--- _id: '2008' abstract: - lang: eng 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. 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). author: - first_name: Anna full_name: Klimova, Anna id: 31934120-F248-11E8-B48F-1D18A9856A87 last_name: Klimova - first_name: Tamás full_name: Rudas, Tamás last_name: Rudas 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 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. 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. ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847. 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. date_created: 2018-12-11T11:55:11Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:54:41Z day: '01' department: - _id: CaUh doi: 10.1111/sjos.12139 intvolume: ' 42' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.3282 month: '09' oa: 1 oa_version: Preprint page: 832 - 847 publication: Scandinavian Journal of Statistics publication_status: published publisher: Wiley publist_id: '5068' quality_controlled: '1' scopus_import: 1 status: public title: Iterative scaling in curved exponential families type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2015' ... --- _id: '2006' 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. ' article_processing_charge: No author: - first_name: Nicolas full_name: Hein, Nicolas last_name: Hein - first_name: Christopher full_name: Hillar, Christopher last_name: Hillar - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin Del Campo Sanchez - first_name: Frank full_name: Sottile, Frank last_name: Sottile - first_name: Zach full_name: Teitler, Zach last_name: Teitler citation: 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 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 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. 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. 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. 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. short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269. date_created: 2018-12-11T11:55:10Z date_published: 2015-06-23T00:00:00Z date_updated: 2021-01-12T06:54:40Z day: '23' department: - _id: CaUh doi: 10.1080/10586458.2014.980044 intvolume: ' 24' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.3436 month: '06' oa: 1 oa_version: Preprint page: 261 - 269 publication: Experimental Mathematics publication_status: published publisher: Taylor & Francis publist_id: '5070' quality_controlled: '1' scopus_import: 1 status: public title: The monotone secant conjecture in the real Schubert calculus type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '2014' 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. author: - first_name: Anna full_name: Klimova, Anna id: 31934120-F248-11E8-B48F-1D18A9856A87 last_name: Klimova - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Tamás full_name: Rudas, Tamás last_name: Rudas citation: 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 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. 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. ista: Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 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. short: A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72. date_created: 2018-12-11T11:55:13Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:54:43Z day: '01' department: - _id: CaUh doi: 10.1016/j.csda.2015.01.017 intvolume: ' 87' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.6617 month: '07' oa: 1 oa_version: Preprint page: 57 - 72 publication: Computational Statistics & Data Analysis publication_status: published publisher: Elsevier publist_id: '5062' quality_controlled: '1' scopus_import: 1 status: public title: Faithfulness and learning hypergraphs from discrete distributions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2015' ... --- _id: '2025' 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. author: - first_name: Daiki full_name: Kawada, Daiki last_name: Kawada - first_name: Hiromu full_name: Kobayashi, Hiromu last_name: Kobayashi - first_name: Tsuyoshi full_name: Tomita, Tsuyoshi last_name: Tomita - first_name: Eisuke full_name: Nakata, Eisuke last_name: Nakata - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Junko full_name: Toshima, Junko last_name: Toshima - first_name: Jiro full_name: Toshimaa, Jiro last_name: Toshimaa citation: 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 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. 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. 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. 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. date_created: 2018-12-11T11:55:17Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:54:48Z day: '01' ddc: - '570' department: - _id: DaSi doi: 10.1016/j.bbamcr.2014.10.009 file: - access_level: open_access checksum: 5bb328edebb6a91337cadd7d63f961b7 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:18Z date_updated: 2020-07-14T12:45:25Z file_id: '4936' file_name: IST-2016-615-v1+1_BBAMCR.pdf file_size: 926685 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 1853' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 144 - 156 publication: Biochimica et Biophysica Acta - Molecular Cell Research publication_status: published publisher: Elsevier publist_id: '5047' pubrep_id: '615' quality_controlled: '1' scopus_import: 1 status: public title: The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1853 year: '2015' ... --- _id: '2030' 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. author: - first_name: Liang full_name: Shi, Liang id: 374A3F1A-F248-11E8-B48F-1D18A9856A87 last_name: Shi - first_name: Markus full_name: Rampp, Markus last_name: Rampp - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: 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 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 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. 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. 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. short: L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11. date_created: 2018-12-11T11:55:18Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:54:51Z day: '01' department: - _id: BjHo doi: 10.1016/j.compfluid.2014.09.021 intvolume: ' 106' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1311.2481 month: '01' oa: 1 oa_version: Preprint page: 1 - 11 publication: Computers and Fluids publication_status: published publisher: Elsevier publist_id: '5042' quality_controlled: '1' scopus_import: 1 status: public title: A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 106 year: '2015' ... --- _id: '2035' 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" 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. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Grzegorz full_name: Jablonski, Grzegorz id: 4483EF78-F248-11E8-B48F-1D18A9856A87 last_name: Jablonski orcid: 0000-0002-3536-9866 - first_name: Marian full_name: Mrozek, Marian last_name: Mrozek citation: 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. 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. ista: Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244. 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. date_created: 2018-12-11T11:55:20Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:54:53Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s10208-014-9223-y ec_funded: 1 file: - access_level: open_access checksum: 3566f3a8b0c1bc550e62914a88c584ff content_type: application/pdf creator: system date_created: 2018-12-12T10:08:10Z date_updated: 2020-07-14T12:45:26Z file_id: '4670' file_name: IST-2016-486-v1+1_s10208-014-9223-y.pdf file_size: 1317546 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '5' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1213 - 1244 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '5022' pubrep_id: '486' quality_controlled: '1' scopus_import: 1 status: public title: The persistent homology of a self-map tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2015' ... --- _id: '2034' 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. author: - first_name: Béatrice full_name: Bérard, Béatrice last_name: Bérard - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nathalie full_name: Sznajder, Nathalie last_name: Sznajder 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 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 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. 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. ista: Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59. 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. date_created: 2018-12-11T11:55:20Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:54:52Z day: '01' department: - _id: KrCh doi: 10.1016/j.ipl.2014.09.001 ec_funded: 1 intvolume: ' 115' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.4225 month: '01' oa: 1 oa_version: Preprint page: 52 - 59 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ' Information Processing Letters' publication_status: published publisher: Elsevier publist_id: '5025' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic opacity for Markov decision processes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2015' ... --- _id: '2085' abstract: - lang: eng 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. ' author: - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:55:37Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:55:13Z day: '01' department: - _id: RoSe doi: 10.1007/s00205-014-0781-6 intvolume: ' 215' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.1153 month: '02' oa: 1 oa_version: Preprint page: 381 - 417 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '4951' quality_controlled: '1' scopus_import: 1 status: public title: Collective excitations of Bose gases in the mean-field regime type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 215 year: '2015' ... --- _id: '2166' abstract: - lang: eng 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). ' author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles 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' 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' 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.' 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.' 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.' 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. date_created: 2018-12-11T11:56:05Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:55:43Z day: '01' department: - _id: LaEr doi: 10.1007/s00220-014-2119-5 intvolume: ' 333' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5106 month: '02' oa: 1 oa_version: Preprint page: 1365 - 1416 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4818' quality_controlled: '1' scopus_import: 1 status: public title: 'The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 333 year: '2015' ... --- _id: '1832' abstract: - lang: eng 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. ' article_number: '20' article_processing_charge: No article_type: original author: - first_name: Soham full_name: Chakraborty, Soham last_name: Chakraborty - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ali full_name: Sezgin, Ali last_name: Sezgin - first_name: Viktor full_name: Vafeiadis, Viktor last_name: Vafeiadis citation: 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 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 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. 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. ista: Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 11(1), 20. 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). date_created: 2018-12-11T11:54:15Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T10:38:13Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.2168/LMCS-11(1:20)2015 ec_funded: 1 file: - access_level: open_access checksum: 7370e164d0a731f442424a92669efc34 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:27Z date_updated: 2020-07-14T12:45:17Z file_id: '4881' file_name: IST-2015-390-v1+1_1502.07639.pdf file_size: 380203 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '04' oa: 1 oa_version: Published Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Logical Methods in Computer Science publication_status: published publisher: International Federation of Computational Logic publist_id: '5271' pubrep_id: '390' quality_controlled: '1' related_material: record: - id: '2328' relation: earlier_version status: public scopus_import: 1 status: public title: Aspect-oriented linearizability proofs tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '2271' 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. " author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Johan full_name: Thapper, Johan last_name: Thapper - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: 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 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. 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. 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. short: V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36. date_created: 2018-12-11T11:56:41Z date_published: 2015-02-01T00:00:00Z date_updated: 2023-02-23T10:46:30Z day: '01' department: - _id: VlKo doi: 10.1137/130945648 external_id: arxiv: - '1311.4219' intvolume: ' 44' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1311.4219 month: '02' oa: 1 oa_version: Preprint page: 1 - 36 publication: SIAM Journal on Computing publication_status: published publisher: SIAM publist_id: '4673' quality_controlled: '1' related_material: record: - id: '2518' relation: earlier_version status: public scopus_import: 1 status: public title: The power of linear programming for general-valued CSPs type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2015' ... --- _id: '257' 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. 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. author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Ritabrata full_name: Munshi, Ritabrata last_name: Munshi citation: 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 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 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. 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. 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. 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_created: 2018-12-11T11:45:28Z date_published: 2015-07-10T00:00:00Z date_updated: 2021-01-12T06:58:18Z day: '10' doi: 10.1515/forum-2013-6024 extern: 1 intvolume: ' 27' issue: '4' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1302.2434 month: '07' oa: 1 page: 2025 - 2050 publication: Forum Mathematicum publication_status: published publisher: Walter de Gruyter GmbH publist_id: '7645' quality_controlled: 0 status: public title: Pairs of diagonal quadratic forms and linear correlations among sums of two squares type: journal_article volume: 27 year: '2015' ... --- _id: '258' abstract: - lang: eng 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. author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: 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' 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 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. 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. ista: 'Browning TD. 2015.A survey of applications of the circle method to rational points. In: Arithmetic and Geometry. , 89–113.' 