Fast, Scalable Approximations to Posterior Distributions in Extended Latent Gaussian Models

We define a novel class of additive models, called Extended Latent Gaussian Models, that allow for a wide range of response distributions and flexible relationships between the additive predictor and mean response. The new class covers a broad range of interesting models including multi-resolution spatial processes, partial likelihood-based survival models, and multivariate measurement error models. Because computation of the exact posterior distribution is infeasible, we develop a fast, scalable approximate Bayesian inference methodology for this class based on nested Gaussian, Laplace, and adaptive quadrature approximations. We prove that the error in these approximate posteriors is op(1) under standard conditions, and provide numerical evidence suggesting that our method runs faster and scales to larger datasets than methods based on Integrated Nested Laplace Approximations and Markov Chain Monte Carlo, with comparable accuracy. We apply the new method to the mapping of malaria incidence rates in continuous space using aggregated data, mapping leukaemia survival hazards using a Cox Proportional-Hazards model with a continuously-varying spatial process, and estimating the mass of the Milky Way Galaxy using noisy multivariate measurements of the positions and velocities of star clusters in its orbit

Resting behaviour of Anopheles gambiae s.l. and its implication on malaria transmission in Uyui District, western Tanzania

An entomological survey to determine resting behaviour and species composition of malaria vectors was carried out in Uyui District in western Tanzania in May 2009. Mosquitoes were collected using indoor resting catch, window exit trap and outdoor “bed-net” techniques. They mosquitoes were identified using morphological key and polymerase chain reaction (PCR). A total of 672 Anopheles gambiae sensu lato were collected. Of these, 661 (98.4%) were collected outdoor whereas few (1.6%) were collected indoor. The exit trap catch: mechanical aspirator catch ratio was 1:1.75. The overall indoor resting density of An. gambiae s.l. as determined by mechanical aspirator and exit trap was 0.7 and 0.5 mosquitoes per room, respectively. The overall density of the host-seeking as determined by bed net trap outdoor was 44.1 mosquitoes per person. A sample of 44 specimens taken randomly from morphologically identified An.gambiae s.l. population was further analyzed to species level using PCR techniques. Of these 44 specimens 26 (59%) and 18 (41%) were Anopheles arabiensis and Anopheles gambiae sensu stricto respectively. This study contributes to the understanding of the distribution of malaria vectors with respect to species composition and their resting behaviour that could contribute to vector control operations in western Tanzania. A longitudinal study considering dry and wet seasons is recommended to provide more information on the seasonal distribution, abundance and biting behaviour of malaria vectors in the study area

Association between rheumatoid arthritis disease activity, progression of functional limitation and long-term risk of orthopaedic surgery : Combined analysis of two prospective cohorts supports EULAR treat to target DAS thresholds

Objectives: To examine the association between disease activity in early rheumatoid arthritis (RA), functional limitation and long-term orthopaedic episodes. Methods: Health Assessment Questionnaire (HAQ) disability scores were collected from two longitudinal early RA inception cohorts in routine care; Early Rheumatoid Arthritis Study and Early Rheumatoid Arthritis Network from 1986 to 2012. The incidence of major and intermediate orthopaedic surgical episodes over 25 years was collected from national data sets. Disease activity was categorised by mean disease activity score (DAS28) annually between years 1 and 5; remission (RDAS≤2.6), low (LDAS>2.6-3.2), low-moderate (LMDAS≥3.2-4.19), high-moderate (HMDAS 4.2-5.1) and high (HDAS>5.1). Results: Data from 2045 patients were analysed. Patients in RDAS showed no HAQ progression over 5 years, whereas there was a significant relationship between rising DAS28 category and HAQ at 1 year, and the rate of HAQ progression between years 1 and 5. During 27 986 person-years follow-up, 392 intermediate and 591 major surgeries were observed. Compared with the RDAS category, there was a significantly increased cumulative incidence of intermediate surgery in HDAS (OR 2.59 CI 1.49 to 4.52) and HMDAS (OR 1.8 CI 1.05 to 3.11) categories, and for major surgery in HDAS (OR 2.48 CI 1.5 to 4.11), HMDAS (OR 2.16 CI 1.32 to 3.52) and LMDAS (OR 2.07 CI 1.28 to 3.33) categories. There was no significant difference in HAQ progression or orthopaedic episodes between RDAS and LDAS categories. Conclusions: There is an association between disease activity and both poor function and long-term orthopaedic episodes. This illustrates the far from benign consequences of persistent moderate disease activity, and supports European League Against Rheumatism treat to target recommendations to secure low disease activity or remission in all patients.Peer reviewedFinal Published versio

In-Space Assembly Capability Assessment for Potential Human Exploration and Science Applications

Human missions to Mars present several major challenges that must be overcome, including delivering multiple large mass and volume elements, keeping the crew safe and productive, meeting cost constraints, and ensuring a sustainable campaign. Traditional methods for executing human Mars missions minimize or eliminate in-space assembly, which provides a narrow range of options for addressing these challenges and limits the types of missions that can be performed. This paper discusses recent work to evaluate how the inclusion of in-space assembly in space mission architectural concepts could provide novel solutions to address these challenges by increasing operational flexibility, robustness, risk reduction, crew health and safety, and sustainability. A hierarchical framework is presented to characterize assembly strategies, assembly tasks, and the required capabilities to assemble mission systems in space. The framework is used to identify general mission system design considerations and assembly system characteristics by assembly strategy. These general approaches are then applied to identify potential in-space assembly applications to address each challenge. Through this process, several focus areas were identified where applications of in-space assembly could affect multiple challenges. Each focus area was developed to identify functions, potential assembly solutions and operations, key architectural trades, and potential considerations and implications of implementation. This paper helps to identify key areas to investigate were potentially significant gains in addressing the challenges with human missions to Mars may be realized, and creates a foundation on which to further develop and analyze in-space assembly concepts and assembly-based architectures

