[{"title":"The monotone secant conjecture in the real Schubert calculus","isi":1,"arxiv":1,"date_published":"2015-06-23T00:00:00Z","article_processing_charge":"No","volume":24,"publist_id":"5070","month":"06","external_id":{"isi":["000356873900001"],"arxiv":["1109.3436"]},"quality_controlled":"1","date_updated":"2025-09-23T14:07:49Z","publisher":"Taylor & Francis","main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"oa_version":"Preprint","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.","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.","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.","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."},"scopus_import":"1","abstract":[{"lang":"eng","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. "}],"type":"journal_article","status":"public","date_created":"2018-12-11T11:55:10Z","year":"2015","doi":"10.1080/10586458.2014.980044","publication_status":"published","oa":1,"intvolume":" 24","author":[{"full_name":"Hein, Nicolas","first_name":"Nicolas","last_name":"Hein"},{"full_name":"Hillar, Christopher","first_name":"Christopher","last_name":"Hillar"},{"first_name":"Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Del Campo Sanchez, Abraham"},{"first_name":"Frank","last_name":"Sottile","full_name":"Sottile, Frank"},{"full_name":"Teitler, Zach","first_name":"Zach","last_name":"Teitler"}],"language":[{"iso":"eng"}],"page":"261 - 269","department":[{"_id":"CaUh"}],"issue":"3","_id":"2006","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Experimental Mathematics","day":"23"},{"title":"Iterative scaling in curved exponential families","date_published":"2015-09-01T00:00:00Z","arxiv":1,"article_processing_charge":"No","isi":1,"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).","volume":42,"publist_id":"5068","month":"09","external_id":{"isi":["000360077100012"],"arxiv":["1307.3282"]},"date_updated":"2025-09-23T09:25:01Z","quality_controlled":"1","publisher":"Wiley","main_file_link":[{"url":"http://arxiv.org/abs/1307.3282","open_access":"1"}],"citation":{"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","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.","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.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 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","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."},"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"}],"scopus_import":"1","oa_version":"Preprint","type":"journal_article","status":"public","date_created":"2018-12-11T11:55:11Z","year":"2015","publication_status":"published","oa":1,"doi":"10.1111/sjos.12139","intvolume":" 42","language":[{"iso":"eng"}],"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"}],"page":"832 - 847","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2008","issue":"3","department":[{"_id":"CaUh"}],"publication":"Scandinavian Journal of Statistics","day":"01"},{"month":"07","external_id":{"isi":["000352661000005"],"arxiv":["1404.6617"]},"date_updated":"2025-09-23T08:45:54Z","quality_controlled":"1","title":"Faithfulness and learning hypergraphs from discrete distributions","isi":1,"date_published":"2015-07-01T00:00:00Z","arxiv":1,"article_processing_charge":"No","volume":87,"publist_id":"5062","type":"journal_article","status":"public","publisher":"Elsevier","main_file_link":[{"url":"http://arxiv.org/abs/1404.6617","open_access":"1"}],"oa_version":"Preprint","scopus_import":"1","citation":{"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","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.","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.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.","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.","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"},"abstract":[{"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.","lang":"eng"}],"doi":"10.1016/j.csda.2015.01.017","oa":1,"publication_status":"published","intvolume":" 87","author":[{"last_name":"Klimova","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna"},{"orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:13Z","year":"2015","corr_author":"1","publication":"Computational Statistics & Data Analysis","day":"01","page":"57 - 72","issue":"7","department":[{"_id":"CaUh"}],"_id":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"publisher":"Elsevier","abstract":[{"lang":"eng","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."}],"citation":{"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.","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","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.","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.","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.","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"},"scopus_import":"1","oa_version":"Submitted Version","type":"journal_article","status":"public","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","date_published":"2015-01-01T00:00:00Z","article_processing_charge":"No","isi":1,"volume":1853,"publist_id":"5047","month":"01","external_id":{"isi":["000347598100014"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","quality_controlled":"1","date_updated":"2025-09-23T14:51:55Z","page":"144 - 156","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","_id":"2025","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"DaSi"}],"issue":"1","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","day":"01","date_created":"2018-12-11T11:55:17Z","year":"2015","oa":1,"publication_status":"published","doi":"10.1016/j.bbamcr.2014.10.009","file":[{"file_size":926685,"date_updated":"2020-07-14T12:45:25Z","content_type":"application/pdf","relation":"main_file","creator":"system","checksum":"5bb328edebb6a91337cadd7d63f961b7","access_level":"open_access","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","date_created":"2018-12-12T10:12:18Z","file_id":"4936"}],"intvolume":" 1853","file_date_updated":"2020-07-14T12:45:25Z","pubrep_id":"615","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"full_name":"Kawada, Daiki","first_name":"Daiki","last_name":"Kawada"},{"full_name":"Kobayashi, Hiromu","last_name":"Kobayashi","first_name":"Hiromu"},{"full_name":"Tomita, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Tomita"},{"first_name":"Eisuke","last_name":"Nakata","full_name":"Nakata, Eisuke"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"full_name":"Toshimaa, Jiro","first_name":"Jiro","last_name":"Toshimaa"}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2030","department":[{"_id":"BjHo"}],"issue":"1","page":"1 - 11","day":"01","publication":"Computers and Fluids","year":"2015","date_created":"2018-12-11T11:55:18Z","language":[{"iso":"eng"}],"author":[{"last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"intvolume":" 106","publication_status":"published","oa":1,"doi":"10.1016/j.compfluid.2014.09.021","citation":{"short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","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.","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.","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","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."},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1311.2481","open_access":"1"}],"publisher":"Elsevier","status":"public","type":"journal_article","publist_id":"5042","volume":106,"article_processing_charge":"No","date_published":"2015-01-01T00:00:00Z","arxiv":1,"isi":1,"title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","quality_controlled":"1","date_updated":"2025-09-22T14:31:33Z","external_id":{"isi":["000346213200001"],"arxiv":["1311.2481"]},"month":"01"},{"page":"1213 - 1244","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2035","ec_funded":1,"issue":"5","department":[{"_id":"HeEd"}],"publication":"Foundations of Computational Mathematics","day":"01","date_created":"2018-12-11T11:55:20Z","year":"2015","publication_status":"published","oa":1,"file":[{"creator":"system","checksum":"3566f3a8b0c1bc550e62914a88c584ff","access_level":"open_access","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","date_created":"2018-12-12T10:08:10Z","file_id":"4670","file_size":1317546,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:26Z"}],"doi":"10.1007/s10208-014-9223-y","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems"}],"intvolume":" 15","file_date_updated":"2020-07-14T12:45:26Z","pubrep_id":"486","ddc":["000"],"language":[{"iso":"eng"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz","last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866"},{"full_name":"Mrozek, Marian","first_name":"Marian","last_name":"Mrozek"}],"publisher":"Springer","citation":{"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.","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","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","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.","ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244."},"abstract":[{"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","lang":"eng"}],"scopus_import":"1","oa_version":"Published Version","type":"journal_article","status":"public","title":"The persistent homology of a self-map","date_published":"2015-10-01T00:00:00Z","article_processing_charge":"No","isi":1,"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,"publist_id":"5022","month":"10","external_id":{"isi":["000360862900004"]},"license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2025-09-23T14:08:54Z","quality_controlled":"1"},{"language":[{"iso":"eng"}],"author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896"},{"first_name":"Can","last_name":"Zhang","full_name":"Zhang, Can"},{"full_name":"Naibert, Tyler","first_name":"Tyler","last_name":"Naibert"},{"full_name":"Eckstein, James","first_name":"James","last_name":"Eckstein"},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"intvolume":" 60","oa":1,"publication_status":"published","extern":"1","year":"2015","alternative_title":["Bulletin