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. date_created: 2018-12-11T11:45:28Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:58:22Z day: '01' doi: 10.1017/CBO9781316106877.009 extern: '1' language: - iso: eng month: '08' oa_version: None page: 89 - 113 publication: Arithmetic and Geometry publication_status: published publisher: Cambridge University Press publist_id: '7644' quality_controlled: '1' status: public title: A survey of applications of the circle method to rational points type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '259' abstract: - lang: eng text: 'The Hasse principle and weak approximation is established for non-singular cubic hypersurfaces X over the function field ' acknowledgement: "EP/J018260/1\tEngineering and Physical Sciences Research Council EPSRC" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Pankaj full_name: Vishe, Pankaj last_name: Vishe citation: 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 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 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. 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. 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. short: T.D. Browning, P. Vishe, Geometric and Functional Analysis 25 (2015) 671–732. date_created: 2018-12-11T11:45:29Z date_published: 2015-06-11T00:00:00Z date_updated: 2021-01-12T06:58:25Z day: '11' doi: 10.1007/s00039-015-0328-5 extern: 1 intvolume: ' 25' issue: '3' month: '06' page: 671 - 732 publication: Geometric and Functional Analysis publication_status: published publisher: Birkhäuser publist_id: '7643' quality_controlled: 0 status: public title: 'Rational points on cubic hypersurfaces over F_q(t) ' type: journal_article volume: 25 year: '2015' ... --- _id: '1598' 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.' 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" article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Manas full_name: Joglekar, Manas last_name: Joglekar - first_name: Nisarg full_name: Shah, Nisarg last_name: Shah 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:52:56Z date_published: 2015-03-30T00:00:00Z date_updated: 2023-02-23T10:55:03Z day: '30' department: - _id: KrCh doi: 10.1016/j.tcs.2015.01.050 ec_funded: 1 external_id: arxiv: - '1202.4175' intvolume: ' 573' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1202.4175 month: '03' oa: 1 oa_version: Preprint page: 71 - 89 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '5571' quality_controlled: '1' related_material: record: - id: '2715' relation: earlier_version status: public scopus_import: 1 status: public title: Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 573 year: '2015' ... --- _id: '1805' abstract: - lang: eng 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.' author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Olivier full_name: Devillers, Olivier last_name: Devillers - first_name: Marc full_name: Glisse, Marc last_name: Glisse - first_name: André full_name: Lieutier, André last_name: Lieutier citation: 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' 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' 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.' 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.' 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.' 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.' short: 'D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.' date_created: 2018-12-11T11:54:06Z date_published: 2015-06-03T00:00:00Z date_updated: 2023-02-23T10:59:19Z day: '03' department: - _id: HeEd doi: 10.1016/j.comgeo.2014.08.010 ec_funded: 1 intvolume: ' 48' issue: '8' language: - iso: eng month: '06' oa_version: None page: 606 - 621 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '5305' quality_controlled: '1' related_material: record: - id: '2812' relation: earlier_version status: public scopus_import: 1 status: public title: Homological reconstruction and simplification in R3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2015' ... --- _id: '333' 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. ' article_processing_charge: No article_type: original author: - first_name: Marc full_name: Walter, Marc last_name: Walter - first_name: Kostiantyn full_name: Kravchyk, Kostiantyn last_name: Kravchyk - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Maksym full_name: Kovalenko, Maksym last_name: Kovalenko citation: 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 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 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. 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. ista: Walter M, Kravchyk K, Ibáñez M, Kovalenko M. 2015. Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. 27(21), 7452–7458. 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. date_created: 2018-12-11T11:45:52Z date_published: 2015-10-16T00:00:00Z date_updated: 2021-01-12T07:42:42Z day: '16' doi: 10.1021/acs.chemmater.5b03531 extern: '1' intvolume: ' 27' issue: '21' language: - iso: eng month: '10' oa_version: None page: 7452 - 7458 publication: Chemistry of Materials publication_status: published publisher: ACS publist_id: '7507' quality_controlled: '1' status: public title: Efficient and inexpensive sodium magnesium hybrid battery type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '354' abstract: - lang: eng 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. ' 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. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Rachel full_name: Korkosz, Rachel last_name: Korkosz - first_name: Zhishan full_name: Luo, Zhishan last_name: Luo - first_name: Pau full_name: Riba, Pau last_name: Riba - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Silvia full_name: Ortega, Silvia last_name: Ortega - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Mercouri full_name: Kanatzidis, Mercouri last_name: Kanatzidis 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:45:59Z date_published: 2015-03-11T00:00:00Z date_updated: 2021-01-12T07:44:10Z day: '11' doi: 10.1021/jacs.5b00091 extern: '1' intvolume: ' 137' issue: '12' language: - iso: eng month: '03' oa_version: None page: 4046 - 4049 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7470' quality_controlled: '1' status: public title: Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 137 year: '2015' ... --- _id: '360' abstract: - lang: eng 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. ' article_processing_charge: No author: - first_name: Xuelian full_name: Yu, Xuelian last_name: Yu - first_name: Jingjing full_name: Liu, Jingjing last_name: Liu - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Zhishan full_name: Luo, Zhishan last_name: Luo - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Guangjin full_name: Zhang, Guangjin last_name: Zhang - first_name: Yihe full_name: Zhang, Yihe last_name: Zhang - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:01Z date_published: 2015-09-29T00:00:00Z date_updated: 2021-01-12T07:44:34Z day: '29' doi: 10.1021/acs.langmuir.5b02490 extern: '1' intvolume: ' 31' issue: '38' language: - iso: eng month: '09' oa_version: None page: 10555 - 10561 publication: Langmuir publication_status: published publisher: American Chemical Society publist_id: '7467' status: public title: Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '362' 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. ' article_processing_charge: No author: - first_name: Zhishan full_name: Lu, Zhishan last_name: Lu - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Ana full_name: Antolín, Ana last_name: Antolín - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Sandra full_name: Contreras, Sandra last_name: Contreras - first_name: Francesc full_name: Medina, Francesc last_name: Medina - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:02Z date_published: 2015-04-07T00:00:00Z date_updated: 2021-01-12T07:44:42Z day: '07' doi: 10.1021/la504906q extern: '1' intvolume: ' 31' issue: '13' language: - iso: eng month: '04' oa_version: None page: 3952 - 3957 publication: Langmuir publication_status: published publisher: American Chemical Society publist_id: '7469' status: public title: Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '1731' 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. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Hugo full_name: Gimbert, Hugo last_name: Gimbert - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: 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 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 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. 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. 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. short: K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16. date_created: 2018-12-11T11:53:42Z date_published: 2015-12-01T00:00:00Z date_updated: 2023-02-23T11:45:42Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.ic.2015.06.003 ec_funded: 1 intvolume: ' 245' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1006.0673 month: '12' oa: 1 oa_version: Preprint page: 3 - 16 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '5395' quality_controlled: '1' related_material: record: - id: '3856' relation: earlier_version status: public scopus_import: 1 status: public title: Randomness for free type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 245 year: '2015' ... --- _id: '334' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Xuelian full_name: Yu, Xuelian last_name: Yu - first_name: Jingjing full_name: Liu, Jingjing last_name: Liu - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Zhishan full_name: Luo, Zhishan last_name: Luo - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Guangjin full_name: Zhang, Guangjin last_name: Zhang - first_name: Yihe full_name: Zhang, Yihe last_name: Zhang - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:45:52Z date_published: 2015-09-07T00:00:00Z date_updated: 2021-01-12T07:42:46Z day: '07' doi: 10.1021/acs.langmuir.5b02490 extern: '1' intvolume: ' 31' issue: '38' language: - iso: eng month: '09' oa_version: None page: 10555 - 10561 publication: Langmuir publication_status: published publisher: American Chemical Society publist_id: '7508' quality_controlled: '1' status: public title: Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '361' 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. 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. article_processing_charge: No author: - first_name: Xuelian full_name: Yu, Xuelian last_name: Yu - first_name: Xiaoqiang full_name: An, Xiaoqiang last_name: An - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Yihe full_name: Zhang, Yihe last_name: Zhang - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:01Z date_published: 2015-08-26T00:00:00Z date_updated: 2021-01-12T07:44:38Z day: '26' doi: 10.1021/acs.jpcc.5b06199 extern: '1' intvolume: ' 119' issue: '38' language: - iso: eng month: '08' oa_version: None page: 21882 - 21888 publication: Journal of Physical Chemistry C publication_status: published publisher: American Chemical Society publist_id: '7468' status: public title: Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2015' ... --- _id: '1856' abstract: - lang: eng 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.' article_number: '9' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Rohit full_name: Singh, Rohit last_name: Singh 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 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. 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. 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. short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, Journal of the ACM 62 (2015). date_created: 2018-12-11T11:54:23Z date_published: 2015-02-01T00:00:00Z date_updated: 2023-02-23T11:46:04Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1145/2699430 ec_funded: 1 intvolume: ' 62' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1004.0739 month: '02' oa: 1 oa_version: Preprint project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '5244' quality_controlled: '1' related_material: record: - id: '3864' relation: earlier_version status: public scopus_import: 1 status: public title: Measuring and synthesizing systems in probabilistic environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2015' ... --- _id: '388' 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. article_processing_charge: No article_type: original author: - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Gang full_name: Cao, Gang last_name: Cao - first_name: Nuh full_name: Gedik, Nuh last_name: Gedik citation: 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 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 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. 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. 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). 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). date_created: 2018-12-11T11:46:11Z date_published: 2015-07-07T00:00:00Z date_updated: 2021-01-12T07:52:54Z day: '07' doi: 10.1103/PhysRevLett.114.017203 extern: '1' intvolume: ' 114' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://dspace.mit.edu/handle/1721.1/92979 month: '07' oa: 1 oa_version: Published Version publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7441' quality_controlled: '1' status: public title: Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '1661' abstract: - lang: eng 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. 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.' article_number: '7174888' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: 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' 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' 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. 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. 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.' 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. short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:20:05Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2015.34 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprints.cs.univie.ac.at/4368/ month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings - Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '5489' quality_controlled: '1' related_material: record: - id: '464' relation: later_version status: public scopus_import: '1' status: public title: Improved algorithms for one-pair and k-pair Streett objectives type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 2015-July year: '2015' ... --- _id: '473' 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. author: - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Nam full_name: Phan Thanh, Nam id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Phan Thanh - first_name: Nicolas full_name: Rougerie, Nicolas last_name: Rougerie citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:40Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:00:52Z day: '01' ddc: - '539' department: - _id: RoSe doi: 10.5802/jep.18 ec_funded: 1 file: - access_level: open_access checksum: a40eb4016717ddc9927154798a4c164a content_type: application/pdf creator: system date_created: 2018-12-12T10:12:53Z date_updated: 2020-07-14T12:46:35Z file_id: '4974' file_name: IST-2018-951-v1+1_2015_Thanh-Nam_Derivation_of.pdf file_size: 1084254 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 65 - 115 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal de l'Ecole Polytechnique - Mathematiques publication_status: published publisher: Ecole Polytechnique publist_id: '7344' pubrep_id: '951' quality_controlled: '1' scopus_import: 1 status: public title: Derivation of nonlinear gibbs measures from many-body quantum mechanics tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2015' ... --- _id: '477' 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: - first_name: Katrin full_name: Holst, Katrin last_name: Holst - first_name: Daria full_name: Guseva, Daria last_name: Guseva - first_name: Susann full_name: Schindler, Susann last_name: Schindler - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Armin full_name: Braun, Armin last_name: Braun - first_name: Himpriya full_name: Chopra, Himpriya last_name: Chopra - first_name: Oliver full_name: Pabst, Oliver last_name: Pabst - first_name: Evgeni full_name: Ponimaskin, Evgeni last_name: Ponimaskin 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 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 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. 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. 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. 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. 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. date_created: 2018-12-11T11:46:41Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T08:00:54Z day: '15' department: - _id: MiSi doi: 10.1242/jcs.167999 intvolume: ' 128' issue: '15' language: - iso: eng month: '06' oa_version: None page: 2866 - 2880 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '7343' quality_controlled: '1' scopus_import: 1 status: public title: The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '523' 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. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Mickael full_name: Randour, Mickael last_name: Randour - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:57Z date_published: 2015-03-24T00:00:00Z date_updated: 2023-02-23T10:36:02Z day: '24' department: - _id: KrCh doi: 10.1016/j.ic.2015.03.010 ec_funded: 1 intvolume: ' 242' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1302.4248 month: '03' oa: 1 oa_version: Preprint page: 25 - 52 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '7296' quality_controlled: '1' related_material: record: - id: '2279' relation: earlier_version status: public scopus_import: 1 status: public title: Looking at mean-payoff and total-payoff through windows type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 242 year: '2015' ... --- _id: '532' abstract: - lang: eng 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. author: - first_name: Wenyang full_name: Li, Wenyang last_name: Li - first_name: Mengdi full_name: Ma, Mengdi last_name: Ma - first_name: Ying full_name: Feng, Ying last_name: Feng - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Yichuan full_name: Wang, Yichuan last_name: Wang - first_name: Yutong full_name: Ma, Yutong last_name: Ma - first_name: Mingzhe full_name: Li, Mingzhe last_name: Li - first_name: Fengying full_name: An, Fengying last_name: An - first_name: Hongwei full_name: Guo, Hongwei last_name: Guo citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:47:00Z date_published: 2015-10-22T00:00:00Z date_updated: 2021-01-12T08:01:27Z day: '22' department: - _id: JiFr doi: 10.1016/j.cell.2015.09.037 intvolume: ' 163' issue: '3' language: - iso: eng month: '10' oa_version: None page: 670 - 683 publication: Cell publication_status: published publisher: Cell Press publist_id: '7285' quality_controlled: '1' scopus_import: 1 status: public title: EIN2-directed translational regulation of ethylene signaling in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 163 year: '2015' ... --- _id: '524' abstract: - lang: eng 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.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 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 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 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. 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. ista: Chatterjee K, Ibsen-Jensen R. 2015. Qualitative analysis of concurrent mean payoff games. Information and Computation. 242(6), 2–24. 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. date_created: 2018-12-11T11:46:57Z date_published: 2015-10-11T00:00:00Z date_updated: 2023-02-23T12:24:45Z day: '11' department: - _id: KrCh doi: 10.1016/j.ic.2015.03.009 external_id: arxiv: - '1409.5306' intvolume: ' 242' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1409.5306 month: '10' oa: 1 oa_version: Preprint page: 2 - 24 publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '7295' quality_controlled: '1' related_material: record: - id: '5403' relation: earlier_version status: public scopus_import: 1 status: public title: Qualitative analysis of concurrent mean payoff games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 242 year: '2015' ... --- _id: '1481' 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. ' acknowledgement: "A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n" article_processing_charge: No author: - first_name: Umair full_name: Ahmed, Umair last_name: Ahmed - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Sumit full_name: Gulwani, Sumit last_name: Gulwani citation: 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.' 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.' 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. 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. 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.' 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. conference: end_date: 2015-01-30 location: Austin, TX, USA name: 'AAAI: Conference on Artificial Intelligence' start_date: 2015-01-25 date_created: 2018-12-11T11:52:16Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T12:25:07Z day: '01' department: - _id: KrCh ec_funded: 1 intvolume: ' 2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300 month: '01' oa: 1 oa_version: None page: 745 - 752 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence publication_status: published publisher: AAAI Press publist_id: '5713' quality_controlled: '1' related_material: record: - id: '5410' relation: earlier_version status: public scopus_import: 1 status: public title: Automatic generation of alternative starting positions for simple traditional board games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2015' ... --- _id: '1732' 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. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2015-05-30 location: Seattle, WA, United States name: 'ICRA: International Conference on Robotics and Automation' start_date: 2015-05-26 date_created: 2018-12-11T11:53:43Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T12:25:52Z day: '01' department: - _id: KrCh doi: 10.1109/ICRA.2015.7139019 ec_funded: 1 external_id: arxiv: - '1409.3360' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1409.3360 month: '01' oa: 1 oa_version: Preprint page: 325 - 330 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: IEEE publist_id: '5394' quality_controlled: '1' related_material: record: - id: '5424' relation: earlier_version status: public - id: '5426' relation: earlier_version status: public scopus_import: 1 status: public title: Qualitative analysis of POMDPs with temporal logic specifications for robotics applications type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5431' 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Kristoffer full_name: Hansen, Kristoffer last_name: Hansen citation: 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 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 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. ieee: K. Chatterjee, R. Ibsen-Jensen, and K. Hansen, The patience of concurrent stochastic games with safety and reachability objectives. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Hansen K. 2015. The patience of concurrent stochastic games with safety and reachability objectives, IST Austria, 25p. 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. date_created: 2018-12-12T11:39:17Z date_published: 2015-02-19T00:00:00Z date_updated: 2021-01-12T08:02:13Z day: '19' ddc: - '005' - '519' department: - _id: KrCh doi: 10.15479/AT:IST-2015-322-v1-1 file: - access_level: open_access checksum: bfb858262c30445b8e472c40069178a2 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:31Z date_updated: 2020-07-14T12:46:53Z file_id: '5491' file_name: IST-2015-322-v1+1_safetygames.pdf file_size: 661015 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '25' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '322' status: public title: The patience of concurrent stochastic games with safety and reachability objectives type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5434' abstract: - lang: eng 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. alternative_title: - IST Austria Technical Report author: - first_name: '1' full_name: Anonymous, 1 last_name: Anonymous - first_name: '2' full_name: Anonymous, 2 last_name: Anonymous citation: ama: Anonymous 1, Anonymous 2. 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. chicago: Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria, 2015. ieee: 1 Anonymous and 2 Anonymous, 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. 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. date_created: 2018-12-12T11:39:18Z date_published: 2015-02-19T00:00:00Z date_updated: 2020-07-14T23:04:59Z day: '19' ddc: - '000' file: - access_level: open_access checksum: 8542fd0b10aed7811cd41077b8ccb632 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:14Z date_updated: 2020-07-14T12:46:53Z file_id: '5475' file_name: IST-2015-326-v1+1_main.pdf file_size: 378162 relation: main_file - access_level: closed checksum: 84c31c537bdaf7a91909f18d25d640ab content_type: text/plain creator: dernst date_created: 2019-04-16T13:00:33Z date_updated: 2020-07-14T12:46:53Z file_id: '6317' file_name: IST-2015-326-v1+2_authors.txt file_size: 64 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '16' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '326' status: public title: Optimal cost indefinite-horizon reachability in goal DEC-POMDPs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1657' abstract: - lang: eng 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. ' acknowledgement: "A Technical Report of this paper is available at: https://repository.ist.ac.at/327\r\n" alternative_title: - LICS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Komárková, Zuzana last_name: Komárková - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: 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 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' 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. 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. ista: Chatterjee K, Komárková Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes. , 244–256. 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. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:18Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:16Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1109/LICS.2015.32 ec_funded: 1 language: - iso: eng month: '07' oa_version: None page: 244 - 256 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5493' quality_controlled: '1' related_material: record: - id: '466' relation: later_version status: public - id: '5429' relation: earlier_version status: public - id: '5435' relation: earlier_version status: public scopus_import: 1 series_title: LICS status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1656' abstract: - lang: eng 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. 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" article_number: '7174926' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: Proceedings - Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.72' 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' 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. 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. 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.' 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. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:17Z date_published: 2015-07-31T00:00:00Z date_updated: 2023-02-23T12:26:19Z day: '31' department: - _id: KrCh - _id: ToHe doi: 10.1109/LICS.2015.72 ec_funded: 1 external_id: arxiv: - '1606.03598' language: - iso: eng month: '07' oa_version: None project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings - Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '5494' quality_controlled: '1' related_material: record: - id: '467' relation: later_version status: public - id: '5415' relation: earlier_version status: public - id: '5436' relation: earlier_version status: public scopus_import: 1 status: public title: Nested weighted automata type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-July year: '2015' ... --- _id: '5429' abstract: - lang: eng 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.\r\nOur 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. 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Komarkova, Zuzana last_name: Komarkova - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v1-1 apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2015-318-v1-1 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-v1-1. ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria, 2015. ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 41p. mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v1-1. short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015. date_created: 2018-12-12T11:39:17Z date_published: 2015-01-12T00:00:00Z date_updated: 2023-02-23T12:26:16Z day: '12' ddc: - '004' department: - _id: KrCh doi: 10.15479/AT:IST-2015-318-v1-1 file: - access_level: open_access checksum: e4869a584567c506349abda9c8ec7db3 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:11Z date_updated: 2020-07-14T12:46:52Z file_id: '5533' file_name: IST-2015-318-v1+1_main.pdf file_size: 689863 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '41' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '318' related_material: record: - id: '1657' relation: later_version status: public - id: '466' relation: later_version status: public - id: '5435' relation: later_version status: public status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5435' abstract: - lang: eng 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Komarkova, Zuzana last_name: Komarkova - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v2-1 apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2015-318-v2-1 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. ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria, 2015. ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 51p. mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v2-1. short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-02-23T00:00:00Z date_updated: 2023-02-23T12:26:00Z day: '23' ddc: - '004' department: - _id: KrCh doi: 10.15479/AT:IST-2015-318-v2-1 file: - access_level: open_access checksum: 75284adec80baabdfe71ff9ebbc27445 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:03Z date_updated: 2020-07-14T12:46:53Z file_id: '5525' file_name: IST-2015-318-v2+1_main.pdf file_size: 717630 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '51' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '327' related_material: record: - id: '1657' relation: later_version status: public - id: '466' relation: later_version status: public - id: '5429' relation: earlier_version status: public status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5436' abstract: - lang: eng 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.\r\nIn 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-170-v2-2 apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-170-v2-2 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-170-v2-2. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2015. ista: Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria, 29p. mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-170-v2-2. short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-04-24T00:00:00Z date_updated: 2023-02-23T12:25:21Z day: '24' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2015-170-v2-2 file: - access_level: open_access checksum: 3c402f47d3669c28d04d1af405a08e3f content_type: application/pdf creator: system date_created: 2018-12-12T11:54:19Z date_updated: 2020-07-14T12:46:54Z file_id: '5541' file_name: IST-2015-170-v2+2_report.pdf file_size: 569991 relation: main_file file_date_updated: 2020-07-14T12:46:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '331' related_material: record: - id: '1656' relation: later_version status: public - id: '467' relation: later_version status: public - id: '5415' relation: earlier_version status: public status: public title: Nested weighted automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1659' 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.' acknowledgement: 'A technical report of the article is available at: https://research-explorer.app.ist.ac.at/record/5439' article_processing_charge: No author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: 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' apa: 'Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. In LICS (pp. 750–761). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.74' 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. ieee: U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,” in LICS, Kyoto, Japan, 2015, pp. 750–761. ista: 'Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS. LICS: Logic in Computer ScienceLogic in Computer Science, 750–761.' mla: Boker, Udi, et al. “The Target Discounted-Sum Problem.” LICS, IEEE, 2015, pp. 750–61, doi:10.1109/LICS.2015.74. short: U. Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-007-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:27Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/LICS.2015.74 ec_funded: 1 file: - access_level: open_access checksum: 6abebca9c1a620e9e103a8f9222befac content_type: application/pdf creator: dernst date_created: 2020-05-15T08:53:29Z date_updated: 2020-07-14T12:45:10Z file_id: '7852' file_name: 2015_LICS_Boker.pdf file_size: 340215 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 750 - 761 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: LICS publication_identifier: eisbn: - '978-1-4799-8875-4 ' issn: - '1043-6871 ' publication_status: published publisher: IEEE publist_id: '5491' quality_controlled: '1' related_material: record: - id: '5439' relation: earlier_version status: public scopus_import: 1 series_title: Logic in Computer Science status: public title: The target discounted-sum problem type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1610' 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. 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. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: 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' 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' 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. 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.' 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. short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 121–133. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: Automata, Languages and Programming' start_date: 2015-07-06 date_created: 2018-12-11T11:53:01Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:24Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-662-47666-6_10 ec_funded: 1 external_id: arxiv: - '1504.08259' intvolume: ' 9135' issue: Part II language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.08259 month: '07' oa: 1 oa_version: None page: 121 - 133 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: 42nd International Colloquium publication_identifier: isbn: - 978-3-662-47665-9 publication_status: published publisher: Springer Nature publist_id: '5556' pubrep_id: '321' quality_controlled: '1' related_material: record: - id: '465' relation: later_version status: public - id: '5438' relation: earlier_version status: public scopus_import: '1' status: public title: Edit distance for pushdown automata type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9135 year: '2015' ... --- _id: '5437' abstract: - lang: eng 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. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: 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 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 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. ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 27p. 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. date_created: 2018-12-12T11:39:19Z date_published: 2015-04-27T00:00:00Z date_updated: 2023-02-23T12:26:05Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-330-v2-1 file: - access_level: open_access checksum: f5917c20f84018b362d385c000a2e123 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:12Z date_updated: 2020-07-14T12:46:54Z file_id: '5473' file_name: IST-2015-330-v2+1_main.pdf file_size: 1072137 relation: main_file file_date_updated: 2020-07-14T12:46:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '27' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '333' related_material: record: - id: '1607' relation: later_version status: public - id: '5430' relation: earlier_version status: public status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5430' abstract: - lang: eng 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. 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. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: 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 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 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. ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 31p. 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. date_created: 2018-12-12T11:39:17Z date_published: 2015-02-10T00:00:00Z date_updated: 2023-02-23T12:26:22Z day: '10' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-319-v1-1 file: - access_level: open_access checksum: 62c6ea01e342553dcafb88a070fb1ad5 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:21Z date_updated: 2020-07-14T12:46:52Z file_id: '5482' file_name: IST-2015-319-v1+1_long.pdf file_size: 1089651 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '31' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '319' related_material: record: - id: '1607' relation: later_version status: public - id: '5437' relation: later_version status: public status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5439' 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 author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Boker U, Henzinger TA, Otop J. The Target Discounted-Sum Problem. IST Austria; 2015. doi:10.15479/AT:IST-2015-335-v1-1 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 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. ieee: U. Boker, T. A. Henzinger, and J. Otop, The target discounted-sum problem. IST Austria, 2015. ista: Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem, IST Austria, 20p. 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. date_created: 2018-12-12T11:39:20Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T10:08:48Z day: '18' ddc: - '004' - '512' - '513' department: - _id: ToHe doi: 10.15479/AT:IST-2015-335-v1-1 file: - access_level: open_access checksum: 40405907aa012acece1bc26cf0be554d content_type: application/pdf creator: system date_created: 2018-12-12T11:53:55Z date_updated: 2020-07-14T12:46:55Z file_id: '5517' file_name: IST-2015-335-v1+1_report.pdf file_size: 589619 relation: main_file file_date_updated: 2020-07-14T12:46:55Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '20' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '335' related_material: record: - id: '1659' relation: later_version status: public status: public title: The target discounted-sum problem type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5438' 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. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop 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 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. 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. mla: Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1. short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015. date_created: 2018-12-12T11:39:20Z date_published: 2015-05-05T00:00:00Z date_updated: 2023-02-23T12:20:08Z day: '05' ddc: - '004' department: - _id: KrCh doi: 10.15479/AT:IST-2015-334-v1-1 file: - access_level: open_access checksum: 8a5f2d77560e552af87eb1982437a43b content_type: application/pdf creator: system date_created: 2018-12-12T11:53:56Z date_updated: 2020-07-14T12:46:55Z file_id: '5518' file_name: IST-2015-334-v1+1_report.pdf file_size: 422573 relation: main_file file_date_updated: 2020-07-14T12:46:55Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '15' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '334' related_material: record: - id: '1610' relation: later_version status: public - id: '465' relation: later_version status: public status: public title: Edit distance for pushdown automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5440' 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 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.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Martin full_name: Nowak, Martin last_name: Nowak 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-v2-2 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 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. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 18p. 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. date_created: 2018-12-12T11:39:21Z date_published: 2015-06-16T00:00:00Z date_updated: 2023-02-23T12:26:10Z day: '16' ddc: - '005' - '576' department: - _id: KrCh doi: 10.15479/AT:IST-2015-323-v2-2 file: - access_level: open_access checksum: 66aace7d367032af97c15e35c9be9636 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:23Z date_updated: 2020-07-14T12:46:56Z file_id: '5484' file_name: IST-2015-323-v2+2_main.pdf file_size: 466161 relation: main_file file_date_updated: 2020-07-14T12:46:56Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '18' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '338' related_material: record: - id: '5421' relation: earlier_version status: public - id: '5432' relation: earlier_version status: public status: public title: The complexity of evolutionary games on graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5432' 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" alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Martin full_name: Nowak, Martin last_name: Nowak 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 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 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. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 29p. mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:18Z date_published: 2015-02-19T00:00:00Z date_updated: 2023-02-23T12:26:33Z day: '19' ddc: - '005' - '576' department: - _id: KrCh doi: 10.15479/AT:IST-2015-323-v1-1 file: - access_level: open_access checksum: 546c1b291d545e7b24aaaf4199dac671 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:57Z date_updated: 2020-07-14T12:46:53Z file_id: '5519' file_name: IST-2015-323-v1+1_main.pdf file_size: 576347 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '323' related_material: record: - id: '5421' relation: earlier_version status: public - id: '5440' relation: later_version status: public status: public title: The complexity of evolutionary games on graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5444' 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 author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Alvin full_name: Makohon-Moore, Alvin last_name: Makohon-Moore - first_name: Jeffrey full_name: Gerold, Jeffrey last_name: Gerold - first_name: Ivana full_name: Bozic, Ivana last_name: Bozic - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christine full_name: Iacobuzio-Donahue, Christine last_name: Iacobuzio-Donahue - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: 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 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. 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. mla: Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1. 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. date_created: 2018-12-12T11:39:22Z date_published: 2015-12-30T00:00:00Z date_updated: 2020-07-14T23:05:07Z day: '30' ddc: - '000' - '576' department: - _id: KrCh doi: 10.15479/AT:IST-2015-399-v1-1 file: - access_level: open_access checksum: c47d33bdda06181753c0af36f16e7b5d content_type: application/pdf creator: system date_created: 2018-12-12T11:53:24Z date_updated: 2020-07-14T12:46:58Z file_id: '5485' file_name: IST-2015-399-v1+1_treeomics.pdf file_size: 3533200 relation: main_file file_date_updated: 2020-07-14T12:46:58Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '25' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '399' status: public title: Reconstructing robust phylogenies of metastatic cancers type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5443' abstract: - lang: eng 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. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Jessica full_name: Davies, Jessica id: 378E0060-F248-11E8-B48F-1D18A9856A87 last_name: Davies citation: 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 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 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. 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. 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. 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. date_created: 2018-12-12T11:39:22Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-02-21T16:24:05Z day: '06' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-325-v2-1 file: - access_level: open_access checksum: f0fa31ad8161ed655137e94012123ef9 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:05Z date_updated: 2020-07-14T12:46:57Z file_id: '5466' file_name: IST-2015-325-v2+1_main.pdf file_size: 412379 relation: main_file file_date_updated: 2020-07-14T12:46:57Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '23' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '362' related_material: record: - id: '1166' relation: later_version status: public status: public title: A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5804' abstract: - lang: eng 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. author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: 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 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 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. 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. ista: Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 624(4), 56–72. 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. date_created: 2019-01-08T20:44:06Z date_published: 2015-04-18T00:00:00Z date_updated: 2021-01-12T08:03:36Z day: '18' doi: 10.1016/j.tcs.2015.11.018 extern: '1' intvolume: ' 624' issue: '4' language: - iso: eng month: '04' oa_version: None page: 56-72 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: From prima quadraginta octant to lattice sphere through primitive integer operations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 624 year: '2015' ... --- _id: '5807' author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: 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 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 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. 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. ista: Biswas R, Bhowmick P. 2015. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 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. short: R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163. date_created: 2019-01-08T20:44:52Z date_published: 2015-11-09T00:00:00Z date_updated: 2021-01-12T08:03:37Z day: '09' doi: 10.1016/j.tcs.2015.09.003 extern: '1' intvolume: ' 605' issue: '11' language: - iso: eng month: '11' oa_version: None page: 146-163 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: On different topological classes of spherical geodesic paths and circles inZ3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 605 year: '2015' ... --- _id: '5808' author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: Biswas R, Bhowmick P. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797. doi:10.1007/s00371-015-1101-3 apa: Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer. Springer Nature. https://doi.org/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. ieee: R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer, vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015. ista: Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8), 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. short: R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797. date_created: 2019-01-08T20:45:05Z date_published: 2015-05-08T00:00:00Z date_updated: 2021-01-12T08:03:37Z day: '08' doi: 10.1007/s00371-015-1101-3 extern: '1' intvolume: ' 31' issue: 6-8 language: - iso: eng month: '05' oa_version: None page: 787-797 publication: The Visual Computer publication_identifier: issn: - 0178-2789 - 1432-2315 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Layer the sphere type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '594' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Sarah full_name: Sainsbury, Sarah last_name: Sainsbury - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:47:23Z date_published: 2015-03-26T00:00:00Z date_updated: 2021-01-12T08:05:16Z day: '26' doi: 10.1038/nrm3952 extern: '1' intvolume: ' 16' issue: '3' language: - iso: eng month: '03' oa_version: None page: 129 - 143 publication: Nature Reviews Molecular Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '7206' status: public title: Structural basis of transcription initiation by RNA polymerase II type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2015' ... --- _id: '1511' abstract: - lang: eng 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.' 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)." alternative_title: - LIPIcs author: - first_name: Xavier full_name: Goaoc, Xavier last_name: Goaoc - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: 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' 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' 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.' 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.' 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.' 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. conference: end_date: 2015-06-25 location: Eindhoven, Netherlands name: 'SoCG: Symposium on Computational Geometry' start_date: 2015-06-22 date_created: 2018-12-11T11:52:27Z date_published: 2015-06-11T00:00:00Z date_updated: 2023-02-23T12:38:00Z day: '11' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SOCG.2015.476 ec_funded: 1 file: - access_level: open_access checksum: 0945811875351796324189312ca29e9e content_type: application/pdf creator: system date_created: 2018-12-12T10:11:18Z date_updated: 2020-07-14T12:44:59Z file_id: '4871' file_name: IST-2016-502-v1+1_42.pdf file_size: 636735 relation: main_file file_date_updated: 2020-07-14T12:44:59Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 476 - 490 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5666' pubrep_id: '502' quality_controlled: '1' related_material: record: - id: '610' relation: later_version status: public scopus_import: 1 status: public title: 'On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '34 ' year: '2015' ... --- _id: '6118' 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.' author: - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 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 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 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. 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. 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. 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. date_created: 2019-03-19T14:15:50Z date_published: 2015-07-07T00:00:00Z date_updated: 2021-01-12T08:06:12Z day: '07' ddc: - '570' doi: 10.1073/pnas.1423808112 extern: '1' external_id: pmid: - '26100886' file: - access_level: open_access checksum: 3d2da5af8d72467e382a565abc2e003d content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:21:07Z date_updated: 2020-07-14T12:47:20Z file_id: '6119' file_name: 2015_PNAS_Fenk.pdf file_size: 2822681 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 112' issue: '27' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: E3525-E3534 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '6120' abstract: - lang: eng 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. article_number: e04241 author: - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: Zoltan full_name: Soltesz, Zoltan last_name: Soltesz - first_name: Geoffrey M full_name: Nelson, Geoffrey M last_name: Nelson - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Fausto full_name: Arellano-Carbajal, Fausto last_name: Arellano-Carbajal - first_name: Emmanuel full_name: Levy, Emmanuel last_name: Levy - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: 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 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 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. ieee: P. Laurent et al., “Decoding a neural circuit controlling global animal state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015. 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. 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). date_created: 2019-03-19T14:23:51Z date_published: 2015-03-11T00:00:00Z date_updated: 2021-01-12T08:06:13Z day: '11' ddc: - '570' doi: 10.7554/elife.04241 extern: '1' external_id: pmid: - '25760081' file: - access_level: open_access checksum: cf641b7a363aecd0a101755d23dee7e0 content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:29:43Z date_updated: 2020-07-14T12:47:20Z file_id: '6121' file_name: 2015_elife_Laurent.pdf file_size: 6723528 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' status: public title: Decoding a neural circuit controlling global animal state in C. elegans tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '1637' 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. alternative_title: - 56th Annual Symposium on Foundations of Computer Science author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Andrei full_name: Krokhin, Andrei last_name: Krokhin - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: 'Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. In: IEEE; 2015:1246-1258. doi:10.1109/FOCS.2015.80' 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' 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. 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.' 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.' mla: Kolmogorov, Vladimir, et al. The Complexity of General-Valued CSPs. IEEE, 2015, pp. 1246–58, doi:10.1109/FOCS.2015.80. short: V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258. conference: end_date: 2015-10-20 location: Berkeley, CA, United States name: 'FOCS: Foundations of Computer Science' start_date: 2015-10-18 date_created: 2018-12-11T11:53:10Z date_published: 2015-12-01T00:00:00Z date_updated: 2023-02-23T12:44:26Z day: '01' department: - _id: VlKo doi: 10.1109/FOCS.2015.80 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.07327 month: '12' oa: 1 oa_version: Preprint page: 1246 - 1258 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_status: published publisher: IEEE publist_id: '5518' quality_controlled: '1' related_material: record: - id: '644' relation: other status: public scopus_import: 1 status: public title: The complexity of general-valued CSPs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '6507' abstract: - lang: eng 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. author: - first_name: Long full_name: Zhou, Long id: 3E751364-F248-11E8-B48F-1D18A9856A87 last_name: Zhou orcid: 0000-0002-1864-8951 - first_name: J. M. full_name: Hinerman, J. M. last_name: Hinerman - first_name: M. full_name: Blaszczyk, M. last_name: Blaszczyk - first_name: J. L. C. full_name: Miller, J. L. C. last_name: Miller - first_name: D. G. full_name: Conrady, D. G. last_name: Conrady - first_name: A. D. full_name: Barrow, A. D. last_name: Barrow - first_name: D. Y. full_name: Chirgadze, D. Y. last_name: Chirgadze - first_name: D. full_name: Bihan, D. last_name: Bihan - first_name: R. W. full_name: Farndale, R. W. last_name: Farndale - first_name: A. B. full_name: Herr, A. B. last_name: Herr 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 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 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. 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. 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. 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. date_created: 2019-05-31T09:38:50Z date_published: 2015-11-02T00:00:00Z date_updated: 2021-01-12T08:07:47Z day: '02' doi: 10.1182/blood-2015-08-667055 extern: '1' external_id: pmid: - '26552697' intvolume: ' 127' issue: '5' language: - iso: eng month: '11' oa_version: None page: 529-537 pmid: 1 publication: Blood publication_identifier: issn: - 0006-4971 - 1528-0020 publication_status: published publisher: American Society of Hematology quality_controlled: '1' status: public title: Structural basis for collagen recognition by the immune receptor OSCAR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 127 year: '2015' ... --- _id: '6737' 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. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Igal full_name: Sason, Igal last_name: Sason - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: 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 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 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. 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. 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. 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. date_created: 2019-07-31T07:03:38Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T08:08:46Z day: '01' doi: 10.1109/tit.2014.2368555 extern: '1' external_id: arxiv: - '1401.6060' intvolume: ' 61' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1401.6060 month: '02' oa: 1 oa_version: Preprint page: 783-800 publication: IEEE Transactions on Information Theory publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Achieving Marton’s region for broadcast channels using polar codes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '6736' abstract: - lang: eng 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. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: 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 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 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. 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. 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. 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. date_created: 2019-07-31T06:50:34Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T08:08:45Z day: '01' doi: 10.1109/tit.2015.2453315 extern: '1' external_id: arxiv: - '1304.5220' intvolume: ' 61' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.5220 month: '09' oa: 1 oa_version: Preprint page: 4838-4851 publication: IEEE Transactions on Information Theory publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Scaling exponent of list decoders with applications to polar codes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '7070' abstract: - lang: eng 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.' article_number: '180509' article_processing_charge: No article_type: original author: - first_name: Jing Fei full_name: Yu, Jing Fei last_name: Yu - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: I. full_name: Kokanović, I. last_name: Kokanović - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: N. full_name: Harrison, N. last_name: Harrison - first_name: James full_name: Day, James last_name: Day - first_name: Ruixing full_name: Liang, Ruixing last_name: Liang - first_name: W. N. full_name: Hardy, W. N. last_name: Hardy - first_name: D. A. full_name: Bonn, D. A. last_name: Bonn - first_name: A. full_name: McCollam, A. last_name: McCollam - first_name: S. R. full_name: Julian, S. R. last_name: Julian - first_name: J. R. full_name: Cooper, J. R. last_name: Cooper citation: 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 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 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. 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. 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. 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). date_created: 2019-11-19T13:22:06Z date_published: 2015-11-23T00:00:00Z date_updated: 2021-01-12T08:11:42Z day: '23' doi: 10.1103/physrevb.92.180509 extern: '1' intvolume: ' 92' issue: '18' language: - iso: eng month: '11' oa_version: None publication: Physical Review B publication_identifier: issn: - 1098-0121 - 1550-235X publication_status: published publisher: APS quality_controlled: '1' status: public title: Magnetization of underdoped YBa2Cu3Oy above the irreversibility field type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '7456' 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. article_processing_charge: No article_type: original author: - first_name: Daniela full_name: Caruntu, Daniela last_name: Caruntu - first_name: Taha full_name: Rostamzadeh, Taha last_name: Rostamzadeh - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Saman full_name: Salemizadeh Parizi, Saman last_name: Salemizadeh Parizi - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: 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 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 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. 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. 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. 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. date_created: 2020-02-05T14:16:37Z date_published: 2015-08-14T00:00:00Z date_updated: 2023-02-23T13:08:24Z day: '14' doi: 10.1039/c5nr00737b extern: '1' external_id: pmid: - '26168304' intvolume: ' 7' issue: '30' language: - iso: eng month: '08' oa_version: None page: 12955-12969 pmid: 1 publication: Nanoscale publication_identifier: issn: - 2040-3364 - 2040-3372 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2015' ... --- _id: '7457' 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. article_processing_charge: No article_type: original author: - first_name: Saman Salemizadeh full_name: Parizi, Saman Salemizadeh last_name: Parizi - first_name: Gavin full_name: Conley, Gavin last_name: Conley - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Bob full_name: Howell, Bob last_name: Howell - first_name: Axel full_name: Mellinger, Axel last_name: Mellinger - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: 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 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 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. 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. 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. 