@article{7742, abstract = {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).}, author = {Robinson, Matthew Richard and Hemani, Gibran and Medina-Gomez, Carolina and Mezzavilla, Massimo and Esko, Tonu and Shakhbazov, Konstantin and Powell, Joseph E and Vinkhuyzen, Anna and Berndt, Sonja I and Gustafsson, Stefan and Justice, Anne E and Kahali, Bratati and Locke, Adam E and Pers, Tune H and Vedantam, Sailaja and Wood, Andrew R and van Rheenen, Wouter and Andreassen, Ole A and Gasparini, Paolo and Metspalu, Andres and Berg, Leonard H van den and Veldink, Jan H and Rivadeneira, Fernando and Werge, Thomas M and Abecasis, Goncalo R and Boomsma, Dorret I and Chasman, Daniel I and de Geus, Eco J C and Frayling, Timothy M and Hirschhorn, Joel N and Hottenga, Jouke Jan and Ingelsson, Erik and Loos, Ruth J F and Magnusson, Patrik K E and Martin, Nicholas G and Montgomery, Grant W and North, Kari E and Pedersen, Nancy L and Spector, Timothy D and Speliotes, Elizabeth K and Goddard, Michael E and Yang, Jian and Visscher, Peter M}, issn = {1061-4036}, journal = {Nature Genetics}, number = {11}, pages = {1357--1362}, publisher = {Springer Nature}, title = {{Population genetic differentiation of height and body mass index across Europe}}, doi = {10.1038/ng.3401}, volume = {47}, year = {2015}, } @article{7741, abstract = {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.}, author = {Adams, Mark James and Robinson, Matthew Richard and Mannarelli, Maria-Elena and Hatchwell, Ben J.}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, number = {1810}, publisher = {The Royal Society}, title = {{Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird}}, doi = {10.1098/rspb.2015.0689}, volume = {282}, year = {2015}, } @article{7739, abstract = {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.}, author = {Santure, Anna W. and Poissant, Jocelyn and De Cauwer, Isabelle and van Oers, Kees and Robinson, Matthew Richard and Quinn, John L. and Groenen, Martien A. M. and Visser, Marcel E. and Sheldon, Ben C. and Slate, Jon}, issn = {0962-1083}, journal = {Molecular Ecology}, pages = {6148--6162}, publisher = {Wiley}, title = {{Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations}}, doi = {10.1111/mec.13452}, volume = {24}, year = {2015}, } @inproceedings{776, abstract = {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.}, author = {Alistarh, Dan-Adrian and Kopinsky, Justin and Li, Jerry and Shavit, Nir}, pages = {11 -- 20}, publisher = {ACM}, title = {{The SprayList: A scalable relaxed priority queue}}, doi = {10.1145/2688500.2688523}, volume = {2015-January}, year = {2015}, } @article{7765, abstract = {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.}, author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {22}, publisher = {American Physical Society}, title = {{The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior}}, doi = {10.1103/physrevlett.114.225501}, volume = {114}, year = {2015}, } @article{7767, abstract = {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.}, author = {van Drongelen, Ruben and Pal, Anshuman and Goodrich, Carl Peter and Idema, Timon}, issn = {1539-3755}, journal = {Physical Review E}, number = {3}, publisher = {American Physical Society}, title = {{Collective dynamics of soft active particles}}, doi = {10.1103/physreve.91.032706}, volume = {91}, year = {2015}, } @article{7766, abstract = {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.}, author = {Sussman, Daniel M. and Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {1744-683X}, journal = {Soft Matter}, number = {14}, pages = {2745--2751}, publisher = {Royal Society of Chemistry}, title = {{Disordered surface vibrations in jammed sphere packings}}, doi = {10.1039/c4sm02905d}, volume = {11}, year = {2015}, } @inproceedings{777, abstract = {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.}, author = {Alistarh, Dan-Adrian and Iglesias, Jennifer and Vojnović, Milan}, pages = {1900 -- 1908}, publisher = {Neural Information Processing Systems}, title = {{Streaming min-max hypergraph partitioning}}, volume = {2015-January}, year = {2015}, } @inproceedings{778, abstract = {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.}, author = {Alistarh, Dan-Adrian and Kopinsky, Justin and Kuznetsov, Petr and Ravi, Srivatsan and Shavit, Nir}, pages = {185 -- 199}, publisher = {Springer}, title = {{Inherent limitations of hybrid transactional memory}}, doi = {10.1007/978-3-662-48653-5_13}, volume = {9363}, year = {2015}, } @unpublished{7779, abstract = {The fact that a disordered material is not constrained in its properties in the same way as a crystal presents significant and yet largely untapped potential for novel material design. However, unlike their crystalline counterparts, disordered solids are not well understood. One of the primary obstacles is the lack of a theoretical framework for thinking about disorder and its relation to mechanical properties. To this end, we study an idealized system of frictionless athermal soft spheres that, when compressed, undergoes a jamming phase transition with diverging length scales and clean power-law signatures. This critical point is the cornerstone of a much larger "jamming scenario" that has the potential to provide the essential theoretical foundation necessary for a unified understanding of the mechanics of disordered solids. We begin by showing that jammed sphere packings have a valid linear regime despite the presence of "contact nonlinearities." We then investigate the critical nature of the transition, focusing on diverging length scales and finite-size effects. Next, we argue that jamming plays the same role for disordered solids as the perfect crystal plays for crystalline solids. Not only can it be considered an idealized starting point for understanding disordered materials, but it can even influence systems that have a relatively high amount of crystalline order. The behavior of solids can thus be thought of as existing on a spectrum, with the perfect crystal and the jamming transition at opposing ends. Finally, we introduce a new principle wherein the contribution of an individual bond to one global property is independent of its contribution to another. This principle allows the different global responses of a disordered system to be manipulated independently and provides a great deal of flexibility in designing materials with unique, textured and tunable properties.}, author = {Goodrich, Carl Peter}, booktitle = {arXiv:1510.08820}, pages = {242}, title = {{Unearthing the anticrystal: Criticality in the linear response of disordered solids}}, year = {2015}, }