[{"date_published":"2015-09-01T00:00:00Z","page":"832 - 847","publication":"Scandinavian Journal of Statistics","citation":{"mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:10.1111/sjos.12139.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","apa":"Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847, 2015."},"day":"01","scopus_import":1,"oa_version":"Preprint","status":"public","title":"Iterative scaling in curved exponential families","intvolume":" 42","_id":"2008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.","lang":"eng"}],"issue":"3","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/sjos.12139","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1307.3282","open_access":"1"}],"oa":1,"month":"09","date_created":"2018-12-11T11:55:11Z","date_updated":"2021-01-12T06:54:41Z","volume":42,"author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova"},{"last_name":"Rudas","first_name":"Tamás","full_name":"Rudas, Tamás"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"CaUh"}],"acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","year":"2015","publist_id":"5068"},{"title":"The monotone secant conjecture in the real Schubert calculus","status":"public","intvolume":" 24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2006","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. ","lang":"eng"}],"issue":"3","page":"261 - 269","publication":"Experimental Mathematics","citation":{"ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” Experimental Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 2015;24(3):261-269. doi:10.1080/10586458.2014.980044","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis, 2015, pp. 261–69, doi:10.1080/10586458.2014.980044."},"date_published":"2015-06-23T00:00:00Z","scopus_import":1,"day":"23","article_processing_charge":"No","publication_status":"published","publisher":"Taylor & Francis","department":[{"_id":"CaUh"}],"year":"2015","date_created":"2018-12-11T11:55:10Z","date_updated":"2021-01-12T06:54:40Z","volume":24,"author":[{"last_name":"Hein","first_name":"Nicolas","full_name":"Hein, Nicolas"},{"full_name":"Hillar, Christopher","first_name":"Christopher","last_name":"Hillar"},{"full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez","first_name":"Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sottile","first_name":"Frank","full_name":"Sottile, Frank"},{"full_name":"Teitler, Zach","last_name":"Teitler","first_name":"Zach"}],"publist_id":"5070","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1080/10586458.2014.980044","month":"06"},{"department":[{"_id":"CaUh"}],"intvolume":" 87","publisher":"Elsevier","status":"public","title":"Faithfulness and learning hypergraphs from discrete distributions","publication_status":"published","_id":"2014","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":87,"oa_version":"Preprint","date_updated":"2021-01-12T06:54:43Z","date_created":"2018-12-11T11:55:13Z","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"type":"journal_article","publist_id":"5062","issue":"7","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"page":"57 - 72","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"citation":{"chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” Computational Statistics & Data Analysis, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","apa":"Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. Elsevier. https://doi.org/10.1016/j.csda.2015.01.017","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72. doi:10.1016/j.csda.2015.01.017"},"publication":"Computational Statistics & Data Analysis","language":[{"iso":"eng"}],"date_published":"2015-07-01T00:00:00Z","doi":"10.1016/j.csda.2015.01.017","scopus_import":1,"month":"07","day":"01"},{"file":[{"checksum":"5bb328edebb6a91337cadd7d63f961b7","date_created":"2018-12-12T10:12:18Z","date_updated":"2020-07-14T12:45:25Z","relation":"main_file","file_id":"4936","file_size":926685,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-615-v1+1_BBAMCR.pdf"}],"oa_version":"Submitted Version","pubrep_id":"615","intvolume":" 1853","ddc":["570"],"status":"public","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2025","issue":"1","abstract":[{"text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.","lang":"eng"}],"type":"journal_article","date_published":"2015-01-01T00:00:00Z","page":"144 - 156","citation":{"short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009","ieee":"D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156."},"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","has_accepted_license":"1","day":"01","scopus_import":1,"volume":1853,"date_updated":"2021-01-12T06:54:48Z","date_created":"2018-12-11T11:55:17Z","author":[{"last_name":"Kawada","first_name":"Daiki","full_name":"Kawada, Daiki"},{"full_name":"Kobayashi, Hiromu","last_name":"Kobayashi","first_name":"Hiromu"},{"full_name":"Tomita, Tsuyoshi","last_name":"Tomita","first_name":"Tsuyoshi"},{"last_name":"Nakata","first_name":"Eisuke","full_name":"Nakata, Eisuke"},{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"last_name":"Toshimaa","first_name":"Jiro","full_name":"Toshimaa, Jiro"}],"department":[{"_id":"DaSi"}],"publisher":"Elsevier","publication_status":"published","year":"2015","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publist_id":"5047","file_date_updated":"2020-07-14T12:45:25Z","language":[{"iso":"eng"}],"doi":"10.1016/j.bbamcr.2014.10.009","quality_controlled":"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"},"oa":1,"month":"01"},{"day":"01","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","doi":"10.1016/j.compfluid.2014.09.021","page":"1 - 11","quality_controlled":"1","oa":1,"citation":{"short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” Computers and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","apa":"Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11."},"main_file_link":[{"url":"http://arxiv.org/abs/1311.2481","open_access":"1"}],"publication":"Computers and Fluids","issue":"1","publist_id":"5042","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"type":"journal_article","volume":106,"oa_version":"Preprint","date_updated":"2021-01-12T06:54:51Z","date_created":"2018-12-11T11:55:18Z","author":[{"full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","last_name":"Shi","first_name":"Liang"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}],"intvolume":" 106","department":[{"_id":"BjHo"}],"publisher":"Elsevier","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","status":"public","publication_status":"published","year":"2015","_id":"2030","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2015","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","volume":15,"date_created":"2018-12-11T11:55:20Z","date_updated":"2021-01-12T06:54:53Z","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz"},{"full_name":"Mrozek, Marian","last_name":"Mrozek","first_name":"Marian"}],"license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"5022","ec_funded":1,"file_date_updated":"2020-07-14T12:45:26Z","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493","_id":"255D761E-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/s10208-014-9223-y","month":"10","intvolume":" 15","status":"public","title":"The persistent homology of a self-map","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2035","oa_version":"Published Version","file":[{"file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1317546,"creator":"system","relation":"main_file","file_id":"4670","date_updated":"2020-07-14T12:45:26Z","date_created":"2018-12-12T10:08:10Z","checksum":"3566f3a8b0c1bc550e62914a88c584ff"}],"pubrep_id":"486","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n"}],"page":"1213 - 1244","citation":{"ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” Foundations of Computational Mathematics, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","apa":"Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2015). The persistent homology of a self-map. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9223-y","ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. Foundations of Computational Mathematics. 2015;15(5):1213-1244. doi:10.1007/s10208-014-9223-y","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics. Springer, 2015. https://doi.org/10.1007/s10208-014-9223-y.","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:10.1007/s10208-014-9223-y.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244."},"publication":"Foundations of Computational Mathematics","date_published":"2015-10-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"scopus_import":1,"day":"01","page":"52 - 59","citation":{"ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59.","apa":"Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.001","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” Information Processing Letters, vol. 115, no. 1. Elsevier, pp. 52–59, 2015.","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:10.1016/j.ipl.2014.09.001.","short":"B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115 (2015) 52–59.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001."},"publication":" Information Processing Letters","date_published":"2015-01-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers."}],"intvolume":" 115","title":"Probabilistic opacity for Markov decision processes","status":"public","_id":"2034","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"01","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.4225"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.ipl.2014.09.001","publist_id":"5025","ec_funded":1,"publisher":"Elsevier","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2015","volume":115,"date_created":"2018-12-11T11:55:20Z","date_updated":"2021-01-12T06:54:52Z","author":[{"full_name":"Bérard, Béatrice","first_name":"Béatrice","last_name":"Bérard"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Sznajder, Nathalie","last_name":"Sznajder","first_name":"Nathalie"}]},{"doi":"10.1007/s00205-014-0781-6","date_published":"2015-02-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Archive for Rational Mechanics and Analysis","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.1153"}],"citation":{"ista":"Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.","ieee":"P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field regime,” Archive for Rational Mechanics and Analysis, vol. 215, no. 2. Springer, pp. 381–417, 2015.","apa":"Nam, P., & Seiringer, R. (2015). Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-014-0781-6","ama":"Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 2015;215(2):381-417. doi:10.1007/s00205-014-0781-6","chicago":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis. Springer, 2015. https://doi.org/10.1007/s00205-014-0781-6.","mla":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis, vol. 215, no. 2, Springer, 2015, pp. 381–417, doi:10.1007/s00205-014-0781-6.","short":"P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015) 381–417."},"oa":1,"quality_controlled":"1","page":"381 - 417","month":"02","day":"01","scopus_import":1,"author":[{"full_name":"Nam, Phan","first_name":"Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:55:37Z","date_updated":"2021-01-12T06:55:13Z","volume":215,"oa_version":"Preprint","_id":"2085","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publication_status":"published","status":"public","title":"Collective excitations of Bose gases in the mean-field regime","department":[{"_id":"RoSe"}],"publisher":"Springer","intvolume":" 215","abstract":[{"text":"We study the spectrum of a large system of N identical bosons interacting via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov's theory predicts that the spectrum of the N-particle Hamiltonian can be approximated by that of an effective quadratic Hamiltonian acting on Fock space, which describes the fluctuations around a condensed state. Recently, Bogoliubov's theory has been justified rigorously in the case that the low-energy eigenvectors of the N-particle Hamiltonian display complete condensation in the unique minimizer of the corresponding Hartree functional. In this paper, we shall justify Bogoliubov's theory for the high-energy part of the spectrum of the N-particle Hamiltonian corresponding to (non-linear) excited states of the Hartree functional. Moreover, we shall extend the existing results on the excitation spectrum to the case of non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the latter covers the case of rotating Bose gases, when the rotation speed is large enough to break the symmetry and to produce multiple quantized vortices in the Hartree minimizer. ","lang":"eng"}],"issue":"2","publist_id":"4951","type":"journal_article"},{"quality_controlled":"1","page":"1365 - 1416","publication":"Communications in Mathematical Physics","main_file_link":[{"url":"http://arxiv.org/abs/1309.5106","open_access":"1"}],"citation":{"ama":"Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 2015;333(3):1365-1416. doi:10.1007/s00220-014-2119-5","ista":"Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 333(3), 1365–1416.","apa":"Erdös, L., & Knowles, A. (2015). The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2119-5","ieee":"L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case,” Communications in Mathematical Physics, vol. 333, no. 3. Springer, pp. 1365–1416, 2015.","mla":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics, vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:10.1007/s00220-014-2119-5.","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-014-2119-5."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00220-014-2119-5","date_published":"2015-02-01T00:00:00Z","scopus_import":1,"month":"02","day":"01","publication_status":"published","title":"The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case","status":"public","publisher":"Springer","intvolume":" 333","department":[{"_id":"LaEr"}],"_id":"2166","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_created":"2018-12-11T11:56:05Z","date_updated":"2021-01-12T06:55:43Z","volume":333,"oa_version":"Preprint","author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Knowles, Antti","last_name":"Knowles","first_name":"Antti"}],"type":"journal_article","abstract":[{"text":"We consider the spectral statistics of large random band matrices on mesoscopic energy scales. We show that the correlation function of the local eigenvalue density exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta statistics. This law had been predicted in the physics literature by Altshuler and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it describes the correlations of the eigenvalue density in general metallic sampleswith weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas for band matrices. In two dimensions, where the leading term vanishes owing to an algebraic cancellation, we identify the first non-vanishing term and show that it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion (Ann. H. Poincaré. arXiv:1309.5107, 2014). ","lang":"eng"}],"publist_id":"4818","issue":"3"},{"year":"2015","publication_status":"published","publisher":"International Federation of Computational Logic","department":[{"_id":"ToHe"}],"author":[{"last_name":"Chakraborty","first_name":"Soham","full_name":"Chakraborty, Soham"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali"},{"full_name":"Vafeiadis, Viktor","last_name":"Vafeiadis","first_name":"Viktor"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2328"}]},"date_updated":"2023-02-23T10:38:13Z","date_created":"2018-12-11T11:54:15Z","volume":11,"article_number":"20","file_date_updated":"2020-07-14T12:45:17Z","ec_funded":1,"publist_id":"5271","license":"https://creativecommons.org/licenses/by-nd/4.0/","oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"doi":"10.2168/LMCS-11(1:20)2015","language":[{"iso":"eng"}],"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1832","status":"public","ddc":["000"],"title":"Aspect-oriented linearizability proofs","intvolume":" 11","pubrep_id":"390","file":[{"checksum":"7370e164d0a731f442424a92669efc34","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:11:27Z","relation":"main_file","file_id":"4881","content_type":"application/pdf","file_size":380203,"creator":"system","access_level":"open_access","file_name":"IST-2015-390-v1+1_1502.07639.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on the identification of the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof. ","lang":"eng"}],"issue":"1","publication":"Logical Methods in Computer Science","citation":{"mla":"Chakraborty, Soham, et al. “Aspect-Oriented Linearizability Proofs.” Logical Methods in Computer Science, vol. 11, no. 1, 20, International Federation of Computational Logic, 2015, doi:10.2168/LMCS-11(1:20)2015.","short":"S. Chakraborty, T.A. Henzinger, A. Sezgin, V. Vafeiadis, Logical Methods in Computer Science 11 (2015).","chicago":"Chakraborty, Soham, Thomas A Henzinger, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Logical Methods in Computer Science. International Federation of Computational Logic, 2015. https://doi.org/10.2168/LMCS-11(1:20)2015.","ama":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 2015;11(1). doi:10.2168/LMCS-11(1:20)2015","ista":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 11(1), 20.","ieee":"S. Chakraborty, T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” Logical Methods in Computer Science, vol. 11, no. 1. International Federation of Computational Logic, 2015.","apa":"Chakraborty, S., Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2015). Aspect-oriented linearizability proofs. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-11(1:20)2015"},"article_type":"original","date_published":"2015-04-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"month":"02","language":[{"iso":"eng"}],"doi":"10.1137/130945648","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.4219"}],"oa":1,"external_id":{"arxiv":["1311.4219"]},"publist_id":"4673","date_created":"2018-12-11T11:56:41Z","date_updated":"2023-02-23T10:46:30Z","volume":44,"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"full_name":"Thapper, Johan","first_name":"Johan","last_name":"Thapper"},{"first_name":"Stanislav","last_name":"Živný","full_name":"Živný, Stanislav"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2518"}]},"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"SIAM","year":"2015","day":"01","scopus_import":1,"date_published":"2015-02-01T00:00:00Z","page":"1 - 36","publication":"SIAM Journal on Computing","citation":{"short":"V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36.","mla":"Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued CSPs.” SIAM Journal on Computing, vol. 44, no. 1, SIAM, 2015, pp. 1–36, doi:10.1137/130945648.","chicago":"Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of Linear Programming for General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2015. https://doi.org/10.1137/130945648.","ama":"Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 2015;44(1):1-36. doi:10.1137/130945648","apa":"Kolmogorov, V., Thapper, J., & Živný, S. (2015). The power of linear programming for general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/130945648","ieee":"V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming for general-valued CSPs,” SIAM Journal on Computing, vol. 44, no. 1. SIAM, pp. 1–36, 2015.","ista":"Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36."},"abstract":[{"lang":"eng","text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.\r\nUsing these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees. "}],"issue":"1","type":"journal_article","oa_version":"Preprint","status":"public","title":"The power of linear programming for general-valued CSPs","intvolume":" 44","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2271"},{"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"For suitable pairs of diagonal quadratic forms in eight variables we use the circle method to investigate the density of simultaneous integer solutions and relate this to the problem of estimating linear correlations among sums of two squares."}],"issue":"4","publist_id":"7645","status":"public","title":"Pairs of diagonal quadratic forms and linear correlations among sums of two squares","publication_status":"published","intvolume":" 27","publisher":"Walter de Gruyter GmbH","year":"2015","_id":"257","acknowledgement":"While working on this paper the first author was supported by ERC grant 306457 and the second author was supported by SwarnaJayanti Fellowship 2011–12, DST, Government of India.","date_created":"2018-12-11T11:45:28Z","date_updated":"2021-01-12T06:58:18Z","volume":27,"author":[{"full_name":"Timothy Browning","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Munshi","first_name":"Ritabrata","full_name":"Munshi, Ritabrata"}],"day":"10","month":"07","quality_controlled":0,"page":"2025 - 2050","publication":"Forum Mathematicum","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1302.2434"}],"citation":{"ista":"Browning TD, Munshi R. 2015. Pairs of diagonal quadratic forms and linear correlations among sums of two squares. Forum Mathematicum. 27(4), 2025–2050.","ieee":"T. D. Browning and R. Munshi, “Pairs of diagonal quadratic forms and linear correlations among sums of two squares,” Forum Mathematicum, vol. 27, no. 4. Walter de Gruyter GmbH, pp. 2025–2050, 2015.","apa":"Browning, T. D., & Munshi, R. (2015). Pairs of diagonal quadratic forms and linear correlations among sums of two squares. Forum Mathematicum. Walter de Gruyter GmbH. https://doi.org/10.1515/forum-2013-6024","ama":"Browning TD, Munshi R. Pairs of diagonal quadratic forms and linear correlations among sums of two squares. Forum Mathematicum. 2015;27(4):2025-2050. doi:10.1515/forum-2013-6024","chicago":"Browning, Timothy D, and Ritabrata Munshi. “Pairs of Diagonal Quadratic Forms and Linear Correlations among Sums of Two Squares.” Forum Mathematicum. Walter de Gruyter GmbH, 2015. https://doi.org/10.1515/forum-2013-6024.","mla":"Browning, Timothy D., and Ritabrata Munshi. “Pairs of Diagonal Quadratic Forms and Linear Correlations among Sums of Two Squares.” Forum Mathematicum, vol. 27, no. 4, Walter de Gruyter GmbH, 2015, pp. 2025–50, doi:10.1515/forum-2013-6024.","short":"T.D. Browning, R. Munshi, Forum Mathematicum 27 (2015) 2025–2050."},"date_published":"2015-07-10T00:00:00Z","doi":"10.1515/forum-2013-6024"},{"type":"book_chapter","extern":"1","publist_id":"7644","abstract":[{"text":"Given a number field k and a projective algebraic variety X defined over k, the question of whether X contains a k-rational point is both very natural and very difficult. In the event that the set X(k) of k-rational points is not empty, one can also ask how the points of X(k) are distributed. Are they dense in X under the Zariski topology? Are they dense in the set.","lang":"eng"}],"publisher":"Cambridge University Press","status":"public","publication_status":"published","title":"A survey of applications of the circle method to rational points","_id":"258","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2018-12-11T11:45:28Z","date_updated":"2021-01-12T06:58:22Z","author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"}],"day":"01","month":"08","page":"89 - 113","quality_controlled":"1","citation":{"mla":"Browning, Timothy D. “A Survey of Applications of the Circle Method to Rational Points.” Arithmetic and Geometry, Cambridge University Press, 2015, pp. 89–113, doi:10.1017/CBO9781316106877.009.","short":"T.D. Browning, in:, Arithmetic and Geometry, Cambridge University Press, 2015, pp. 89–113.","chicago":"Browning, Timothy D. “A Survey of Applications of the Circle Method to Rational Points.” In Arithmetic and Geometry, 89–113. Cambridge University Press, 2015. https://doi.org/10.1017/CBO9781316106877.009.","ama":"Browning TD. A survey of applications of the circle method to rational points. In: Arithmetic and Geometry. Cambridge University Press; 2015:89-113. doi:10.1017/CBO9781316106877.009","ista":"Browning TD. 2015.A survey of applications of the circle method to rational points. In: Arithmetic and Geometry. , 89–113.","ieee":"T. D. Browning, “A survey of applications of the circle method to rational points,” in Arithmetic and Geometry, Cambridge University Press, 2015, pp. 89–113.","apa":"Browning, T. D. (2015). A survey of applications of the circle method to rational points. In Arithmetic and Geometry (pp. 89–113). Cambridge University Press. https://doi.org/10.1017/CBO9781316106877.009"},"publication":"Arithmetic and Geometry","language":[{"iso":"eng"}],"doi":"10.1017/CBO9781316106877.009","date_published":"2015-08-01T00:00:00Z"},{"day":"11","month":"06","date_published":"2015-06-11T00:00:00Z","doi":"10.1007/s00039-015-0328-5","page":"671 - 732","quality_controlled":0,"citation":{"apa":"Browning, T. D., & Vishe, P. (2015). Rational points on cubic hypersurfaces over F_q(t) . Geometric and Functional Analysis. Birkhäuser. https://doi.org/10.1007/s00039-015-0328-5","ieee":"T. D. Browning and P. Vishe, “Rational points on cubic hypersurfaces over F_q(t) ,” Geometric and Functional Analysis, vol. 25, no. 3. Birkhäuser, pp. 671–732, 2015.","ista":"Browning TD, Vishe P. 2015. Rational points on cubic hypersurfaces over F_q(t) . Geometric and Functional Analysis. 25(3), 671–732.","ama":"Browning TD, Vishe P. Rational points on cubic hypersurfaces over F_q(t) . Geometric and Functional Analysis. 2015;25(3):671-732. doi:10.1007/s00039-015-0328-5","chicago":"Browning, Timothy D, and Pankaj Vishe. “Rational Points on Cubic Hypersurfaces over F_q(T) .” Geometric and Functional Analysis. Birkhäuser, 2015. https://doi.org/10.1007/s00039-015-0328-5.","short":"T.D. Browning, P. Vishe, Geometric and Functional Analysis 25 (2015) 671–732.","mla":"Browning, Timothy D., and Pankaj Vishe. “Rational Points on Cubic Hypersurfaces over F_q(T) .” Geometric and Functional Analysis, vol. 25, no. 3, Birkhäuser, 2015, pp. 671–732, doi:10.1007/s00039-015-0328-5."},"publication":"Geometric and Functional Analysis","extern":1,"issue":"3","publist_id":"7643","abstract":[{"text":"The Hasse principle and weak approximation is established for non-singular cubic hypersurfaces X over the function field ","lang":"eng"}],"type":"journal_article","volume":25,"date_updated":"2021-01-12T06:58:25Z","date_created":"2018-12-11T11:45:29Z","author":[{"full_name":"Timothy Browning","first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177"},{"full_name":"Vishe, Pankaj","last_name":"Vishe","first_name":"Pankaj"}],"publisher":"Birkhäuser","intvolume":" 25","publication_status":"published","title":"Rational points on cubic hypersurfaces over F_q(t) ","status":"public","_id":"259","acknowledgement":"EP/J018260/1\tEngineering and Physical Sciences Research Council EPSRC","year":"2015"},{"_id":"1598","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 573","status":"public","title":"Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure winning vertices such that the objective can be ensured with probability 1 from these vertices. We study for the first time the average-case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average-case running time is linear (as compared to the worst-case linear number of iterations and quadratic time complexity). Second, for the average-case analysis over all MDPs we show that the expected number of iterations is constant and the average-case running time is linear (again as compared to the worst-case linear number of iterations and quadratic time complexity). Finally we also show that when all MDPs are equally likely, the probability that the classical algorithm requires more than a constant number of iterations is exponentially small."