[{"ddc":["530"],"fulldoi":"https://doi.org/10.1126/sciadv.1500692","month":"10","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","_id":"19805","date_created":"2025-06-10T09:09:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-10T13:09:49Z","oa":1,"title":"Nearly free electrons in a 5d delafossite oxide metal","intvolume":"         1","day":"01","status":"public","article_type":"original","article_number":"1500692","quality_controlled":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"abstract":[{"lang":"eng","text":"Understanding the role of electron correlations in strong spin-orbit transition-metal oxides is key to the realization of numerous exotic phases including spin-orbit–assisted Mott insulators, correlated topological solids, and prospective new high-temperature superconductors. To date, most attention has been focused on the 5d iridium-based oxides. We instead consider the Pt-based delafossite oxide PtCoO2. Our transport measurements, performed on single-crystal samples etched to well-defined geometries using focused ion beam techniques, yield a room temperature resistivity of only 2.1 microhm·cm (μΩ-cm), establishing PtCoO2 as the most conductive oxide known. From angle-resolved photoemission and density functional theory, we show that the underlying Fermi surface is a single cylinder of nearly hexagonal cross-section, with very weak dispersion along kz. Despite being predominantly composed of d-orbital character, the conduction band is remarkably steep, with an average effective mass of only 1.14me. Moreover, the sharp spectral features observed in photoemission remain well defined with little additional broadening for more than 500 meV below EF, pointing to suppressed electron-electron scattering. Together, our findings establish PtCoO2 as a model nearly-free–electron system in a 5d delafossite transition-metal oxide."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciadv.1500692"}],"date_published":"2015-10-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Science Advances","publication_identifier":{"issn":["2375-2548"]},"issue":"9","author":[{"full_name":"Kushwaha, Pallavi","last_name":"Kushwaha","first_name":"Pallavi"},{"full_name":"Sunko, Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","last_name":"Sunko","first_name":"Veronika","orcid":"0000-0003-2724-3523"},{"last_name":"Moll","first_name":"Philip J. W.","full_name":"Moll, Philip J. W."},{"full_name":"Bawden, Lewis","first_name":"Lewis","last_name":"Bawden"},{"last_name":"Riley","first_name":"Jonathon M.","full_name":"Riley, Jonathon M."},{"full_name":"Nandi, Nabhanila","first_name":"Nabhanila","last_name":"Nandi"},{"last_name":"Rosner","first_name":"Helge","full_name":"Rosner, Helge"},{"full_name":"Schmidt, Marcus P.","first_name":"Marcus P.","last_name":"Schmidt"},{"full_name":"Arnold, Frank","first_name":"Frank","last_name":"Arnold"},{"full_name":"Hassinger, Elena","last_name":"Hassinger","first_name":"Elena"},{"last_name":"Kim","first_name":"Timur K.","full_name":"Kim, Timur K."},{"first_name":"Moritz","last_name":"Hoesch","full_name":"Hoesch, Moritz"},{"full_name":"Mackenzie, Andrew P.","first_name":"Andrew P.","last_name":"Mackenzie"},{"full_name":"King, Phil D. C.","last_name":"King","first_name":"Phil D. C."}],"DOAJ_listed":"1","OA_place":"publisher","year":"2015","doi":"10.1126/sciadv.1500692","citation":{"ieee":"P. Kushwaha <i>et al.</i>, “Nearly free electrons in a 5d delafossite oxide metal,” <i>Science Advances</i>, vol. 1, no. 9. American Association for the Advancement of Science, 2015.","ista":"Kushwaha P, Sunko V, Moll PJW, Bawden L, Riley JM, Nandi N, Rosner H, Schmidt MP, Arnold F, Hassinger E, Kim TK, Hoesch M, Mackenzie AP, King PDC. 2015. Nearly free electrons in a 5d delafossite oxide metal. Science Advances. 1(9), 1500692.","ama":"Kushwaha P, Sunko V, Moll PJW, et al. Nearly free electrons in a 5d delafossite oxide metal. <i>Science Advances</i>. 2015;1(9). doi:<a href=\"https://doi.org/10.1126/sciadv.1500692\">10.1126/sciadv.1500692</a>","chicago":"Kushwaha, Pallavi, Veronika Sunko, Philip J. W. Moll, Lewis Bawden, Jonathon M. Riley, Nabhanila Nandi, Helge Rosner, et al. “Nearly Free Electrons in a 5d Delafossite Oxide Metal.” <i>Science Advances</i>. American Association for the Advancement of Science, 2015. <a href=\"https://doi.org/10.1126/sciadv.1500692\">https://doi.org/10.1126/sciadv.1500692</a>.","apa":"Kushwaha, P., Sunko, V., Moll, P. J. W., Bawden, L., Riley, J. M., Nandi, N., … King, P. D. C. (2015). Nearly free electrons in a 5d delafossite oxide metal. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.1500692\">https://doi.org/10.1126/sciadv.1500692</a>","mla":"Kushwaha, Pallavi, et al. “Nearly Free Electrons in a 5d Delafossite Oxide Metal.” <i>Science Advances</i>, vol. 1, no. 9, 1500692, American Association for the Advancement of Science, 2015, doi:<a href=\"https://doi.org/10.1126/sciadv.1500692\">10.1126/sciadv.1500692</a>.","short":"P. Kushwaha, V. Sunko, P.J.W. Moll, L. Bawden, J.M. Riley, N. Nandi, H. Rosner, M.P. Schmidt, F. Arnold, E. Hassinger, T.K. Kim, M. Hoesch, A.P. Mackenzie, P.D.C. King, Science Advances 1 (2015)."},"volume":1,"OA_type":"gold","type":"journal_article","scopus_import":"1","oa_version":"Published Version","extern":"1","publication_status":"published"},{"acknowledgement":"Funded by      University of Alaska Center for Global Change Student Research     Cooperative Institute for Alaska Research and the Rasmuson Foundation","type":"journal_article","status":"public","extern":"1","oa_version":"None","article_type":"review","publication_status":"published","intvolume":"        53","doi":"10.1111/jzs.12079","year":"2015","title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","day":"01","volume":53,"citation":{"ista":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2015. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 53(1), 1–17.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1. Wiley, pp. 1–17, 2015.","ama":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. 2015;53(1):1-17. doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>","apa":"Garvin, M., Bielawski, J., Sazanov, L. A., &#38; Gharrett, A. (2015). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>","chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>.","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2015) 1–17.","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1, Wiley, 2015, pp. 1–17, doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>."},"issue":"1","page":"1 - 17","publist_id":"5102","author":[{"first_name":"Michael","last_name":"Garvin","full_name":"Garvin, Michael"},{"first_name":"Joseph","last_name":"Bielawski","full_name":"Bielawski, Joseph"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"},{"full_name":"Gharrett, Anthony","first_name":"Anthony","last_name":"Gharrett"}],"date_created":"2018-12-11T11:55:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-08-05T14:47:50Z","abstract":[{"text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may pro-vide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.","lang":"eng"}],"publisher":"Wiley","language":[{"iso":"eng"}],"date_published":"2015-02-01T00:00:00Z","fulldoi":"https://doi.org/10.1111/jzs.12079","month":"02","article_processing_charge":"No","publication":"Journal of Zoological Systematics and Evolutionary Research","_id":"1981"},{"file_date_updated":"2020-07-14T12:45:22Z","citation":{"short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","mla":"Gupta, Ashutosh, et al. <i>Succinct Representation of Concurrent Trace Sets</i>. ACM, 2015, pp. 433–44, doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., &#38; Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444."},"doi":"10.1145/2676726.2677008","year":"2015","oa_version":"Submitted Version","has_accepted_license":"1","publication_status":"published","type":"conference","department":[{"_id":"ToHe"}],"scopus_import":"1","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"abstract":[{"lang":"eng","text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula."}],"file":[{"content_type":"application/pdf","creator":"system","file_size":399462,"file_name":"IST-2015-317-v1+1_author_version.pdf","date_updated":"2020-07-14T12:45:22Z","date_created":"2018-12-12T10:17:56Z","file_id":"5314","relation":"main_file","access_level":"open_access","checksum":"f0d4395b600f410a191256ac0b73af32"}],"language":[{"iso":"eng"}],"date_published":"2015-01-15T00:00:00Z","page":"433 - 444","author":[{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"last_name":"Samanta","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha"},{"orcid":"0000-0003-4409-8487","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","full_name":"Tarrach, Thorsten"}],"day":"15","conference":{"end_date":"2015-01-17","location":"Mumbai, India","start_date":"2015-01-15","name":"POPL: Principles of Programming Languages"},"title":"Succinct representation of concurrent trace sets","quality_controlled":"1","status":"public","article_processing_charge":"No","pubrep_id":"317","_id":"1992","ddc":["005"],"fulldoi":"https://doi.org/10.1145/2676726.2677008","month":"01","publisher":"ACM","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-03-07T08:44:29Z","date_created":"2018-12-11T11:55:05Z","publist_id":"5091"},{"author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Tragust, Simon"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"isi":1,"issue":"1799","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","external_id":{"isi":["000345624600008"],"pmid":["25473011"]},"language":[{"iso":"eng"}],"date_published":"2015-01-22T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. ","lang":"eng"}],"publication_status":"published","oa_version":"Submitted Version","scopus_import":"1","department":[{"_id":"SyCr"}],"acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","type":"journal_article","volume":282,"related_material":{"record":[{"id":"9740","status":"public","relation":"research_data"}]},"citation":{"ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1799). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799. The Royal Society, 2015.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>.","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>"},"corr_author":"1","doi":"10.1098/rspb.2014.1976","year":"2015","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa":1,"publist_id":"5090","date_created":"2018-12-11T11:55:06Z","date_updated":"2025-09-23T07:55:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1993","article_processing_charge":"No","publisher":"The Royal Society","month":"01","fulldoi":"https://doi.org/10.1098/rspb.2014.1976","quality_controlled":"1","article_number":"20141976","article_type":"original","status":"public","ec_funded":1,"pmid":1,"day":"22","intvolume":"       282","title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host"},{"title":"The three-state toric homogeneous Markov chain model has Markov degree two","arxiv":1,"day":"01","status":"public","quality_controlled":"1","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.jsc.2014.09.014","month":"05","_id":"1997","article_processing_charge":"No","publist_id":"5082","date_created":"2018-12-11T11:55:07Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T14:17:34Z","oa":1,"year":"2015","doi":"10.1016/j.jsc.2014.09.014","volume":"68/Part 2","citation":{"apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. 