of the American Physical Society"],"date_created":"2022-02-08T10:17:09Z","day":"01","publication":"APS March Meeting 2015","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10748","conference":{"name":"APS: American Physical Society","end_date":"2015-03-06","start_date":"2015-03-02","location":"San Antonio, TX, United States"},"issue":"1","date_updated":"2022-02-08T10:42:53Z","quality_controlled":"1","month":"03","volume":60,"article_processing_charge":"No","date_published":"2015-03-01T00:00:00Z","title":"Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy","status":"public","type":"conference","publication_identifier":{"issn":["0003-0503"]},"article_number":"G16.00009","citation":{"short":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March Meeting 2015, American Physical Society, 2015.","ista":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015. APS: American Physical Society, Bulletin of the American Physical Society, vol. 60, G16.00009.","mla":"Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” APS March Meeting 2015, vol. 60, no. 1, G16.00009, American Physical Society, 2015.","chicago":"Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” In APS March Meeting 2015, Vol. 60. American Physical Society, 2015.","apa":"Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., & Budakian, R. (2015). Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In APS March Meeting 2015 (Vol. 60). San Antonio, TX, United States: American Physical Society.","ama":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In: APS March Meeting 2015. Vol 60. American Physical Society; 2015.","ieee":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in APS March Meeting 2015, San Antonio, TX, United States, 2015, vol. 60, no. 1."},"abstract":[{"text":"The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR15/Event/238442"}],"publisher":"American Physical Society"},{"oa_version":"Published Version","article_number":"42","citation":{"ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042","apa":"Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42."},"abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"keyword":["General Environmental Science"],"scopus_import":"1","publisher":"Frontiers","publication_identifier":{"issn":["2296-665X"]},"type":"journal_article","status":"public","volume":3,"title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","date_published":"2015-06-10T00:00:00Z","article_processing_charge":"No","quality_controlled":"1","date_updated":"2025-04-15T06:50:01Z","month":"06","ec_funded":1,"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"_id":"10794","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"10","corr_author":"1","publication":"Frontiers in Environmental Science","year":"2015","date_created":"2022-02-25T11:42:25Z","article_type":"original","file_date_updated":"2022-02-25T11:55:26Z","author":[{"full_name":"Parise, Francesca","last_name":"Parise","first_name":"Francesca"},{"full_name":"Lygeros, John","first_name":"John","last_name":"Lygeros"},{"orcid":"0000-0003-1615-3282","first_name":"Jakob","last_name":"Ruess","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000","570"],"language":[{"iso":"eng"}],"file":[{"file_size":1371201,"date_updated":"2022-02-25T11:55:26Z","relation":"main_file","content_type":"application/pdf","date_created":"2022-02-25T11:55:26Z","success":1,"file_id":"10795","checksum":"26c222487564e1be02a11d688d6f769d","creator":"dernst","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","access_level":"open_access"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.3389/fenvs.2015.00042","publication_status":"published","oa":1,"intvolume":" 3"},{"ec_funded":1,"issue":"1","conference":{"location":"San Diego, CA, United States","end_date":"2015-01-06","name":"SODA: Symposium on Discrete Algorithms","start_date":"2015-01-04"},"department":[{"_id":"KrCh"}],"_id":"10796","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1018-1029","day":"01","publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","OA_place":"publisher","corr_author":"1","year":"2015","date_created":"2022-02-25T12:18:43Z","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}],"language":[{"iso":"eng"}],"intvolume":" 2015","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":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"doi":"10.1137/1.9781611973730.69","oa":1,"publication_status":"published","oa_version":"Preprint","scopus_import":"1","abstract":[{"lang":"eng","text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy)."}],"citation":{"mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69.","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29. SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029. doi:10.1137/1.9781611973730.69","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1409.6690","open_access":"1"}],"publisher":"SIAM","OA_type":"green","status":"public","publication_identifier":{"isbn":["978-161197374-7"]},"type":"conference","volume":2015,"acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","article_processing_charge":"No","arxiv":1,"date_published":"2015-01-01T00:00:00Z","title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","quality_controlled":"1","date_updated":"2025-06-26T06:54:08Z","external_id":{"arxiv":["1409.6690"]},"month":"01"},{"volume":24,"year":"2015","article_processing_charge":"No","date_published":"2015-12-10T00:00:00Z","article_type":"original","title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","date_created":"2020-04-30T10:51:01Z","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"Santure","first_name":"Anna W.","full_name":"Santure, Anna W."},{"first_name":"Jocelyn","last_name":"Poissant","full_name":"Poissant, Jocelyn"},{"last_name":"De Cauwer","first_name":"Isabelle","full_name":"De Cauwer, Isabelle"},{"last_name":"van Oers","first_name":"Kees","full_name":"van Oers, Kees"},{"last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"full_name":"Quinn, John L.","last_name":"Quinn","first_name":"John L."},{"last_name":"Groenen","first_name":"Martien A. M.","full_name":"Groenen, Martien A. M."},{"full_name":"Visser, Marcel E.","last_name":"Visser","first_name":"Marcel E."},{"full_name":"Sheldon, Ben C.","last_name":"Sheldon","first_name":"Ben C."},{"full_name":"Slate, Jon","last_name":"Slate","first_name":"Jon"}],"date_updated":"2021-01-12T08:15:12Z","intvolume":" 24","publication_status":"published","oa":1,"extern":"1","doi":"10.1111/mec.13452","month":"12","citation":{"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.","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","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.","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","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.","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.","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."},"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"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7739","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.13452"}],"page":"6148-6162","publisher":"Wiley","day":"10","status":"public","publication":"Molecular Ecology","type":"journal_article","publication_identifier":{"issn":["0962-1083"]}},{"main_file_link":[{"url":"https://doi.org/10.1098/rspb.2015.0689","open_access":"1"}],"publisher":"The Royal Society","oa_version":"Published Version","article_number":"20150689","abstract":[{"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.","lang":"eng"}],"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.","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015).","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.","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.","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","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","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."},"status":"public","publication_identifier":{"issn":["0962-8452","1471-2954"]},"type":"journal_article","date_published":"2015-07-07T00:00:00Z","article_processing_charge":"No","title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","volume":282,"month":"07","quality_controlled":"1","date_updated":"2021-01-12T08:15:12Z","external_id":{"pmid":["26063846"]},"pmid":1,"issue":"1810","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7741","publication":"Proceedings of the Royal Society B: Biological Sciences","day":"07","article_type":"original","date_created":"2020-04-30T10:58:07Z","year":"2015","intvolume":" 282","doi":"10.1098/rspb.2015.0689","oa":1,"extern":"1","publication_status":"published","author":[{"full_name":"Adams, Mark James","first_name":"Mark James","last_name":"Adams"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"},{"full_name":"Mannarelli, Maria-Elena","last_name":"Mannarelli","first_name":"Maria-Elena"},{"full_name":"Hatchwell, Ben J.","first_name":"Ben J.","last_name":"Hatchwell"}],"language":[{"iso":"eng"}]},{"day":"14","type":"journal_article","publication_identifier":{"issn":["1061-4036","1546-1718"]},"publication":"Nature Genetics","status":"public","_id":"7742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"11","citation":{"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.","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","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.","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.","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.","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"},"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)."}],"oa_version":"None","publisher":"Springer Nature","page":"1357-1362","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:15:13Z","quality_controlled":"1","author":[{"orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Hemani, Gibran","last_name":"Hemani","first_name":"Gibran"},{"full_name":"Medina-Gomez, Carolina","first_name":"Carolina","last_name":"Medina-Gomez"},{"full_name":"Mezzavilla, Massimo","last_name":"Mezzavilla","first_name":"Massimo"},{"full_name":"Esko, Tonu","last_name":"Esko","first_name":"Tonu"},{"first_name":"Konstantin","last_name":"Shakhbazov","full_name":"Shakhbazov, Konstantin"},{"first_name":"Joseph E","last_name":"Powell","full_name":"Powell, Joseph E"},{"last_name":"Vinkhuyzen","first_name":"Anna","full_name":"Vinkhuyzen, Anna"},{"full_name":"Berndt, Sonja I","last_name":"Berndt","first_name":"Sonja I"},{"first_name":"Stefan","last_name":"Gustafsson","full_name":"Gustafsson, Stefan"},{"full_name":"Justice, Anne E","last_name":"Justice","first_name":"Anne E"},{"last_name":"Kahali","first_name":"Bratati","full_name":"Kahali, Bratati"},{"last_name":"Locke","first_name":"Adam E","full_name":"Locke, Adam E"},{"last_name":"Pers","first_name":"Tune H","full_name":"Pers, Tune H"},{"last_name":"Vedantam","first_name":"Sailaja","full_name":"Vedantam, Sailaja"},{"last_name":"Wood","first_name":"Andrew R","full_name":"Wood, Andrew R"},{"full_name":"van Rheenen, Wouter","last_name":"van Rheenen","first_name":"Wouter"},{"full_name":"Andreassen, Ole A","last_name":"Andreassen","first_name":"Ole A"},{"full_name":"Gasparini, Paolo","first_name":"Paolo","last_name":"Gasparini"},{"first_name":"Andres","last_name":"Metspalu","full_name":"Metspalu, Andres"},{"first_name":"Leonard H van den","last_name":"Berg","full_name":"Berg, Leonard H van den"},{"full_name":"Veldink, Jan H","first_name":"Jan H","last_name":"Veldink"},{"full_name":"Rivadeneira, Fernando","last_name":"Rivadeneira","first_name":"Fernando"},{"full_name":"Werge, Thomas M","last_name":"Werge","first_name":"Thomas M"},{"first_name":"Goncalo R","last_name":"Abecasis","full_name":"Abecasis, Goncalo R"},{"full_name":"Boomsma, Dorret I","last_name":"Boomsma","first_name":"Dorret I"},{"full_name":"Chasman, Daniel I","last_name":"Chasman","first_name":"Daniel I"},{"full_name":"de Geus, Eco J C","first_name":"Eco J C","last_name":"de Geus"},{"full_name":"Frayling, Timothy M","first_name":"Timothy M","last_name":"Frayling"},{"full_name":"Hirschhorn, Joel N","last_name":"Hirschhorn","first_name":"Joel N"},{"first_name":"Jouke Jan","last_name":"Hottenga","full_name":"Hottenga, Jouke Jan"},{"first_name":"Erik","last_name":"Ingelsson","full_name":"Ingelsson, Erik"},{"last_name":"Loos","first_name":"Ruth J F","full_name":"Loos, Ruth J F"},{"last_name":"Magnusson","first_name":"Patrik K E","full_name":"Magnusson, Patrik K E"},{"first_name":"Nicholas G","last_name":"Martin","full_name":"Martin, Nicholas G"},{"first_name":"Grant W","last_name":"Montgomery","full_name":"Montgomery, Grant W"},{"first_name":"Kari E","last_name":"North","full_name":"North, Kari E"},{"full_name":"Pedersen, Nancy L","first_name":"Nancy L","last_name":"Pedersen"},{"last_name":"Spector","first_name":"Timothy D","full_name":"Spector, Timothy D"},{"first_name":"Elizabeth K","last_name":"Speliotes","full_name":"Speliotes, Elizabeth K"},{"last_name":"Goddard","first_name":"Michael E","full_name":"Goddard, Michael E"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"full_name":"Visscher, Peter M","last_name":"Visscher","first_name":"Peter M"}],"publication_status":"published","extern":"1","month":"09","doi":"10.1038/ng.3401","intvolume":" 47","volume":47,"year":"2015","title":"Population genetic differentiation of height and body mass index across Europe","date_created":"2020-04-30T10:58:23Z","date_published":"2015-09-14T00:00:00Z","article_processing_charge":"No","article_type":"original"},{"year":"2015","publist_id":"6878","title":"The SprayList: A scalable relaxed priority queue","date_created":"2018-12-11T11:48:26Z","date_published":"2015-01-24T00:00:00Z","article_processing_charge":"No","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.","language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2026-05-18T12:40:58Z","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"publication_status":"published","extern":"1","doi":"10.1145/2688500.2688523","month":"01","_id":"776","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","conference":{"location":"San Francisco, CA, United States","name":"PPoPP: Principles and Practice of Parallel Pogramming","end_date":"2015-02-11","start_date":"2015-02-07"},"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","citation":{"ama":"Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. ACM; 2015:11-20. doi:10.1145/2688500.2688523","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” in Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Francisco, CA, United States, 2015, pp. 11–20.","mla":"Alistarh, Dan-Adrian, et al. “The SprayList: A Scalable Relaxed Priority Queue.” Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, ACM, 2015, pp. 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. Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Principles and Practice of Parallel Pogramming, 11–20.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, ACM, 2015, pp. 11–20.