}],"citation":{"ama":"Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. 2015;573(3):71-89. doi:10.1016/j.tcs.2015.01.050","ista":"Chatterjee K, Joglekar M, Shah N. 2015. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. 573(3), 71–89.","ieee":"K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives,” Theoretical Computer Science, vol. 573, no. 3. Elsevier, pp. 71–89, 2015.","apa":"Chatterjee, K., Joglekar, M., & Shah, N. (2015). Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.050","mla":"Chatterjee, Krishnendu, et al. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.” Theoretical Computer Science, vol. 573, no. 3, Elsevier, 2015, pp. 71–89, doi:10.1016/j.tcs.2015.01.050.","short":"K. Chatterjee, M. Joglekar, N. Shah, Theoretical Computer Science 573 (2015) 71–89.","chicago":"Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.050."},"publication":"Theoretical Computer Science","page":"71 - 89","date_published":"2015-03-30T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"30","year":"2015","acknowledgement":"The research was supported by FWF Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start Grant (279307: Graph Games), and the Microsoft Faculty Fellows Award. Nisarg Shah is also supported by NSF Grant CCF-1215883.\r\n","department":[{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2715"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Manas","last_name":"Joglekar","full_name":"Joglekar, Manas"},{"last_name":"Shah","first_name":"Nisarg","full_name":"Shah, Nisarg"}],"volume":573,"date_updated":"2023-02-23T10:55:03Z","date_created":"2018-12-11T11:52:56Z","ec_funded":1,"publist_id":"5571","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.4175"}],"external_id":{"arxiv":["1202.4175"]},"oa":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1016/j.tcs.2015.01.050","language":[{"iso":"eng"}],"month":"03"},{"publist_id":"5305","ec_funded":1,"related_material":{"record":[{"id":"2812","status":"public","relation":"earlier_version"}]},"author":[{"last_name":"Attali","first_name":"Dominique","full_name":"Attali, Dominique"},{"full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","first_name":"Ulrich","last_name":"Bauer"},{"first_name":"Olivier","last_name":"Devillers","full_name":"Devillers, Olivier"},{"full_name":"Glisse, Marc","last_name":"Glisse","first_name":"Marc"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"}],"volume":48,"date_updated":"2023-02-23T10:59:19Z","date_created":"2018-12-11T11:54:06Z","year":"2015","department":[{"_id":"HeEd"}],"publisher":"Elsevier","publication_status":"published","month":"06","doi":"10.1016/j.comgeo.2014.08.010","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"quality_controlled":"1","issue":"8","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"1805","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 48","status":"public","title":"Homological reconstruction and simplification in R3","day":"03","scopus_import":1,"date_published":"2015-06-03T00:00:00Z","citation":{"short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” Computational Geometry: Theory and Applications, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:10.1016/j.comgeo.2014.08.010.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.010.","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 2015;48(8):606-621. doi:10.1016/j.comgeo.2014.08.010","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” Computational Geometry: Theory and Applications, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2015). Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.010","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621."},"publication":"Computational Geometry: Theory and Applications","page":"606 - 621"},{"day":"16","month":"10","article_processing_charge":"No","publication":"Chemistry of Materials","citation":{"mla":"Walter, Marc, et al. “Efficient and Inexpensive Sodium Magnesium Hybrid Battery.” Chemistry of Materials, vol. 27, no. 21, ACS, 2015, pp. 7452–58, doi:10.1021/acs.chemmater.5b03531.","short":"M. Walter, K. Kravchyk, M. Ibáñez, M. Kovalenko, Chemistry of Materials 27 (2015) 7452–7458.","chicago":"Walter, Marc, Kostiantyn Kravchyk, Maria Ibáñez, and Maksym Kovalenko. “Efficient and Inexpensive Sodium Magnesium Hybrid Battery.” Chemistry of Materials. ACS, 2015. https://doi.org/10.1021/acs.chemmater.5b03531.","ama":"Walter M, Kravchyk K, Ibáñez M, Kovalenko M. Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. 2015;27(21):7452-7458. doi:10.1021/acs.chemmater.5b03531","ista":"Walter M, Kravchyk K, Ibáñez M, Kovalenko M. 2015. Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. 27(21), 7452–7458.","apa":"Walter, M., Kravchyk, K., Ibáñez, M., & Kovalenko, M. (2015). Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.5b03531","ieee":"M. Walter, K. Kravchyk, M. Ibáñez, and M. Kovalenko, “Efficient and inexpensive sodium magnesium hybrid battery,” Chemistry of Materials, vol. 27, no. 21. ACS, pp. 7452–7458, 2015."},"article_type":"original","quality_controlled":"1","page":"7452 - 7458","date_published":"2015-10-16T00:00:00Z","doi":"10.1021/acs.chemmater.5b03531","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present a hybrid intercalation battery based on a sodium/magnesium (Na/Mg) dual salt electrolyte, metallic magnesium anode, and a cathode based on FeS2 nanocrystals (NCs). Compared to lithium or sodium, metallic magnesium anode is safer due to dendrite-free electroplating and offers extremely high volumetric (3833 mAh cm-3) and gravimetric capacities (2205 mAh g-1). Na-ion cathodes, FeS2 NCs in the present study, may serve as attractive alternatives to Mg-ion cathodes due to the higher voltage of operation and fast, highly reversible insertion of Na-ions. In this proof-of-concept study, electrochemical cycling of the Na/Mg hybrid battery was characterized by high rate capability, high Coulombic efficiency of 99.8%, and high energy density. In particular, with an average discharge voltage of ∼1.1 V and a cathodic capacity of 189 mAh g-1 at a current of 200 mA g-1, the presented Mg/FeS2 hybrid battery delivers energy densities of up to 210 Wh kg-1, comparable to commercial Li-ion batteries and approximately twice as high as state-of-the-art Mg-ion batteries based on Mo6S8 cathodes. Further significant gains in the energy density are expected from the development of Na/Mg electrolytes with a broader electrochemical stability window. Fully based on Earth-abundant elements, hybrid Na-Mg batteries are highly promising for large-scale stationary energy storage. "}],"issue":"21","publist_id":"7507","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"333","year":"2015","status":"public","publication_status":"published","title":"Efficient and inexpensive sodium magnesium hybrid battery","intvolume":" 27","publisher":"ACS","author":[{"full_name":"Walter, Marc","last_name":"Walter","first_name":"Marc"},{"full_name":"Kravchyk, Kostiantyn","first_name":"Kostiantyn","last_name":"Kravchyk"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Kovalenko, Maksym","last_name":"Kovalenko","first_name":"Maksym"}],"date_created":"2018-12-11T11:45:52Z","date_updated":"2021-01-12T07:42:42Z","volume":27,"oa_version":"None"},{"author":[{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Korkosz, Rachel","first_name":"Rachel","last_name":"Korkosz"},{"last_name":"Luo","first_name":"Zhishan","full_name":"Luo, Zhishan"},{"first_name":"Pau","last_name":"Riba","full_name":"Riba, Pau"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"first_name":"Silvia","last_name":"Ortega","full_name":"Ortega, Silvia"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"last_name":"Kanatzidis","first_name":"Mercouri","full_name":"Kanatzidis, Mercouri"}],"date_created":"2018-12-11T11:45:59Z","date_updated":"2021-01-12T07:44:10Z","volume":137,"oa_version":"None","_id":"354","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"At IREC, work was supported by European Regional Development Funds and the Framework 7 program under project UNION (FP7-NMP 310250). M.I. and S.O. thank AGAUR for their Beatriu i Pinós postdoctoral grant and the PhD grant, respectively. At Northwestern, work was supported by the Revolutionary Materials for Solid State Energy Conversion, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, and Office of Basic Energy Sciences under Award Number DE-SC0001054.","status":"public","publication_status":"published","title":"Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement","intvolume":" 137","publisher":"American Chemical Society","abstract":[{"text":"A simple and effective method to introduce precise amounts of doping in nanomaterials produced from the bottom-up assembly of colloidal nanoparticles (NPs) is described. The procedure takes advantage of a ligand displacement step to incorporate controlled concentrations of halide ions while removing carboxylic acids from the NP surface. Upon consolidation of the NPs into dense pellets, halide ions diffuse within the crystal structure, doping the anion sublattice and achieving n-type electrical doping. Through the characterization of the thermoelectric properties of nanocrystalline PbS, we demonstrate this strategy to be effective to control charge transport properties on thermoelectric nanomaterials assembled from NP building blocks. This approach is subsequently extended to PbTexSe1-x@PbS core-shell NPs, where a significant enhancement of the thermoelectric figure of merit is achieved. ","lang":"eng"}],"publist_id":"7470","issue":"12","extern":"1","type":"journal_article","date_published":"2015-03-11T00:00:00Z","doi":"10.1021/jacs.5b00091","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","citation":{"ama":"Ibáñez M, Korkosz R, Luo Z, et al. Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement. Journal of the American Chemical Society. 2015;137(12):4046-4049. doi:10.1021/jacs.5b00091","ista":"Ibáñez M, Korkosz R, Luo Z, Riba P, Cadavid D, Ortega S, Cabot A, Kanatzidis M. 2015. Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement. Journal of the American Chemical Society. 137(12), 4046–4049.","ieee":"M. Ibáñez et al., “Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement,” Journal of the American Chemical Society, vol. 137, no. 12. American Chemical Society, pp. 4046–4049, 2015.","apa":"Ibáñez, M., Korkosz, R., Luo, Z., Riba, P., Cadavid, D., Ortega, S., … Kanatzidis, M. (2015). Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.5b00091","mla":"Ibáñez, Maria, et al. “Electron Doping in Bottom up Engineered Thermoelectric Nanomaterials through HCl Mediated Ligand Displacement.” Journal of the American Chemical Society, vol. 137, no. 12, American Chemical Society, 2015, pp. 4046–49, doi:10.1021/jacs.5b00091.","short":"M. Ibáñez, R. Korkosz, Z. Luo, P. Riba, D. Cadavid, S. Ortega, A. Cabot, M. Kanatzidis, Journal of the American Chemical Society 137 (2015) 4046–4049.","chicago":"Ibáñez, Maria, Rachel Korkosz, Zhishan Luo, Pau Riba, Doris Cadavid, Silvia Ortega, Andreu Cabot, and Mercouri Kanatzidis. “Electron Doping in Bottom up Engineered Thermoelectric Nanomaterials through HCl Mediated Ligand Displacement.” Journal of the American Chemical Society. American Chemical Society, 2015. https://doi.org/10.1021/jacs.5b00091."},"article_type":"original","quality_controlled":"1","page":"4046 - 4049","day":"11","month":"03","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"date_published":"2015-09-29T00:00:00Z","doi":"10.1021/acs.langmuir.5b02490","page":"10555 - 10561","citation":{"mla":"Yu, Xuelian, et al. “Cu2ZnSnS4-Ag2S Nanoscale p-n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir, vol. 31, no. 38, American Chemical Society, 2015, pp. 10555–61, doi:10.1021/acs.langmuir.5b02490.","short":"X. Yu, J. Liu, A. Genç, M. Ibáñez, Z. Luo, A. Shavel, J. Arbiol, G. Zhang, Y. Zhang, A. Cabot, Langmuir 31 (2015) 10555–10561.","chicago":"Yu, Xuelian, Jingjing Liu, Aziz Genç, Maria Ibáñez, Zhishan Luo, Alexey Shavel, Jordi Arbiol, Guangjin Zhang, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4-Ag2S Nanoscale p-n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/acs.langmuir.5b02490.","ama":"Yu X, Liu J, Genç A, et al. Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 2015;31(38):10555-10561. doi:10.1021/acs.langmuir.5b02490","ista":"Yu X, Liu J, Genç A, Ibáñez M, Luo Z, Shavel A, Arbiol J, Zhang G, Zhang Y, Cabot A. 2015. Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 31(38), 10555–10561.","ieee":"X. Yu et al., “Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting,” Langmuir, vol. 31, no. 38. American Chemical Society, pp. 10555–10561, 2015.","apa":"Yu, X., Liu, J., Genç, A., Ibáñez, M., Luo, Z., Shavel, A., … Cabot, A. (2015). Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. American Chemical Society. https://doi.org/10.1021/acs.langmuir.5b02490"},"publication":"Langmuir","article_processing_charge":"No","day":"29","month":"09","oa_version":"None","volume":31,"date_updated":"2021-01-12T07:44:34Z","date_created":"2018-12-11T11:46:01Z","author":[{"last_name":"Yu","first_name":"Xuelian","full_name":"Yu, Xuelian"},{"full_name":"Liu, Jingjing","first_name":"Jingjing","last_name":"Liu"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"full_name":"Luo, Zhishan","first_name":"Zhishan","last_name":"Luo"},{"last_name":"Shavel","first_name":"Alexey","full_name":"Shavel, Alexey"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"full_name":"Zhang, Guangjin","last_name":"Zhang","first_name":"Guangjin"},{"first_name":"Yihe","last_name":"Zhang","full_name":"Zhang, Yihe"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"intvolume":" 31","publisher":"American Chemical Society","title":"Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting","status":"public","publication_status":"published","_id":"360","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"38","publist_id":"7467","abstract":[{"text":"A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles with controlled composition. We report a detailed study of the formation of such CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for photocatalytic water splitting provides superior photocurrents. We associate this experimental fact to a higher separation efficiency of the photogenerated electron-hole pairs. We believe this and other type-II nanoheterostructures will open the door to the use of CZTS, with excellent light absorption properties and made of abundant and environmental friendly elements, to the field of photocatalysis. ","lang":"eng"}],"type":"journal_article"},{"date_published":"2015-04-07T00:00:00Z","doi":"10.1021/la504906q","language":[{"iso":"eng"}],"publication":"Langmuir","citation":{"chicago":"Lu, Zhishan, Maria Ibáñez, Ana Antolín, Aziz Genç, Alexey Shavel, Sandra Contreras, Francesc Medina, Jordi Arbiol, and Andreu Cabot. “Size and Aspect Ratio Control of Pd Inf 2 Inf Sn Nanorods and Their Water Denitration Properties.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504906q.","mla":"Lu, Zhishan, et al. “Size and Aspect Ratio Control of Pd Inf 2 Inf Sn Nanorods and Their Water Denitration Properties.” Langmuir, vol. 31, no. 13, American Chemical Society, 2015, pp. 3952–57, doi:10.1021/la504906q.","short":"Z. Lu, M. Ibáñez, A. Antolín, A. Genç, A. Shavel, S. Contreras, F. Medina, J. Arbiol, A. Cabot, Langmuir 31 (2015) 3952–3957.","ista":"Lu Z, Ibáñez M, Antolín A, Genç A, Shavel A, Contreras S, Medina F, Arbiol J, Cabot A. 2015. Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties. Langmuir. 31(13), 3952–3957.","apa":"Lu, Z., Ibáñez, M., Antolín, A., Genç, A., Shavel, A., Contreras, S., … Cabot, A. (2015). Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties. Langmuir. American Chemical Society. https://doi.org/10.1021/la504906q","ieee":"Z. Lu et al., “Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties,” Langmuir, vol. 31, no. 13. American Chemical Society, pp. 3952–3957, 2015.","ama":"Lu Z, Ibáñez M, Antolín A, et al. Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties. Langmuir. 2015;31(13):3952-3957. doi:10.1021/la504906q"},"page":"3952 - 3957","month":"04","day":"07","article_processing_charge":"No","author":[{"full_name":"Lu, Zhishan","last_name":"Lu","first_name":"Zhishan"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"last_name":"Antolín","first_name":"Ana","full_name":"Antolín, Ana"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"last_name":"Contreras","first_name":"Sandra","full_name":"Contreras, Sandra"},{"last_name":"Medina","first_name":"Francesc","full_name":"Medina, Francesc"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_created":"2018-12-11T11:46:02Z","date_updated":"2021-01-12T07:44:42Z","oa_version":"None","volume":31,"_id":"362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publication_status":"published","title":"Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties","status":"public","publisher":"American Chemical Society","intvolume":" 31","abstract":[{"lang":"eng","text":"Monodisperse Pd2Sn nanorods with tuned size and aspect ratio were prepared by co-reduction of metal salts in the presence of trioctylphosphine, amine, and chloride ions. Asymmetric Pd2Sn nanostructures were achieved by the selective desorption of a surfactant mediated by chlorine ions. A preliminary evaluation of the geometry influence on catalytic properties evidenced Pd2Sn nanorods to have improved catalytic performance. In view of these results, Pd2Sn nanorods were also evaluated for water denitration. "}],"issue":"13","publist_id":"7469","extern":"1","type":"journal_article"},{"doi":"10.1016/j.ic.2015.06.003","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1006.0673","open_access":"1"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","month":"12","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3856"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"full_name":"Gimbert, Hugo","first_name":"Hugo","last_name":"Gimbert"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"volume":245,"date_created":"2018-12-11T11:53:42Z","date_updated":"2023-02-23T11:45:42Z","year":"2015","publisher":"Elsevier","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","publist_id":"5395","ec_funded":1,"date_published":"2015-12-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger. “Randomness for Free.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.06.003.","short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16.","mla":"Chatterjee, Krishnendu, et al. “Randomness for Free.” Information and Computation, vol. 245, no. 12, Elsevier, 2015, pp. 3–16, doi:10.1016/j.ic.2015.06.003.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Henzinger, T. A. (2015). Randomness for free. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.06.003","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for free,” Information and Computation, vol. 245, no. 12. Elsevier, pp. 3–16, 2015.","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free. Information and Computation. 245(12), 3–16.","ama":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. Information and Computation. 2015;245(12):3-16. doi:10.1016/j.ic.2015.06.003"},"publication":"Information and Computation","page":"3 - 16","day":"01","scopus_import":1,"oa_version":"Preprint","_id":"1731","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 245","status":"public","title":"Randomness for free","issue":"12","abstract":[{"lang":"eng","text":"We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (both players interact simultaneously); and (b) turn-based (both players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. In this work we present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. "}],"type":"journal_article"},{"extern":"1","abstract":[{"text":"A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles with controlled composition. We report a detailed study of the formation of such CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for photocatalytic water splitting provides superior photocurrents. We associate this experimental fact to a higher separation efficiency of the photogenerated electron-hole pairs. We believe this and other type-II nanoheterostructures will open the door to the use of CZTS, with excellent light absorption properties and made of abundant and environmental friendly elements, to the field of photocatalysis.","lang":"eng"}],"issue":"38","publist_id":"7508","type":"journal_article","date_updated":"2021-01-12T07:42:46Z","date_created":"2018-12-11T11:45:52Z","volume":31,"oa_version":"None","author":[{"full_name":"Yu, Xuelian","first_name":"Xuelian","last_name":"Yu"},{"full_name":"Liu, Jingjing","last_name":"Liu","first_name":"Jingjing"},{"full_name":"Genç, Aziz","last_name":"Genç","first_name":"Aziz"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Luo","first_name":"Zhishan","full_name":"Luo, Zhishan"},{"last_name":"Shavel","first_name":"Alexey","full_name":"Shavel, Alexey"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Zhang, Guangjin","first_name":"Guangjin","last_name":"Zhang"},{"full_name":"Zhang, Yihe","first_name":"Yihe","last_name":"Zhang"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"publication_status":"published","status":"public","title":"Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting","publisher":"American Chemical Society","intvolume":" 31","_id":"334","acknowledgement":"This work was supported by the European Regional Development Funds, the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486), the Spanish MINECO under Contract ENE2013-46624-C4-3-R and Fundamental Research Funds for the Central Universities (2652015086). Authors acknowledge the funding from Generalitat de Catalunya 2014 SGR 1638.","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","day":"07","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1021/acs.langmuir.5b02490","date_published":"2015-09-07T00:00:00Z","article_type":"original","quality_controlled":"1","page":"10555 - 10561","publication":"Langmuir","citation":{"ama":"Yu X, Liu J, Genç A, et al. Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 2015;31(38):10555-10561. doi:10.1021/acs.langmuir.5b02490","ista":"Yu X, Liu J, Genç A, Ibáñez M, Luo Z, Shavel A, Arbiol J, Zhang G, Zhang Y, Cabot A. 2015. Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 31(38), 10555–10561.","apa":"Yu, X., Liu, J., Genç, A., Ibáñez, M., Luo, Z., Shavel, A., … Cabot, A. (2015). Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. American Chemical Society. https://doi.org/10.1021/acs.langmuir.5b02490","ieee":"X. Yu et al., “Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting,” Langmuir, vol. 31, no. 38. American Chemical Society, pp. 10555–10561, 2015.","mla":"Yu, Xuelian, et al. “Cu2ZnSnS4–Ag2S Nanoscale p–n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir, vol. 31, no. 38, American Chemical Society, 2015, pp. 10555–61, doi:10.1021/acs.langmuir.5b02490.","short":"X. Yu, J. Liu, A. Genç, M. Ibáñez, Z. Luo, A. Shavel, J. Arbiol, G. Zhang, Y. Zhang, A. Cabot, Langmuir 31 (2015) 10555–10561.","chicago":"Yu, Xuelian, Jingjing Liu, Aziz Genç, Maria Ibáñez, Zhishan Luo, Alexey Shavel, Jordi Arbiol, Guangjin Zhang, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4–Ag2S Nanoscale p–n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/acs.langmuir.5b02490."}},{"page":"21882 - 21888","publication":"Journal of Physical Chemistry C","citation":{"mla":"Yu, Xuelian, et al. “Cu2ZnSnS4–PtM (M = Co, Ni) Nanoheterostructures for Photocatalytic Hydrogen Evolution.” Journal of Physical Chemistry C, vol. 119, no. 38, American Chemical Society, 2015, pp. 21882–88, doi:10.1021/acs.jpcc.5b06199.","short":"X. Yu, X. An, A. Genç, M. Ibáñez, J. Arbiol, Y. Zhang, A. Cabot, Journal of Physical Chemistry C 119 (2015) 21882–21888.","chicago":"Yu, Xuelian, Xiaoqiang An, Aziz Genç, Maria Ibáñez, Jordi Arbiol, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4–PtM (M = Co, Ni) Nanoheterostructures for Photocatalytic Hydrogen Evolution.” Journal of Physical Chemistry C. American Chemical Society, 2015. https://doi.org/10.1021/acs.jpcc.5b06199.","ama":"Yu X, An X, Genç A, et al. Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal of Physical Chemistry C. 2015;119(38):21882-21888. doi:10.1021/acs.jpcc.5b06199","ista":"Yu X, An X, Genç A, Ibáñez M, Arbiol J, Zhang Y, Cabot A. 2015. Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal of Physical Chemistry C. 119(38), 21882–21888.","apa":"Yu, X., An, X., Genç, A., Ibáñez, M., Arbiol, J., Zhang, Y., & Cabot, A. (2015). Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.5b06199","ieee":"X. Yu et al., “Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution,” Journal of Physical Chemistry C, vol. 119, no. 38. American Chemical Society, pp. 21882–21888, 2015."},"language":[{"iso":"eng"}],"doi":"10.1021/acs.jpcc.5b06199","date_published":"2015-08-26T00:00:00Z","day":"26","month":"08","article_processing_charge":"No","publication_status":"published","title":"Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution","status":"public","intvolume":" 119","publisher":"American Chemical Society","_id":"361","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the National Natural Science Foundation of China (Grant 21401212), Fundamental Research Funds for the Central Universities (2652015086), the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486), and the MICINN project ENE2013-46624-C4-3-R. Authors acknowledge the funding from Generalitat de Catalunya 2014 SGR 1638.","date_created":"2018-12-11T11:46:01Z","date_updated":"2021-01-12T07:44:38Z","oa_version":"None","volume":119,"author":[{"full_name":"Yu, Xuelian","last_name":"Yu","first_name":"Xuelian"},{"last_name":"An","first_name":"Xiaoqiang","full_name":"An, Xiaoqiang"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Zhang, Yihe","first_name":"Yihe","last_name":"Zhang"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"We report the synthesis and photocatalytic and magnetic characterization of colloidal nanoheterostructures formed by combining a Pt-based magnetic metal alloy (PtCo, PtNi) with Cu2ZnSnS4 (CZTS). While CZTS is one of the main candidate materials for solar energy conversion, the introduction of a Pt-based alloy on its surface strongly influences its chemical and electronic properties, ultimately determining its functionality. In this regard, up to a 15-fold increase of the photocatalytic hydrogen evolution activity was obtained with CZTS–PtCo when compared with CZTS. Furthermore, two times higher hydrogen evolution rates were obtained for CZTS–PtCo when compared with CZTS–Pt, in spite of the lower precious metal loading of the former. Besides, the magnetic properties of the PtCo nanoparticles attached to the CZTS nanocrystals were retained in the heterostructures, which could facilitate catalyst purification and recovery for its posterior recycling and/or reutilization."}],"publist_id":"7468","issue":"38"},{"date_published":"2015-02-01T00:00:00Z","citation":{"ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. 2015;62(1). doi:10.1145/2699430","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Singh, R. (2015). Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. ACM. https://doi.org/10.1145/2699430","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “Measuring and synthesizing systems in probabilistic environments,” Journal of the ACM, vol. 62, no. 1. ACM, 2015.","ista":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2015. Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. 62(1), 9.","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, Journal of the ACM 62 (2015).","mla":"Chatterjee, Krishnendu, et al. “Measuring and Synthesizing Systems in Probabilistic Environments.” Journal of the ACM, vol. 62, no. 1, 9, ACM, 2015, doi:10.1145/2699430.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “Measuring and Synthesizing Systems in Probabilistic Environments.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2699430."},"publication":"Journal of the ACM","day":"01","scopus_import":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1856","intvolume":" 62","status":"public","title":"Measuring and synthesizing systems in probabilistic environments","issue":"1","abstract":[{"text":"The traditional synthesis question given a specification asks for the automatic construction of a system that satisfies the specification, whereas often there exists a preference order among the different systems that satisfy the given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification under the input assumption, synthesize a system that optimizes the measured value. For safety specifications and quantitative measures that are defined by mean-payoff automata, the optimal synthesis problem reduces to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be achieved in polynomial time. For general omega-regular specifications along with mean-payoff automata, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. Our algorithm constructs optimal strategies that consist of two memoryless strategies and a counter. The counter is in general not bounded. To obtain a finite-state system, we show how to construct an ε-optimal strategy with a bounded counter, for all ε > 0. Furthermore, we show how to decide in polynomial time if it is possible to construct an optimal finite-state system (i.e., a system without a counter) for a given specification. We have implemented our approach and the underlying algorithms in a tool that takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. We present some experimental results showing optimal systems that were automatically generated in this way.","lang":"eng"}],"type":"journal_article","doi":"10.1145/2699430","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.0739"}],"oa":1,"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","month":"02","related_material":{"record":[{"id":"3864","relation":"earlier_version","status":"public"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"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":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"volume":62,"date_created":"2018-12-11T11:54:23Z","date_updated":"2023-02-23T11:46:04Z","year":"2015","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","publist_id":"5244","ec_funded":1,"article_number":"9"},{"publist_id":"7441","issue":"1","abstract":[{"lang":"eng","text":"We use ultrafast optical spectroscopy to observe binding of charged single-particle excitations (SE) in the magnetically frustrated Mott insulator Na2IrO3. Above the antiferromagnetic ordering temperature (TN) the system response is due to both Hubbard excitons (HE) and their constituent unpaired SE. The SE response becomes strongly suppressed immediately below TN. We argue that this increase in binding energy is due to a unique interplay between the frustrated Kitaev and the weak Heisenberg-type ordering term in the Hamiltonian, mediating an effective interaction between the spin-singlet SE. This interaction grows with distance causing the SE to become trapped in the HE, similar to quark confinement inside hadrons. This binding of charged particles, induced by magnetic ordering, is a result of a confinement-deconfinement transition of spin excitations. This observation provides evidence for spin liquid type behavior which is expected in Na2IrO3."}],"extern":"1","type":"journal_article","author":[{"full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","last_name":"Alpichshev"},{"last_name":"Mahmood","first_name":"Fahad","full_name":"Mahmood, Fahad"},{"full_name":"Cao, Gang","first_name":"Gang","last_name":"Cao"},{"full_name":"Gedik, Nuh","last_name":"Gedik","first_name":"Nuh"}],"oa_version":"Published Version","volume":114,"date_updated":"2021-01-12T07:52:54Z","date_created":"2018-12-11T11:46:11Z","_id":"388","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","intvolume":" 114","publisher":"American Physical Society","status":"public","title":"Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3","publication_status":"published","article_processing_charge":"No","month":"07","day":"07","date_published":"2015-07-07T00:00:00Z","doi":"10.1103/PhysRevLett.114.017203","language":[{"iso":"eng"}],"citation":{"mla":"Alpichshev, Zhanybek, et al. “Confinement Deconfinement Transition as an Indication of Spin Liquid Type Behavior in Na2IrO3.” Physical Review Letters, vol. 114, no. 1, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.017203.","short":"Z. Alpichshev, F. Mahmood, G. Cao, N. Gedik, Physical Review Letters 114 (2015).","chicago":"Alpichshev, Zhanybek, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Confinement Deconfinement Transition as an Indication of Spin Liquid Type Behavior in Na2IrO3.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.017203.","ama":"Alpichshev Z, Mahmood F, Cao G, Gedik N. Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters. 2015;114(1). doi:10.1103/PhysRevLett.114.017203","ista":"Alpichshev Z, Mahmood F, Cao G, Gedik N. 2015. Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters. 114(1).","ieee":"Z. Alpichshev, F. Mahmood, G. Cao, and N. Gedik, “Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3,” Physical Review Letters, vol. 114, no. 1. American Physical Society, 2015.","apa":"Alpichshev, Z., Mahmood, F., Cao, G., & Gedik, N. (2015). Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.017203"},"main_file_link":[{"open_access":"1","url":"https://dspace.mit.edu/handle/1721.1/92979"}],"oa":1,"publication":"Physical Review Letters","article_type":"original","quality_controlled":"1"},{"month":"07","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","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"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprints.cs.univie.ac.at/4368/"}],"language":[{"iso":"eng"}],"doi":"10.1109/LICS.2015.34","conference":{"name":"LICS: Logic in Computer Science","start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10"},"article_number":"7174888","ec_funded":1,"publist_id":"5489","publisher":"IEEE","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"K. C. is supported by the Austrian Science Fund (FWF): P23499-N23 and S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award. M. H. is supported by the Austrian Science Fund (FWF): P23499-N23 and the Vienna Science and Technology Fund (WWTF) grant ICT10-002. V. L. is supported by the Vienna Science and Technology Fund (WWTF) grant ICT10-002. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement no. 340506.","year":"2015","volume":"2015-July","date_created":"2018-12-11T11:53:19Z","date_updated":"2023-02-23T12:20:05Z","related_material":{"record":[{"id":"464","status":"public","relation":"later_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for One-Pair and k-Pair Streett Objectives.” Proceedings - Symposium on Logic in Computer Science, vol. 2015–July, 7174888, IEEE, 2015, doi:10.1109/LICS.2015.34.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for One-Pair and k-Pair Streett Objectives.” In Proceedings - Symposium on Logic in Computer Science, Vol. 2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.34.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for one-pair and k-pair Streett objectives. In: Proceedings - Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.34","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for one-pair and k-pair Streett objectives,” in Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015, vol. 2015–July.","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2015). Improved algorithms for one-pair and k-pair Streett objectives. In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.34","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2015. Improved algorithms for one-pair and k-pair Streett objectives. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174888."},"publication":"Proceedings - Symposium on Logic in Computer Science","date_published":"2015-07-01T00:00:00Z","type":"conference","abstract":[{"text":"The computation of the winning set for one-pair Streett objectives and for k-pair Streett objectives in (standard) graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formed ness of specifications, and the synthesis of reactive systems. We give faster algorithms for the computation of the winning set for (1) one-pair Streett objectives (aka parity-3 problem) in game graphs and (2) for k-pair Streett objectives in graphs. For both problems this represents the first improvement in asymptotic running time in 15 years.","lang":"eng"}],"status":"public","title":"Improved algorithms for one-pair and k-pair Streett objectives","_id":"1661","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Submitted Version"},{"page":"65 - 115","publication":"Journal de l'Ecole Polytechnique - Mathematiques","citation":{"mla":"Lewin, Mathieu, et al. “Derivation of Nonlinear Gibbs Measures from Many-Body Quantum Mechanics.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 2, Ecole Polytechnique, 2015, pp. 65–115, doi:10.5802/jep.18.","short":"M. Lewin, P. Nam, N. Rougerie, Journal de l’Ecole Polytechnique - Mathematiques 2 (2015) 65–115.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “Derivation of Nonlinear Gibbs Measures from Many-Body Quantum Mechanics.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2015. https://doi.org/10.5802/jep.18.","ama":"Lewin M, Nam P, Rougerie N. Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. 2015;2:65-115. doi:10.5802/jep.18","ista":"Lewin M, Nam P, Rougerie N. 2015. Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. 2, 65–115.","apa":"Lewin, M., Nam, P., & Rougerie, N. (2015). Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.18","ieee":"M. Lewin, P. Nam, and N. Rougerie, “Derivation of nonlinear gibbs measures from many-body quantum mechanics,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 2. Ecole Polytechnique, pp. 65–115, 2015."},"date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","ddc":["539"],"title":"Derivation of nonlinear gibbs measures from many-body quantum mechanics","status":"public","intvolume":" 2","_id":"473","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"4974","relation":"main_file","date_created":"2018-12-12T10:12:53Z","date_updated":"2020-07-14T12:46:35Z","checksum":"a40eb4016717ddc9927154798a4c164a","file_name":"IST-2018-951-v1+1_2015_Thanh-Nam_Derivation_of.pdf","access_level":"open_access","creator":"system","file_size":1084254,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"951","type":"journal_article","abstract":[{"lang":"eng","text":"We prove that nonlinear Gibbs measures can be obtained from the corresponding many-body, grand-canonical, quantum Gibbs states, in a mean-field limit where the temperature T diverges and the interaction strength behaves as 1/T. We proceed by characterizing the interacting Gibbs state as minimizing a functional counting the free-energy relatively to the non-interacting case. We then perform an infinite-dimensional analogue of phase-space semiclassical analysis, using fine properties of the quantum relative entropy, the link between quantum de Finetti measures and upper/lower symbols in a coherent state basis, as well as Berezin-Lieb type inequalities. Our results cover the measure built on the defocusing nonlinear Schrödinger functional on a finite interval, as well as smoother interactions in dimensions d 2."}],"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.5802/jep.18","month":"01","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Ecole Polytechnique","year":"2015","date_created":"2018-12-11T11:46:40Z","date_updated":"2021-01-12T08:00:52Z","volume":2,"author":[{"last_name":"Lewin","first_name":"Mathieu","full_name":"Lewin, Mathieu"},{"last_name":"Phan Thanh","first_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan Thanh, Nam"},{"first_name":"Nicolas","last_name":"Rougerie","full_name":"Rougerie, Nicolas"}],"file_date_updated":"2020-07-14T12:46:35Z","publist_id":"7344","ec_funded":1},{"citation":{"ama":"Holst K, Guseva D, Schindler S, et al. The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. 2015;128(15):2866-2880. doi:10.1242/jcs.167999","ieee":"K. Holst et al., “The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells,” Journal of Cell Science, vol. 128, no. 15. Company of Biologists, pp. 2866–2880, 2015.","apa":"Holst, K., Guseva, D., Schindler, S., Sixt, M. K., Braun, A., Chopra, H., … Ponimaskin, E. (2015). The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.167999","ista":"Holst K, Guseva D, Schindler S, Sixt MK, Braun A, Chopra H, Pabst O, Ponimaskin E. 2015. The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. 128(15), 2866–2880.","short":"K. Holst, D. Guseva, S. Schindler, M.K. Sixt, A. Braun, H. Chopra, O. Pabst, E. Ponimaskin, Journal of Cell Science 128 (2015) 2866–2880.","mla":"Holst, Katrin, et al. “The Serotonin Receptor 5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.” Journal of Cell Science, vol. 128, no. 15, Company of Biologists, 2015, pp. 2866–80, doi:10.1242/jcs.167999.","chicago":"Holst, Katrin, Daria Guseva, Susann Schindler, Michael K Sixt, Armin Braun, Himpriya Chopra, Oliver Pabst, and Evgeni Ponimaskin. “The Serotonin Receptor 5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.167999."},"publication":"Journal of Cell Science","page":"2866 - 2880","quality_controlled":"1","date_published":"2015-06-15T00:00:00Z","doi":"10.1242/jcs.167999","language":[{"iso":"eng"}],"scopus_import":1,"day":"15","month":"06","_id":"477","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"intvolume":" 128","title":"The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells","publication_status":"published","status":"public","author":[{"full_name":"Holst, Katrin","first_name":"Katrin","last_name":"Holst"},{"full_name":"Guseva, Daria","first_name":"Daria","last_name":"Guseva"},{"full_name":"Schindler, Susann","first_name":"Susann","last_name":"Schindler"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Armin","last_name":"Braun","full_name":"Braun, Armin"},{"full_name":"Chopra, Himpriya","last_name":"Chopra","first_name":"Himpriya"},{"first_name":"Oliver","last_name":"Pabst","full_name":"Pabst, Oliver"},{"full_name":"Ponimaskin, Evgeni","first_name":"Evgeni","last_name":"Ponimaskin"}],"volume":128,"oa_version":"None","date_updated":"2021-01-12T08:00:54Z","date_created":"2018-12-11T11:46:41Z","type":"journal_article","publist_id":"7343","issue":"15","abstract":[{"lang":"eng","text":"Dendritic cells are potent antigen-presenting cells endowed with the unique ability to initiate adaptive immune responses upon inflammation. Inflammatory processes are often associated with an increased production of serotonin, which operates by activating specific receptors. However, the functional role of serotonin receptors in regulation of dendritic cell functions is poorly understood. Here, we demonstrate that expression of serotonin receptor 5-HT7 (5-HT7TR) as well as its downstream effector Cdc42 is upregulated in dendritic cells upon maturation. Although dendritic cell maturation was independent of 5-HT7TR, receptor stimulation affected dendritic cell morphology through Cdc42-mediated signaling. In addition, basal activity of 5-HT7TR was required for the proper expression of the chemokine receptor CCR7, which is a key factor that controls dendritic cell migration. Consistent with this, we observed that 5-HT7TR enhances chemotactic motility of dendritic cells in vitro by modulating their directionality and migration velocity. Accordingly, migration of dendritic cells in murine colon explants was abolished after pharmacological receptor inhibition. Our results indicate that there is a crucial role for 5-HT7TR-Cdc42-mediated signaling in the regulation of dendritic cell morphology and motility, suggesting that 5-HT7TR could be a new target for treatment of a variety of inflammatory and immune disorders."}]},{"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"first_name":"Mickael","last_name":"Randour","full_name":"Randour, Mickael"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2279"}]},"date_created":"2018-12-11T11:46:57Z","date_updated":"2023-02-23T10:36:02Z","volume":242,"year":"2015","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"publist_id":"7296","ec_funded":1,"doi":"10.1016/j.ic.2015.03.010","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1302.4248","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"03","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"523","title":"Looking at mean-payoff and total-payoff through windows","status":"public","intvolume":" 242","abstract":[{"lang":"eng","text":"We consider two-player games played on weighted directed graphs with mean-payoff and total-payoff objectives, two classical quantitative objectives. While for single-dimensional games the complexity and memory bounds for both objectives coincide, we show that in contrast to multi-dimensional mean-payoff games that are known to be coNP-complete, multi-dimensional total-payoff games are undecidable. We introduce conservative approximations of these objectives, where the payoff is considered over a local finite window sliding along a play, instead of the whole play. For single dimension, we show that (i) if the window size is polynomial, deciding the winner takes polynomial time, and (ii) the existence of a bounded window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff games. For multiple dimensions, we show that (i) the problem with fixed window size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to decide the existence of a bounded window."}],"issue":"6","type":"journal_article","date_published":"2015-03-24T00:00:00Z","publication":"Information and Computation","citation":{"mla":"Chatterjee, Krishnendu, et al. “Looking at Mean-Payoff and Total-Payoff through Windows.” Information and Computation, vol. 242, no. 6, Elsevier, 2015, pp. 25–52, doi:10.1016/j.ic.2015.03.010.","short":"K. Chatterjee, L. Doyen, M. Randour, J. Raskin, Information and Computation 242 (2015) 25–52.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin. “Looking at Mean-Payoff and Total-Payoff through Windows.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.010.","ama":"Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff through windows. Information and Computation. 2015;242(6):25-52. doi:10.1016/j.ic.2015.03.010","ista":"Chatterjee K, Doyen L, Randour M, Raskin J. 2015. Looking at mean-payoff and total-payoff through windows. Information and Computation. 242(6), 25–52.","apa":"Chatterjee, K., Doyen, L., Randour, M., & Raskin, J. (2015). Looking at mean-payoff and total-payoff through windows. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.010","ieee":"K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” Information and Computation, vol. 242, no. 6. Elsevier, pp. 25–52, 2015."},"page":"25 - 52","day":"24","scopus_import":1},{"language":[{"iso":"eng"}],"date_published":"2015-10-22T00:00:00Z","doi":"10.1016/j.cell.2015.09.037","quality_controlled":"1","page":"670 - 683","publication":"Cell","citation":{"chicago":"Li, Wenyang, Mengdi Ma, Ying Feng, Hongjiang Li, Yichuan Wang, Yutong Ma, Mingzhe Li, Fengying An, and Hongwei Guo. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.09.037.","mla":"Li, Wenyang, et al. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” Cell, vol. 163, no. 3, Cell Press, 2015, pp. 670–83, doi:10.1016/j.cell.2015.09.037.","short":"W. Li, M. Ma, Y. Feng, H. Li, Y. Wang, Y. Ma, M. Li, F. An, H. Guo, Cell 163 (2015) 670–683.","ista":"Li W, Ma M, Feng Y, Li H, Wang Y, Ma Y, Li M, An F, Guo H. 2015. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 163(3), 670–683.","ieee":"W. Li et al., “EIN2-directed translational regulation of ethylene signaling in arabidopsis,” Cell, vol. 163, no. 3. Cell Press, pp. 670–683, 2015.","apa":"Li, W., Ma, M., Feng, Y., Li, H., Wang, Y., Ma, Y., … Guo, H. (2015). EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.09.037","ama":"Li W, Ma M, Feng Y, et al. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 2015;163(3):670-683. doi:10.1016/j.cell.2015.09.037"},"month":"10","day":"22","scopus_import":1,"date_created":"2018-12-11T11:47:00Z","date_updated":"2021-01-12T08:01:27Z","oa_version":"None","volume":163,"author":[{"first_name":"Wenyang","last_name":"Li","full_name":"Li, Wenyang"},{"full_name":"Ma, Mengdi","first_name":"Mengdi","last_name":"Ma"},{"full_name":"Feng, Ying","first_name":"Ying","last_name":"Feng"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","last_name":"Li","full_name":"Li, Hongjiang"},{"full_name":"Wang, Yichuan","first_name":"Yichuan","last_name":"Wang"},{"last_name":"Ma","first_name":"Yutong","full_name":"Ma, Yutong"},{"full_name":"Li, Mingzhe","first_name":"Mingzhe","last_name":"Li"},{"first_name":"Fengying","last_name":"An","full_name":"An, Fengying"},{"last_name":"Guo","first_name":"Hongwei","full_name":"Guo, Hongwei"}],"status":"public","title":"EIN2-directed translational regulation of ethylene signaling in arabidopsis","publication_status":"published","department":[{"_id":"JiFr"}],"intvolume":" 163","publisher":"Cell Press","_id":"532","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","abstract":[{"text":"Ethylene is a gaseous phytohormone that plays vital roles in plant growth and development. Previous studies uncovered EIN2 as an essential signal transducer linking ethylene perception on ER to transcriptional regulation in the nucleus through a “cleave and shuttle” model. In this study, we report another mechanism of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational repression and identify multiple poly-uridylates (PolyU) motifs as functional cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2 to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body (P-body) through interacting with multiple P-body factors, including EIN5 and PABs. Our study illustrates translational regulation as a key step in ethylene signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense and relay cellular signaling in plants.","lang":"eng"}],"publist_id":"7285","issue":"3","type":"journal_article"},{"publist_id":"7295","date_created":"2018-12-11T11:46:57Z","date_updated":"2023-02-23T12:24:45Z","volume":242,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}],"related_material":{"record":[{"id":"5403","status":"public","relation":"earlier_version"}]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"year":"2015","month":"10","language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2015.03.009","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1409.5306"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.5306"}],"abstract":[{"text":"We consider concurrent games played by two players on a finite-state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to each transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question of whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show that for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies, or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of turn-based deterministic mean-payoff games) that is not known to be solvable in polynomial time.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Preprint","status":"public","title":"Qualitative analysis of concurrent mean payoff games","intvolume":" 242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"524","day":"11","scopus_import":1,"date_published":"2015-10-11T00:00:00Z","page":"2 - 24","publication":"Information and Computation","citation":{"ama":"Chatterjee K, Ibsen-Jensen R. Qualitative analysis of concurrent mean payoff games. Information and Computation. 2015;242(6):2-24. doi:10.1016/j.ic.2015.03.009","ista":"Chatterjee K, Ibsen-Jensen R. 2015. Qualitative analysis of concurrent mean payoff games. Information and Computation. 242(6), 2–24.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Qualitative analysis of concurrent mean payoff games,” Information and Computation, vol. 242, no. 6. Elsevier, pp. 2–24, 2015.","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2015). Qualitative analysis of concurrent mean payoff games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.009","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent Mean Payoff Games.” Information and Computation, vol. 242, no. 6, Elsevier, 2015, pp. 2–24, doi:10.1016/j.ic.2015.03.009.","short":"K. Chatterjee, R. Ibsen-Jensen, Information and Computation 242 (2015) 2–24.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent Mean Payoff Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.009."}},{"month":"01","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"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2015-01-30","location":"Austin, TX, USA","start_date":"2015-01-25","name":"AAAI: Conference on Artificial Intelligence"},"publist_id":"5713","ec_funded":1,"publication_status":"published","publisher":"AAAI Press","department":[{"_id":"KrCh"}],"year":"2015","acknowledgement":"A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n","date_updated":"2023-02-23T12:25:07Z","date_created":"2018-12-11T11:52:16Z","volume":2,"author":[{"full_name":"Ahmed, Umair","first_name":"Umair","last_name":"Ahmed"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Gulwani, Sumit","last_name":"Gulwani","first_name":"Sumit"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5410"}]},"scopus_import":1,"day":"01","article_processing_charge":"No","page":"745 - 752","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence","citation":{"chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2:745–52. AAAI Press, 2015.","mla":"Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, vol. 2, AAAI Press, 2015, pp. 745–52.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.","ista":"Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative starting positions for simple traditional board games. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2, 745–752.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative starting positions for simple traditional board games,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, Austin, TX, USA, 2015, vol. 2, pp. 745–752.","apa":"Ahmed, U., Chatterjee, K., & Gulwani, S. (2015). Automatic generation of alternative starting positions for simple traditional board games. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 2, pp. 745–752). Austin, TX, USA: AAAI Press.","ama":"Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting positions for simple traditional board games. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. Vol 2. AAAI Press; 2015:745-752."},"date_published":"2015-01-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. "}],"status":"public","title":"Automatic generation of alternative starting positions for simple traditional board games","intvolume":" 2","_id":"1481","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None"},{"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IEEE","year":"2015","date_created":"2018-12-11T11:53:43Z","date_updated":"2023-02-23T12:25:52Z","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"},{"last_name":"Gupta","first_name":"Raghav","full_name":"Gupta, Raghav"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"}],"related_material":{"record":[{"id":"5424","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"5426"}]},"ec_funded":1,"publist_id":"5394","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"external_id":{"arxiv":["1409.3360"]},"main_file_link":[{"url":"http://arxiv.org/abs/1409.3360","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICRA: International Conference on Robotics and Automation","location":"Seattle, WA, United States","start_date":"2015-05-26","end_date":"2015-05-30"},"doi":"10.1109/ICRA.2015.7139019","month":"01","status":"public","title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","_id":"1732","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty."}],"page":"325 - 330","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. ICRA: International Conference on Robotics and Automation, 325–330.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications (pp. 325–330). Presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States: IEEE. https://doi.org/10.1109/ICRA.2015.7139019","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Qualitative analysis of POMDPs with temporal logic specifications for robotics applications,” presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States, 2015, pp. 325–330.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. In: IEEE; 2015:325-330. doi:10.1109/ICRA.2015.7139019","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications,” 325–30. IEEE, 2015. https://doi.org/10.1109/ICRA.2015.7139019.","mla":"Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IEEE, 2015, pp. 325–30, doi:10.1109/ICRA.2015.7139019.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, IEEE, 2015, pp. 325–330."},"date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01"},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:53Z","abstract":[{"lang":"eng","text":"We consider finite-state concurrent stochastic games, played by k>=2 players for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. We consider reachability objectives that given a target set of states require that some state in the target set is visited, and the dual safety objectives that given a target set require that only states in the target set are visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed.\r\n\r\n Our main results are as follows: We show that in two-player zero-sum concurrent stochastic games (with reachability objective for one player and the complementary safety objective for the other player): (i) the optimal bound on the patience of optimal and epsilon-optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. In general we study the class of non-zero-sum games admitting epsilon-Nash equilibria. We show that if there is at least one player with reachability objective, then doubly-exponential patience is needed in general for epsilon-Nash equilibrium strategies, whereas in contrast if all players have safety objectives, then the optimal bound on patience for epsilon-Nash equilibrium strategies is only exponential."}],"year":"2015","_id":"5431","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IST Austria","department":[{"_id":"KrCh"}],"title":"The patience of concurrent stochastic games with safety and reachability objectives","status":"public","publication_status":"published","ddc":["005","519"],"pubrep_id":"322","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Hansen, Kristoffer","first_name":"Kristoffer","last_name":"Hansen"}],"file":[{"file_id":"5491","relation":"main_file","date_created":"2018-12-12T11:53:31Z","date_updated":"2020-07-14T12:46:53Z","checksum":"bfb858262c30445b8e472c40069178a2","file_name":"IST-2015-322-v1+1_safetygames.pdf","access_level":"open_access","creator":"system","file_size":661015,"content_type":"application/pdf"}],"oa_version":"Published Version","date_updated":"2021-01-12T08:02:13Z","date_created":"2018-12-12T11:39:17Z","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"19","month":"02","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Hansen K. 2015. The patience of concurrent stochastic games with safety and reachability objectives, IST Austria, 25p.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Hansen, K. (2015). The patience of concurrent stochastic games with safety and reachability objectives. IST Austria. https://doi.org/10.15479/AT:IST-2015-322-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and K. Hansen, The patience of concurrent stochastic games with safety and reachability objectives. IST Austria, 2015.","ama":"Chatterjee K, Ibsen-Jensen R, Hansen K. The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives. IST Austria; 2015. doi:10.15479/AT:IST-2015-322-v1-1","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Kristoffer Hansen. The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-322-v1-1.","mla":"Chatterjee, Krishnendu, et al. The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives. IST Austria, 2015, doi:10.15479/AT:IST-2015-322-v1-1.","short":"K. Chatterjee, R. Ibsen-Jensen, K. Hansen, The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives, IST Austria, 2015."},"oa":1,"page":"25","date_published":"2015-02-19T00:00:00Z","doi":"10.15479/AT:IST-2015-322-v1-1","language":[{"iso":"eng"}]},{"month":"02","day":"19","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"date_published":"2015-02-19T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"mla":"Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria, 2015.","short":"1 Anonymous, 2 Anonymous, Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs, IST Austria, 2015.","chicago":"Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria, 2015.","ama":"Anonymous 1, Anonymous 2. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria; 2015.","ista":"Anonymous 1, Anonymous 2. 2015. Optimal cost indefinite-horizon reachability in goal DEC-POMDPs, IST Austria, 16p.","ieee":"1 Anonymous and 2 Anonymous, Optimal cost indefinite-horizon reachability in goal DEC-POMDPs. IST Austria, 2015.","apa":"Anonymous, 1, & Anonymous, 2. (2015). Optimal cost indefinite-horizon reachability in goal DEC-POMDPs. IST Austria."},"page":"16","abstract":[{"text":"DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. DEC-POMDPs have been studied with finite-horizon and infinite-horizon discounted-sum objectives, and there exist solvers both for exact and approximate solutions. 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 method to solve the problem that extends methods for finite-horizon DEC- POMDPs and the RTDP-Bel approach for POMDPs. We present experimental results on several examples, and show our approach presents promising results.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:53Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"author":[{"last_name":"Anonymous","first_name":"1","full_name":"Anonymous, 1"},{"full_name":"Anonymous, 2","last_name":"Anonymous","first_name":"2"}],"pubrep_id":"326","date_updated":"2020-07-14T23:04:59Z","date_created":"2018-12-12T11:39:18Z","oa_version":"Published Version","file":[{"file_size":378162,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-326-v1+1_main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:53Z","date_created":"2018-12-12T11:53:14Z","checksum":"8542fd0b10aed7811cd41077b8ccb632","relation":"main_file","file_id":"5475"},{"access_level":"closed","file_name":"IST-2015-326-v1+2_authors.txt","creator":"dernst","file_size":64,"content_type":"text/plain","file_id":"6317","relation":"main_file","checksum":"84c31c537bdaf7a91909f18d25d640ab","date_created":"2019-04-16T13:00:33Z","date_updated":"2020-07-14T12:46:53Z"}],"year":"2015","_id":"5434","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Optimal cost indefinite-horizon reachability in goal DEC-POMDPs","ddc":["000"],"status":"public","publication_status":"published","publisher":"IST Austria"},{"series_title":"LICS","scopus_import":1,"day":"01","page":"244 - 256","citation":{"ista":"Chatterjee K, Komárková Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes. , 244–256.","apa":"Chatterjee, K., Komárková, Z., & Kretinsky, J. (2015). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.32","ieee":"K. Chatterjee, Z. Komárková, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes.” IEEE, pp. 244–256, 2015.","ama":"Chatterjee K, Komárková Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. 2015:244-256. doi:10.1109/LICS.2015.32","chicago":"Chatterjee, Krishnendu, Zuzana Komárková, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” LICS. IEEE, 2015. https://doi.org/10.1109/LICS.2015.32.","mla":"Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IEEE, 2015, pp. 244–56, doi:10.1109/LICS.2015.32.","short":"K. Chatterjee, Z. Komárková, J. Kretinsky, (2015) 244–256."},"date_published":"2015-07-01T00:00:00Z","alternative_title":["LICS"],"type":"conference","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) ~the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) ~the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., Ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems, which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ","lang":"eng"}],"status":"public","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1657","oa_version":"None","month":"07","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1109/LICS.2015.32","conference":{"location":"Kyoto, Japan","start_date":"2015-07-06","end_date":"2015-07-10","name":"LICS: Logic in Computer Science"},"publist_id":"5493","ec_funded":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","year":"2015","acknowledgement":"A Technical Report of this paper is available at: https://repository.ist.ac.at/327\r\n","date_created":"2018-12-11T11:53:18Z","date_updated":"2023-02-23T12:26:16Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"466"},{"status":"public","relation":"earlier_version","id":"5429"},{"status":"public","relation":"earlier_version","id":"5435"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Komárková","first_name":"Zuzana","full_name":"Komárková, Zuzana"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"}]},{"publist_id":"5494","ec_funded":1,"article_number":"7174926","date_updated":"2023-02-23T12:26:19Z","date_created":"2018-12-11T11:53:17Z","volume":"2015-July","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"467"},{"id":"5415","status":"public","relation":"earlier_version"},{"id":"5436","status":"public","relation":"earlier_version"}]},"publication_status":"published","publisher":"IEEE","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available at: \r\nhttps://repository.ist.ac.at/331/\r\n","year":"2015","month":"07","language":[{"iso":"eng"}],"conference":{"start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10","name":"LICS: Logic in Computer Science"},"doi":"10.1109/LICS.2015.72","quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1606.03598"]},"abstract":[{"text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.","lang":"eng"}],"type":"conference","oa_version":"None","status":"public","title":"Nested weighted automata","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1656","day":"31","scopus_import":1,"date_published":"2015-07-31T00:00:00Z","publication":"Proceedings - Symposium on Logic in Computer Science","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” In Proceedings - Symposium on Logic in Computer Science, Vol. 2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.72.","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” Proceedings - Symposium on Logic in Computer Science, vol. 2015–July, 7174926, IEEE, 2015, doi:10.1109/LICS.2015.72.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174926.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015, vol. 2015–July.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata. In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.72","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: Proceedings - Symposium on Logic in Computer Science. Vol 2015-July. 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We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions.\r\nFinally, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem."}],"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":"Komarkova, Zuzana","last_name":"Komarkova","first_name":"Zuzana"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"pubrep_id":"318","related_material":{"record":[{"relation":"later_version","status":"public","id":"1657"},{"status":"public","relation":"later_version","id":"466"},{"relation":"later_version","status":"public","id":"5435"}]},"date_updated":"2023-02-23T12:26:16Z","date_created":"2018-12-12T11:39:17Z","file":[{"file_name":"IST-2015-318-v1+1_main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":689863,"file_id":"5533","relation":"main_file","date_created":"2018-12-12T11:54:11Z","date_updated":"2020-07-14T12:46:52Z","checksum":"e4869a584567c506349abda9c8ec7db3"}],"oa_version":"Published Version","_id":"5429","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","ddc":["004"],"publication_status":"published","publisher":"IST Austria","department":[{"_id":"KrCh"}]},{"publication_status":"published","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","ddc":["004"],"status":"public","department":[{"_id":"KrCh"}],"publisher":"IST Austria","_id":"5435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_updated":"2023-02-23T12:26:00Z","date_created":"2018-12-12T11:39:19Z","oa_version":"Published Version","file":[{"creator":"system","file_size":717630,"content_type":"application/pdf","file_name":"IST-2015-318-v2+1_main.pdf","access_level":"open_access","date_created":"2018-12-12T11:54:03Z","date_updated":"2020-07-14T12:46:53Z","checksum":"75284adec80baabdfe71ff9ebbc27445","file_id":"5525","relation":"main_file"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Komarkova","first_name":"Zuzana","full_name":"Komarkova, Zuzana"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"}],"pubrep_id":"327","related_material":{"record":[{"relation":"later_version","status":"public","id":"1657"},{"status":"public","relation":"later_version","id":"466"},{"id":"5429","relation":"earlier_version","status":"public"}]},"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:53Z","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. \r\nThere have been two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. \r\nWe consider the problem where the goal is to optimize the expectation under the constraint that the satisfaction semantics is ensured, and thus consider a generalization that unifies the existing semantics. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensures certain probabilistic guarantee).\r\nOur main results are algorithms for the decision problem which are always polynomial in the size of the MDP.\r\nWe also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Finally, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem.","lang":"eng"}],"page":"51","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v2-1.","mla":"Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. 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Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761.","chicago":"Boker, Udi, Thomas A Henzinger, and Jan Otop. “The Target Discounted-Sum Problem.” In LICS, 750–61. Logic in Computer Science. IEEE, 2015. https://doi.org/10.1109/LICS.2015.74.","ama":"Boker U, Henzinger TA, Otop J. The target discounted-sum problem. In: LICS. Logic in Computer Science. IEEE; 2015:750-761. doi:10.1109/LICS.2015.74","ista":"Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS. LICS: Logic in Computer ScienceLogic in Computer Science, 750–761.","ieee":"U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,” in LICS, Kyoto, Japan, 2015, pp. 750–761.","apa":"Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. In LICS (pp. 750–761). 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The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata."}],"type":"conference"},{"year":"2015","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer Nature","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"}],"related_material":{"record":[{"id":"465","status":"public","relation":"later_version"},{"id":"5438","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T12:26:24Z","date_created":"2018-12-11T11:53:01Z","volume":9135,"ec_funded":1,"publist_id":"5556","external_id":{"arxiv":["1504.08259"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.08259","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10"},"doi":"10.1007/978-3-662-47666-6_10","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"isbn":["978-3-662-47665-9"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1610","title":"Edit distance for pushdown automata","status":"public","intvolume":" 9135","pubrep_id":"321","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1,L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to pushdown automata is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k.","lang":"eng"}],"issue":"Part II","publication":"42nd International Colloquium","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. In 42nd International Colloquium (Vol. 9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, no. Part II, pp. 121–133.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 121–133.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:121-133. doi:10.1007/978-3-662-47666-6_10","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium, 9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 121–133.","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” 42nd International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp. 121–33, doi:10.1007/978-3-662-47666-6_10."},"page":"121 - 133","date_published":"2015-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"doi":"10.15479/AT:IST-2015-330-v2-1","date_published":"2015-04-27T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 27p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-330-v2-1","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-330-v2-1","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-330-v2-1.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-330-v2-1.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015."},"oa":1,"page":"27","month":"04","day":"27","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"pubrep_id":"333","related_material":{"record":[{"id":"1607","status":"public","relation":"later_version"},{"id":"5430","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-12T11:39:19Z","date_updated":"2023-02-23T12:26:05Z","file":[{"relation":"main_file","file_id":"5473","date_updated":"2020-07-14T12:46:54Z","date_created":"2018-12-12T11:53:12Z","checksum":"f5917c20f84018b362d385c000a2e123","file_name":"IST-2015-330-v2+1_main.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1072137,"creator":"system"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5437","year":"2015","ddc":["000"],"status":"public","title":"Faster algorithms for quantitative verification in constant treewidth graphs","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IST Austria","abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. \r\nThe algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let $n$ denote the number of nodes of a graph, $m$ the number of edges (for constant treewidth graphs $m=O(n)$) and $W$ the largest absolute value of the weights.\r\nOur main theoretical results are as follows.\r\nFirst, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of $\\epsilon$ in time $O(n \\cdot \\log (n/\\epsilon))$ and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time $O(n \\cdot \\log (|a\\cdot b|))=O(n\\cdot\\log (n\\cdot W))$, when the output is $\\frac{a}{b}$, as compared to the previously best known algorithm with running time $O(n^2 \\cdot \\log (n\\cdot W))$. Third, for the minimum initial credit problem we show that (i)~for general graphs the problem can be solved in $O(n^2\\cdot m)$ time and the associated decision problem can be solved in $O(n\\cdot m)$ time, improving the previous known $O(n^3\\cdot m\\cdot \\log (n\\cdot W))$ and $O(n^2 \\cdot m)$ bounds, respectively; and (ii)~for constant treewidth graphs we present an algorithm that requires $O(n\\cdot \\log n)$ time, improving the previous known $O(n^4 \\cdot \\log (n \\cdot W))$ bound.\r\nWe have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:54Z","type":"technical_report","alternative_title":["IST Austria Technical Report"]},{"oa":1,"citation":{"mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-319-v1-1.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-319-v1-1.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-319-v1-1","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 31p.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-319-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. 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The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m = O ( n ) ) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a mul- tiplicative factor of ∊ in time O ( n · log( n/∊ )) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O ( n · log( | a · b · n | )) = O ( n · log( n · W )) , when the output is a b , as compared to the previously best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O ( n 2 · m ) time and the associated decision problem can be solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n · W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O ( n · log n ) time, improving the previous known O ( n 4 · log( n · W )) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}]},{"day":"18","month":"05","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"date_published":"2015-05-18T00:00:00Z","doi":"10.15479/AT:IST-2015-335-v1-1","page":"20","citation":{"mla":"Boker, Udi, et al. The Target Discounted-Sum Problem. IST Austria, 2015, doi:10.15479/AT:IST-2015-335-v1-1.","short":"U. Boker, T.A. Henzinger, J. Otop, The Target Discounted-Sum Problem, IST Austria, 2015.","chicago":"Boker, Udi, Thomas A Henzinger, and Jan Otop. The Target Discounted-Sum Problem. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-335-v1-1.","ama":"Boker U, Henzinger TA, Otop J. The Target Discounted-Sum Problem. IST Austria; 2015. doi:10.15479/AT:IST-2015-335-v1-1","ista":"Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem, IST Austria, 20p.","apa":"Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. IST Austria. https://doi.org/10.15479/AT:IST-2015-335-v1-1","ieee":"U. Boker, T. A. Henzinger, and J. Otop, The target discounted-sum problem. IST Austria, 2015."},"oa":1,"file_date_updated":"2020-07-14T12:46:55Z","abstract":[{"lang":"eng","text":"The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata. "}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","date_created":"2018-12-12T11:39:20Z","date_updated":"2023-02-23T10:08:48Z","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:55Z","date_created":"2018-12-12T11:53:55Z","checksum":"40405907aa012acece1bc26cf0be554d","relation":"main_file","file_id":"5517","content_type":"application/pdf","file_size":589619,"creator":"system","file_name":"IST-2015-335-v1+1_report.pdf","access_level":"open_access"}],"author":[{"full_name":"Boker, Udi","first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"related_material":{"record":[{"id":"1659","relation":"later_version","status":"public"}]},"pubrep_id":"335","ddc":["004","512","513"],"publication_status":"published","status":"public","title":"The target discounted-sum problem","department":[{"_id":"ToHe"}],"publisher":"IST Austria","_id":"5439","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"05","month":"05","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"date_published":"2015-05-05T00:00:00Z","doi":"10.15479/AT:IST-2015-334-v1-1","page":"15","citation":{"ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance for pushdown automata. IST Austria, 2015.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata, IST Austria, 15p.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1."},"oa":1,"abstract":[{"lang":"eng","text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses.\r\nThe problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k. 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The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v2-2","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 18p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v2-2","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v2-2.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v2-2."},"oa":1,"month":"06","day":"16","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:21Z","date_updated":"2023-02-23T12:26:10Z","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":466161,"file_name":"IST-2015-323-v2+2_main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:56Z","date_created":"2018-12-12T11:53:23Z","checksum":"66aace7d367032af97c15e35c9be9636","file_id":"5484","relation":"main_file"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"pubrep_id":"338","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5421"},{"status":"public","relation":"earlier_version","id":"5432"}]},"title":"The complexity of evolutionary games on graphs","publication_status":"published","status":"public","ddc":["005","576"],"department":[{"_id":"KrCh"}],"publisher":"IST Austria","_id":"5440","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom for payoff in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. The fitness (or the reproductive rate) is a non-negative number, and depends on the payoff. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are as follows: First, we consider a special case of the general problem, where the residents do not reproduce. We show that the qualitative question is NP-complete, and the quantitative approximation question is #P-complete, and the hardness results hold even in the special case where the interaction and the replacement graphs coincide. Second, we show that in general both the qualitative and the quantitative approximation questions are PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds even when the fitness is always positive.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:56Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5432","year":"2015","title":"The complexity of evolutionary games on graphs","ddc":["005","576"],"publication_status":"published","status":"public","department":[{"_id":"KrCh"}],"publisher":"IST Austria","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"pubrep_id":"323","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5421"},{"relation":"later_version","status":"public","id":"5440"}]},"date_updated":"2023-02-23T12:26:33Z","date_created":"2018-12-12T11:39:18Z","file":[{"date_created":"2018-12-12T11:53:57Z","date_updated":"2020-07-14T12:46:53Z","checksum":"546c1b291d545e7b24aaaf4199dac671","relation":"main_file","file_id":"5519","file_size":576347,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-323-v1+1_main.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:53Z","abstract":[{"lang":"eng","text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution.The replacement graph specifies who competes with whom for reproduction. \r\nThe vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. \r\nOur main results are:\r\n(1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure).\r\n(2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.\r\n"}],"oa":1,"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v1-1","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 29p.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v1-1."},"page":"29","date_published":"2015-02-19T00:00:00Z","doi":"10.15479/AT:IST-2015-323-v1-1","language":[{"iso":"eng"}],"month":"02","day":"19","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1"},{"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2015-399-v1-1","date_published":"2015-12-30T00:00:00Z","page":"25","oa":1,"citation":{"short":"J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue, B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers, IST Austria, 2015.","mla":"Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1.","chicago":"Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1.","ama":"Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1","apa":"Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers. IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1","ieee":"J. Reiter et al., Reconstructing robust phylogenies of metastatic cancers. IST Austria, 2015.","ista":"Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic cancers, IST Austria, 25p."},"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"30","month":"12","file":[{"checksum":"c47d33bdda06181753c0af36f16e7b5d","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:53:24Z","file_id":"5485","relation":"main_file","creator":"system","file_size":3533200,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2015-399-v1+1_treeomics.pdf"}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:22Z","date_updated":"2020-07-14T23:05:07Z","pubrep_id":"399","author":[{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter"},{"full_name":"Makohon-Moore, Alvin","first_name":"Alvin","last_name":"Makohon-Moore"},{"last_name":"Gerold","first_name":"Jeffrey","full_name":"Gerold, Jeffrey"},{"full_name":"Bozic, Ivana","first_name":"Ivana","last_name":"Bozic"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Christine","last_name":"Iacobuzio-Donahue","full_name":"Iacobuzio-Donahue, Christine"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"title":"Reconstructing robust phylogenies of metastatic cancers","publication_status":"published","status":"public","ddc":["000","576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5444","year":"2015","file_date_updated":"2020-07-14T12:46:58Z","abstract":[{"lang":"eng","text":"A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal."}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report"},{"page":"23","citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-325-v2-1.","mla":"Chatterjee, Krishnendu, et al. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria, 2015, doi:10.15479/AT:IST-2015-325-v2-1.","short":"K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.","ista":"Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.","apa":"Chatterjee, K., Chmelik, M., & Davies, J. (2015). A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs. IST Austria. https://doi.org/10.15479/AT:IST-2015-325-v2-1","ieee":"K. Chatterjee, M. Chmelik, and J. Davies, A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs. IST Austria, 2015.","ama":"Chatterjee K, Chmelik M, Davies J. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria; 2015. doi:10.15479/AT:IST-2015-325-v2-1"},"oa":1,"language":[{"iso":"eng"}],"date_published":"2015-11-06T00:00:00Z","doi":"10.15479/AT:IST-2015-325-v2-1","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"06","month":"11","department":[{"_id":"KrCh"}],"publisher":"IST Austria","status":"public","ddc":["000"],"publication_status":"published","title":"A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs","_id":"5443","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","file":[{"checksum":"f0fa31ad8161ed655137e94012123ef9","date_updated":"2020-07-14T12:46:57Z","date_created":"2018-12-12T11:53:05Z","file_id":"5466","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":412379,"access_level":"open_access","file_name":"IST-2015-325-v2+1_main.pdf"}],"oa_version":"Published Version","date_updated":"2023-02-21T16:24:05Z","date_created":"2018-12-12T11:39:22Z","related_material":{"record":[{"id":"1166","relation":"later_version","status":"public"}]},"pubrep_id":"362","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"full_name":"Davies, Jessica","first_name":"Jessica","last_name":"Davies","id":"378E0060-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","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 EXPTIME-complete, 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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:57Z"},{"publication_status":"published","title":"From prima quadraginta octant to lattice sphere through primitive integer operations","status":"public","publisher":"Elsevier","intvolume":" 624","year":"2015","_id":"5804","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-01-08T20:44:06Z","date_updated":"2021-01-12T08:03:36Z","oa_version":"None","volume":624,"author":[{"orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","first_name":"Ranita","full_name":"Biswas, Ranita"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"type":"journal_article","extern":"1","abstract":[{"text":"We present here the first integer-based algorithm for constructing a well-defined lattice sphere specified by integer radius and integer center. The algorithm evolves from a unique correspondence between the lattice points comprising the sphere and the distribution of sum of three square numbers in integer intervals. We characterize these intervals to derive a useful set of recurrences, which, in turn, aids in efficient computation. Each point of the lattice sphere is determined by resorting to only a few primitive operations in the integer domain. The symmetry of its quadraginta octants provides an added advantage by confining the computation to its prima quadraginta octant. Detailed theoretical analysis and experimental results have been furnished to demonstrate its simplicity and elegance.","lang":"eng"}],"issue":"4","quality_controlled":"1","page":"56-72","publication":"Theoretical Computer Science","citation":{"chicago":"Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.11.018.","mla":"Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” Theoretical Computer Science, vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:10.1016/j.tcs.2015.11.018.","short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72.","ista":"Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 624(4), 56–72.","apa":"Biswas, R., & Bhowmick, P. (2015). From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.11.018","ieee":"R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere through primitive integer operations,” Theoretical Computer Science, vol. 624, no. 4. Elsevier, pp. 56–72, 2015.","ama":"Biswas R, Bhowmick P. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 2015;624(4):56-72. doi:10.1016/j.tcs.2015.11.018"},"language":[{"iso":"eng"}],"date_published":"2015-04-18T00:00:00Z","doi":"10.1016/j.tcs.2015.11.018","month":"04","day":"18","publication_identifier":{"issn":["0304-3975"]}},{"issue":"11","extern":"1","type":"journal_article","author":[{"full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"date_created":"2019-01-08T20:44:52Z","date_updated":"2021-01-12T08:03:37Z","oa_version":"None","volume":605,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5807","year":"2015","status":"public","publication_status":"published","title":"On different topological classes of spherical geodesic paths and circles inZ3","publisher":"Elsevier","intvolume":" 605","month":"11","day":"09","publication_identifier":{"issn":["0304-3975"]},"date_published":"2015-11-09T00:00:00Z","doi":"10.1016/j.tcs.2015.09.003","language":[{"iso":"eng"}],"publication":"Theoretical Computer Science","citation":{"ieee":"R. Biswas and P. Bhowmick, “On different topological classes of spherical geodesic paths and circles inZ3,” Theoretical Computer Science, vol. 605, no. 11. Elsevier, pp. 146–163, 2015.","apa":"Biswas, R., & Bhowmick, P. (2015). On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.09.003","ista":"Biswas R, Bhowmick P. 2015. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163.","ama":"Biswas R, Bhowmick P. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 2015;605(11):146-163. doi:10.1016/j.tcs.2015.09.003","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.09.003.","short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163.","mla":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science, vol. 605, no. 11, Elsevier, 2015, pp. 146–63, doi:10.1016/j.tcs.2015.09.003."},"quality_controlled":"1","page":"146-163"},{"author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"date_updated":"2021-01-12T08:03:37Z","date_created":"2019-01-08T20:45:05Z","oa_version":"None","volume":31,"_id":"5808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","title":"Layer the sphere","status":"public","publication_status":"published","intvolume":" 31","publisher":"Springer Nature","issue":"6-8","extern":"1","type":"journal_article","doi":"10.1007/s00371-015-1101-3","date_published":"2015-05-08T00:00:00Z","language":[{"iso":"eng"}],"publication":"The Visual Computer","citation":{"ieee":"R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer, vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.","apa":"Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer. Springer Nature. https://doi.org/10.1007/s00371-015-1101-3","ista":"Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8), 787–797.","ama":"Biswas R, Bhowmick P. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797. doi:10.1007/s00371-015-1101-3","chicago":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer. Springer Nature, 2015. https://doi.org/10.1007/s00371-015-1101-3.","short":"R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.","mla":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer, vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:10.1007/s00371-015-1101-3."},"quality_controlled":"1","page":"787-797","month":"05","day":"08","publication_identifier":{"issn":["0178-2789","1432-2315"]}},{"month":"03","day":"26","article_processing_charge":"No","page":"129 - 143","publication":"Nature Reviews Molecular Cell Biology","citation":{"ista":"Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3), 129–143.","apa":"Sainsbury, S., Bernecky, C., & Cramer, P. (2015). Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3952","ieee":"S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription initiation by RNA polymerase II,” Nature Reviews Molecular Cell Biology, vol. 16, no. 3. Nature Publishing Group, pp. 129–143, 2015.","ama":"Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 2015;16(3):129-143. doi:10.1038/nrm3952","chicago":"Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3952.","mla":"Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular Cell Biology, vol. 16, no. 3, Nature Publishing Group, 2015, pp. 129–43, doi:10.1038/nrm3952.","short":"S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology 16 (2015) 129–143."},"language":[{"iso":"eng"}],"date_published":"2015-03-26T00:00:00Z","doi":"10.1038/nrm3952","type":"journal_article","extern":"1","abstract":[{"text":"Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.","lang":"eng"}],"publist_id":"7206","issue":"3","publication_status":"published","status":"public","title":"Structural basis of transcription initiation by RNA polymerase II","publisher":"Nature Publishing Group","intvolume":" 16","_id":"594","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:05:16Z","date_created":"2018-12-11T11:47:23Z","oa_version":"None","volume":16,"author":[{"last_name":"Sainsbury","first_name":"Sarah","full_name":"Sainsbury, Sarah"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A"},{"full_name":"Cramer, Patrick","first_name":"Patrick","last_name":"Cramer"}]},{"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.","lang":"eng"}],"ddc":["510"],"title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","status":"public","_id":"1511","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","file_size":636735,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-502-v1+1_42.pdf","checksum":"0945811875351796324189312ca29e9e","date_updated":"2020-07-14T12:44:59Z","date_created":"2018-12-12T10:11:18Z","file_id":"4871","relation":"main_file"}],"pubrep_id":"502","scopus_import":1,"day":"11","has_accepted_license":"1","page":"476 - 490","citation":{"ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.476","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 476–490.","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490. doi:10.4230/LIPIcs.SOCG.2015.476","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.476.","mla":"Goaoc, Xavier, et al. On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:10.4230/LIPIcs.SOCG.2015.476.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490."},"date_published":"2015-06-11T00:00:00Z","file_date_updated":"2020-07-14T12:44:59Z","ec_funded":1,"publist_id":"5666","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"acknowledgement":"The work by Z. P. was partially supported by the Charles University Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948).","year":"2015","date_updated":"2023-02-23T12:38:00Z","date_created":"2018-12-11T11:52:27Z","volume":"34 ","author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","first_name":"Zuzana","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"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":"610"}]},"month":"06","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"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"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2015-06-22","location":"Eindhoven, Netherlands","end_date":"2015-06-25"},"doi":"10.4230/LIPIcs.SOCG.2015.476"},{"_id":"6118","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","ddc":["570"],"title":"Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity","status":"public","file":[{"access_level":"open_access","file_name":"2015_PNAS_Fenk.pdf","file_size":2822681,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6119","checksum":"3d2da5af8d72467e382a565abc2e003d","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-19T14:21:07Z"}],"oa_version":"Published Version","type":"journal_article","issue":"27","abstract":[{"lang":"eng","text":"Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry."}],"citation":{"ama":"Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534. doi:10.1073/pnas.1423808112","ista":"Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.","apa":"Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1423808112","ieee":"L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity,” Proceedings of the National Academy of Sciences, vol. 112, no. 27. National Academy of Sciences, pp. E3525–E3534, 2015.","mla":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” Proceedings of the National Academy of Sciences, vol. 112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112.","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112 (2015) E3525–E3534.","chicago":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112."},"publication":"Proceedings of the National Academy of Sciences","page":"E3525-E3534","date_published":"2015-07-07T00:00:00Z","has_accepted_license":"1","day":"07","pmid":1,"year":"2015","publisher":"National Academy of Sciences","publication_status":"published","author":[{"full_name":"Fenk, Lorenz A.","last_name":"Fenk","first_name":"Lorenz A."},{"full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"volume":112,"date_updated":"2021-01-12T08:06:12Z","date_created":"2019-03-19T14:15:50Z","file_date_updated":"2020-07-14T12:47:20Z","extern":"1","external_id":{"pmid":["26100886"]},"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.1423808112","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"07"},{"abstract":[{"text":"Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed.","lang":"eng"}],"type":"journal_article","file":[{"file_size":6723528,"content_type":"application/pdf","creator":"kschuh","file_name":"2015_elife_Laurent.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-19T14:29:43Z","checksum":"cf641b7a363aecd0a101755d23dee7e0","relation":"main_file","file_id":"6121"}],"oa_version":"Published Version","title":"Decoding a neural circuit controlling global animal state in C. elegans","status":"public","ddc":["570"],"intvolume":" 4","_id":"6120","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"11","has_accepted_license":"1","date_published":"2015-03-11T00:00:00Z","publication":"eLife","citation":{"ista":"Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono M. 2015. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 4, e04241.","ieee":"P. Laurent et al., “Decoding a neural circuit controlling global animal state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015.","apa":"Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy, E., & de Bono, M. (2015). Decoding a neural circuit controlling global animal state in C. elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.04241","ama":"Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 2015;4. doi:10.7554/elife.04241","chicago":"Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/elife.04241.","mla":"Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” ELife, vol. 4, e04241, eLife Sciences Publications, 2015, doi:10.7554/elife.04241.","short":"P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy, M. de Bono, ELife 4 (2015)."},"extern":"1","file_date_updated":"2020-07-14T12:47:20Z","article_number":"e04241","date_created":"2019-03-19T14:23:51Z","date_updated":"2021-01-12T08:06:13Z","volume":4,"author":[{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"full_name":"Soltesz, Zoltan","last_name":"Soltesz","first_name":"Zoltan"},{"full_name":"Nelson, Geoffrey M","first_name":"Geoffrey M","last_name":"Nelson"},{"last_name":"Chen","first_name":"Changchun","full_name":"Chen, Changchun"},{"full_name":"Arellano-Carbajal, Fausto","last_name":"Arellano-Carbajal","first_name":"Fausto"},{"first_name":"Emmanuel","last_name":"Levy","full_name":"Levy, Emmanuel"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"}],"publication_status":"published","publisher":"eLife Sciences Publications","year":"2015","pmid":1,"month":"03","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/elife.04241","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"},"external_id":{"pmid":["25760081"]}},{"status":"public","title":"The complexity of general-valued CSPs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1637","oa_version":"Preprint","alternative_title":["56th Annual Symposium on Foundations of Computer Science"],"type":"conference","abstract":[{"lang":"eng","text":"An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs."}],"page":"1246 - 1258","citation":{"chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs,” 1246–58. IEEE, 2015. https://doi.org/10.1109/FOCS.2015.80.","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258.","mla":"Kolmogorov, Vladimir, et al. The Complexity of General-Valued CSPs. IEEE, 2015, pp. 1246–58, doi:10.1109/FOCS.2015.80.","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States, 2015, pp. 1246–1258.","apa":"Kolmogorov, V., Krokhin, A., & Rolinek, M. (2015). The complexity of general-valued CSPs (pp. 1246–1258). Presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States: IEEE. https://doi.org/10.1109/FOCS.2015.80","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2015. The complexity of general-valued CSPs. FOCS: Foundations of Computer Science, 56th Annual Symposium on Foundations of Computer Science, , 1246–1258.","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. In: IEEE; 2015:1246-1258. doi:10.1109/FOCS.2015.80"},"date_published":"2015-12-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","publisher":"IEEE","department":[{"_id":"VlKo"}],"year":"2015","date_updated":"2023-02-23T12:44:26Z","date_created":"2018-12-11T11:53:10Z","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","first_name":"Michal"}],"related_material":{"record":[{"relation":"other","status":"public","id":"644"}]},"ec_funded":1,"publist_id":"5518","quality_controlled":"1","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.07327"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2015-10-20","start_date":"2015-10-18","location":"Berkeley, CA, United States","name":"FOCS: Foundations of Computer Science"},"doi":"10.1109/FOCS.2015.80","month":"12"},{"day":"02","month":"11","publication_identifier":{"issn":["0006-4971","1528-0020"]},"doi":"10.1182/blood-2015-08-667055","date_published":"2015-11-02T00:00:00Z","language":[{"iso":"eng"}],"publication":"Blood","citation":{"ama":"Zhou L, Hinerman JM, Blaszczyk M, et al. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 2015;127(5):529-537. doi:10.1182/blood-2015-08-667055","ista":"Zhou L, Hinerman JM, Blaszczyk M, Miller JLC, Conrady DG, Barrow AD, Chirgadze DY, Bihan D, Farndale RW, Herr AB. 2015. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 127(5), 529–537.","ieee":"L. Zhou et al., “Structural basis for collagen recognition by the immune receptor OSCAR,” Blood, vol. 127, no. 5. American Society of Hematology, pp. 529–537, 2015.","apa":"Zhou, L., Hinerman, J. M., Blaszczyk, M., Miller, J. L. C., Conrady, D. G., Barrow, A. D., … Herr, A. B. (2015). Structural basis for collagen recognition by the immune receptor OSCAR. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2015-08-667055","mla":"Zhou, Long, et al. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood, vol. 127, no. 5, American Society of Hematology, 2015, pp. 529–37, doi:10.1182/blood-2015-08-667055.","short":"L. Zhou, J.M. Hinerman, M. Blaszczyk, J.L.C. Miller, D.G. Conrady, A.D. Barrow, D.Y. Chirgadze, D. Bihan, R.W. Farndale, A.B. Herr, Blood 127 (2015) 529–537.","chicago":"Zhou, Long, J. M. Hinerman, M. Blaszczyk, J. L. C. Miller, D. G. Conrady, A. D. Barrow, D. Y. Chirgadze, D. Bihan, R. W. Farndale, and A. B. Herr. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood. American Society of Hematology, 2015. https://doi.org/10.1182/blood-2015-08-667055."},"external_id":{"pmid":["26552697"]},"quality_controlled":"1","page":"529-537","abstract":[{"text":"The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor with important roles in dendritic cell maturation and activation of inflammatory monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR ectodomain is presented, both free and in complex with a consensus triple-helical peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like domain (D1 and D2). The THP binds near a predicted collagen-binding groove in D1, but a more extensive interaction with D2 is facilitated by the unusually wide D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI) and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows a higher affinity (KD 1.5 μM) when binding to a solid-phase THP, most likely due to an avidity effect. These data suggest a 2-stage model for the interaction of OSCAR with a collagen fibril, with transient, low-affinity interactions initiated by the membrane-distal D1, followed by firm adhesion to the primary binding site in D2.","lang":"eng"}],"issue":"5","extern":"1","type":"journal_article","author":[{"orcid":"0000-0002-1864-8951","id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou","first_name":"Long","full_name":"Zhou, Long"},{"full_name":"Hinerman, J. M.","first_name":"J. M.","last_name":"Hinerman"},{"last_name":"Blaszczyk","first_name":"M.","full_name":"Blaszczyk, M."},{"full_name":"Miller, J. L. C.","last_name":"Miller","first_name":"J. L. C."},{"full_name":"Conrady, D. G.","first_name":"D. G.","last_name":"Conrady"},{"last_name":"Barrow","first_name":"A. D.","full_name":"Barrow, A. D."},{"first_name":"D. Y.","last_name":"Chirgadze","full_name":"Chirgadze, D. Y."},{"first_name":"D.","last_name":"Bihan","full_name":"Bihan, D."},{"full_name":"Farndale, R. W.","first_name":"R. W.","last_name":"Farndale"},{"full_name":"Herr, A. B.","first_name":"A. B.","last_name":"Herr"}],"date_created":"2019-05-31T09:38:50Z","date_updated":"2021-01-12T08:07:47Z","oa_version":"None","volume":127,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6507","year":"2015","pmid":1,"publication_status":"published","title":"Structural basis for collagen recognition by the immune receptor OSCAR","status":"public","intvolume":" 127","publisher":"American Society of Hematology"},{"type":"journal_article","abstract":[{"lang":"eng","text":"This paper presents polar coding schemes for the two-user discrete memoryless broadcast channel (DM-BC) which achieve Marton's region with both common and private messages. This is the best achievable rate region known to date, and it is tight for all classes of two-user DM-BCs whose capacity regions are known. To accomplish this task, we first construct polar codes for both the superposition as well as binning strategy. By combining these two schemes, we obtain Marton's region with private messages only. Finally, we show how to handle the case of common information. The proposed coding schemes possess the usual advantages of polar codes, i.e., they have low encoding and decoding complexity and a superpolynomial decay rate of the error probability. We follow the lead of Goela, Abbe, and Gastpar, who recently introduced polar codes emulating the superposition and binning schemes. To align the polar indices, for both schemes, their solution involves some degradedness constraints that are assumed to hold between the auxiliary random variables and channel outputs. To remove these constraints, we consider the transmission of k blocks and employ a chaining construction that guarantees the proper alignment of the polarized indices. The techniques described in this paper are quite general, and they can be adopted to many other multiterminal scenarios whenever there polar indices need to be aligned."