2015;68/Part 2(May-June):285-296. doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>"},"corr_author":"1","scopus_import":"1","department":[{"_id":"CaUh"}],"type":"journal_article","publication_status":"published","oa_version":"Preprint","date_published":"2015-05-01T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0077"}],"abstract":[{"text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.","lang":"eng"}],"publication":"Journal of Symbolic Computation","external_id":{"arxiv":["1207.0077"],"isi":["000347767600016"]},"author":[{"last_name":"Noren","id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik","full_name":"Noren, Patrik"}],"isi":1,"issue":"May-June","page":"285 - 296"},{"isi":1,"issue":"3","page":"261 - 269","author":[{"full_name":"Hein, Nicolas","last_name":"Hein","first_name":"Nicolas"},{"full_name":"Hillar, Christopher","first_name":"Christopher","last_name":"Hillar"},{"full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez","first_name":"Abraham"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"},{"full_name":"Teitler, Zach","first_name":"Zach","last_name":"Teitler"}],"publication":"Experimental Mathematics","external_id":{"isi":["000356873900001"],"arxiv":["1109.3436"]},"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. "}],"date_published":"2015-06-23T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"oa_version":"Preprint","publication_status":"published","type":"journal_article","scopus_import":"1","department":[{"_id":"CaUh"}],"volume":24,"citation":{"chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., &#38; Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>, vol. 24, no. 3, Taylor &#38; Francis, 2015, pp. 261–69, doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>.","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.","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” <i>Experimental Mathematics</i>, vol. 24, no. 3. Taylor &#38; Francis, pp. 261–269, 2015.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. 2015;24(3):261-269. doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>"},"year":"2015","doi":"10.1080/10586458.2014.980044","oa":1,"publist_id":"5070","date_created":"2018-12-11T11:55:10Z","date_updated":"2025-09-23T14:07:49Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","_id":"2006","publisher":"Taylor & Francis","fulldoi":"https://doi.org/10.1080/10586458.2014.980044","month":"06","quality_controlled":"1","status":"public","day":"23","arxiv":1,"intvolume":"        24","title":"The monotone secant conjecture in the real Schubert calculus"},{"status":"public","quality_controlled":"1","title":"Iterative scaling in curved exponential families","intvolume":"        42","arxiv":1,"day":"01","date_created":"2018-12-11T11:55:11Z","date_updated":"2025-09-23T09:25:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5068","oa":1,"month":"09","fulldoi":"https://doi.org/10.1111/sjos.12139","publisher":"Wiley","_id":"2008","article_processing_charge":"No","department":[{"_id":"CaUh"}],"scopus_import":"1","type":"journal_article","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).","publication_status":"published","oa_version":"Preprint","doi":"10.1111/sjos.12139","year":"2015","citation":{"apa":"Klimova, A., &#38; Rudas, T. (2015). Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. Wiley. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. 2015;42(3):832-847. doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>"},"volume":42,"author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova","full_name":"Klimova, Anna"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"issue":"3","page":"832 - 847","isi":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.3282","open_access":"1"}],"language":[{"iso":"eng"}],"date_published":"2015-09-01T00:00:00Z","abstract":[{"text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.","lang":"eng"}],"external_id":{"isi":["000360077100012"],"arxiv":["1307.3282"]},"publication":"Scandinavian Journal of Statistics"},{"article_processing_charge":"No","_id":"2014","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.csda.2015.01.017","month":"07","oa":1,"publist_id":"5062","date_updated":"2025-09-23T08:45:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:55:13Z","day":"01","arxiv":1,"intvolume":"        87","title":"Faithfulness and learning hypergraphs from discrete distributions","quality_controlled":"1","status":"public","publication":"Computational Statistics & Data Analysis","external_id":{"isi":["000352661000005"],"arxiv":["1404.6617"]},"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."}],"date_published":"2015-07-01T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1404.6617","open_access":"1"}],"isi":1,"issue":"7","page":"57 - 72","author":[{"full_name":"Klimova, Anna","first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"corr_author":"1","volume":87,"citation":{"short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics &#38; Data Analysis 87 (2015) 57–72.","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>.","apa":"Klimova, A., Uhler, C., &#38; Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. 2015;87(7):57-72. doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7. Elsevier, pp. 57–72, 2015."},"doi":"10.1016/j.csda.2015.01.017","year":"2015","oa_version":"Preprint","publication_status":"published","type":"journal_article","scopus_import":"1","department":[{"_id":"CaUh"}]},{"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","day":"01","intvolume":"      1853","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","oa":1,"publist_id":"5047","date_updated":"2025-09-23T14:51:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:55:17Z","_id":"2025","pubrep_id":"615","article_processing_charge":"No","publisher":"Elsevier","month":"01","fulldoi":"https://doi.org/10.1016/j.bbamcr.2014.10.009","ddc":["570"],"has_accepted_license":"1","publication_status":"published","oa_version":"Submitted Version","scopus_import":"1","department":[{"_id":"DaSi"}],"type":"journal_article","volume":1853,"citation":{"mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>.","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.","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.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>.","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. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(1):144-156. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>","ieee":"D. Kawada <i>et al.</i>, “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, 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."},"file_date_updated":"2020-07-14T12:45:25Z","doi":"10.1016/j.bbamcr.2014.10.009","year":"2015","author":[{"full_name":"Kawada, Daiki","first_name":"Daiki","last_name":"Kawada"},{"last_name":"Kobayashi","first_name":"Hiromu","full_name":"Kobayashi, Hiromu"},{"full_name":"Tomita, Tsuyoshi","last_name":"Tomita","first_name":"Tsuyoshi"},{"full_name":"Nakata, Eisuke","first_name":"Eisuke","last_name":"Nakata"},{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","full_name":"Siekhaus, Daria E"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"last_name":"Toshimaa","first_name":"Jiro","full_name":"Toshimaa, Jiro"}],"isi":1,"issue":"1","page":"144 - 156","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","external_id":{"isi":["000347598100014"]},"date_published":"2015-01-01T00:00:00Z","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","creator":"system","file_size":926685,"file_name":"IST-2016-615-v1+1_BBAMCR.pdf","date_created":"2018-12-12T10:12:18Z","date_updated":"2020-07-14T12:45:25Z","access_level":"open_access","relation":"main_file","file_id":"4936","checksum":"5bb328edebb6a91337cadd7d63f961b7"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.","lang":"eng"}]},{"publist_id":"5042","date_created":"2018-12-11T11:55:18Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:31:33Z","oa":1,"publisher":"Elsevier","month":"01","fulldoi":"https://doi.org/10.1016/j.compfluid.2014.09.021","_id":"2030","article_processing_charge":"No","status":"public","quality_controlled":"1","intvolume":"       106","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","arxiv":1,"day":"01","author":[{"last_name":"Shi","first_name":"Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","full_name":"Shi, Liang"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"isi":1,"page":"1 - 11","issue":"1","language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1311.2481","open_access":"1"}],"abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"publication":"Computers and Fluids","external_id":{"isi":["000346213200001"],"arxiv":["1311.2481"]},"scopus_import":"1","department":[{"_id":"BjHo"}],"type":"journal_article","publication_status":"published","oa_version":"Preprint","year":"2015","doi":"10.1016/j.compfluid.2014.09.021","volume":106,"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. <i>Computers and Fluids</i>. 2015;106(1):1-11. doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>","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,” <i>Computers and Fluids</i>, 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.” <i>Computers and Fluids</i>, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","apa":"Shi, L., Rampp, M., Hof, B., &#38; Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>","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.” <i>Computers and Fluids</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>."}},{"day":"01","intvolume":"        15","title":"The persistent homology of a self-map","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","ec_funded":1,"article_processing_charge":"No","_id":"2035","pubrep_id":"486","ddc":["000"],"publisher":"Springer","fulldoi":"https://doi.org/10.1007/s10208-014-9223-y","month":"10","oa":1,"publist_id":"5022","date_updated":"2025-09-23T14:08:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:55:20Z","file_date_updated":"2020-07-14T12:45:26Z","volume":15,"citation":{"ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. 2015;15(5):1213-1244. doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>","apa":"Edelsbrunner, H., Jablonski, G., &#38; Mrozek, M. (2015). The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>."},"year":"2015","doi":"10.1007/s10208-014-9223-y","oa_version":"Published Version","publication_status":"published","has_accepted_license":"1","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","type":"journal_article","scopus_import":"1","department":[{"_id":"HeEd"}],"publication":"Foundations of Computational Mathematics","external_id":{"isi":["000360862900004"]},"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"license":"https://creativecommons.org/licenses/by/4.0/","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"}],"date_published":"2015-10-01T00:00:00Z","language":[{"iso":"eng"}],"file":[{"creator":"system","content_type":"application/pdf","file_size":1317546,"file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","date_created":"2018-12-12T10:08:10Z","date_updated":"2020-07-14T12:45:26Z","file_id":"4670","relation":"main_file","access_level":"open_access","checksum":"3566f3a8b0c1bc550e62914a88c584ff"}],"isi":1,"issue":"5","page":"1213 - 1244","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Jablonski, Grzegorz","last_name":"Jablonski","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866"},{"full_name":"Mrozek, Marian","first_name":"Marian","last_name":"Mrozek"}]},{"year":"2015","citation":{"apa":"Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., &#38; Budakian, R. (2015). Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In <i>APS March Meeting 2015</i> (Vol. 60). San Antonio, TX, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” In <i>APS March Meeting 2015</i>, Vol. 60. American Physical Society, 2015.","short":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March Meeting 2015, American Physical Society, 2015.","mla":"Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” <i>APS March Meeting 2015</i>, vol. 60, no. 1, G16.00009, American Physical Society, 2015.","ista":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015. APS: American Physical Society, Bulletin of the American Physical Society, vol. 60, G16.00009.","ieee":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in <i>APS March Meeting 2015</i>, San Antonio, TX, United States, 2015, vol. 60, no. 1.","ama":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In: <i>APS March Meeting 2015</i>. Vol 60. American Physical Society; 2015."},"volume":60,"alternative_title":["Bulletin of the American Physical Society"],"type":"conference","publication_status":"published","oa_version":"Published Version","extern":"1","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR15/Event/238442","open_access":"1"}],"date_published":"2015-03-01T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"text":"The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed.","lang":"eng"}],"publication_identifier":{"issn":["0003-0503"]},"publication":"APS March Meeting 2015","author":[{"orcid":"0000-0001-8223-8896","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhang, Can","last_name":"Zhang","first_name":"Can"},{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"first_name":"James","last_name":"Eckstein","full_name":"Eckstein, James"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"issue":"1","title":"Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy","intvolume":"        60","day":"01","conference":{"end_date":"2015-03-06","location":"San Antonio, TX, United States","name":"APS: American Physical Society","start_date":"2015-03-02"},"status":"public","quality_controlled":"1","article_number":"G16.00009","month":"03","publisher":"American Physical Society","_id":"10748","article_processing_charge":"No","date_created":"2022-02-08T10:17:09Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-02-08T10:42:53Z","oa":1},{"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"scopus_import":"1","type":"journal_article","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","has_accepted_license":"1","publication_status":"published","oa_version":"Published Version","year":"2015","doi":"10.3389/fenvs.2015.00042","citation":{"mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>.","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42."},"volume":3,"corr_author":"1","file_date_updated":"2022-02-25T11:55:26Z","author":[{"last_name":"Parise","first_name":"Francesca","full_name":"Parise, Francesca"},{"last_name":"Lygeros","first_name":"John","full_name":"Lygeros, John"},{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob"}],"file":[{"date_created":"2022-02-25T11:55:26Z","date_updated":"2022-02-25T11:55:26Z","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","checksum":"26c222487564e1be02a11d688d6f769d","file_id":"10795","access_level":"open_access","relation":"main_file","file_size":1371201,"content_type":"application/pdf","creator":"dernst","success":1}],"date_published":"2015-06-10T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation.","lang":"eng"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_identifier":{"issn":["2296-665X"]},"publication":"Frontiers in Environmental Science","status":"public","ec_funded":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_type":"original","article_number":"42","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","intvolume":"         3","day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T06:50:01Z","date_created":"2022-02-25T11:42:25Z","keyword":["General Environmental Science"],"oa":1,"fulldoi":"https://doi.org/10.3389/fenvs.2015.00042","month":"06","publisher":"Frontiers","ddc":["000","570"],"_id":"10794","article_processing_charge":"No"},{"abstract":[{"text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).","lang":"eng"}],"date_published":"2015-01-01T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1409.6690","open_access":"1"}],"publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","external_id":{"arxiv":["1409.6690"]},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication_identifier":{"isbn":["978-161197374-7"]},"page":"1018-1029","issue":"1","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389"}],"doi":"10.1137/1.9781611973730.69","OA_place":"publisher","year":"2015","corr_author":"1","volume":2015,"citation":{"ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2015. SIAM; 2015:1018-1029. doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2015:1018–29. SIAM, 2015. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>"},"acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","OA_type":"green","type":"conference","scopus_import":"1","department":[{"_id":"KrCh"}],"oa_version":"Preprint","publication_status":"published","publisher":"SIAM","fulldoi":"https://doi.org/10.1137/1.9781611973730.69","month":"01","article_processing_charge":"No","_id":"10796","date_created":"2022-02-25T12:18:43Z","date_updated":"2025-06-26T06:54:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"arxiv":1,"intvolume":"      2015","title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","conference":{"location":"San Diego, CA, United States","end_date":"2015-01-06","name":"SODA: Symposium on Discrete Algorithms","start_date":"2015-01-04"},"day":"01","ec_funded":1,"status":"public","quality_controlled":"1"},{"oa":1,"date_updated":"2021-01-12T08:15:12Z","date_created":"2020-04-30T10:51:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"7739","publisher":"Wiley","fulldoi":"https://doi.org/10.1111/mec.13452","month":"12","article_type":"original","quality_controlled":"1","status":"public","day":"10","intvolume":"        24","title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","page":"6148-6162","author":[{"last_name":"Santure","first_name":"Anna W.","full_name":"Santure, Anna W."},{"first_name":"Jocelyn","last_name":"Poissant","full_name":"Poissant, Jocelyn"},{"last_name":"De Cauwer","first_name":"Isabelle","full_name":"De Cauwer, Isabelle"},{"last_name":"van Oers","first_name":"Kees","full_name":"van Oers, Kees"},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard"},{"last_name":"Quinn","first_name":"John L.","full_name":"Quinn, John L."},{"full_name":"Groenen, Martien A. M.","last_name":"Groenen","first_name":"Martien A. M."},{"full_name":"Visser, Marcel E.","first_name":"Marcel E.","last_name":"Visser"},{"full_name":"Sheldon, Ben C.","last_name":"Sheldon","first_name":"Ben C."},{"last_name":"Slate","first_name":"Jon","full_name":"Slate, Jon"}],"publication":"Molecular Ecology","publication_identifier":{"issn":["0962-1083"]},"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."}],"language":[{"iso":"eng"}],"date_published":"2015-12-10T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.13452"}],"oa_version":"Published Version","extern":"1","publication_status":"published","type":"journal_article","volume":24,"citation":{"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. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.13452\">https://doi.org/10.1111/mec.13452</a>","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.” <i>Molecular Ecology</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/mec.13452\">https://doi.org/10.1111/mec.13452</a>.","mla":"Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” <i>Molecular Ecology</i>, vol. 24, Wiley, 2015, pp. 6148–62, doi:<a href=\"https://doi.org/10.1111/mec.13452\">10.1111/mec.13452</a>.","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.","ieee":"A. W. Santure <i>et al.</i>, “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” <i>Molecular Ecology</i>, 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.","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. <i>Molecular Ecology</i>. 2015;24:6148-6162. doi:<a href=\"https://doi.org/10.1111/mec.13452\">10.1111/mec.13452</a>"},"year":"2015","doi":"10.1111/mec.13452"},{"intvolume":"       282","title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","day":"07","status":"public","pmid":1,"quality_controlled":"1","article_number":"20150689","article_type":"original","publisher":"The Royal Society","month":"07","fulldoi":"https://doi.org/10.1098/rspb.2015.0689","_id":"7741","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:12Z","date_created":"2020-04-30T10:58:07Z","oa":1,"doi":"10.1098/rspb.2015.0689","year":"2015","volume":282,"citation":{"mla":"Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2015.0689\">10.1098/rspb.2015.0689</a>.","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015).","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.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2015.0689\">https://doi.org/10.1098/rspb.2015.0689</a>.","apa":"Adams, M. J., Robinson, M. R., Mannarelli, M.-E., &#38; Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2015.0689\">https://doi.org/10.1098/rspb.2015.0689</a>","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. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2015;282(1810). doi:<a href=\"https://doi.org/10.1098/rspb.2015.0689\">10.1098/rspb.2015.0689</a>","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,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, 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."},"type":"journal_article","publication_status":"published","extern":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"date_published":"2015-07-07T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rspb.2015.0689"}],"abstract":[{"text":"Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population.","lang":"eng"}],"publication_identifier":{"issn":["0962-8452","1471-2954"]},"publication":"Proceedings of the Royal Society B: Biological Sciences","external_id":{"pmid":["26063846"]},"author":[{"full_name":"Adams, Mark James","first_name":"Mark James","last_name":"Adams"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Mannarelli, Maria-Elena","first_name":"Maria-Elena","last_name":"Mannarelli"},{"full_name":"Hatchwell, Ben J.","first_name":"Ben J.","last_name":"Hatchwell"}],"issue":"1810"},{"status":"public","type":"journal_article","quality_controlled":"1","publication_status":"published","extern":"1","oa_version":"None","article_type":"original","intvolume":"        47","doi":"10.1038/ng.3401","title":"Population genetic differentiation of height and body mass index across Europe","year":"2015","volume":47,"citation":{"ama":"Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. <i>Nature Genetics</i>. 2015;47(11):1357-1362. doi:<a href=\"https://doi.org/10.1038/ng.3401\">10.1038/ng.3401</a>","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.","ieee":"M. R. Robinson <i>et al.</i>, “Population genetic differentiation of height and body mass index across Europe,” <i>Nature Genetics</i>, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015.","short":"M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.","mla":"Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” <i>Nature Genetics</i>, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:<a href=\"https://doi.org/10.1038/ng.3401\">10.1038/ng.3401</a>.","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. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ng.3401\">https://doi.org/10.1038/ng.3401</a>","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.” <i>Nature Genetics</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/ng.3401\">https://doi.org/10.1038/ng.3401</a>."},"day":"14","author":[{"orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"full_name":"Hemani, Gibran","first_name":"Gibran","last_name":"Hemani"},{"last_name":"Medina-Gomez","first_name":"Carolina","full_name":"Medina-Gomez, Carolina"},{"full_name":"Mezzavilla, Massimo","last_name":"Mezzavilla","first_name":"Massimo"},{"full_name":"Esko, Tonu","last_name":"Esko","first_name":"Tonu"},{"full_name":"Shakhbazov, Konstantin","last_name":"Shakhbazov","first_name":"Konstantin"},{"first_name":"Joseph E","last_name":"Powell","full_name":"Powell, Joseph E"},{"first_name":"Anna","last_name":"Vinkhuyzen","full_name":"Vinkhuyzen, Anna"},{"full_name":"Berndt, Sonja I","last_name":"Berndt","first_name":"Sonja I"},{"full_name":"Gustafsson, Stefan","first_name":"Stefan","last_name":"Gustafsson"},{"full_name":"Justice, Anne E","last_name":"Justice","first_name":"Anne E"},{"last_name":"Kahali","first_name":"Bratati","full_name":"Kahali, Bratati"},{"first_name":"Adam E","last_name":"Locke","full_name":"Locke, Adam E"},{"first_name":"Tune H","last_name":"Pers","full_name":"Pers, Tune H"},{"first_name":"Sailaja","last_name":"Vedantam","full_name":"Vedantam, Sailaja"},{"full_name":"Wood, Andrew R","first_name":"Andrew R","last_name":"Wood"},{"full_name":"van Rheenen, Wouter","first_name":"Wouter","last_name":"van Rheenen"},{"last_name":"Andreassen","first_name":"Ole A","full_name":"Andreassen, Ole A"},{"full_name":"Gasparini, Paolo","first_name":"Paolo","last_name":"Gasparini"},{"full_name":"Metspalu, Andres","first_name":"Andres","last_name":"Metspalu"},{"full_name":"Berg, Leonard H van den","first_name":"Leonard H van den","last_name":"Berg"},{"full_name":"Veldink, Jan H","first_name":"Jan H","last_name":"Veldink"},{"first_name":"Fernando","last_name":"Rivadeneira","full_name":"Rivadeneira, Fernando"},{"full_name":"Werge, Thomas M","last_name":"Werge","first_name":"Thomas M"},{"last_name":"Abecasis","first_name":"Goncalo R","full_name":"Abecasis, Goncalo R"},{"last_name":"Boomsma","first_name":"Dorret I","full_name":"Boomsma, Dorret I"},{"full_name":"Chasman, Daniel I","first_name":"Daniel I","last_name":"Chasman"},{"full_name":"de Geus, Eco J C","first_name":"Eco J C","last_name":"de Geus"},{"full_name":"Frayling, Timothy M","first_name":"Timothy M","last_name":"Frayling"},{"full_name":"Hirschhorn, Joel N","first_name":"Joel N","last_name":"Hirschhorn"},{"full_name":"Hottenga, Jouke Jan","last_name":"Hottenga","first_name":"Jouke Jan"},{"last_name":"Ingelsson","first_name":"Erik","full_name":"Ingelsson, Erik"},{"last_name":"Loos","first_name":"Ruth J F","full_name":"Loos, Ruth J F"},{"first_name":"Patrik K E","last_name":"Magnusson","full_name":"Magnusson, Patrik K E"},{"full_name":"Martin, Nicholas G","last_name":"Martin","first_name":"Nicholas G"},{"full_name":"Montgomery, Grant W","last_name":"Montgomery","first_name":"Grant W"},{"full_name":"North, Kari E","last_name":"North","first_name":"Kari E"},{"full_name":"Pedersen, Nancy L","last_name":"Pedersen","first_name":"Nancy L"},{"full_name":"Spector, Timothy D","last_name":"Spector","first_name":"Timothy D"},{"last_name":"Speliotes","first_name":"Elizabeth K","full_name":"Speliotes, Elizabeth K"},{"first_name":"Michael E","last_name":"Goddard","full_name":"Goddard, Michael E"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"first_name":"Peter M","last_name":"Visscher","full_name":"Visscher, Peter M"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T10:58:23Z","date_updated":"2021-01-12T08:15:13Z","issue":"11","page":"1357-1362","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_published":"2015-09-14T00:00:00Z","fulldoi":"https://doi.org/10.1038/ng.3401","month":"09","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)."}],"_id":"7742","publication_identifier":{"issn":["1061-4036","1546-1718"]},"publication":"Nature Genetics","article_processing_charge":"No"},{"citation":{"chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue.” In <i>Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 11–20. ACM, 2015. <a href=\"https://doi.org/10.1145/2688500.2688523\">https://doi.org/10.1145/2688500.2688523</a>.