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue. In Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 11–20). San Francisco, CA, United States: ACM. https://doi.org/10.1145/2688500.2688523","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue.” In Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523."},"oa_version":"None","publisher":"ACM","page":"11 - 20","OA_type":"closed access","day":"24","type":"conference","publication_identifier":{"isbn":["9781450332057"]},"publication":"Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","status":"public"},{"doi":"10.1103/physrevlett.114.225501","month":"06","publication_status":"published","extern":"1","intvolume":" 114","author":[{"first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}],"quality_controlled":"1","date_updated":"2021-01-12T08:15:23Z","language":[{"iso":"eng"}],"date_created":"2020-04-30T11:41:08Z","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","article_type":"original","date_published":"2015-06-04T00:00:00Z","article_processing_charge":"No","year":"2015","volume":114,"publication_identifier":{"issn":["0031-9007","1079-7114"]},"type":"journal_article","publication":"Physical Review Letters","status":"public","day":"04","publisher":"American Physical Society","issue":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7765","oa_version":"None","citation":{"short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).","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.","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.","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","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."},"article_number":"225501","abstract":[{"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.","lang":"eng"}]},{"type":"journal_article","publication_identifier":{"issn":["1744-683X","1744-6848"]},"status":"public","publication":"Soft Matter","day":"15","page":"2745-2751","publisher":"Royal Society of Chemistry","_id":"7766","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"14","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."}],"citation":{"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.","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","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","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.","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751."},"oa_version":"None","extern":"1","publication_status":"published","doi":"10.1039/c4sm02905d","month":"02","intvolume":" 11","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:15:23Z","author":[{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}],"quality_controlled":"1","title":"Disordered surface vibrations in jammed sphere packings","date_created":"2020-04-30T11:41:23Z","article_processing_charge":"No","date_published":"2015-02-15T00:00:00Z","article_type":"original","volume":11,"year":"2015"},{"publisher":"American Physical Society","issue":"3","_id":"7767","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","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.","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.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706.","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","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."},"abstract":[{"lang":"eng","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."}],"article_number":"032706","publication_identifier":{"issn":["1539-3755","1550-2376"]},"type":"journal_article","publication":"Physical Review E","status":"public","day":"01","date_created":"2020-04-30T11:41:38Z","title":"Collective dynamics of soft active particles","article_type":"original","date_published":"2015-03-01T00:00:00Z","article_processing_charge":"No","year":"2015","volume":91,"doi":"10.1103/physreve.91.032706","month":"03","publication_status":"published","extern":"1","intvolume":" 91","author":[{"full_name":"van Drongelen, Ruben","first_name":"Ruben","last_name":"van Drongelen"},{"first_name":"Anshuman","last_name":"Pal","full_name":"Pal, Anshuman"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"}],"quality_controlled":"1","date_updated":"2021-01-12T08:15:24Z","language":[{"iso":"eng"}]},{"citation":{"chicago":"Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015.","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, Montréal, Canada: Neural Information Processing Systems.","short":"D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, 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.","mla":"Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.","ieee":"D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph partitioning,” presented at the NIPS: Neural Information Processing Systems, Montréal, Canada, 2015, vol. 2015–January, pp. 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."},"abstract":[{"lang":"eng","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."