BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

<p>Abstract</p> <p>Background</p> <p>In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.</p> <p>Results</p> <p>Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (<it>P </it>< 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (<it>P </it>≤ 0.005), and nearly so for the superfamily Drepanoidea as currently defined (<it>P </it>< 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.</p> <p>Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data.</p> <p>Conclusion</p> <p>Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.</p

Superior performance of cone beam tomography in detecting a calcaneus fracture

Cone beam computed tomography is a state-of-the-art imaging tool, initially developed for dental and maxillofacial application. With its high resolution and low radiation dose, cone beam tomography has been expanding its application fields, for example, to diagnosis of traumata and fractures in the head and neck area. In this study, we demonstrate superior and satisfactory performance of cone beam tomography for the imaging of a calcaneus fracture in comparison to conventional and computed tomography

Small renal masses in the elderly: Contemporary treatment approaches and comparative oncological outcomes of nonsurgical and surgical strategies

Over the last decades, there has been a significant stage migration in renal cell carcinoma and especially older patients are getting diagnosed more frequently with low stage disease, such as small renal masses ≤4 cm of size. Considering the particular risk profile of an older population, often presenting with a nonnegligible comorbidity profile and progressive renal dysfunction, treatment approaches beyond aggressive radical surgical procedures have come to the fore. We sought to give a contemporary overview of the available different treatment strategies for incidental small renal masses in an elderly population with the focus on comparative oncological outcomes of nonsurgical and surgical modalities

Drug addiction. Is it a disease or is it based on choice? A review of Gene Heyman's Addiction: A disorder of choice.

In Addiction: A disorder of choice, Gene Heyman surveys a broad array of evidence—historical, anthropological, survey, clinical, and laboratory-based to build an argument about the role of basic choice processes in the phenomena that comprise drug addiction. He makes a compelling, multifaceted argument that conceptualizing drug addiction as a chronic disease (like schizophrenia or diabetes) is both misleading and erroneous. In developing his argument, he points out that the best survey data available indicate that most drug addicts quit their addiction, a fact inconsistent with a chronic-disease model. He illustrates how basic, normal choice processes can lead to addiction, arguing that people do not choose to be addicts, but that normal choice dynamics can lead them to that condition. He points to a variety of factors that keep most from becoming addicted, with a focus on the role of choice governed by choice-by-choice contingencies versus choice governed by the outcome of sequences of choices, a difference in an under-described activity called framing. His view is consistent with the most effective treatments currently available, and provides a basis for continued basic research on choice as well as research on treatment and prevention

Prediction of Meniscal and Ligamentous Injuries in Lateral Tibial Plateau Fractures Based on Measurements of Lateral Plateau Widening on Multidetector Computed Tomography Scans

Background. The influence of increasing lateral plateau widening on the frequency of meniscal and ligamentous lesions in lateral tibial plateau fractures has been examined in very few studies using plain radiographs. Because the amount of this parameter cannot be measured accurately on plain radiographs, the purpose of this survey was to look for a possible correlation between the extent of lateral plateau widening, as measured on multidetector CT (MDCT) scans, and different soft-tissue injuries determined from magnetic resonance imaging (MRI). Materials and Methods. 55 patients with a lateral tibial plateau fracture were included in this retrospective case series. Patient age averaged 52.6 years (SD = 18.0). The degree of lateral plateau widening was measured on CT images. MRIs were screened for meniscal and ligamentous injuries. Results. We found a significant effect of increasing lateral plateau widening on the incidence of lateral meniscus lesions (P = 0.021), lateral collateral ligament tears (P = 0.047), and the overall quantity of meniscal and ligamentous lesions (P = 0.001). Discussion. MRIs are not widely used as a diagnostic tool in lateral plateau fractures of the tibia. Reasons might be the costs and the fact that it is a time-consuming examination. The results of this study may help to estimate the probability of specific soft-tissue lesions in lateral tibial plateau fractures based on measurements of lateral plateau widening on MDCT scans, and they may guide the decision for additional MRI and/or arthroscopically assisted repair

Inter- and Intraobserver reproducibility of T2 relaxation times of the discus interpubicus: A feasibility study at 3 Tesla.

OBJECTIVE:To quantify standard values of the discus interpubicus in healthy subjects and to determine reliability and repeatability using T2 relaxation time measurements at 3T. METHODS:20 asymptomatic participants (10 male, 10 female; mean age: 27.3 years ±4.1, BMI: 22.2 ±1.8) underwent a 3T Magnetic Resonance Imaging (MRI) of the pelvic region in a supine position. We included sagittal and para-axial T2w sequences centred over the pubic symphysis in order to identify the complete discus interpubicus. For quantitative analysis, a multi-echo Turbo Spin Echo (TSE) sequence (including 12 echo times between 6.4 and 76.8 ms) was acquired and analysed by using an in-house developed quantification plugin tool (qMapIt) extending ImageJ. Two readers in consensus defined three central slices of the pubic symphysis with the greatest length. For each slice, both readers separately placed three regions-of-interest (ROI) covering the whole discus interpubicus. Both readers repeated the ROI placements in identical fashion after a four-week interval on the original MRI images. Statistical analysis included intraclass correlation coefficient (ICC), nonparametric Wilcoxon test, Fisher exact test and mean relaxation time in ms and 95% confidence intervals. RESULTS:T2 relaxation time analysis was performed for all 20 participants. In total, a mean relaxation time of all analysed segments for both observers was 48.6 (±6.3 ms), with a mean relaxation time for observer 1 of 48.7 (±6.0 ms) and for observer 2 of 48.5 ms (±6.6ms). The calculated ICC comparing inter- and intrarater reproducibility was excellent in all segments (≥0.75). CONCLUSION:T2 mapping of the discus interpubicus demonstrates good inter- and intrarater repeatability as well as reliability. Mean relaxation times were calculated with 48.6ms in healthy volunteers