--- _id: '7742' abstract: - lang: eng text: Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58). article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Gibran full_name: Hemani, Gibran last_name: Hemani - first_name: Carolina full_name: Medina-Gomez, Carolina last_name: Medina-Gomez - first_name: Massimo full_name: Mezzavilla, Massimo last_name: Mezzavilla - first_name: Tonu full_name: Esko, Tonu last_name: Esko - first_name: Konstantin full_name: Shakhbazov, Konstantin last_name: Shakhbazov - first_name: Joseph E full_name: Powell, Joseph E last_name: Powell - first_name: Anna full_name: Vinkhuyzen, Anna last_name: Vinkhuyzen - first_name: Sonja I full_name: Berndt, Sonja I last_name: Berndt - first_name: Stefan full_name: Gustafsson, Stefan last_name: Gustafsson - first_name: Anne E full_name: Justice, Anne E last_name: Justice - first_name: Bratati full_name: Kahali, Bratati last_name: Kahali - first_name: Adam E full_name: Locke, Adam E last_name: Locke - first_name: Tune H full_name: Pers, Tune H last_name: Pers - first_name: Sailaja full_name: Vedantam, Sailaja last_name: Vedantam - first_name: Andrew R full_name: Wood, Andrew R last_name: Wood - first_name: Wouter full_name: van Rheenen, Wouter last_name: van Rheenen - first_name: Ole A full_name: Andreassen, Ole A last_name: Andreassen - first_name: Paolo full_name: Gasparini, Paolo last_name: Gasparini - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Leonard H van den full_name: Berg, Leonard H van den last_name: Berg - first_name: Jan H full_name: Veldink, Jan H last_name: Veldink - first_name: Fernando full_name: Rivadeneira, Fernando last_name: Rivadeneira - first_name: Thomas M full_name: Werge, Thomas M last_name: Werge - first_name: Goncalo R full_name: Abecasis, Goncalo R last_name: Abecasis - first_name: Dorret I full_name: Boomsma, Dorret I last_name: Boomsma - first_name: Daniel I full_name: Chasman, Daniel I last_name: Chasman - first_name: Eco J C full_name: de Geus, Eco J C last_name: de Geus - first_name: Timothy M full_name: Frayling, Timothy M last_name: Frayling - first_name: Joel N full_name: Hirschhorn, Joel N last_name: Hirschhorn - first_name: Jouke Jan full_name: Hottenga, Jouke Jan last_name: Hottenga - first_name: Erik full_name: Ingelsson, Erik last_name: Ingelsson - first_name: Ruth J F full_name: Loos, Ruth J F last_name: Loos - first_name: Patrik K E full_name: Magnusson, Patrik K E last_name: Magnusson - first_name: Nicholas G full_name: Martin, Nicholas G last_name: Martin - first_name: Grant W full_name: Montgomery, Grant W last_name: Montgomery - first_name: Kari E full_name: North, Kari E last_name: North - first_name: Nancy L full_name: Pedersen, Nancy L last_name: Pedersen - first_name: Timothy D full_name: Spector, Timothy D last_name: Spector - first_name: Elizabeth K full_name: Speliotes, Elizabeth K last_name: Speliotes - first_name: Michael E full_name: Goddard, Michael E last_name: Goddard - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M full_name: Visscher, Peter M last_name: Visscher citation: ama: Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362. doi:10.1038/ng.3401 apa: Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., … Visscher, P. M. (2015). Population genetic differentiation of height and body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401 chicago: Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401. ieee: M. R. Robinson et al., “Population genetic differentiation of height and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015. ista: Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362. mla: Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401. short: M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362. date_created: 2020-04-30T10:58:23Z date_published: 2015-09-14T00:00:00Z date_updated: 2021-01-12T08:15:13Z day: '14' doi: 10.1038/ng.3401 extern: '1' intvolume: ' 47' issue: '11' language: - iso: eng month: '09' oa_version: None page: 1357-1362 publication: Nature Genetics publication_identifier: issn: - 1061-4036 - 1546-1718 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Population genetic differentiation of height and body mass index across Europe type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2015' ... --- _id: '7741' abstract: - lang: eng text: Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population. article_number: '20150689' article_processing_charge: No article_type: original author: - first_name: Mark James full_name: Adams, Mark James last_name: Adams - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Maria-Elena full_name: Mannarelli, Maria-Elena last_name: Mannarelli - first_name: Ben J. full_name: Hatchwell, Ben J. last_name: Hatchwell citation: ama: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689' apa: 'Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689' chicago: 'Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.' ieee: 'M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.' ista: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689.' mla: 'Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.' short: 'M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015).' date_created: 2020-04-30T10:58:07Z date_published: 2015-07-07T00:00:00Z date_updated: 2021-01-12T08:15:12Z day: '07' doi: 10.1098/rspb.2015.0689 extern: '1' external_id: pmid: - '26063846' intvolume: ' 282' issue: '1810' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rspb.2015.0689 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: 'Proceedings of the Royal Society B: Biological Sciences' publication_identifier: issn: - 0962-8452 - 1471-2954 publication_status: published publisher: The Royal Society quality_controlled: '1' status: public title: Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2015' ... --- _id: '7739' abstract: - lang: eng text: Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations. article_processing_charge: No article_type: original author: - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Jocelyn full_name: Poissant, Jocelyn last_name: Poissant - first_name: Isabelle full_name: De Cauwer, Isabelle last_name: De Cauwer - first_name: Kees full_name: van Oers, Kees last_name: van Oers - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: John L. full_name: Quinn, John L. last_name: Quinn - first_name: Martien A. M. full_name: Groenen, Martien A. M. last_name: Groenen - first_name: Marcel E. full_name: Visser, Marcel E. last_name: Visser - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452 apa: Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452 chicago: Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452. ieee: A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015. ista: Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162. mla: Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452. short: A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162. date_created: 2020-04-30T10:51:01Z date_published: 2015-12-10T00:00:00Z date_updated: 2021-01-12T08:15:12Z day: '10' doi: 10.1111/mec.13452 extern: '1' intvolume: ' 24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/mec.13452 month: '12' oa: 1 oa_version: Published Version page: 6148-6162 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '776' abstract: - lang: eng text: High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by "spraying" themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution. acknowledgement: "Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Jerry full_name: Li, Jerry last_name: Li - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523' apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523' chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523.' ieee: 'D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2015, vol. 2015–January, pp. 11–20.' ista: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming vol. 2015–January, 11–20.' mla: 'Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.' short: D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20. conference: name: 'PPoPP: Principles and Practice of Parallel Pogramming' date_created: 2018-12-11T11:48:26Z date_published: 2015-01-24T00:00:00Z date_updated: 2023-02-23T13:16:43Z day: '24' doi: 10.1145/2688500.2688523 extern: '1' language: - iso: eng month: '01' oa_version: None page: 11 - 20 publication_status: published publisher: ACM publist_id: '6878' status: public title: 'The SprayList: A scalable relaxed priority queue' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-January year: '2015' ... --- _id: '7765' abstract: - lang: eng text: 'We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior.' article_number: '225501' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: 'Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501' apa: 'Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501' chicago: 'Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501.' ieee: 'C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.' ista: 'Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.' mla: 'Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.' short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015). date_created: 2020-04-30T11:41:08Z date_published: 2015-06-04T00:00:00Z date_updated: 2021-01-12T08:15:23Z day: '04' doi: 10.1103/physrevlett.114.225501 extern: '1' intvolume: ' 114' issue: '22' language: - iso: eng month: '06' oa_version: None publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: 'The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '7767' abstract: - lang: eng text: We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food. article_number: '032706' article_processing_charge: No article_type: original author: - first_name: Ruben full_name: van Drongelen, Ruben last_name: van Drongelen - first_name: Anshuman full_name: Pal, Anshuman last_name: Pal - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Timon full_name: Idema, Timon last_name: Idema citation: ama: van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706 apa: van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective dynamics of soft active particles. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.91.032706 chicago: Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema. “Collective Dynamics of Soft Active Particles.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706. ieee: R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics of soft active particles,” Physical Review E, vol. 91, no. 3. American Physical Society, 2015. ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706. mla: van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.” Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015, doi:10.1103/physreve.91.032706. short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015). date_created: 2020-04-30T11:41:38Z date_published: 2015-03-01T00:00:00Z date_updated: 2021-01-12T08:15:24Z day: '01' doi: 10.1103/physreve.91.032706 extern: '1' intvolume: ' 91' issue: '3' language: - iso: eng month: '03' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 - 1550-2376 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Collective dynamics of soft active particles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '7766' abstract: - lang: eng text: We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached. article_processing_charge: No article_type: original author: - first_name: Daniel M. full_name: Sussman, Daniel M. last_name: Sussman - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d apa: Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d chicago: Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d. ieee: D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015. ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751. mla: Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d. short: D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751. date_created: 2020-04-30T11:41:23Z date_published: 2015-02-15T00:00:00Z date_updated: 2021-01-12T08:15:23Z day: '15' doi: 10.1039/c4sm02905d extern: '1' intvolume: ' 11' issue: '14' language: - iso: eng month: '02' oa_version: None page: 2745-2751 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Disordered surface vibrations in jammed sphere packings type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '777' abstract: - lang: eng text: 'In many applications, the data is of rich structure that can be represented by a hypergraph, where the data items are represented by vertices and the associations among items are represented by hyperedges. Equivalently, we are given an input bipartite graph with two types of vertices: items, and associations (which we refer to as topics). We consider the problem of partitioning the set of items into a given number of components such that the maximum number of topics covered by a component is minimized. This is a clustering problem with various applications, e.g. partitioning of a set of information objects such as documents, images, and videos, and load balancing in the context of modern computation platforms.Inthis paper, we focus on the streaming computation model for this problem, in which items arrive online one at a time and each item must be assigned irrevocably to a component at its arrival time. Motivated by scalability requirements, we focus on the class of streaming computation algorithms with memory limited to be at most linear in the number of components. We show that a greedy assignment strategy is able to recover a hidden co-clustering of items under a natural set of recovery conditions. We also report results of an extensive empirical evaluation, which demonstrate that this greedy strategy yields superior performance when compared with alternative approaches.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Jennifer full_name: Iglesias, Jennifer last_name: Iglesias - first_name: Milan full_name: Vojnović, Milan last_name: Vojnović citation: ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning. In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.' apa: 'Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.' chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015. ieee: 'D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015, vol. 2015–January, pp. 1900–1908.' ista: 'Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.' mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08. short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908. conference: name: 'NIPS: Neural Information Processing Systems' date_created: 2018-12-11T11:48:27Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T13:17:09Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning month: '01' oa_version: None page: 1900 - 1908 publication_status: published publisher: Neural Information Processing Systems publist_id: '6879' status: public title: Streaming min-max hypergraph partitioning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-January year: '2015' ... --- _id: '778' abstract: - lang: eng text: Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead. acknowledgement: P. Kuznetsov-The author is supported by the Agence Nationale de la Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations. alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Petr full_name: Kuznetsov, Petr last_name: Kuznetsov - first_name: Srivatsan full_name: Ravi, Srivatsan last_name: Ravi - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13' apa: 'Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13' chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13. ieee: 'D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent limitations of hybrid transactional memory,” presented at the DISC: Distributed Computing, 2015, vol. 9363, pp. 185–199.' ista: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363, 185–199.' mla: Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13. short: D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199. conference: name: 'DISC: Distributed Computing' date_created: 2018-12-11T11:48:27Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T13:17:35Z day: '01' doi: 10.1007/978-3-662-48653-5_13 extern: '1' external_id: arxiv: - '1405.5689' intvolume: ' 9363' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1405.5689 month: '01' oa: 1 oa_version: None page: 185 - 199 publication_status: published publisher: Springer publist_id: '6880' quality_controlled: '1' status: public title: Inherent limitations of hybrid transactional memory type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9363 year: '2015' ... --- _id: '7779' abstract: - lang: eng text: "The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties." article_processing_charge: No author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 citation: ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of  disordered solids. arXiv:151008820. 2015.' apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of  disordered solids. arXiv:1510.08820.' chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of  Disordered Solids.” ArXiv:1510.08820, 2015.' ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of  disordered solids,” arXiv:1510.08820. 2015.' ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear response of  disordered solids. arXiv:1510.08820, .' mla: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of  Disordered Solids.” ArXiv:1510.08820, 2015.' short: C.P. Goodrich, ArXiv:1510.08820 (2015). date_created: 2020-04-30T12:16:18Z date_published: 2015-10-29T00:00:00Z date_updated: 2021-01-12T08:15:28Z day: '29' extern: '1' external_id: arxiv: - '1510.08820' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.08820 month: '10' oa: 1 oa_version: Preprint page: '242' publication: arXiv:1510.08820 publication_status: published status: public title: 'Unearthing the anticrystal: Criticality in the linear response of disordered solids' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ...