SUMMARYThe material point method (MPM) has demonstrated itself as a computationally effective particle method for solving solid mechanics problems involving large deformations and/or fragmentation of structures, which are sometimes problematic for finite element methods (FEMs). However, similar to most methods that employ mixed Lagrangian (particle) and Eulerian strategies, analysis of the method is not straightforward. The lack of an analysis framework for MPM, as is found in FEMs, makes it challenging to explain anomalies found in its employment and makes it difficult to propose methodology improvements with predictable outcomes.In this paper we present an analysis of the quadrature errors found in the computation of (material) internal force in MPM and use this analysis to direct proposed improvements. In particular, we demonstrate that lack of regularity in the grid functions used for representing the solution to the equations of motion can hamper spatial convergence of the method. We propose the use of a quadratic B-spline basis for representing solutions on the grid, and we demonstrate computationally and explain theoretically why such a small change can have a significant impact on the reduction in the internal force quadrature error (and corresponding 'grid crossing error') often experienced when using MPM.

Life-history modes can profoundly impact the biology of a species, and a classic example is the dichotomy between metamorphic(biphasic) and paedomorphic (permanently aquatic) life-history strategies in salamanders. However, despite centuries of research on this system, several basic questions about the evolution of paedomorphosis in salamanders have not been addressed. Here, we use a nearly comprehensive, time-calibrated phylogeny of spelerpine plethodontids to reconstruct the evolution of paedomorphosis and to test if paedomorphosis is (1) reversible; (2) associated with living in caves; (3) associated with relatively dry climatic conditions on the surface; and (4) correlated with limited range size and geographic dispersal. We find that paedomorphosis arose multiple times in spelerpines. We also find evidence for re-evolution of metamorphosis after several million years of paedomorphosis in a lineage of Eurycea from the Edwards Plateau region of Texas. We also show for the first time using phylogenetic comparative methods that paedomorphosis is highly correlated with cave-dwelling, arid surface environments, and small geographic range sizes, providing insights into both the causes and consequences of this major life history transition. K E Y W O R D S :Amphibians, biogeography, climate, development, life history, phylogeny.

BACKGROUND:We previously reported improved neurodevelopmental outcomes at 2 years among infants treated with the erythropoiesis-stimulating agents (ESAs) darbepoetin alfa (darbepoetin) or erythropoietin. Here we characterize 4-year outcomes.

While it is well known that the genome can affect social behavior, recent models posit that social lifestyles can, in turn, influence genome evolution. Here, we perform the most phylogenetically comprehensive comparative analysis of 16 bee genomes to date: incorporating two published and four new carpenter bee genomes (Apidae: Xylocopinae) for a first-ever genomic comparison with a monophyletic clade containing solitary through advanced eusocial taxa. We find that eusocial lineages have undergone more gene family expansions, feature more signatures of positive selection, and have higher counts of taxonomically restricted genes than solitary and weakly social lineages. Transcriptomic data reveal that caste-affiliated genes are deeply-conserved; gene regulatory and functional elements are more closely tied to social phenotype than phylogenetic lineage; and regulatory complexity increases steadily with social complexity. Overall, our study provides robust empirical evidence that social evolution can act as a major and surprisingly consistent driver of macroevolutionary genomic change.

Despite a strong history of theoretical work on the mechanisms of social evolution, relatively little is known of the molecular genetic changes that accompany transitions from solitary to eusocial forms. Here, we provide the first genome of an incipiently social bee that shows both solitary and social colony organization in sympatry, the Australian carpenter bee Ceratina australensis. Through comparative analysis, we provide support for the role of conserved genes and cis-regulation of gene expression in the phenotypic plasticity observed in nest-sharing, a rudimentary form of sociality. Additionally, we find that these conserved genes are associated with caste differences in advanced eusocial species, suggesting these types of mechanisms could pave the molecular pathway from solitary to eusocial living. Genes associated with social nesting in this species show signatures of being deeply conserved, in contrast to previous studies in other bees showing novel and faster-evolving genes are associated with derived sociality. Our data provide support for the idea that the earliest social transitions are driven by changes in gene regulation of deeply conserved genes.

BackgroundDisentangling evolutionary shifts in developmental timing (heterochony) is dependent upon accurate estimates of ancestral patterns. However, many classic assessments of heterochronic patterns predate robust phylogenetic hypotheses and methods for trait reconstruction, and therefore may have been polarized with untested ‘primitive’ conditions. Here we revisit the heterochronic modes of development that underlie the evolution of metamorphosis, maturation, and paedomorphosis in plethodontid salamanders. We focus on the tribe Spelerpini, which is a diverse clade that exhibits tremendous variation in timing of metamorphosis and maturation, as well as multiple independent instances of larval form paedomorphosis. Based on morphology and biogeography, early investigators concluded that the most recent common ancestors of plethodontids, and also spelerpines, were large salamanders, with very long larval periods and late maturation times. This prevailing assumption influenced subsequent heterochronic assessments, which concluded that most modern spelerpines (with shorter larval periods) were derived through multiple independent accelerations in larval development. It was also concluded that most occurrences of larval form paedomorphosis in this clade resulted from progenesis (acceleration of gonadal development relative to metamorphosis).ResultsBy reconstructing the time to metamorphosis on a molecular-based phylogeny of plethodontids, we find that ancestral spelerpines likely had relatively shorter larval periods than previously proposed. Taken together with the credibility interval from our ancestral state estimation we show that very long larval periods are likely derived decelerations, only a few lineages have undergone appreciable accelerations in metamorphic timing, and the remaining taxa have lower probabilities of being different than the ancestral condition (possibly due to stasis). Reconstructing maturation age across nodes concomitant with the evolution of larval form paedomorphosis in one large radiation does not show clear evidence of progenesis, but more likely indicates a case of neoteny (delayed metamorphosis).ConclusionsThis study demonstrates cases in plethodontid salamanders where phylogenetic-based character reconstructions reject previously hypothesized ancestral life history conditions. As a result, several prior hypotheses of heterochronic evolution in this family are reversed.

Abstract-Streamline integration of fields produced by computational fluid mechanics simulations is a commonly used tool for the investigation and analysis of fluid flow phenomena. Integration is often accomplished through the application of ordinary differential equation (ODE) integrators-integrators whose error characteristics are predicated on the smoothness of the field through which the streamline is being integrated, which is not available at the interelement level of finite volume and finite element data. Adaptive error control techniques are often used to ameliorate the challenge posed by interelement discontinuities. As the root of the difficulties is the discontinuous nature of the data, we present a complementary approach of applying smoothness-increasing accuracy-conserving filters to the data prior to streamline integration. We investigate whether such an approach applied to uniform quadrilateral discontinuous Galerkin (high-order finite volume) data can be used to augment current adaptive error control approaches. We discuss and demonstrate through a numerical example the computational trade-offs exhibited when one applies such a strategy.

As integrated circuits (ICs) continue to have an overwhelming presence in our digital information-dominated world, having trust in their manufacture and distribution mechanisms is crucial. However, with ever-shrinking transistor technologies, the cost of new fabrication facilities is becoming prohibitive, pushing industry to make greater use of potentially less reliable foreign sources for their IC supply. The 2008 Computer Security Awareness Week (CSAW) Embedded Systems Challenge at the Polytechnic Institute of NYU highlighted some of the vulnerabilities of the IC supply chain in the form of a hardware hacking challenge. This paper explores the design and implementation of our winning entry.