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., &#38; Shavit, N. (2015). The SprayList: A scalable relaxed priority queue. In <i>Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 11–20). San Francisco, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2688500.2688523\">https://doi.org/10.1145/2688500.2688523</a>","short":"D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, ACM, 2015, pp. 11–20.","mla":"Alistarh, Dan-Adrian, et al. “The SprayList: A Scalable Relaxed Priority Queue.” <i>Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, ACM, 2015, pp. 11–20, doi:<a href=\"https://doi.org/10.1145/2688500.2688523\">10.1145/2688500.2688523</a>.","ista":"Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Principles and Practice of Parallel Pogramming, 11–20.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” in <i>Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, San Francisco, CA, United States, 2015, pp. 11–20.","ama":"Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: <i>Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. ACM; 2015:11-20. doi:<a href=\"https://doi.org/10.1145/2688500.2688523\">10.1145/2688500.2688523</a>"},"doi":"10.1145/2688500.2688523","year":"2015","publication_status":"published","extern":"1","oa_version":"None","scopus_import":"1","type":"conference","OA_type":"closed access","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.","publication_identifier":{"isbn":["9781450332057"]},"publication":"Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","language":[{"iso":"eng"}],"date_published":"2015-01-24T00:00:00Z","abstract":[{"text":"High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by &quot;spraying&quot; themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution.","lang":"eng"}],"author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Kopinsky, Justin","first_name":"Justin","last_name":"Kopinsky"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"page":"11 - 20","day":"24","conference":{"location":"San Francisco, CA, United States","end_date":"2015-02-11","start_date":"2015-02-07","name":"PPoPP: Principles and Practice of Parallel Pogramming"},"title":"The SprayList: A scalable relaxed priority queue","quality_controlled":"1","status":"public","_id":"776","article_processing_charge":"No","month":"01","fulldoi":"https://doi.org/10.1145/2688500.2688523","publisher":"ACM","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-18T12:40:58Z","date_created":"2018-12-11T11:48:26Z","publist_id":"6878"},{"intvolume":"       114","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","doi":"10.1103/physrevlett.114.225501","year":"2015","volume":114,"citation":{"mla":"Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” <i>Physical Review Letters</i>, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/physrevlett.114.225501\">10.1103/physrevlett.114.225501</a>.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.114.225501\">https://doi.org/10.1103/physrevlett.114.225501</a>","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.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/physrevlett.114.225501\">https://doi.org/10.1103/physrevlett.114.225501</a>.","ama":"Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. <i>Physical Review Letters</i>. 2015;114(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.114.225501\">10.1103/physrevlett.114.225501</a>","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,” <i>Physical Review Letters</i>, 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."},"day":"04","status":"public","type":"journal_article","quality_controlled":"1","publication_status":"published","oa_version":"None","article_number":"225501","extern":"1","article_type":"original","language":[{"iso":"eng"}],"publisher":"American Physical Society","date_published":"2015-06-04T00:00:00Z","month":"06","fulldoi":"https://doi.org/10.1103/physrevlett.114.225501","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."}],"_id":"7765","publication_identifier":{"issn":["0031-9007","1079-7114"]},"article_processing_charge":"No","publication":"Physical Review Letters","author":[{"orcid":"0000-0002-1307-5074","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:23Z","date_created":"2020-04-30T11:41:08Z","issue":"22"},{"day":"15","citation":{"ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. <i>Soft Matter</i>. 2015;11(14):2745-2751. doi:<a href=\"https://doi.org/10.1039/c4sm02905d\">10.1039/c4sm02905d</a>","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751.","ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” <i>Soft Matter</i>, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” <i>Soft Matter</i>, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:<a href=\"https://doi.org/10.1039/c4sm02905d\">10.1039/c4sm02905d</a>.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c4sm02905d\">https://doi.org/10.1039/c4sm02905d</a>","chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” <i>Soft Matter</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c4sm02905d\">https://doi.org/10.1039/c4sm02905d</a>."},"volume":11,"title":"Disordered surface vibrations in jammed sphere packings","year":"2015","doi":"10.1039/c4sm02905d","intvolume":"        11","article_type":"original","extern":"1","oa_version":"None","publication_status":"published","quality_controlled":"1","type":"journal_article","status":"public","publication":"Soft Matter","article_processing_charge":"No","publication_identifier":{"issn":["1744-683X","1744-6848"]},"_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."}],"fulldoi":"https://doi.org/10.1039/c4sm02905d","month":"02","language":[{"iso":"eng"}],"date_published":"2015-02-15T00:00:00Z","publisher":"Royal Society of Chemistry","issue":"14","page":"2745-2751","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:23Z","date_created":"2020-04-30T11:41:23Z","author":[{"last_name":"Sussman","first_name":"Daniel M.","full_name":"Sussman, Daniel M."},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}]}]