}],"oa_version":"None","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"777","conference":{"location":"Montréal, Canada","name":"NIPS: Neural Information Processing Systems","end_date":"2015-12-12","start_date":"2015-12-07"},"main_file_link":[{"url":"http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning"}],"page":"1900 - 1908","publisher":"Neural Information Processing Systems","day":"01","status":"public","type":"conference","publication_identifier":{"isbn":["9781510825024"]},"publist_id":"6879","volume":"2015-January","year":"2015","article_processing_charge":"No","date_published":"2015-01-01T00:00:00Z","title":"Streaming min-max hypergraph partitioning","date_created":"2018-12-11T11:48:27Z","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jennifer","last_name":"Iglesias","full_name":"Iglesias, Jennifer"},{"last_name":"Vojnović","first_name":"Milan","full_name":"Vojnović, Milan"}],"date_updated":"2026-05-19T08:39:02Z","extern":"1","publication_status":"published","month":"01"},{"external_id":{"arxiv":["1510.08820"]},"author":[{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"date_updated":"2025-06-26T10:26:40Z","language":[{"iso":"eng"}],"month":"10","doi":"10.48550/arXiv.1510.08820","publication_status":"submitted","extern":"1","oa":1,"year":"2015","date_created":"2020-04-30T12:16:18Z","title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","article_processing_charge":"No","date_published":"2015-10-29T00:00:00Z","arxiv":1,"OA_type":"green","day":"29","type":"preprint","publication":"arXiv","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7779","oa_version":"Preprint","article_number":"1510.08820","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"}],"citation":{"ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv. doi:10.48550/arXiv.1510.08820","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv. .","mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv, 1510.08820, doi:10.48550/arXiv.1510.08820.","ista":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv, 1510.08820.","short":"C.P. Goodrich, ArXiv (n.d.).","apa":"Goodrich, C. P. (n.d.). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv. https://doi.org/10.48550/arXiv.1510.08820","chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1510.08820."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.08820"}]},{"year":"2015","date_created":"2018-12-11T11:48:27Z","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"first_name":"Petr","last_name":"Kuznetsov","full_name":"Kuznetsov, Petr"},{"first_name":"Srivatsan","last_name":"Ravi","full_name":"Ravi, Srivatsan"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"publication_status":"published","extern":"1","oa":1,"doi":"10.1007/978-3-662-48653-5_13","intvolume":" 9363","_id":"778","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"DISC: Distributed Computing"},"page":"185 - 199","day":"01","volume":9363,"publist_id":"6880","title":"Inherent limitations of hybrid transactional memory","article_processing_charge":"No","arxiv":1,"date_published":"2015-01-01T00:00:00Z","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.","external_id":{"arxiv":["1405.5689"]},"quality_controlled":"1","date_updated":"2023-02-23T13:17:35Z","month":"01","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."}],"citation":{"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.","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","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.","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","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.","short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, 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."},"oa_version":"None","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.5689"}],"type":"conference","status":"public"},{"publication_status":"published","extern":"1","doi":"10.1145/2755573.2755600","month":"06","language":[{"iso":"eng"}],"date_updated":"2023-02-23T12:35:42Z","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":"Alexander","last_name":"Matveev","full_name":"Matveev, Alexander"},{"full_name":"Leiserson, William","last_name":"Leiserson","first_name":"William"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"date_published":"2015-06-13T00:00:00Z","article_processing_charge":"No","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.","title":"ThreadScan: Automatic and scalable memory reclamation","date_created":"2018-12-11T11:48:27Z","publist_id":"6876","volume":"2015-June","year":"2015","status":"public","type":"conference","day":"13","related_material":{"record":[{"relation":"later_version","id":"6001","status":"public"}]},"publisher":"ACM","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.","short":"D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132.","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.","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.","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"},"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."}],"oa_version":"None","_id":"779","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"}}]