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. date_created: 2020-02-05T14:17:26Z date_published: 2015-09-01T00:00:00Z date_updated: 2023-02-23T13:08:26Z day: '01' doi: 10.1039/c5ra11347d extern: '1' intvolume: ' 5' issue: '93' language: - iso: eng month: '09' oa_version: Submitted Version page: 76356-76362 publication: RSC Advances publication_identifier: issn: - 2046-2069 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2015' ... --- _id: '7742' 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). article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Gibran full_name: Hemani, Gibran last_name: Hemani - first_name: Carolina full_name: Medina-Gomez, Carolina last_name: Medina-Gomez - first_name: Massimo full_name: Mezzavilla, Massimo last_name: Mezzavilla - first_name: Tonu full_name: Esko, Tonu last_name: Esko - first_name: Konstantin full_name: Shakhbazov, Konstantin last_name: Shakhbazov - first_name: Joseph E full_name: Powell, Joseph E last_name: Powell - first_name: Anna full_name: Vinkhuyzen, Anna last_name: Vinkhuyzen - first_name: Sonja I full_name: Berndt, Sonja I last_name: Berndt - first_name: Stefan full_name: Gustafsson, Stefan last_name: Gustafsson - first_name: Anne E full_name: Justice, Anne E last_name: Justice - first_name: Bratati full_name: Kahali, Bratati last_name: Kahali - first_name: Adam E full_name: Locke, Adam E last_name: Locke - first_name: Tune H full_name: Pers, Tune H last_name: Pers - first_name: Sailaja full_name: Vedantam, Sailaja last_name: Vedantam - first_name: Andrew R full_name: Wood, Andrew R last_name: Wood - first_name: Wouter full_name: van Rheenen, Wouter last_name: van Rheenen - first_name: Ole A full_name: Andreassen, Ole A last_name: Andreassen - first_name: Paolo full_name: Gasparini, Paolo last_name: Gasparini - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Leonard H van den full_name: Berg, Leonard H van den last_name: Berg - first_name: Jan H full_name: Veldink, Jan H last_name: Veldink - first_name: Fernando full_name: Rivadeneira, Fernando last_name: Rivadeneira - first_name: Thomas M full_name: Werge, Thomas M last_name: Werge - first_name: Goncalo R full_name: Abecasis, Goncalo R last_name: Abecasis - first_name: Dorret I full_name: Boomsma, Dorret I last_name: Boomsma - first_name: Daniel I full_name: Chasman, Daniel I last_name: Chasman - first_name: Eco J C full_name: de Geus, Eco J C last_name: de Geus - first_name: Timothy M full_name: Frayling, Timothy M last_name: Frayling - first_name: Joel N full_name: Hirschhorn, Joel N last_name: Hirschhorn - first_name: Jouke Jan full_name: Hottenga, Jouke Jan last_name: Hottenga - first_name: Erik full_name: Ingelsson, Erik last_name: Ingelsson - first_name: Ruth J F full_name: Loos, Ruth J F last_name: Loos - first_name: Patrik K E full_name: Magnusson, Patrik K E last_name: Magnusson - first_name: Nicholas G full_name: Martin, Nicholas G last_name: Martin - first_name: Grant W full_name: Montgomery, Grant W last_name: Montgomery - first_name: Kari E full_name: North, Kari E last_name: North - first_name: Nancy L full_name: Pedersen, Nancy L last_name: Pedersen - first_name: Timothy D full_name: Spector, Timothy D last_name: Spector - first_name: Elizabeth K full_name: Speliotes, Elizabeth K last_name: Speliotes - first_name: Michael E full_name: Goddard, Michael E last_name: Goddard - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M full_name: Visscher, Peter M last_name: Visscher citation: 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 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 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. 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. 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. 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. date_created: 2020-04-30T10:58:23Z date_published: 2015-09-14T00:00:00Z date_updated: 2021-01-12T08:15:13Z day: '14' doi: 10.1038/ng.3401 extern: '1' intvolume: ' 47' issue: '11' language: - iso: eng month: '09' oa_version: None page: 1357-1362 publication: Nature Genetics publication_identifier: issn: - 1061-4036 - 1546-1718 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Population genetic differentiation of height and body mass index across Europe type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2015' ... --- _id: '7741' 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. article_number: '20150689' article_processing_charge: No article_type: original author: - first_name: Mark James full_name: Adams, Mark James last_name: Adams - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Maria-Elena full_name: Mannarelli, Maria-Elena last_name: Mannarelli - first_name: Ben J. full_name: Hatchwell, Ben J. last_name: Hatchwell citation: 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' 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' 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.' 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.' 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.' 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).' date_created: 2020-04-30T10:58:07Z date_published: 2015-07-07T00:00:00Z date_updated: 2021-01-12T08:15:12Z day: '07' doi: 10.1098/rspb.2015.0689 extern: '1' external_id: pmid: - '26063846' intvolume: ' 282' issue: '1810' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rspb.2015.0689 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: 'Proceedings of the Royal Society B: Biological Sciences' publication_identifier: issn: - 0962-8452 - 1471-2954 publication_status: published publisher: The Royal Society quality_controlled: '1' status: public title: Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2015' ... --- _id: '7739' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Jocelyn full_name: Poissant, Jocelyn last_name: Poissant - first_name: Isabelle full_name: De Cauwer, Isabelle last_name: De Cauwer - first_name: Kees full_name: van Oers, Kees last_name: van Oers - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: John L. full_name: Quinn, John L. last_name: Quinn - first_name: Martien A. M. full_name: Groenen, Martien A. M. last_name: Groenen - first_name: Marcel E. full_name: Visser, Marcel E. last_name: Visser - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: 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 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 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. 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. 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. 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. date_created: 2020-04-30T10:51:01Z date_published: 2015-12-10T00:00:00Z date_updated: 2021-01-12T08:15:12Z day: '10' doi: 10.1111/mec.13452 extern: '1' intvolume: ' 24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/mec.13452 month: '12' oa: 1 oa_version: Published Version page: 6148-6162 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '776' 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. 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." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Jerry full_name: Li, Jerry last_name: Li - first_name: Nir full_name: Shavit, Nir last_name: Shavit 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' 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' 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.' 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.' 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.' 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. conference: name: 'PPoPP: Principles and Practice of Parallel Pogramming' date_created: 2018-12-11T11:48:26Z date_published: 2015-01-24T00:00:00Z date_updated: 2023-02-23T13:16:43Z day: '24' doi: 10.1145/2688500.2688523 extern: '1' language: - iso: eng month: '01' oa_version: None page: 11 - 20 publication_status: published publisher: ACM publist_id: '6878' status: public title: 'The SprayList: A scalable relaxed priority queue' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-January year: '2015' ... --- _id: '7765' 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.' article_number: '225501' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel 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' 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' 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.' 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.' 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.' short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015). date_created: 2020-04-30T11:41:08Z date_published: 2015-06-04T00:00:00Z date_updated: 2021-01-12T08:15:23Z day: '04' doi: 10.1103/physrevlett.114.225501 extern: '1' intvolume: ' 114' issue: '22' language: - iso: eng month: '06' oa_version: None publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: 'The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '7767' 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' article_processing_charge: No article_type: original author: - first_name: Ruben full_name: van Drongelen, Ruben last_name: van Drongelen - first_name: Anshuman full_name: Pal, Anshuman last_name: Pal - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Timon full_name: Idema, Timon last_name: Idema 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 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. 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. ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706. 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). date_created: 2020-04-30T11:41:38Z date_published: 2015-03-01T00:00:00Z date_updated: 2021-01-12T08:15:24Z day: '01' doi: 10.1103/physreve.91.032706 extern: '1' intvolume: ' 91' issue: '3' language: - iso: eng month: '03' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 - 1550-2376 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Collective dynamics of soft active particles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '7766' 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. article_processing_charge: No article_type: original author: - first_name: Daniel M. full_name: Sussman, Daniel M. last_name: Sussman - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: 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. 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. ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751. 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. date_created: 2020-04-30T11:41:23Z date_published: 2015-02-15T00:00:00Z date_updated: 2021-01-12T08:15:23Z day: '15' doi: 10.1039/c4sm02905d extern: '1' intvolume: ' 11' issue: '14' language: - iso: eng month: '02' oa_version: None page: 2745-2751 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Disordered surface vibrations in jammed sphere packings type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '777' 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.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Jennifer full_name: Iglesias, Jennifer last_name: Iglesias - first_name: Milan full_name: Vojnović, Milan last_name: Vojnović citation: ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning. In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.' 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.' chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015. 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.' mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08. short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908. conference: name: 'NIPS: Neural Information Processing Systems' date_created: 2018-12-11T11:48:27Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T13:17:09Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning month: '01' oa_version: None page: 1900 - 1908 publication_status: published publisher: Neural Information Processing Systems publist_id: '6879' status: public title: Streaming min-max hypergraph partitioning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-January year: '2015' ... --- _id: '778' 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. 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. alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Petr full_name: Kuznetsov, Petr last_name: Kuznetsov - first_name: Srivatsan full_name: Ravi, Srivatsan last_name: Ravi - first_name: Nir full_name: Shavit, Nir last_name: Shavit 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' 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' 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. 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.' 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.' 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. conference: name: 'DISC: Distributed Computing' date_created: 2018-12-11T11:48:27Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T13:17:35Z day: '01' doi: 10.1007/978-3-662-48653-5_13 extern: '1' external_id: arxiv: - '1405.5689' intvolume: ' 9363' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1405.5689 month: '01' oa: 1 oa_version: None page: 185 - 199 publication_status: published publisher: Springer publist_id: '6880' quality_controlled: '1' status: public title: Inherent limitations of hybrid transactional memory type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9363 year: '2015' ... --- _id: '7779' abstract: - lang: eng 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." article_processing_charge: No author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 citation: ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of  disordered solids. arXiv:151008820. 2015.' apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of  disordered solids. arXiv:1510.08820.' chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of  Disordered Solids.” ArXiv:1510.08820, 2015.' ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of  disordered solids,” arXiv:1510.08820. 2015.' ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear response of  disordered solids. arXiv:1510.08820, .' 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). date_created: 2020-04-30T12:16:18Z date_published: 2015-10-29T00:00:00Z date_updated: 2021-01-12T08:15:28Z day: '29' extern: '1' external_id: arxiv: - '1510.08820' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.08820 month: '10' oa: 1 oa_version: Preprint page: '242' publication: arXiv:1510.08820 publication_status: published status: public title: 'Unearthing the anticrystal: Criticality in the linear response of disordered solids' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '779' 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.' 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. article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: William full_name: Leiserson, William last_name: Leiserson - first_name: Nir full_name: Shavit, Nir last_name: Shavit 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' 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' 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.' 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.' 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.' short: D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132. conference: name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' date_created: 2018-12-11T11:48:27Z date_published: 2015-06-13T00:00:00Z date_updated: 2023-02-23T12:35:42Z day: '13' doi: 10.1145/2755573.2755600 extern: '1' language: - iso: eng month: '06' oa_version: None page: 123 - 132 publication_status: published publisher: ACM publist_id: '6876' related_material: record: - id: '6001' relation: later_version status: public status: public title: 'ThreadScan: Automatic and scalable memory reclamation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-June year: '2015' ... --- _id: '780' 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.' 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.” author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili citation: 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' 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' 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. 