Scalable Bayesian nonparametric regression via a Plackett-Luce model for conditional ranks

We present a novel Bayesian nonparametric regression model for covariates X and continuous, real response variable Y. The model is parametrized in terms of marginal distributions for Y and X and a regression function which tunes the stochastic ordering of the conditional distributions F(y|x). By adopting an approximate composite likelihood approach, we show that the resulting posterior inference can be decoupled for the separate components of the model. This procedure can scale to very large datasets and allows for the use of standard, existing, software from Bayesian nonparametric density estimation and Plackett-Luce ranking estimation to be applied. As an illustration, we show an application of our approach to a US Census dataset, with over 1,300,000 data points and more than 100 covariates

A Hierarchical Bayesian Framework for Constructing Sparsity-inducing Priors

Variable selection techniques have become increasingly popular amongst statisticians due to an increased number of regression and classification applications involving high-dimensional data where we expect some predictors to be unimportant. In this context, Bayesian variable selection techniques involving Markov chain Monte Carlo exploration of the posterior distribution over models can be prohibitively computationally expensive and so there has been attention paid to quasi-Bayesian approaches such as maximum a posteriori (MAP) estimation using priors that induce sparsity in such estimates. We focus on this latter approach, expanding on the hierarchies proposed to date to provide a Bayesian interpretation and generalization of state-of-the-art penalized optimization approaches and providing simultaneously a natural way to include prior information about parameters within this framework. We give examples of how to use this hierarchy to compute MAP estimates for linear and logistic regression as well as sparse precision-matrix estimates in Gaussian graphical models. In addition, an adaptive group lasso method is derived using the framework.Comment: Submitted for publication; corrected typo

The realities of storing carbon dioxide - A response to CO2 storage capacity issues raised by Ehlig-Economides & Economides

In a recent publication, Ehlig-Economides & Economides (2010) have sought to demonstrate that carbon dioxide capture and storage (CCS) is not technically or economically feasible, based on a supposed lack of underground storage capacity. We consider this to be a serious misrepresentation of the scientific, engineering and operational facts surrounding CCS. Ehlig-Economides & Economides raise a number of storage related issues: reservoir boundaries, capacity, pressure management, storage integrity, dissolution and storage in depleted reservoirs. We take each one in turn, highlighting specific errors in the paper but also drawing attention to more general background issues. Finally, we discuss in more detail some inconsistencies in the paper surrounding the reservoir engineering calculations

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 10(4) and 10(5) copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 10(5) copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.Peer reviewe

A framework for comprehensive analysis of a swing in sports using low-cost inertial sensors

We present a novel framework to monitor the three- dimensional trajectory (orientation and position) of a golf swing using miniaturized inertial sensors. Firstly we employed a highly accurate and computationally efficient revised gradient descent algorithm to obtain the orientation of a golf club. Secondly, we designed a series of digital filters to determine the backward and forward segments of the swing, enabling us to calculate drift-free linear velocity along with the relative 3D position of the golf club during the entire swing. Finally, the calculated motion trajectory was verified against a ground truth VICON system using Iterative Closest Point (ICP) in conjunction with Principal Component Analysis (PCA). The computationally efficient framework present here achieves a high level of accuracy (r = 0.9885, p < 0.0001) for such a low-cost system. This framework can be utilized for reliable movement technique evaluation and can provide near real-time feedback for athletes in various unconstrained environments. It is envisaged that the proposed framework is applicable to other racket based sports (e.g. tennis, cricket and hurling)

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality

Automatic activity classification and movement assessment during a sports training session using wearable inertial sensors

Motion analysis technologies have been widely used to monitor the potential for injury and enhance athlete performance. However, most of these technologies are expensive, can only be used in laboratory environments and examine only a few trials of each movement action. In this paper, we present a novel ambulatory motion analysis framework using wearable inertial sensors to accurately assess all of an athlete’s activities in an outdoor training environment. We firstly present a system that automatically classifies a large range of training activities using the Discrete Wavelet Transform (DWT) in conjunction with a Random forest classifier. The classifier is capable of successfully classifying various activities with up to 98% accuracy. Secondly, a computationally efficient gradient descent algorithm is used to estimate the relative orientations of the wearable inertial sensors mounted on the thigh and shank of a subject, from which the flexion-extension knee angle is calculated. Finally, a curve shift registration technique is applied to both generate normative data and determine if a subject’s movement technique differed to the normative data in order to identify potential injury related factors. It is envisaged that the proposed framework could be utilized for accurate and automatic sports activity classification and reliable movement technique evaluation in various unconstrained environments

Towards automatic activity classification and movement assessment during a sports training session

Abstract—Motion analysis technologies have been widely used to monitor the potential for injury and enhance athlete perfor- mance. However, most of these technologies are expensive, can only be used in laboratory environments and examine only a few trials of each movement action. In this paper, we present a novel ambulatory motion analysis framework using wearable inertial sensors to accurately assess all of an athlete’s activities in real training environment. We firstly present a system that automatically classifies a large range of training activities using the Discrete Wavelet Transform (DWT) in conjunction with a Random forest classifier. The classifier is capable of successfully classifying various activities with up to 98% accuracy. Secondly, a computationally efficient gradient descent algorithm is used to estimate the relative orientations of the wearable inertial sensors mounted on the shank, thigh and pelvis of a subject, from which the flexion-extension knee and hip angles are calculated. These angles, along with sacrum impact accelerations, are automatically extracted for each stride during jogging. Finally, normative data is generated and used to determine if a subject’s movement technique differed to the normative data in order to identify potential injury related factors. For the joint angle data this is achieved using a curve-shift registration technique. It is envisaged that the proposed framework could be utilized for accurate and automatic sports activity classification and reliable movement technique evaluation in various unconstrained environments for both injury management and performance enhancement

A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination. with increased transmissibility and an unfamiliar molecular mechanism of virulence.Peer reviewe