The Profumo affair in popular culture: The Keeler Affair (1963) and ‘the commercial exploitation of a public scandal’

This article demonstrates that the Profumo affair, which obsessed Britain for large parts of 1963, was not simply a political scandal, but was also an important cultural event. Focussing on the production of The Keeler Affair, a feature film that figured prominently in contemporary coverage of the scandal but which has been largely overlooked since, the article shows that this film emerged from a situation in which cultural entrepreneurs, many of them associated with the satire boom, sought to exploit the scandal for financial gain. Many Profumo-related cultural products found an audience, and thus formed an integral part of, and helped to shape public attitudes towards, the Profumo affair. However, these products did not go uncontested, and resistance to them, and especially to the idea that Keeler might benefit materially from her role in the scandal, speak to concerns about cultural mediations of sex, politics and humour in early-1960s Britain

Specialty Care Use in US Patients with Chronic Diseases

Despite efforts to eliminate health disparities, racial, ethnic, and geographic groups continue lag behind their counterparts in health outcomes in the United States. The purpose of this study is to determine variation in specialty care utilization by chronic disease status. Data were extracted from the Commonwealth Fund 2006 Health Care Quality Survey (n = 2475). A stratified minority sample design was employed to ensure a representative sample. Logistic regression was used in analyses to predict specialty care utilization in the sample. Poor perceived health, minority status, and lack of insurance was associated with reduced specialty care use and chronic disease diagnosis

On the analysis of sedimentation velocity in the study of protein complexes

Sedimentation velocity analytical ultracentrifugation has experienced a significant transformation, precipitated by the possibility of efficiently fitting Lamm equation solutions to the experimental data. The precision of this approach depends on the ability to account for the imperfections of the experiment, both regarding the sample and the instrument. In the present work, we explore in more detail the relationship between the sedimentation process, its detection, and the model used in the mathematical data analysis. We focus on configurations that produce steep and fast-moving sedimentation boundaries, such as frequently encountered when studying large multi-protein complexes. First, as a computational tool facilitating the analysis of heterogeneous samples, we introduce the strategy of partial boundary modeling. It can simplify the modeling by restricting the direct boundary analysis to species with sedimentation coefficients in a predefined range. Next, we examine factors related to the experimental detection, including the magnitude of optical aberrations generated by out-of-focus solution columns at high protein concentrations, the relationship between the experimentally recorded signature of the meniscus and the meniscus parameter in the data analysis, and the consequences of the limited radial and temporal resolution of the absorbance optical scanning system. Surprisingly, we find that large errors can be caused by the finite scanning speed of the commercial absorbance optics, exceeding the statistical errors in the measured sedimentation coefficients by more than an order of magnitude. We describe how these effects can be computationally accounted for in SEDFIT and SEDPHAT

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

Abstract—As parallel algorithms and architectures drive the longest molecular dynamics (MD) simulations towards the millisecond scale, traditional sequential post-simulation data analysis methods are becoming increasingly untenable. Inspired by the programming interface of Google’s MapReduce, we have built a new parallel analysis framework called HiMach, which allows users to write trajectory analysis programs sequentially, and carries out the parallel execution of the programs automatically. We introduce (1) a new MD trajectory data analysis model that is amenable to parallel processing, (2) a new interface for defining trajectories to be analyzed, (3) a novel method to make use of an existing sequential analysis tool called VMD, and (4) an extension to the original MapReduce model to support multiple rounds of analysis. Performance evaluations on up to 512 cores demonstrate the efficiency and scalability of the HiMach framework on a Linux cluster. I

Area deprivation and its association with health in a cross-sectional study: are the results biased by recent migration?

<p>Abstract</p> <p>Background</p> <p>The association between area deprivation and health has mostly been examined in cross-sectional studies or prospective studies with short follow-up. These studies have rarely taken migration into account. This is a possible source of misclassification of exposure, i.e. an unknown number of study participants are attributed an exposure of area deprivation that they may have experienced too short for it to have any influence. The aim of this article was to examine to what extent associations between area deprivation and health outcomes were biased by recent migration.</p> <p>Methods</p> <p>Based on data from the Oslo Health Study, a cross-sectional study conducted in 2000 in Oslo, Norway, we used six health outcomes (self rated health, mental health, coronary heart disease, chronic obstructive pulmonary disease, smoking and exercise) and considered migration nine years prior to the study conduct. Migration into Oslo, between the areas of Oslo, and the changes in area deprivation during the period were taken into account. Associations were investigated by multilevel logistic regression analyses.</p> <p>Results</p> <p>After adjustment for individual socio-demographic variables we found significant associations between area deprivation and all health outcomes. Accounting for migration into Oslo and between areas of Oslo did not change these associations much. However, the people who migrated into Oslo were younger and had lower prevalences of unfavourable health outcomes than those who were already living in Oslo. But since they were evenly distributed across the area deprivation quintiles, they had little influence on the associations between area deprivation and health. Evidence of selective migration within Oslo was weak, as both moving up and down in the deprivation hierarchy was associated with significantly worse health than not moving.</p> <p>Conclusion</p> <p>We have documented significant associations between area deprivation and health outcomes in Oslo after adjustment for socio-demographic variables in a cross-sectional study. These associations were weakly biased by recent migration. From our results it still appears that migration prior to study conduct may be relevant to investigate even within a relatively short period of time, whereas changes in area deprivation during such a period is of limited interest.</p