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.' 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. short: D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491. conference: name: 'ICALP: International Colloquium on Automota, Languages and Programming' date_created: 2018-12-11T11:48:28Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T13:18:11Z day: '01' doi: 10.1007/978-3-662-47666-6_38 extern: '1' external_id: arxiv: - '1502.05745' intvolume: ' 9135' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1502.05745 month: '01' oa: 1 oa_version: Preprint page: 479 - 491 publication_status: published publisher: Springer publist_id: '6877' status: public title: Polylogarithmic-time leader election in population protocols type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9135 year: '2015' ... --- _id: '781' 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.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili - first_name: Milan full_name: Vojnović, Milan last_name: Vojnović citation: 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' 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' 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. 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.' 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. short: D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:28Z date_published: 2015-07-21T00:00:00Z date_updated: 2023-02-23T13:18:35Z day: '21' doi: 10.1145/2767386.2767429 extern: '1' language: - iso: eng month: '07' oa_version: None page: 47 - 56 publication_status: published publisher: ACM publist_id: '6873' status: public title: Fast and exact majority in population protocols type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-July year: '2015' ... --- _id: '782' abstract: - lang: eng 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.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Thomas full_name: Sauerwald, Thomas last_name: Sauerwald - first_name: Milan full_name: Vojnović, Milan last_name: Vojnović citation: 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' 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' 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. 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.' 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.' 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. short: D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:28Z date_published: 2015-07-21T00:00:00Z date_updated: 2023-02-23T13:18:50Z day: '21' doi: 10.1145/2767386.2767430 extern: '1' language: - iso: eng month: '07' oa_version: None page: 251 - 260 publication_status: published publisher: ACM publist_id: '6874' status: public title: Lock-Free algorithms under stochastic schedulers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-July year: '2015' ... --- _id: '783' 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.' 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." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili - first_name: Adrian full_name: Vladu, Adrian last_name: Vladu citation: 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' 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' 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. 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.' 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.' 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. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:28Z date_published: 2015-07-21T00:00:00Z date_updated: 2023-02-23T13:18:55Z day: '21' doi: 10.1145/2767386.2767420 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1411.1001 month: '07' oa: 1 oa_version: None page: 365 - 374 publication_status: published publisher: ACM publist_id: '6875' status: public title: How to elect a leader faster than a tournament type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-July year: '2015' ... --- _id: '784' abstract: - lang: eng 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. author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Hitesh full_name: Ballani, Hitesh last_name: Ballani - first_name: Paolo full_name: Costa, Paolo last_name: Costa - first_name: Adam full_name: Funnell, Adam last_name: Funnell - first_name: Joshua full_name: Benjamin, Joshua last_name: Benjamin - first_name: Philip full_name: Watts, Philip last_name: Watts - first_name: Benn full_name: Thomsen, Benn last_name: Thomsen citation: 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' 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' 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. 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.' 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.' 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. short: D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368. conference: end_date: 2015-08-21 location: London, United Kindgdom name: 'SIGCOMM: Special Interest Group on Data Communication' start_date: 2015-08-17 date_created: 2018-12-11T11:48:29Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T13:18:57Z day: '01' doi: 10.1145/2785956.2790035 extern: '1' language: - iso: eng month: '01' oa_version: None page: 367 - 368 publication_identifier: isbn: - 978-1-4503-3542-3 publication_status: published publisher: ACM publist_id: '6872' quality_controlled: '1' status: public title: A high-radix, low-latency optical switch for data centers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '802' abstract: - lang: eng 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. author: - first_name: Jakob full_name: Engel, Jakob last_name: Engel - first_name: Philipp S full_name: Schmalhorst, Philipp S id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Anke full_name: Kruger, Anke last_name: Kruger - first_name: Christina full_name: Muller, Christina last_name: Muller - first_name: Falk full_name: Buettner, Falk last_name: Buettner - first_name: Françoise full_name: Routier, Françoise last_name: Routier citation: 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 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 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. 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. 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. short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430. date_created: 2018-12-11T11:48:35Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T08:16:33Z day: '01' department: - _id: CaHe doi: 10.1093/glycob/cwv059 external_id: pmid: - '26306635' intvolume: ' 25' issue: '12' language: - iso: eng month: '12' oa_version: None page: 1423 - 1430 pmid: 1 publication: Glycobiology publication_status: published publisher: Oxford University Press publist_id: '6851' quality_controlled: '1' scopus_import: 1 status: public title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '815' 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" author: - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Robert full_name: Dick, Robert last_name: Dick - first_name: Wim full_name: Hagen, Wim last_name: Hagen - first_name: Volker full_name: Vogt, Volker last_name: Vogt - first_name: John full_name: Briggs, John last_name: Briggs citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:48:39Z date_published: 2015-09-22T00:00:00Z date_updated: 2021-01-12T08:17:09Z day: '22' doi: 10.1128/JVI.01502-15 extern: '1' external_id: pmid: - '26223638' intvolume: ' 89' issue: '20' language: - iso: eng month: '09' oa_version: None page: 10294 - 10302 pmid: 1 publication: Journal of Virology publication_status: published publisher: ASM publist_id: '6837' quality_controlled: '1' status: public title: The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2015' ... --- _id: '814' abstract: - lang: eng 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. 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. author: - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Wim full_name: Hagen, Wim J last_name: Hagen - first_name: Michaela full_name: Rumlová, Michaela last_name: Rumlová - first_name: Tomáš full_name: Ruml, Tomáš last_name: Ruml - first_name: B full_name: Müller B last_name: Müller - first_name: Hans full_name: Kraüsslich, Hans Georg last_name: Kraüsslich - first_name: John full_name: Briggs, John A last_name: Briggs citation: 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 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 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. 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. 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. 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. short: F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508. date_created: 2018-12-11T11:48:39Z date_published: 2015-01-22T00:00:00Z date_updated: 2021-01-12T08:17:08Z day: '22' doi: 10.1038/nature13838 extern: 1 intvolume: ' 517' issue: '7535' month: '01' page: 505 - 508 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6836' quality_controlled: 0 status: public title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution type: journal_article volume: 517 year: '2015' ... --- _id: '8242' article_number: AB101 article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Einhorn, Lukas last_name: Einhorn - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Martina full_name: Muhr, Martina last_name: Muhr - first_name: Alexandra full_name: Schoos, Alexandra last_name: Schoos - first_name: Kumiko full_name: Oida, Kumiko last_name: Oida - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Lucia full_name: Panakova, Lucia last_name: Panakova - first_name: Krisztina full_name: Manzano-Szalai, Krisztina last_name: Manzano-Szalai - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: 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 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 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. 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. 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. 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). date_created: 2020-08-10T11:54:09Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T08:17:42Z day: '01' doi: 10.1016/j.jaci.2014.12.1263 extern: '1' intvolume: ' 135' issue: '2' language: - iso: eng month: '02' oa_version: None publication: Journal of Allergy and Clinical Immunology publication_identifier: issn: - 0091-6749 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2015' ... --- _id: '832' 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. 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). " author: - first_name: Peter full_name: Peter Marhavy id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 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 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 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. 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. ista: Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8). 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). date_created: 2018-12-11T11:48:44Z date_published: 2015-04-20T00:00:00Z date_updated: 2021-01-12T08:18:07Z day: '20' doi: 10.21769/BioProtoc.1446 extern: 1 intvolume: ' 5' issue: '8' month: '04' publication: Bio-protocol publication_status: published publisher: Bio-protocol LLC publist_id: '6816' quality_controlled: 0 status: public title: Real time analysis of lateral root organogenesis in arabidopsis type: journal_article volume: 5 year: '2015' ... --- _id: '8456' abstract: - lang: eng 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. article_number: '8361' article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Yi full_name: Xue, Yi last_name: Xue - first_name: Nicolas full_name: Coquelle, Nicolas last_name: Coquelle - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Tairan full_name: Yuwen, Tairan last_name: Yuwen - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Oleg full_name: Mikhailovskii, Oleg last_name: Mikhailovskii - first_name: Dieter full_name: Willbold, Dieter last_name: Willbold - first_name: Jacques-Philippe full_name: Colletier, Jacques-Philippe last_name: Colletier - first_name: Nikolai R. full_name: Skrynnikov, Nikolai R. last_name: Skrynnikov - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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 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 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. ieee: P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015. 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. 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). date_created: 2020-09-18T10:07:36Z date_published: 2015-10-05T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '05' doi: 10.1038/ncomms9361 extern: '1' intvolume: ' 6' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '10' oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Observing the overall rocking motion of a protein in a crystal type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '8457' 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. article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' 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' 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.' 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.' ista: 'Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 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.' short: P. Ma, P. Schanda, EMagRes 4 (2015) 699–708. date_created: 2020-09-18T10:07:45Z date_published: 2015-09-10T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '10' doi: 10.1002/9780470034590.emrstm1418 extern: '1' intvolume: ' 4' issue: '3' language: - iso: eng month: '09' oa_version: None page: 699-708 publication: eMagRes publication_identifier: isbn: - '9780470034590' - '9780470058213' publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'Conformational exchange processes in biological systems: Detection by solid-state NMR' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '848' abstract: - lang: eng 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. author: - first_name: Dinara full_name: Usmanova, Dinara last_name: Usmanova - first_name: Luca full_name: Ferretti, Luca last_name: Ferretti - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Peter full_name: Vlasov, Peter last_name: Vlasov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: 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 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 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. 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. 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. 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. short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554. date_created: 2018-12-11T11:48:49Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T08:19:33Z day: '01' doi: 10.1093/molbev/msu318 extern: '1' intvolume: ' 32' issue: '2' language: - iso: eng month: '02' oa_version: None page: 542 - 554 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6804' quality_controlled: '1' status: public title: A model of substitution trajectories in sequence space and long-term protein evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2015' ... --- _id: '8498' 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]." article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: K full_name: Zhang, K last_name: Zhang citation: 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 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 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. 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. 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. 