}],"issue":"2","extern":"1","_id":"6737","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","title":"Achieving Marton’s region for broadcast channels using polar codes","status":"public","publication_status":"published","publisher":"IEEE","intvolume":" 61","author":[{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"last_name":"Sason","first_name":"Igal","full_name":"Sason, Igal"},{"first_name":"Rudiger","last_name":"Urbanke","full_name":"Urbanke, Rudiger"}],"date_created":"2019-07-31T07:03:38Z","date_updated":"2021-01-12T08:08:46Z","oa_version":"Preprint","volume":61,"month":"02","day":"01","publication":"IEEE Transactions on Information Theory","external_id":{"arxiv":["1401.6060"]},"oa":1,"citation":{"mla":"Mondelli, Marco, et al. “Achieving Marton’s Region for Broadcast Channels Using Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no. 2, IEEE, 2015, pp. 783–800, doi:10.1109/tit.2014.2368555.","short":"M. Mondelli, H. Hassani, I. Sason, R. Urbanke, IEEE Transactions on Information Theory 61 (2015) 783–800.","chicago":"Mondelli, Marco, Hamed Hassani, Igal Sason, and Rudiger Urbanke. “Achieving Marton’s Region for Broadcast Channels Using Polar Codes.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/tit.2014.2368555.","ama":"Mondelli M, Hassani H, Sason I, Urbanke R. Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. 2015;61(2):783-800. doi:10.1109/tit.2014.2368555","ista":"Mondelli M, Hassani H, Sason I, Urbanke R. 2015. Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. 61(2), 783–800.","ieee":"M. Mondelli, H. Hassani, I. Sason, and R. Urbanke, “Achieving Marton’s region for broadcast channels using polar codes,” IEEE Transactions on Information Theory, vol. 61, no. 2. IEEE, pp. 783–800, 2015.","apa":"Mondelli, M., Hassani, H., Sason, I., & Urbanke, R. (2015). Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2014.2368555"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.6060"}],"quality_controlled":"1","page":"783-800","date_published":"2015-02-01T00:00:00Z","doi":"10.1109/tit.2014.2368555","language":[{"iso":"eng"}]},{"day":"01","month":"09","language":[{"iso":"eng"}],"date_published":"2015-09-01T00:00:00Z","doi":"10.1109/tit.2015.2453315","quality_controlled":"1","page":"4838-4851","publication":"IEEE Transactions on Information Theory","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.5220"}],"oa":1,"external_id":{"arxiv":["1304.5220"]},"citation":{"mla":"Mondelli, Marco, et al. “Scaling Exponent of List Decoders with Applications to Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no. 9, IEEE, 2015, pp. 4838–51, doi:10.1109/tit.2015.2453315.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 61 (2015) 4838–4851.","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “Scaling Exponent of List Decoders with Applications to Polar Codes.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/tit.2015.2453315.","ama":"Mondelli M, Hassani H, Urbanke R. Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. 2015;61(9):4838-4851. doi:10.1109/tit.2015.2453315","ista":"Mondelli M, Hassani H, Urbanke R. 2015. Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. 61(9), 4838–4851.","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “Scaling exponent of list decoders with applications to polar codes,” IEEE Transactions on Information Theory, vol. 61, no. 9. IEEE, pp. 4838–4851, 2015.","apa":"Mondelli, M., Hassani, H., & Urbanke, R. (2015). Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2015.2453315"},"extern":"1","abstract":[{"text":"Motivated by the significant performance gains which polar codes experience under successive cancellation list decoding, their scaling exponent is studied as a function of the list size. In particular, the error probability is fixed, and the tradeoff between the block length and back-off from capacity is analyzed. A lower bound is provided on the error probability under MAP decoding with list size L for any binary-input memoryless output-symmetric channel and for any class of linear codes such that their minimum distance is unbounded as the block length grows large. Then, it is shown that under MAP decoding, although the introduction of a list can significantly improve the involved constants, the scaling exponent itself, i.e., the speed at which capacity is approached, stays unaffected for any finite list size. In particular, this result applies to polar codes, since their minimum distance tends to infinity as the block length increases. A similar result is proved for genie-aided successive cancellation decoding when transmission takes place over the binary erasure channel, namely, the scaling exponent remains constant for any fixed number of helps from the genie. Note that since genie-aided successive cancellation decoding might be strictly worse than successive cancellation list decoding, the problem of establishing the scaling exponent of the latter remains open.","lang":"eng"}],"issue":"9","type":"journal_article","date_updated":"2021-01-12T08:08:45Z","date_created":"2019-07-31T06:50:34Z","volume":61,"oa_version":"Preprint","author":[{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"full_name":"Urbanke, Rudiger","first_name":"Rudiger","last_name":"Urbanke"}],"status":"public","publication_status":"published","title":"Scaling exponent of list decoders with applications to polar codes","intvolume":" 61","publisher":"IEEE","_id":"6736","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7070","year":"2015","title":"Magnetization of underdoped YBa2Cu3Oy above the irreversibility field","publication_status":"published","status":"public","publisher":"APS","intvolume":" 92","author":[{"full_name":"Yu, Jing Fei","last_name":"Yu","first_name":"Jing Fei"},{"full_name":"Ramshaw, B. J.","last_name":"Ramshaw","first_name":"B. J."},{"last_name":"Kokanović","first_name":"I.","full_name":"Kokanović, I."},{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","last_name":"Modic","full_name":"Modic, Kimberly A"},{"full_name":"Harrison, N.","last_name":"Harrison","first_name":"N."},{"full_name":"Day, James","first_name":"James","last_name":"Day"},{"first_name":"Ruixing","last_name":"Liang","full_name":"Liang, Ruixing"},{"last_name":"Hardy","first_name":"W. N.","full_name":"Hardy, W. N."},{"full_name":"Bonn, D. A.","last_name":"Bonn","first_name":"D. A."},{"full_name":"McCollam, A.","last_name":"McCollam","first_name":"A."},{"last_name":"Julian","first_name":"S. R.","full_name":"Julian, S. R."},{"first_name":"J. R.","last_name":"Cooper","full_name":"Cooper, J. R."}],"date_created":"2019-11-19T13:22:06Z","date_updated":"2021-01-12T08:11:42Z","oa_version":"None","volume":92,"article_number":"180509","type":"journal_article","abstract":[{"text":"Torque magnetization measurements on YBa2Cu3Oy (YBCO) at doping y=6.67 (p=0.12), in dc fields (B) up to 33 T and temperatures down to 4.5 K, show that weak diamagnetism persists above the extrapolated irreversibility field Hirr(T=0)≈24 T. The differential susceptibility dM/dB, however, is more rapidly suppressed for B≳16 T than expected from the properties of the low field superconducting state, and saturates at a low value for fields B≳24 T. In addition, torque measurements on a p=0.11 YBCO crystal in pulsed field up to 65 T and temperatures down to 8 K show similar behavior, with no additional features at higher fields. We offer two candidate scenarios to explain these observations: (a) superconductivity survives but is heavily suppressed at high field by competition with charge-density-wave (CDW) order; (b) static superconductivity disappears near 24 T and is followed by a region of fluctuating superconductivity, which causes dM/dB to saturate at high field. The diamagnetic signal observed above 50 T for the p=0.11 crystal at 40 K and below may be caused by changes in the normal state susceptibility rather than bulk or fluctuating superconductivity. There will be orbital (Landau) diamagnetism from electron pockets and possibly a reduction in spin susceptibility caused by the stronger three-dimensional ordered CDW.","lang":"eng"}],"issue":"18","extern":"1","publication":"Physical Review B","citation":{"chicago":"Yu, Jing Fei, B. J. Ramshaw, I. Kokanović, Kimberly A Modic, N. Harrison, James Day, Ruixing Liang, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility Field.” Physical Review B. APS, 2015. https://doi.org/10.1103/physrevb.92.180509.","short":"J.F. Yu, B.J. Ramshaw, I. Kokanović, K.A. Modic, N. Harrison, J. Day, R. Liang, W.N. Hardy, D.A. Bonn, A. McCollam, S.R. Julian, J.R. Cooper, Physical Review B 92 (2015).","mla":"Yu, Jing Fei, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility Field.” Physical Review B, vol. 92, no. 18, 180509, APS, 2015, doi:10.1103/physrevb.92.180509.","apa":"Yu, J. F., Ramshaw, B. J., Kokanović, I., Modic, K. A., Harrison, N., Day, J., … Cooper, J. R. (2015). Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. APS. https://doi.org/10.1103/physrevb.92.180509","ieee":"J. F. Yu et al., “Magnetization of underdoped YBa2Cu3Oy above the irreversibility field,” Physical Review B, vol. 92, no. 18. APS, 2015.","ista":"Yu JF, Ramshaw BJ, Kokanović I, Modic KA, Harrison N, Day J, Liang R, Hardy WN, Bonn DA, McCollam A, Julian SR, Cooper JR. 2015. Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. 92(18), 180509.","ama":"Yu JF, Ramshaw BJ, Kokanović I, et al. Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. 2015;92(18). doi:10.1103/physrevb.92.180509"},"article_type":"original","quality_controlled":"1","date_published":"2015-11-23T00:00:00Z","doi":"10.1103/physrevb.92.180509","language":[{"iso":"eng"}],"day":"23","month":"11","article_processing_charge":"No","publication_identifier":{"issn":["1098-0121","1550-235X"]}},{"type":"journal_article","abstract":[{"lang":"eng","text":"The rational design of monodisperse ferroelectric nanocrystals with controlled size and shape and their organization into hierarchical structures has been a critical step for understanding the polar ordering in nanoscale ferroelectrics, as well as the design of nanocrystal-based functional materials which harness the properties of individual nanoparticles and the collective interactions between them. We report here on the synthesis and self-assembly of aggregate-free, single-crystalline titanium-based perovskite nanoparticles with controlled morphology and surface composition by using a simple, easily scalable and highly versatile colloidal route. Single-crystalline, non-aggregated BaTiO3 colloidal nanocrystals, used as a model system, have been prepared under solvothermal conditions at temperatures as low as 180 °C. The shape of the nanocrystals was tuned from spheroidal to cubic upon changing the polarity of the solvent, whereas their size was varied from 16 to 30 nm for spheres and 5 to 78 nm for cubes by changing the concentration of the precursors and the reaction time, respectively. The hydrophobic, oleic acid-passivated nanoparticles exhibit very good solubility in non-polar solvents and can be rendered dispersible in polar solvents by a simple process involving the oxidative cleavage of the double bond upon treating the nanopowders with the Lemieux–von Rudloff reagent. Lattice dynamic analysis indicated that regardless of their size, BaTiO3 nanocrystals present local disorder within the perovskite unit cell, associated with the existence of polar ordering. We also demonstrate for the first time that, in addition to being used for fabricating large area, crack-free, highly uniform films, BaTiO3 nanocubes can serve as building blocks for the design of 2D and 3D mesoscale structures, such as superlattices and superparticles. Interestingly, the type of superlattice structure (simple cubic or face centered cubic) appears to be determined by the type of solvent in which the nanocrystals were dispersed. This approach provides an excellent platform for the synthesis of other titanium-based perovskite colloidal nanocrystals with controlled chemical composition, surface structure and morphology and for their assembly into complex architectures, therefore opening the door for the design of novel mesoscale functional materials/nanocomposites with potential applications in energy conversion, data storage and the biomedical field."}],"issue":"30","status":"public","title":"Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals","intvolume":" 7","_id":"7456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"14","article_processing_charge":"No","article_type":"original","page":"12955-12969","publication":"Nanoscale","citation":{"chicago":"Caruntu, Daniela, Taha Rostamzadeh, Tommaso Costanzo, Saman Salemizadeh Parizi, and Gabriel Caruntu. “Solvothermal Synthesis and Controlled Self-Assembly of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale. RSC, 2015. https://doi.org/10.1039/c5nr00737b.","mla":"Caruntu, Daniela, et al. “Solvothermal Synthesis and Controlled Self-Assembly of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale, vol. 7, no. 30, RSC, 2015, pp. 12955–69, doi:10.1039/c5nr00737b.","short":"D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, G. Caruntu, Nanoscale 7 (2015) 12955–12969.","ista":"Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. 2015. Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. 7(30), 12955–12969.","apa":"Caruntu, D., Rostamzadeh, T., Costanzo, T., Salemizadeh Parizi, S., & Caruntu, G. (2015). Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. RSC. https://doi.org/10.1039/c5nr00737b","ieee":"D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, and G. Caruntu, “Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals,” Nanoscale, vol. 7, no. 30. RSC, pp. 12955–12969, 2015.","ama":"Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. 2015;7(30):12955-12969. doi:10.1039/c5nr00737b"},"date_published":"2015-08-14T00:00:00Z","extern":"1","publication_status":"published","publisher":"RSC","year":"2015","pmid":1,"date_created":"2020-02-05T14:16:37Z","date_updated":"2023-02-23T13:08:24Z","volume":7,"author":[{"full_name":"Caruntu, Daniela","first_name":"Daniela","last_name":"Caruntu"},{"first_name":"Taha","last_name":"Rostamzadeh","full_name":"Rostamzadeh, Taha"},{"full_name":"Costanzo, Tommaso","last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"first_name":"Saman","last_name":"Salemizadeh Parizi","full_name":"Salemizadeh Parizi, Saman"},{"full_name":"Caruntu, Gabriel","first_name":"Gabriel","last_name":"Caruntu"}],"month":"08","publication_identifier":{"issn":["2040-3364","2040-3372"]},"quality_controlled":"1","external_id":{"pmid":["26168304"]},"language":[{"iso":"eng"}],"doi":"10.1039/c5nr00737b"},{"author":[{"full_name":"Parizi, Saman Salemizadeh","last_name":"Parizi","first_name":"Saman Salemizadeh"},{"full_name":"Conley, Gavin","first_name":"Gavin","last_name":"Conley"},{"first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"last_name":"Howell","first_name":"Bob","full_name":"Howell, Bob"},{"full_name":"Mellinger, Axel","last_name":"Mellinger","first_name":"Axel"},{"last_name":"Caruntu","first_name":"Gabriel","full_name":"Caruntu, Gabriel"}],"date_created":"2020-02-05T14:17:26Z","date_updated":"2023-02-23T13:08:26Z","volume":5,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7457","year":"2015","title":"Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors","status":"public","publication_status":"published","publisher":"RSC","intvolume":" 5","abstract":[{"lang":"eng","text":"A new organic–inorganic ferroelectric hybrid capacitor designed by uniformly incorporating surface modified monodisperse 15 nm ferroelectric BaTiO3 nanocubes into non-polar polymer blends of poly(methyl methacrylate) (PMMA) polymer and acrylonitrile-butadiene-styrene (ABS) terpolymer is described. The investigation of spatial distribution of nanofillers via a non-distractive thermal pulse method illustrates that the surface functionalization of nanocubes plays a key role in the uniform distribution of charge polarization within the polymer matrix. The discharged energy density of the nanocomposite with 30 vol% BaTiO3 nanocubes is ∼44 × 10−3 J cm−3, which is almost six times higher than that of the neat polymer. The facile processing, along with the superior mechanical and electrical properties of the BaTiO3/PMMA–ABS nanocomposites make them suitable for implementation into capacitive electrical energy storage devices."}],"issue":"93","extern":"1","type":"journal_article","date_published":"2015-09-01T00:00:00Z","doi":"10.1039/c5ra11347d","language":[{"iso":"eng"}],"publication":"RSC Advances","citation":{"mla":"Parizi, Saman Salemizadeh, et al. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric Capacitors.” RSC Advances, vol. 5, no. 93, RSC, 2015, pp. 76356–62, doi:10.1039/c5ra11347d.","short":"S.S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, G. Caruntu, RSC Advances 5 (2015) 76356–76362.","chicago":"Parizi, Saman Salemizadeh, Gavin Conley, Tommaso Costanzo, Bob Howell, Axel Mellinger, and Gabriel Caruntu. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric Capacitors.” RSC Advances. RSC, 2015. https://doi.org/10.1039/c5ra11347d.","ama":"Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. 2015;5(93):76356-76362. doi:10.1039/c5ra11347d","ista":"Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. 2015. Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. 5(93), 76356–76362.","apa":"Parizi, S. S., Conley, G., Costanzo, T., Howell, B., Mellinger, A., & Caruntu, G. (2015). Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. RSC. https://doi.org/10.1039/c5ra11347d","ieee":"S. S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, and G. Caruntu, “Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors,” RSC Advances, vol. 5, no. 93. RSC, pp. 76356–76362, 2015."},"quality_controlled":"1","article_type":"original","page":"76356-76362","month":"09","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["2046-2069"]}},{"date_published":"2015-09-14T00:00:00Z","doi":"10.1038/ng.3401","language":[{"iso":"eng"}],"citation":{"ista":"Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.","apa":"Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., … Visscher, P. M. (2015). Population genetic differentiation of height and body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401","ieee":"M. R. Robinson et al., “Population genetic differentiation of height and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015.","ama":"Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362. doi:10.1038/ng.3401","chicago":"Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401.","mla":"Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401.","short":"M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362."},"publication":"Nature Genetics","page":"1357-1362","article_type":"original","quality_controlled":"1","publication_identifier":{"issn":["1061-4036","1546-1718"]},"article_processing_charge":"No","month":"09","day":"14","author":[{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"first_name":"Gibran","last_name":"Hemani","full_name":"Hemani, Gibran"},{"full_name":"Medina-Gomez, Carolina","last_name":"Medina-Gomez","first_name":"Carolina"},{"last_name":"Mezzavilla","first_name":"Massimo","full_name":"Mezzavilla, Massimo"},{"full_name":"Esko, Tonu","first_name":"Tonu","last_name":"Esko"},{"full_name":"Shakhbazov, Konstantin","first_name":"Konstantin","last_name":"Shakhbazov"},{"full_name":"Powell, Joseph E","first_name":"Joseph E","last_name":"Powell"},{"first_name":"Anna","last_name":"Vinkhuyzen","full_name":"Vinkhuyzen, Anna"},{"full_name":"Berndt, Sonja I","last_name":"Berndt","first_name":"Sonja I"},{"full_name":"Gustafsson, Stefan","last_name":"Gustafsson","first_name":"Stefan"},{"last_name":"Justice","first_name":"Anne E","full_name":"Justice, Anne E"},{"full_name":"Kahali, Bratati","first_name":"Bratati","last_name":"Kahali"},{"full_name":"Locke, Adam E","last_name":"Locke","first_name":"Adam E"},{"first_name":"Tune H","last_name":"Pers","full_name":"Pers, Tune H"},{"full_name":"Vedantam, Sailaja","first_name":"Sailaja","last_name":"Vedantam"},{"first_name":"Andrew R","last_name":"Wood","full_name":"Wood, Andrew R"},{"last_name":"van Rheenen","first_name":"Wouter","full_name":"van Rheenen, Wouter"},{"full_name":"Andreassen, Ole A","first_name":"Ole A","last_name":"Andreassen"},{"first_name":"Paolo","last_name":"Gasparini","full_name":"Gasparini, Paolo"},{"last_name":"Metspalu","first_name":"Andres","full_name":"Metspalu, Andres"},{"last_name":"Berg","first_name":"Leonard H van den","full_name":"Berg, Leonard H van den"},{"first_name":"Jan H","last_name":"Veldink","full_name":"Veldink, Jan H"},{"last_name":"Rivadeneira","first_name":"Fernando","full_name":"Rivadeneira, Fernando"},{"first_name":"Thomas M","last_name":"Werge","full_name":"Werge, Thomas M"},{"last_name":"Abecasis","first_name":"Goncalo R","full_name":"Abecasis, Goncalo R"},{"last_name":"Boomsma","first_name":"Dorret I","full_name":"Boomsma, Dorret I"},{"last_name":"Chasman","first_name":"Daniel I","full_name":"Chasman, Daniel I"},{"full_name":"de Geus, Eco J C","last_name":"de Geus","first_name":"Eco J C"},{"last_name":"Frayling","first_name":"Timothy M","full_name":"Frayling, Timothy M"},{"first_name":"Joel N","last_name":"Hirschhorn","full_name":"Hirschhorn, Joel N"},{"first_name":"Jouke Jan","last_name":"Hottenga","full_name":"Hottenga, Jouke Jan"},{"first_name":"Erik","last_name":"Ingelsson","full_name":"Ingelsson, Erik"},{"full_name":"Loos, Ruth J F","first_name":"Ruth J F","last_name":"Loos"},{"full_name":"Magnusson, Patrik K E","first_name":"Patrik K E","last_name":"Magnusson"},{"last_name":"Martin","first_name":"Nicholas G","full_name":"Martin, Nicholas G"},{"full_name":"Montgomery, Grant W","first_name":"Grant W","last_name":"Montgomery"},{"full_name":"North, Kari E","last_name":"North","first_name":"Kari E"},{"first_name":"Nancy L","last_name":"Pedersen","full_name":"Pedersen, Nancy L"},{"full_name":"Spector, Timothy D","last_name":"Spector","first_name":"Timothy D"},{"full_name":"Speliotes, Elizabeth K","last_name":"Speliotes","first_name":"Elizabeth K"},{"full_name":"Goddard, Michael E","first_name":"Michael E","last_name":"Goddard"},{"last_name":"Yang","first_name":"Jian","full_name":"Yang, Jian"},{"last_name":"Visscher","first_name":"Peter M","full_name":"Visscher, Peter M"}],"volume":47,"oa_version":"None","date_updated":"2021-01-12T08:15:13Z","date_created":"2020-04-30T10:58:23Z","_id":"7742","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","intvolume":" 47","status":"public","publication_status":"published","title":"Population genetic differentiation of height and body mass index across Europe","issue":"11","abstract":[{"lang":"eng","text":"Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58)."}],"extern":"1","type":"journal_article"},{"publication_identifier":{"issn":["0962-8452","1471-2954"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1098/rspb.2015.0689","quality_controlled":"1","external_id":{"pmid":["26063846"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rspb.2015.0689"}],"oa":1,"extern":"1","article_number":"20150689","volume":282,"date_updated":"2021-01-12T08:15:12Z","date_created":"2020-04-30T10:58:07Z","author":[{"last_name":"Adams","first_name":"Mark James","full_name":"Adams, Mark James"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"first_name":"Maria-Elena","last_name":"Mannarelli","full_name":"Mannarelli, Maria-Elena"},{"first_name":"Ben J.","last_name":"Hatchwell","full_name":"Hatchwell, Ben J."}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"year":"2015","article_processing_charge":"No","day":"07","date_published":"2015-07-07T00:00:00Z","article_type":"original","citation":{"ista":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689.","apa":"Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689","ieee":"M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.","ama":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689","chicago":"Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.","mla":"Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015)."},"publication":"Proceedings of the Royal Society B: Biological Sciences","issue":"1810","abstract":[{"lang":"eng","text":"Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 282","title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","status":"public","_id":"7741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2020-04-30T10:51:01Z","date_updated":"2021-01-12T08:15:12Z","volume":24,"oa_version":"Published Version","author":[{"full_name":"Santure, Anna W.","first_name":"Anna W.","last_name":"Santure"},{"last_name":"Poissant","first_name":"Jocelyn","full_name":"Poissant, Jocelyn"},{"full_name":"De Cauwer, Isabelle","last_name":"De Cauwer","first_name":"Isabelle"},{"full_name":"van Oers, Kees","last_name":"van Oers","first_name":"Kees"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard"},{"full_name":"Quinn, John L.","first_name":"John L.","last_name":"Quinn"},{"full_name":"Groenen, Martien A. M.","first_name":"Martien A. M.","last_name":"Groenen"},{"full_name":"Visser, Marcel E.","last_name":"Visser","first_name":"Marcel E."},{"first_name":"Ben C.","last_name":"Sheldon","full_name":"Sheldon, Ben C."},{"full_name":"Slate, Jon","last_name":"Slate","first_name":"Jon"}],"status":"public","publication_status":"published","title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","intvolume":" 24","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7739","year":"2015","extern":"1","abstract":[{"text":"Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"date_published":"2015-12-10T00:00:00Z","doi":"10.1111/mec.13452","article_type":"original","quality_controlled":"1","page":"6148-6162","publication":"Molecular Ecology","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.13452"}],"citation":{"mla":"Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.","short":"A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162.","chicago":"Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452.","ama":"Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452","ista":"Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162.","apa":"Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452","ieee":"A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015."