Accelerating epistasis analysis in human genetics with consumer graphics hardware

BACKGROUND: Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR) is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs) have more memory bandwidth and computational capability than Central Processing Units (CPUs) and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions. FINDINGS: We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C++ cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized C++ implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective performance while leaving the CPU available for other tasks. The GPU workstation containing three GPUs costs $2000 while obtaining similar performance on a Beowulf cluster requires 150 CPU cores which, including the added infrastructure and support cost of the cluster system, cost approximately$82,500. CONCLUSION: Graphics hardware based computing provides a cost effective means to perform genetic analysis of epistasis using MDR on large datasets without the infrastructure of a computing cluster

Absence of Street Lighting May Prevent Vehicle Crime, but Spatial and Temporal Displacement Remains a Concern

OBJECTIVES: This paper estimates the effect of changes in street lighting at night on levels of crime at street-level. Analyses investigate spatial and temporal displacement of crime into adjacent streets. METHODS: Offense data (burglaries, robberies, theft of and theft from vehicles, and violent crime) were obtained from Thames Valley Police, UK. Street lighting data (switching lights off at midnight, dimming, and white light) were obtained from local authorities. Monthly counts of crime at street-level were analyzed using a conditional fixed-effects Poisson regression model, adjusting for seasonal and temporal variation. Two sets of models analyzed: (1) changes in night-time crimes adjusting for changes in day-time crimes and (2) changes in crimes at all times of the day. RESULTS: Switching lights off at midnight was strongly associated with a reduction in night-time theft from vehicles relative to daytime (rate ratio RR 0.56; 0.41–0.78). Adjusted for changes in daytime, night-time theft from vehicles increased (RR 1.55; 1.14–2.11) in adjacent roads where street lighting remained unchanged. CONCLUSION: Theft from vehicle offenses reduced in streets where street lighting was switched off at midnight but may have been displaced to better-lit adjacent streets. Relative to daytime, night-time theft from vehicle offenses reduced in streets with dimming while theft from vehicles at all times of the day increased, thus suggesting temporal displacement. These findings suggest that the absence of street lighting may prevent theft from vehicles, but there is a danger of offenses being temporally or spatially displaced

Growth and dislocation studies of β-HMX

Background: The defect structure of organic materials is important as it plays a major role in their crystal growth properties. It also can play a subcritical role in “hot-spot” detonation processes of energetics and one such energetic is cyclotetramethylene-tetranitramine, in the commonly used beta form (β-HMX). Results: The as-grown crystals grown by evaporation from acetone show prismatic, tabular and columnar habits, all with {011}, {110}, (010) and (101) faces. Etching on (010) surfaces revealed three different types of etch pits, two of which could be identified with either pure screw or pure edge dislocations, the third is shown to be an artifact of the twinning process that this material undergoes. Examination of the {011} and {110} surfaces show only one type of etch pit on each surface; however their natural asymmetry precludes the easy identification of their Burgers vector or dislocation type. Etching of cleaved {011} surfaces demonstrates that the etch pits can be associated with line dislocations. All dislocations appear randomly on the crystal surfaces and do not form alignments characteristic of mechanical deformation by dislocation slip. Conclusions: Crystals of β-HMX grown from acetone show good morphological agreement with that predicted by modelling, with three distinct crystal habits observed depending upon the supersaturation of the growth solution. Prismatic habit was favoured at low supersaturation, while tabular and columnar crystals were predominant at higher super saturations. The twin plane in β-HMX was identified as a (101) reflection plane. The low plasticity of β-HMX is shown by the lack of etch pit alignments corresponding to mechanically induced dislocation arrays. On untwinned {010} faces, two types of dislocations exist, pure edge dislocations with b = [010] and pure screw dislocations with b = [010]. On twinned (010) faces, a third dislocation type exists and it is proposed that these pits are associated with pure screw dislocations with b = [010]

Comparing videofluoroscopy and endoscopy to assess swallowing in bottle-fed young infants in the neonatal intensive care unit

Contains fulltext : 235605.pdf (Publisher’s version ) (Closed access

The effect of seating preferences of the medical students on educational achievement

Background: The seat selection and classroom dynamics may have mutual influence on the student performance and participation in both assigned and random seating arrangement. Purpose: The aim of the study was to understand the influence of seat selection on educational achievement. Methods: The seating positions of the medical students were recorded on an architectural plan during each class session and the means and standard deviations of the students’ locations were calculated in X and Y orientations. The locations of the students in the class were analyzed based on three architectural classifications: interactional zone, distance from the board, and access to the aisles. Final exam scores were used to measure the students’ educational achievement. Results: Our results demonstrate that there is a statistically significant relationship between the student's locations in the class and their attendance and educational achievements. Conclusion: Two factors may effect on educational achievement: student seating in the high interactional zone and minimal changes in seating location. Seating in the high interaction zone was directly associated with higher performance and inversely correlated with the percentage of absences. This observation is consistent with the view that students in the front of the classroom are likely more motivated and interact with the lecturer more than their classmates

Integrating model-based design of experiments and computer-aided solvent design

Computer-aided molecular design (CAMD) methods can be used to generate promising solvents with enhanced reaction kinetics, given a reliable model of solvent effects on reaction rates. Herein, we use a surrogate model parameterised from computer experiments, more specifically, quantum-mechanical (QM) data on rate constants. The choice of solvents in which these computer experiments are performed is critical, considering the cost and difficulty of these QM calculations. We investigate the use of model-based design of experiments (MBDoE) to identify an information-rich solvent set and integrate this within a QM-CAMD framework. We find it beneficial to consider a wide range of solvents in designing the solvent set, using group contribution techniques to predict missing solvent properties. We demonstrate, via three case studies, that the use of MBDoE yields surrogate models with good statistics and leads to the identification of solvents with enhanced predicted performance with few iterations and at low computational cost