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. short: V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720. date_created: 2020-09-18T10:46:43Z date_published: 2015-06-30T00:00:00Z date_updated: 2021-01-12T08:19:41Z day: '30' doi: 10.1088/0951-7715/28/8/2699 extern: '1' intvolume: ' 28' issue: '8' keyword: - Mathematical Physics - General Physics and Astronomy - Applied Mathematics - Statistical and Nonlinear Physics language: - iso: eng month: '06' oa_version: None page: 2699-2720 publication: Nonlinearity publication_identifier: issn: - 0951-7715 - 1361-6544 publication_status: published publisher: IOP Publishing quality_controlled: '1' status: public title: Arnold diffusion for smooth convex systems of two and a half degrees of freedom type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2015' ... --- _id: '8499' 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 0Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499 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 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. 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. 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. 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. date_created: 2020-09-18T10:46:50Z date_published: 2015-02-05T00:00:00Z date_updated: 2021-01-12T08:19:41Z day: '05' doi: 10.4171/jems/499 extern: '1' intvolume: ' 17' issue: '1' language: - iso: eng month: '02' oa_version: None page: 71-149 publication: Journal of the European Mathematical Society publication_identifier: issn: - 1435-9855 publication_status: published publisher: European Mathematical Society Publishing House quality_controlled: '1' status: public title: Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '9057' abstract: - lang: eng text: Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes. article_number: e1400214 article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: Anaïs full_name: Abramian, Anaïs last_name: Abramian - first_name: Jérémie full_name: Barral, Jérémie last_name: Barral - first_name: Kasey full_name: Hanson, Kasey last_name: Hanson - first_name: Alexander Y. full_name: Grosberg, Alexander Y. last_name: Grosberg - first_name: David J. full_name: Pine, David J. last_name: Pine - first_name: Paul M. full_name: Chaikin, Paul M. last_name: Chaikin citation: ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214 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 chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/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. 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. 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. 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). date_created: 2021-02-02T13:15:02Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-23T13:47:52Z day: '01' ddc: - '530' doi: 10.1126/sciadv.1400214 extern: '1' external_id: arxiv: - '1505.05111' pmid: - '26601175' file: - access_level: open_access checksum: b97d62433581875c1b85210c5f6ae370 content_type: application/pdf creator: cziletti date_created: 2021-02-02T13:22:19Z date_updated: 2021-02-02T13:22:19Z file_id: '9058' file_name: 2015_ScienceAdvances_Palacci.pdf file_size: 2416780 relation: main_file success: 1 file_date_updated: 2021-02-02T13:22:19Z has_accepted_license: '1' intvolume: ' 1' issue: '4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: 'American Association for the Advancement of Science ' quality_controlled: '1' scopus_import: '1' status: public title: Artificial rheotaxis tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 1 year: '2015' ... --- _id: '906' abstract: - lang: eng 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. 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.' author: - first_name: Oksana full_name: Arkhipova, Oksana V last_name: Arkhipova - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Galina full_name: Mikoulinskaia, Galina V last_name: Mikoulinskaia - first_name: Marina full_name: Zakharova, Marina V last_name: Zakharova - first_name: Alexander full_name: Galushko, Alexander S last_name: Galushko - first_name: Vasilii full_name: Akimenko, Vasilii K last_name: Akimenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 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 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 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. 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. 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). 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. short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015). date_created: 2018-12-11T11:49:08Z date_published: 2015-05-11T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '11' doi: 10.1371/journal.pone.0125888 extern: 1 intvolume: ' 10' issue: '5' month: '05' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6742' quality_controlled: 0 status: public title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 10 year: '2015' ... --- _id: '9141' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Adrien full_name: Lefauve, Adrien last_name: Lefauve - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Angélique full_name: Melet, Angélique last_name: Melet citation: 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' 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' 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.' 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.' 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.' 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.' date_created: 2021-02-15T14:21:49Z date_published: 2015-06-08T00:00:00Z date_updated: 2022-01-24T13:45:41Z day: '08' doi: 10.1002/2014jc010598 extern: '1' intvolume: ' 120' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2014JC010598 month: '06' oa: 1 oa_version: Published Version page: 4760-4777 publication: 'Journal of Geophysical Research: Oceans' publication_identifier: issn: - 2169-9275 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: A three-dimensional map of tidal dissipation over abyssal hills type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 120 year: '2015' ... --- _id: '928' abstract: - lang: eng 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. article_number: e09206 author: - first_name: Ivonne full_name: Sehring, Ivonne last_name: Sehring - first_name: Pierre full_name: Recho, Pierre last_name: Recho - first_name: Elsa full_name: Denker, Elsa last_name: Denker - first_name: Matthew full_name: Kourakis, Matthew last_name: Kourakis - first_name: Birthe full_name: Mathiesen, Birthe last_name: Mathiesen - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Di full_name: Jiang, Di last_name: Jiang 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 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 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. ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015. 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. 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). date_created: 2018-12-11T11:49:15Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T08:21:58Z day: '21' ddc: - '539' - '570' doi: 10.7554/eLife.09206 extern: '1' file: - access_level: open_access checksum: 1e4024b3161adcae4a53a0b3dc8a946e content_type: application/pdf creator: dernst date_created: 2018-12-20T15:50:56Z date_updated: 2020-07-14T12:48:15Z file_id: '5769' file_name: 2015_eLife_Sehring.pdf file_size: 7202224 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '6512' quality_controlled: '1' status: public title: Assembly and positioning of actomyosin rings by contractility and planar cell polarity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '9575' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Krivelevich, Michael last_name: Krivelevich - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: 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 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. 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. 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. short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187. date_created: 2021-06-21T06:40:34Z date_published: 2015-11-01T00:00:00Z date_updated: 2023-02-23T14:01:28Z day: '01' doi: 10.1016/j.endm.2015.06.027 extern: '1' external_id: arxiv: - '1501.04816' intvolume: ' 49' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1501.04816 month: '11' oa: 1 oa_version: Preprint page: 181-187 publication: Electronic Notes in Discrete Mathematics publication_identifier: issn: - 1571-0653 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cycles and matchings in randomly perturbed digraphs and hypergraphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 49 year: '2015' ... --- _id: '9673' 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. article_processing_charge: No article_type: original author: - first_name: H.S. full_name: Leung, H.S. last_name: Leung - first_name: P.S.S. full_name: Leung, P.S.S. last_name: Leung - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: A.H.W. full_name: Ngan, A.H.W. last_name: Ngan citation: 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 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 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. 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. 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. 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. date_created: 2021-07-15T14:09:32Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T14:04:28Z day: '01' doi: 10.1016/j.ijplas.2014.09.009 extern: '1' intvolume: ' 67' language: - iso: eng month: '04' oa_version: None page: 1-25 publication: International Journal of Plasticity publication_identifier: issn: - 0749-6419 publication_status: published publisher: Elsevier scopus_import: '1' status: public title: A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 67 year: '2015' ... --- _id: '9688' abstract: - lang: eng 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. article_number: '180102' article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Gareth A. full_name: Tribello, Gareth A. last_name: Tribello - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: 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 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 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. 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. 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. 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). date_created: 2021-07-19T10:07:22Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-08-09T12:38:49Z day: '01' doi: 10.1103/physrevb.92.180102 extern: '1' external_id: arxiv: - '1511.08668' intvolume: ' 92' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.08668 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: eissn: - 1550-235X issn: - 1098-0121 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Solid-liquid interfacial free energy out of equilibrium type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 92 year: '2015' ... --- _id: '9711' article_processing_charge: No author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Tugce full_name: Batur, Tugce last_name: Batur - first_name: Aysegul full_name: Guvenek, Aysegul last_name: Guvenek - first_name: Dilay Hazal full_name: Ayhan, Dilay Hazal last_name: Ayhan - first_name: Erdal full_name: Toprak, Erdal last_name: Toprak - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: 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 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 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. ieee: G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015. 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. 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). date_created: 2021-07-23T11:53:50Z date_published: 2015-11-18T00:00:00Z date_updated: 2023-02-23T10:07:02Z day: '18' department: - _id: ToBo doi: 10.1371/journal.pbio.1002299.s001 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1619' relation: used_in_publication status: public status: public title: Excel file containing the raw data for all figures type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1855' abstract: - lang: eng text: 'Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.' 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. article_processing_charge: No article_type: original author: - first_name: Dino full_name: Mcmahon, Dino last_name: Mcmahon - first_name: Matthias full_name: Fürst, Matthias id: 393B1196-F248-11E8-B48F-1D18A9856A87 last_name: Fürst orcid: 0000-0002-3712-925X - first_name: Jesicca full_name: Caspar, Jesicca last_name: Caspar - first_name: Panagiotis full_name: Theodorou, Panagiotis last_name: Theodorou - first_name: Mark full_name: Brown, Mark last_name: Brown - first_name: Robert full_name: Paxton, Robert last_name: Paxton citation: 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' 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.' 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.' 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.' short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624. date_created: 2018-12-11T11:54:23Z date_published: 2015-03-03T00:00:00Z date_updated: 2023-02-23T14:06:09Z day: '03' ddc: - '570' department: - _id: SyCr doi: 10.1111/1365-2656.12345 external_id: pmid: - '25646973' file: - access_level: open_access checksum: 542a0b9b07e78050a81b35f26f0b82da content_type: application/pdf creator: system date_created: 2018-12-12T10:18:29Z date_updated: 2020-07-14T12:45:19Z file_id: '5350' file_name: IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf file_size: 1823045 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 84' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 615 - 624 pmid: 1 publication: Journal of Animal Ecology publication_status: published publisher: Wiley publist_id: '5245' pubrep_id: '460' quality_controlled: '1' related_material: record: - id: '9720' relation: research_data status: public scopus_import: '1' status: public title: 'A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 84 year: '2015' ... --- _id: '1830' 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. 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. article_processing_charge: No article_type: original author: - first_name: Fabian full_name: Theis, Fabian last_name: Theis - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: 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 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 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. 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. 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). 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. short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015). date_created: 2018-12-11T11:54:15Z date_published: 2015-05-26T00:00:00Z date_updated: 2023-02-23T14:06:12Z day: '26' department: - _id: SyCr doi: 10.1098/rstb.2014.0108 ec_funded: 1 external_id: pmid: - '25870394' intvolume: ' 370' issue: '1669' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25DDF0F0-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '302004' name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach' - _id: 25E0E184-B435-11E9-9278-68D0E5697425 name: Antnet - _id: 25E24DB2-B435-11E9-9278-68D0E5697425 name: Fellowship of Wissenschaftskolleg zu Berlin publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: Royal Society, The publist_id: '5273' quality_controlled: '1' related_material: record: - id: '9721' relation: research_data status: public scopus_import: '1' status: public title: Opposing effects of allogrooming on disease transmission in ant societies type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 370 year: '2015' ...