},"day":"10","month":"12","publication_identifier":{"issn":["0962-1083"]},"article_processing_charge":"No"},{"page":"11 - 20","citation":{"ama":"Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523","ista":"Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming vol. 2015–January, 11–20.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2015, vol. 2015–January, pp. 11–20.","mla":"Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523."},"language":[{"iso":"eng"}],"doi":"10.1145/2688500.2688523","date_published":"2015-01-24T00:00:00Z","conference":{"name":"PPoPP: Principles and Practice of Parallel Pogramming"},"article_processing_charge":"No","month":"01","day":"24","publisher":"ACM","publication_status":"published","title":"The SprayList: A scalable relaxed priority queue","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"776","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations.","year":"2015","volume":"2015-January","oa_version":"None","date_created":"2018-12-11T11:48:26Z","date_updated":"2023-02-23T13:16:43Z","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"first_name":"Jerry","last_name":"Li","full_name":"Li, Jerry"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"type":"conference","extern":"1","publist_id":"6878","abstract":[{"lang":"eng","text":"High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by "spraying" themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution."}]},{"oa_version":"None","volume":114,"date_created":"2020-04-30T11:41:08Z","date_updated":"2021-01-12T08:15:23Z","author":[{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"publisher":"American Physical Society","intvolume":" 114","publication_status":"published","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","status":"public","year":"2015","_id":"7765","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"22","abstract":[{"lang":"eng","text":"We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior."}],"type":"journal_article","article_number":"225501","language":[{"iso":"eng"}],"date_published":"2015-06-04T00:00:00Z","doi":"10.1103/physrevlett.114.225501","article_type":"original","quality_controlled":"1","citation":{"ama":"Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501","ista":"Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).","mla":"Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501."},"publication":"Physical Review Letters","publication_identifier":{"issn":["0031-9007","1079-7114"]},"article_processing_charge":"No","month":"06","day":"04"},{"author":[{"full_name":"van Drongelen, Ruben","first_name":"Ruben","last_name":"van Drongelen"},{"last_name":"Pal","first_name":"Anshuman","full_name":"Pal, Anshuman"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"}],"date_updated":"2021-01-12T08:15:24Z","date_created":"2020-04-30T11:41:38Z","oa_version":"None","volume":91,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7767","year":"2015","title":"Collective dynamics of soft active particles","status":"public","publication_status":"published","publisher":"American Physical Society","intvolume":" 91","abstract":[{"text":"We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food.","lang":"eng"}],"issue":"3","extern":"1","article_number":"032706","type":"journal_article","date_published":"2015-03-01T00:00:00Z","doi":"10.1103/physreve.91.032706","language":[{"iso":"eng"}],"publication":"Physical Review E","citation":{"ama":"van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706","ieee":"R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics of soft active particles,” Physical Review E, vol. 91, no. 3. American Physical Society, 2015.","apa":"van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective dynamics of soft active particles. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.91.032706","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","mla":"van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.” Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015, doi:10.1103/physreve.91.032706.","chicago":"Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema. “Collective Dynamics of Soft Active Particles.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706."},"quality_controlled":"1","article_type":"original","day":"01","month":"03","publication_identifier":{"issn":["1539-3755","1550-2376"]},"article_processing_charge":"No"},{"month":"02","day":"15","article_processing_charge":"No","publication_identifier":{"issn":["1744-683X","1744-6848"]},"quality_controlled":"1","article_type":"original","page":"2745-2751","publication":"Soft Matter","citation":{"chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.","mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751.","ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d","ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d"},"language":[{"iso":"eng"}],"doi":"10.1039/c4sm02905d","date_published":"2015-02-15T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached."}],"issue":"14","title":"Disordered surface vibrations in jammed sphere packings","status":"public","publication_status":"published","publisher":"Royal Society of Chemistry","intvolume":" 11","_id":"7766","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:23Z","date_created":"2020-04-30T11:41:23Z","volume":11,"oa_version":"None","author":[{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}]},{"conference":{"name":"NIPS: Neural Information Processing Systems"},"date_published":"2015-01-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"apa":"Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","ieee":"D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015, vol. 2015–January, pp. 1900–1908.","ista":"Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.","ama":"Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning. In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.","chicago":"Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015.","short":"D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908.","mla":"Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08."},"main_file_link":[{"url":"http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning"}],"page":"1900 - 1908","day":"01","month":"01","article_processing_charge":"No","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Jennifer","last_name":"Iglesias","full_name":"Iglesias, Jennifer"},{"full_name":"Vojnović, Milan","last_name":"Vojnović","first_name":"Milan"}],"date_updated":"2023-02-23T13:17:09Z","date_created":"2018-12-11T11:48:27Z","oa_version":"None","volume":"2015-January","_id":"777","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Streaming min-max hypergraph partitioning","publication_status":"published","publisher":"Neural Information Processing Systems","abstract":[{"text":"In many applications, the data is of rich structure that can be represented by a hypergraph, where the data items are represented by vertices and the associations among items are represented by hyperedges. Equivalently, we are given an input bipartite graph with two types of vertices: items, and associations (which we refer to as topics). We consider the problem of partitioning the set of items into a given number of components such that the maximum number of topics covered by a component is minimized. This is a clustering problem with various applications, e.g. partitioning of a set of information objects such as documents, images, and videos, and load balancing in the context of modern computation platforms.Inthis paper, we focus on the streaming computation model for this problem, in which items arrive online one at a time and each item must be assigned irrevocably to a component at its arrival time. Motivated by scalability requirements, we focus on the class of streaming computation algorithms with memory limited to be at most linear in the number of components. We show that a greedy assignment strategy is able to recover a hidden co-clustering of items under a natural set of recovery conditions. We also report results of an extensive empirical evaluation, which demonstrate that this greedy strategy yields superior performance when compared with alternative approaches.","lang":"eng"}],"publist_id":"6879","extern":"1","type":"conference"},{"abstract":[{"lang":"eng","text":"Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"778","title":"Inherent limitations of hybrid transactional memory","status":"public","intvolume":" 9363","day":"01","article_processing_charge":"No","date_published":"2015-01-01T00:00:00Z","citation":{"ama":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13","ista":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363, 185–199.","apa":"Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13","ieee":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent limitations of hybrid transactional memory,” presented at the DISC: Distributed Computing, 2015, vol. 9363, pp. 185–199.","mla":"Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.","short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13."},"page":"185 - 199","publist_id":"6880","extern":"1","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Kopinsky, Justin","first_name":"Justin","last_name":"Kopinsky"},{"full_name":"Kuznetsov, Petr","first_name":"Petr","last_name":"Kuznetsov"},{"full_name":"Ravi, Srivatsan","last_name":"Ravi","first_name":"Srivatsan"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"date_created":"2018-12-11T11:48:27Z","date_updated":"2023-02-23T13:17:35Z","volume":9363,"year":"2015","acknowledgement":"P. Kuznetsov-The author is supported by the Agence Nationale de la Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.","publication_status":"published","publisher":"Springer","month":"01","conference":{"name":"DISC: Distributed Computing"},"doi":"10.1007/978-3-662-48653-5_13","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1405.5689","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1405.5689"]},"quality_controlled":"1"},{"page":"242","publication":"arXiv:1510.08820","external_id":{"arxiv":["1510.08820"]},"oa":1,"citation":{"mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","short":"C.P. Goodrich, ArXiv:1510.08820 (2015).","chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:151008820. 2015.","ista":"Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820, .","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv:1510.08820. 2015.","apa":"Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.08820"}],"language":[{"iso":"eng"}],"date_published":"2015-10-29T00:00:00Z","day":"29","month":"10","article_processing_charge":"No","publication_status":"published","status":"public","title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7779","year":"2015","date_created":"2020-04-30T12:16:18Z","date_updated":"2021-01-12T08:15:28Z","oa_version":"Preprint","author":[{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"}],"type":"preprint","extern":"1","abstract":[{"text":"The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties.","lang":"eng"}]},{"extern":"1","publist_id":"6876","abstract":[{"lang":"eng","text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. In this paper, we take a new approach to concurrent memory reclamation: instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free."}],"type":"conference","oa_version":"None","volume":"2015-June","date_updated":"2023-02-23T12:35:42Z","date_created":"2018-12-11T11:48:27Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"6001"}]},"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"last_name":"Leiserson","first_name":"William","full_name":"Leiserson, William"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"publisher":"ACM","publication_status":"published","status":"public","title":"ThreadScan: Automatic and scalable memory reclamation","_id":"779","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable Synchronization Research Group for very useful feedback on earlier drafts of this paper.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","article_processing_charge":"No","month":"06","day":"13","language":[{"iso":"eng"}],"doi":"10.1145/2755573.2755600","date_published":"2015-06-13T00:00:00Z","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"page":"123 - 132","citation":{"ama":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:10.1145/2755573.2755600","ieee":"D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.","apa":"Alistarh, D.-A., Matveev, A., Leiserson, W., & Shavit, N. (2015). ThreadScan: Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2755573.2755600","ista":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms and Architectures vol. 2015–June, 123–132.","short":"D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132.","mla":"Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.","chicago":"Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM, 2015. https://doi.org/10.1145/2755573.2755600."}},{"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"oa_version":"Preprint","volume":9135,"date_updated":"2023-02-23T13:18:11Z","date_created":"2018-12-11T11:48:28Z","_id":"780","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”","year":"2015","publisher":"Springer","intvolume":" 9135","publication_status":"published","title":"Polylogarithmic-time leader election in population protocols","status":"public","publist_id":"6877","abstract":[{"lang":"eng","text":"Population protocols are networks of finite-state agents, interacting randomly, and updating their states using simple rules. Despite their extreme simplicity, these systems have been shown to cooperatively perform complex computational tasks, such as simulating register machines to compute standard arithmetic functions. The election of a unique leader agent is a key requirement in such computational constructions. Yet, the fastest currently known population protocol for electing a leader only has linear convergence time, and it has recently been shown that no population protocol using a constant number of states per node may overcome this linear bound. In this paper, we give the first population protocol for leader election with polylogarithmic convergence time, using polylogarithmic memory states per node. The protocol structure is quite simple: each node has an associated value, and is either a leader (still in contention) or a minion (following some leader). A leader keeps incrementing its value and “defeats” other leaders in one-to-one interactions, and will drop from contention and become a minion if it meets a leader with higher value. Importantly, a leader also drops out if it meets a minion with higher absolute value. While these rules are quite simple, the proof that this algorithm achieves polylogarithmic convergence time is non-trivial. In particular, the argument combines careful use of concentration inequalities with anti-concentration bounds, showing that the leaders’ values become spread apart as the execution progresses, which in turn implies that straggling leaders get quickly eliminated. We complement our analysis with empirical results, showing that our protocol converges extremely fast, even for large network sizes."}],"extern":"1","type":"conference","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-662-47666-6_38","conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"language":[{"iso":"eng"}],"citation":{"apa":"Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP: International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38","ieee":"D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in population protocols,” presented at the ICALP: International Colloquium on Automota, Languages and Programming, 2015, vol. 9135, pp. 479–491.","ista":"Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in population protocols. ICALP: International Colloquium on Automota, Languages and Programming vol. 9135, 479–491.","ama":"Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38","chicago":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.","short":"D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.","mla":"Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38."},"oa":1,"external_id":{"arxiv":["1502.05745"]},"main_file_link":[{"url":"https://arxiv.org/abs/1502.05745","open_access":"1"}],"page":"479 - 491","month":"01","day":"01"},{"doi":"10.1145/2767386.2767429","date_published":"2015-07-21T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"citation":{"apa":"Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429","ieee":"D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority in population protocols,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 47–56.","ista":"Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in population protocols. PODC: Principles of Distributed Computing vol. 2015–July, 47–56.","ama":"Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.","short":"D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.","mla":"Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols. Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429."},"page":"47 - 56","article_processing_charge":"No","day":"21","month":"07","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"last_name":"Vojnović","first_name":"Milan","full_name":"Vojnović, Milan"}],"oa_version":"None","volume":"2015-July","date_created":"2018-12-11T11:48:28Z","date_updated":"2023-02-23T13:18:35Z","year":"2015","_id":"781","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","publication_status":"published","status":"public","title":"Fast and exact majority in population protocols","publist_id":"6873","abstract":[{"lang":"eng","text":"Population protocols, roughly defined as systems consisting of large numbers of simple identical agents, interacting at random and updating their state following simple rules, are an important research topic at the intersection of distributed computing and biology. One of the fundamental tasks that a population protocol may solve is majority: each node starts in one of two states; the goal is for all nodes to reach a correct consensus on which of the two states was initially the majority. Despite considerable research effort, known protocols for this problem are either exact but slow (taking linear parallel time to converge), or fast but approximate (with non-zero probability of error). In this paper, we show that this trade-off between preciasion and speed is not inherent. We present a new protocol called Average and Conquer (AVC) that solves majority ex-actly in expected parallel convergence time O(log n/(sε) + log n log s), where n is the number of nodes, εn is the initial node advantage of the majority state, and s = Ω(log n log log n) is the number of states the protocol employs. This shows that the majority problem can be solved exactly in time poly-logarithmic in n, provided that the memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case of four memory states per node, and a lower bound of Ω(logn) parallel time for protocols using any number of memory states per node.per node, and a lower bound of (log n) parallel time for protocols using any number of memory states per node."}],"extern":"1","type":"conference"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"782","year":"2015","publisher":"ACM","status":"public","publication_status":"published","title":"Lock-Free algorithms under stochastic schedulers","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sauerwald, Thomas","last_name":"Sauerwald","first_name":"Thomas"},{"full_name":"Vojnović, Milan","first_name":"Milan","last_name":"Vojnović"}],"volume":"2015-July","oa_version":"None","date_updated":"2023-02-23T13:18:50Z","date_created":"2018-12-11T11:48:28Z","type":"conference","publist_id":"6874","abstract":[{"text":"In this work, we consider the following random process, mo- Tivated by the analysis of lock-free concurrent algorithms under high memory contention. In each round, a new scheduling step is allocated to one of n threads, according to a distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability pi. When some thread first reaches a set threshold of executed steps, it registers a win, completing its current operation, and resets its step count to 1. At the same time, threads whose step count was close to the threshold also get reset because of the win, but to 0 steps, being penalized for almost winning. We are interested in two questions: how often does some thread complete an operation (system latency), and how often does a specific thread complete an operation (individual latency)? We provide asymptotically tight bounds for the system and individual latency of this general concurrency pattern, for arbitrary scheduling distributions p. Surprisingly, a sim- ple characterization exists: in expectation, the system will complete a new operation every Θ(1/p 2) steps, while thread i will complete a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right, as it requires a careful analysis of how the higher norms of the vector p inuence the thread step counts and latencies in this random process. Our result offers a simple connection between the scheduling distribution and the average performance of concurrent algorithms, which has several applications.","lang":"eng"}],"extern":"1","citation":{"chicago":"Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430.","short":"D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.","mla":"Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers. Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.","ieee":"D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under stochastic schedulers,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 251–260.","apa":"Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430","ista":"Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.","ama":"Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430"},"page":"251 - 260","date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767430","conference":{"name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"article_processing_charge":"No","day":"21","month":"07"},{"article_processing_charge":"No","day":"21","month":"07","citation":{"mla":"Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament. Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.","short":"D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.","ama":"Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament. In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420","ista":"Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.","apa":"Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420","ieee":"D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster than a tournament,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 365–374."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.1001"}],"oa":1,"page":"365 - 374","doi":"10.1145/2767386.2767420","date_published":"2015-07-21T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"type":"conference","publist_id":"6875","abstract":[{"lang":"eng","text":"The problem of electing a leader from among n contenders is one of the fundamental questions in distributed computing. In its simplest formulation, the task is as follows: given n processors, all participants must eventually return a win or lose indication, such that a single contender may win. Despite a considerable amount of work on leader election, the following question is still open: can we elect a leader in an asynchronous fault-prone system faster than just running a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper, we answer this question in the affirmative, improving on a decades-old upper bound. We introduce two new algorithmic ideas to reduce the time complexity of electing a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application of our algorithm is a new upper bound for the tight renaming problem, assigning n items to the n participants in expected O(log2 n) time and O(n2) messages. We complement our results with lower bound of Ω(n2) messages for solving these two problems, closing the question of their message complexity."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"783","year":"2015","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement during this work, and the anonymous reviewers for their very useful suggestions.","publisher":"ACM","title":"How to elect a leader faster than a tournament","status":"public","publication_status":"published","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Vladu, Adrian","first_name":"Adrian","last_name":"Vladu"}],"volume":"2015-July","oa_version":"None","date_updated":"2023-02-23T13:18:55Z","date_created":"2018-12-11T11:48:28Z"},{"abstract":[{"text":"We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.","lang":"eng"}],"publist_id":"6872","extern":"1","type":"conference","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Hitesh","last_name":"Ballani","full_name":"Ballani, Hitesh"},{"full_name":"Costa, Paolo","first_name":"Paolo","last_name":"Costa"},{"last_name":"Funnell","first_name":"Adam","full_name":"Funnell, Adam"},{"first_name":"Joshua","last_name":"Benjamin","full_name":"Benjamin, Joshua"},{"first_name":"Philip","last_name":"Watts","full_name":"Watts, Philip"},{"full_name":"Thomsen, Benn","first_name":"Benn","last_name":"Thomsen"}],"date_updated":"2023-02-23T13:18:57Z","date_created":"2018-12-11T11:48:29Z","oa_version":"None","_id":"784","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A high-radix, low-latency optical switch for data centers","publication_status":"published","status":"public","publisher":"ACM","month":"01","day":"01","publication_identifier":{"isbn":["978-1-4503-3542-3"]},"conference":{"end_date":"2015-08-21","start_date":"2015-08-17","location":"London, United Kindgdom","name":"SIGCOMM: Special Interest Group on Data Communication"},"doi":"10.1145/2785956.2790035","date_published":"2015-01-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ieee":"D.-A. Alistarh et al., “A high-radix, low-latency optical switch for data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom, 2015, pp. 367–368.","apa":"Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts, P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035","ista":"Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special Interest Group on Data Communication, 367–368.","ama":"Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035","chicago":"Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.","short":"D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368.","mla":"Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035."},"quality_controlled":"1","page":"367 - 368"},{"abstract":[{"text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.","lang":"eng"}],"publist_id":"6851","issue":"12","type":"journal_article","author":[{"first_name":"Jakob","last_name":"Engel","full_name":"Engel, Jakob"},{"full_name":"Schmalhorst, Philipp S","first_name":"Philipp S","last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5795-0133"},{"last_name":"Kruger","first_name":"Anke","full_name":"Kruger, Anke"},{"first_name":"Christina","last_name":"Muller","full_name":"Muller, Christina"},{"first_name":"Falk","last_name":"Buettner","full_name":"Buettner, Falk"},{"last_name":"Routier","first_name":"Françoise","full_name":"Routier, Françoise"}],"date_created":"2018-12-11T11:48:35Z","date_updated":"2021-01-12T08:16:33Z","volume":25,"oa_version":"None","year":"2015","_id":"802","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"status":"public","publication_status":"published","title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","department":[{"_id":"CaHe"}],"publisher":"Oxford University Press","intvolume":" 25","month":"12","day":"01","scopus_import":1,"doi":"10.1093/glycob/cwv059","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Glycobiology","citation":{"chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:10.1093/glycob/cwv059.","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., & Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430. doi:10.1093/glycob/cwv059"},"external_id":{"pmid":["26306635"]},"quality_controlled":"1","page":"1423 - 1430"},{"doi":"10.1128/JVI.01502-15","date_published":"2015-09-22T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"pmid":["26223638"]},"citation":{"ista":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.","apa":"Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15","ieee":"F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20. ASM, pp. 10294–10302, 2015.","ama":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15","chicago":"Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology. ASM, 2015. https://doi.org/10.1128/JVI.01502-15.","mla":"Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.","short":"F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89 (2015) 10294–10302."},"publication":"Journal of Virology","page":"10294 - 10302","quality_controlled":"1","month":"09","day":"22","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur","full_name":"Schur, Florian"},{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"full_name":"Hagen, Wim","first_name":"Wim","last_name":"Hagen"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John"}],"oa_version":"None","volume":89,"date_updated":"2021-01-12T08:17:09Z","date_created":"2018-12-11T11:48:39Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"815","year":"2015","intvolume":" 89","publisher":"ASM","publication_status":"published","status":"public","title":"The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly","issue":"20","publist_id":"6837","abstract":[{"lang":"eng","text":"The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation.\r\n"}],"extern":"1","type":"journal_article"},{"type":"journal_article","extern":1,"publist_id":"6836","issue":"7535","abstract":[{"text":"Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments.","lang":"eng"}],"intvolume":" 517","publisher":"Nature Publishing Group","title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","status":"public","publication_status":"published","_id":"814","year":"2015","acknowledgement":"This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples, and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich and T. Bharat for technical support and/or discussion. This study was technically supported by the European Molecular Biology Laboratory IT services unit.","volume":517,"date_updated":"2021-01-12T08:17:08Z","date_created":"2018-12-11T11:48:39Z","author":[{"full_name":"Florian Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim J"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"full_name":"Ruml, Tomáš","last_name":"Ruml","first_name":"Tomáš"},{"full_name":"Müller B","first_name":"B","last_name":"Müller"},{"full_name":"Kraüsslich, Hans Georg","first_name":"Hans","last_name":"Kraüsslich"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John A"}],"month":"01","day":"22","page":"505 - 508","quality_controlled":0,"citation":{"ieee":"F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature Publishing Group, pp. 505–508, 2015.","apa":"Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H., & Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838","ista":"Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 517(7535), 505–508.","ama":"Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508. doi:10.1038/nature13838","chicago":"Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature13838.","short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508.","mla":"Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838."},"publication":"Nature","date_published":"2015-01-22T00:00:00Z","doi":"10.1038/nature13838"},{"extern":"1","issue":"2","type":"journal_article","article_number":"AB101","volume":135,"oa_version":"None","date_created":"2020-08-10T11:54:09Z","date_updated":"2021-01-12T08:17:42Z","author":[{"full_name":"Einhorn, Lukas","last_name":"Einhorn","first_name":"Lukas"},{"orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","first_name":"Judit","full_name":"Fazekas, Judit"},{"last_name":"Muhr","first_name":"Martina","full_name":"Muhr, Martina"},{"full_name":"Schoos, Alexandra","first_name":"Alexandra","last_name":"Schoos"},{"full_name":"Oida, Kumiko","last_name":"Oida","first_name":"Kumiko"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"first_name":"Lucia","last_name":"Panakova","full_name":"Panakova, Lucia"},{"last_name":"Manzano-Szalai","first_name":"Krisztina","full_name":"Manzano-Szalai, Krisztina"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"}],"intvolume":" 135","publisher":"Elsevier","status":"public","title":"Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients","publication_status":"published","_id":"8242","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0091-6749"]},"article_processing_charge":"No","month":"02","day":"01","language":[{"iso":"eng"}],"doi":"10.1016/j.jaci.2014.12.1263","date_published":"2015-02-01T00:00:00Z","article_type":"original","quality_controlled":"1","citation":{"mla":"Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.","short":"L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova, K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 135 (2015).","chicago":"Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida, Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.","ama":"Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263","ista":"Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 135(2), AB101.","apa":"Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim, E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263","ieee":"L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients,” Journal of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015."},"publication":"Journal of Allergy and Clinical Immunology"},{"author":[{"full_name":"Peter Marhavy","first_name":"Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741"},{"full_name":"Eva Benková","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:44Z","date_updated":"2021-01-12T08:18:07Z","volume":5,"year":"2015","_id":"832","acknowledgement":"European Research Council with a Starting Independent Research grant: ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas Fendrych for critical reading and comments. The protocol was developed based on previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). ","title":"Real time analysis of lateral root organogenesis in arabidopsis","publication_status":"published","status":"public","intvolume":" 5","publisher":"Bio-protocol LLC","abstract":[{"lang":"eng","text":"Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis."}],"publist_id":"6816","issue":"8","extern":1,"type":"journal_article","doi":"10.21769/BioProtoc.1446","date_published":"2015-04-20T00:00:00Z","publication":"Bio-protocol","citation":{"ama":"Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446","ista":"Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8).","apa":"Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446","ieee":"P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.","mla":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.","short":"P. Marhavý, E. Benková, Bio-Protocol 5 (2015).","chicago":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446."},"quality_controlled":0,"month":"04","day":"20"},{"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"month":"10","day":"05","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","article_type":"original","quality_controlled":"1","publication":"Nature Communications","citation":{"mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361.","short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015).","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361","ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361.","ieee":"P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.","apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9361","date_published":"2015-10-05T00:00:00Z","article_number":"8361","type":"journal_article","extern":"1","abstract":[{"text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.","lang":"eng"}],"status":"public","publication_status":"published","title":"Observing the overall rocking motion of a protein in a crystal","intvolume":" 6","publisher":"Springer Nature","_id":"8456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_updated":"2021-01-12T08:19:24Z","date_created":"2020-09-18T10:07:36Z","oa_version":"Published Version","volume":6,"author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"full_name":"Xue, Yi","first_name":"Yi","last_name":"Xue"},{"last_name":"Coquelle","first_name":"Nicolas","full_name":"Coquelle, Nicolas"},{"last_name":"Haller","first_name":"Jens D.","full_name":"Haller, Jens D."},{"first_name":"Tairan","last_name":"Yuwen","full_name":"Yuwen, Tairan"},{"full_name":"Ayala, Isabel","first_name":"Isabel","last_name":"Ayala"},{"first_name":"Oleg","last_name":"Mikhailovskii","full_name":"Mikhailovskii, Oleg"},{"full_name":"Willbold, Dieter","first_name":"Dieter","last_name":"Willbold"},{"full_name":"Colletier, Jacques-Philippe","last_name":"Colletier","first_name":"Jacques-Philippe"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"}]},{"type":"journal_article","extern":"1","issue":"3","abstract":[{"lang":"eng","text":"We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed."}],"publisher":"Wiley","intvolume":" 4","title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","publication_status":"published","status":"public","_id":"8457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","oa_version":"None","volume":4,"date_created":"2020-09-18T10:07:45Z","date_updated":"2021-01-12T08:19:24Z","author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"publication_identifier":{"isbn":["9780470034590","9780470058213"]},"article_processing_charge":"No","day":"10","month":"09","page":"699-708","article_type":"original","quality_controlled":"1","citation":{"short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.","mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.","chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015. https://doi.org/10.1002/9780470034590.emrstm1418.","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418","ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708, 2015.","apa":"Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418","ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708."},"publication":"eMagRes","language":[{"iso":"eng"}],"date_published":"2015-09-10T00:00:00Z","doi":"10.1002/9780470034590.emrstm1418"},{"citation":{"ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318","ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318","chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318.","short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318."},"publication":"Molecular Biology and Evolution","page":"542 - 554","quality_controlled":"1","doi":"10.1093/molbev/msu318","date_published":"2015-02-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","month":"02","_id":"848","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","intvolume":" 32","publisher":"Oxford University Press","status":"public","publication_status":"published","title":"A model of substitution trajectories in sequence space and long-term protein evolution","author":[{"last_name":"Usmanova","first_name":"Dinara","full_name":"Usmanova, Dinara"},{"full_name":"Ferretti, Luca","last_name":"Ferretti","first_name":"Luca"},{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"first_name":"Peter","last_name":"Vlasov","full_name":"Vlasov, Peter"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"}],"volume":32,"oa_version":"None","date_created":"2018-12-11T11:48:49Z","date_updated":"2021-01-12T08:19:33Z","type":"journal_article","issue":"2","publist_id":"6804","abstract":[{"text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.","lang":"eng"}],"extern":"1"},{"type":"journal_article","abstract":[{"lang":"eng","text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]."}],"issue":"8","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8498","year":"2015","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","status":"public","publication_status":"published","intvolume":" 28","publisher":"IOP Publishing","author":[{"full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"},{"full_name":"Zhang, K","first_name":"K","last_name":"Zhang"}],"date_updated":"2021-01-12T08:19:41Z","date_created":"2020-09-18T10:46:43Z","oa_version":"None","volume":28,"keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"month":"06","day":"30","publication_identifier":{"issn":["0951-7715","1361-6544"]},"article_processing_charge":"No","publication":"Nonlinearity","citation":{"short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015. https://doi.org/10.1088/0951-7715/28/8/2699.","ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","apa":"Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720."},"article_type":"original","quality_controlled":"1","page":"2699-2720","doi":"10.1088/0951-7715/28/8/2699","date_published":"2015-06-30T00:00:00Z","language":[{"iso":"eng"}]},{"page":"71-149","quality_controlled":"1","article_type":"original","citation":{"ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499","ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149.","apa":"Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” Journal of the European Mathematical Society, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:10.4171/jems/499.","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149.","chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499."},"publication":"Journal of the European Mathematical Society","language":[{"iso":"eng"}],"doi":"10.4171/jems/499","date_published":"2015-02-05T00:00:00Z","publication_identifier":{"issn":["1435-9855"]},"article_processing_charge":"No","day":"05","month":"02","publisher":"European Mathematical Society Publishing House","intvolume":" 17","status":"public","title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","publication_status":"published","year":"2015","_id":"8499","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":17,"date_created":"2020-09-18T10:46:50Z","date_updated":"2021-01-12T08:19:41Z","author":[{"full_name":"Guardia, Marcel","last_name":"Guardia","first_name":"Marcel"},{"first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"}],"type":"journal_article","extern":"1","issue":"1","abstract":[{"lang":"eng","text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214.","ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214"},"publication":"Science Advances","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"intvolume":" 10","publisher":"Public Library of Science","publication_status":"published","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","status":"public","acknowledgement":"Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, \"Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)\" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","_id":"906","year":"2015","volume":10,"date_updated":"2021-01-12T08:21:48Z","date_created":"2018-12-11T11:49:08Z","author":[{"last_name":"Arkhipova","first_name":"Oksana","full_name":"Arkhipova, Oksana V"},{"full_name":"Meer, Margarita V","last_name":"Meer","first_name":"Margarita"},{"full_name":"Mikoulinskaia, Galina V","first_name":"Galina","last_name":"Mikoulinskaia"},{"first_name":"Marina","last_name":"Zakharova","full_name":"Zakharova, Marina V"},{"last_name":"Galushko","first_name":"Alexander","full_name":"Galushko, Alexander S"},{"full_name":"Akimenko, Vasilii K","last_name":"Akimenko","first_name":"Vasilii"},{"full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","extern":1,"publist_id":"6742","issue":"5","abstract":[{"text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.","lang":"eng"}],"quality_controlled":0,"citation":{"ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888."},"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"},"publication":"PLoS One","doi":"10.1371/journal.pone.0125888","date_published":"2015-05-11T00:00:00Z","month":"05","day":"11"},{"article_processing_charge":"No","day":"08","citation":{"chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598"},"publication":"Journal of Geophysical Research: Oceans","page":"4760-4777","article_type":"original","date_published":"2015-06-08T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9141","intvolume":" 120","status":"public","title":"A three-dimensional map of tidal dissipation over abyssal hills","oa_version":"Published Version","publication_identifier":{"issn":["2169-9275"]},"month":"06","main_file_link":[{"url":"https://doi.org/10.1002/2014JC010598","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1002/2014jc010598","language":[{"iso":"eng"}],"extern":"1","year":"2015","publisher":"American Geophysical Union","publication_status":"published","author":[{"first_name":"Adrien","last_name":"Lefauve","full_name":"Lefauve, Adrien"},{"full_name":"Muller, Caroline J","last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"full_name":"Melet, Angélique","last_name":"Melet","first_name":"Angélique"}],"volume":120,"date_updated":"2022-01-24T13:45:41Z","date_created":"2021-02-15T14:21:49Z"},{"publication_status":"published","publisher":"eLife Sciences Publications","year":"2015","date_updated":"2021-01-12T08:21:58Z","date_created":"2018-12-11T11:49:15Z","volume":4,"author":[{"full_name":"Sehring, Ivonne","last_name":"Sehring","first_name":"Ivonne"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"full_name":"Denker, Elsa","first_name":"Elsa","last_name":"Denker"},{"last_name":"Kourakis","first_name":"Matthew","full_name":"Kourakis, Matthew"},{"full_name":"Mathiesen, Birthe","last_name":"Mathiesen","first_name":"Birthe"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Dong, Bo","first_name":"Bo","last_name":"Dong"},{"full_name":"Jiang, Di","first_name":"Di","last_name":"Jiang"}],"article_number":"e09206","extern":"1","file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6512","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":"10.7554/eLife.09206","month":"10","ddc":["539","570"],"title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","status":"public","intvolume":" 4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"928","file":[{"file_id":"5769","relation":"main_file","date_created":"2018-12-20T15:50:56Z","date_updated":"2020-07-14T12:48:15Z","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","file_name":"2015_eLife_Sehring.pdf","access_level":"open_access","creator":"dernst","file_size":7202224,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.","lang":"eng"}],"publication":"eLife","citation":{"ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015.","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206."},"date_published":"2015-10-21T00:00:00Z","day":"21","has_accepted_license":"1"},{"extern":"1","publisher":"Elsevier","publication_status":"published","year":"2015","volume":49,"date_created":"2021-06-21T06:40:34Z","date_updated":"2023-02-23T14:01:28Z","author":[{"last_name":"Krivelevich","first_name":"Michael","full_name":"Krivelevich, Michael"},{"full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567"},{"first_name":"Benny","last_name":"Sudakov","full_name":"Sudakov, Benny"}],"publication_identifier":{"issn":["1571-0653"]},"month":"11","quality_controlled":"1","external_id":{"arxiv":["1501.04816"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.endm.2015.06.027","type":"journal_article","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"intvolume":" 49","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","status":"public","_id":"9575","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"181-187","article_type":"original","citation":{"short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187."},"publication":"Electronic Notes in Discrete Mathematics","date_published":"2015-11-01T00:00:00Z"},{"scopus_import":"1","month":"04","day":"01","publication_identifier":{"issn":["0749-6419"]},"article_processing_charge":"No","article_type":"original","page":"1-25","publication":"International Journal of Plasticity","citation":{"ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25."},"language":[{"iso":"eng"}],"date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.ijplas.2014.09.009","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation."}],"publication_status":"published","status":"public","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","intvolume":" 67","publisher":"Elsevier","year":"2015","_id":"9673","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-15T14:09:32Z","date_updated":"2023-02-23T14:04:28Z","volume":67,"oa_version":"None","author":[{"first_name":"H.S.","last_name":"Leung","full_name":"Leung, H.S."},{"last_name":"Leung","first_name":"P.S.S.","full_name":"Leung, P.S.S."},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"},{"first_name":"A.H.W.","last_name":"Ngan","full_name":"Ngan, A.H.W."}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2015-11-01T00:00:00Z","citation":{"chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102"},"publication":"Physical Review B - Condensed Matter and Materials Physics","article_type":"original","issue":"18","abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"9688","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":" 92","title":"Solid-liquid interfacial free energy out of equilibrium","status":"public","publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"month":"11","doi":"10.1103/physrevb.92.180102","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1511.08668"]},"quality_controlled":"1","extern":"1","article_number":"180102","author":[{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"volume":92,"date_updated":"2021-08-09T12:38:49Z","date_created":"2021-07-19T10:07:22Z","year":"2015","publisher":"American Physical Society","publication_status":"published"},{"day":"18","month":"11","article_processing_charge":"No","citation":{"mla":"Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001","ieee":"G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015."},"doi":"10.1371/journal.pbio.1002299.s001","date_published":"2015-11-18T00:00:00Z","type":"research_data_reference","_id":"9711","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Excel file containing the raw data for all figures","department":[{"_id":"ToBo"}],"publisher":"Public Library of Science","author":[{"first_name":"Guillaume","last_name":"Chevereau","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume"},{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"full_name":"Guvenek, Aysegul","first_name":"Aysegul","last_name":"Guvenek"},{"last_name":"Ayhan","first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal"},{"last_name":"Toprak","first_name":"Erdal","full_name":"Toprak, Erdal"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias"}],"related_material":{"record":[{"id":"1619","status":"public","relation":"used_in_publication"}]},"date_created":"2021-07-23T11:53:50Z","date_updated":"2023-02-23T10:07:02Z","oa_version":"Published Version"},{"title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","ddc":["570"],"status":"public","intvolume":" 84","_id":"1855","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","file":[{"file_id":"5350","relation":"main_file","checksum":"542a0b9b07e78050a81b35f26f0b82da","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:18:29Z","access_level":"open_access","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","creator":"system","content_type":"application/pdf","file_size":1823045}],"oa_version":"Published Version","pubrep_id":"460","type":"journal_article","abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"issue":"3","article_type":"original","page":"615 - 624","publication":"Journal of Animal Ecology","citation":{"short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624."},"date_published":"2015-03-03T00:00:00Z","scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Wiley","department":[{"_id":"SyCr"}],"year":"2015","acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 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.","pmid":1,"date_created":"2018-12-11T11:54:23Z","date_updated":"2023-02-23T14:06:09Z","volume":84,"author":[{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias","full_name":"Fürst, Matthias"},{"full_name":"Caspar, Jesicca","last_name":"Caspar","first_name":"Jesicca"},{"last_name":"Theodorou","first_name":"Panagiotis","full_name":"Theodorou, Panagiotis"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9720"}]},"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5245","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"},"external_id":{"pmid":["25646973"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/1365-2656.12345","month":"03"},{"pmid":1,"year":"2015","acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9721"}]},"author":[{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"last_name":"Marr","first_name":"Carsten","full_name":"Marr, Carsten"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"volume":370,"date_created":"2018-12-11T11:54:15Z","date_updated":"2023-02-23T14:06:12Z","publist_id":"5273","ec_funded":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"external_id":{"pmid":["25870394"]},"oa":1,"project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","grant_number":"302004"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"},{"name":"Fellowship of Wissenschaftskolleg zu Berlin","_id":"25E24DB2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1098/rstb.2014.0108","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"month":"05","_id":"1830","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":" 370","title":"Opposing effects of allogrooming on disease transmission in ant societies","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"1669","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"citation":{"ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, The, 2015.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2014.0108","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","article_type":"original","date_published":"2015-05-26T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"26"}]