Unbiased Markov chain Monte Carlo for intractable target distributions

Performing numerical integration when the integrand itself cannot be evaluated point-wise is a challenging task that arises in statistical analysis, notably in Bayesian inference for models with intractable likelihood functions. Markov chain Monte Carlo (MCMC) algorithms have been proposed for this setting, such as the pseudo-marginal method for latent variable models and the exchange algorithm for a class of undirected graphical models. As with any MCMC algorithm, the resulting estimators are justified asymptotically in the limit of the number of iterations, but exhibit a bias for any fixed number of iterations due to the Markov chains starting outside of stationarity. This "burn-in" bias is known to complicate the use of parallel processors for MCMC computations. We show how to use coupling techniques to generate unbiased estimators in finite time, building on recent advances for generic MCMC algorithms. We establish the theoretical validity of some of these procedures by extending existing results to cover the case of polynomially ergodic Markov chains. The efficiency of the proposed estimators is compared with that of standard MCMC estimators, with theoretical arguments and numerical experiments including state space models and Ising models.Comment: 40 page

Knowledge, attitudes, beliefs and behaviour intentions for three bowel management practices in intensive care: effects of a targeted protocol implementation for nursing and medical staff.

Background Bowel management protocols have the potential to minimize complications for critically ill patients. Targeted implementation can increase the uptake of protocols by clinicians into practice. The theory of planned behaviour offers a framework in which to investigate clinicians’ intention to perform the behaviour of interest. This study aimed to evaluate the effect of implementing a bowel management protocol on intensive care nursing and medical staffs’ knowledge, attitude, subjective norms, perceived behavioural control, behaviour intentions, role perceptions and past behaviours in relation to three bowel management practices. Methods A descriptive before and after survey using a self-administered questionnaire sent to nursing and medical staff working within three intensive care units before and after implementation of our bowel management protocol (pre: May – June 2008; post: Feb – May 2009). Results Participants had significantly higher knowledge scores post-implementation of our protocol (pre mean score 17.6; post mean score 19.3; p = 0.004). Post-implementation there was a significant increase in: self-reported past behaviour (pre mean score 5.38; post mean score 7.11; p = 0.002) and subjective norms scores (pre mean score 3.62; post mean score 4.18; p = 0.016) for bowel assessment; and behaviour intention (pre mean score 5.22; post mean score 5.65; p = 0.048) for administration of enema. Conclusion This evaluation, informed by the theory of planned behaviour, has provided useful insights into factors that influence clinician intentions to perform evidence-based bowel management practices in intensive care. Addressing factors such as knowledge, attitudes and beliefs can assist in targeting implementation strategies to positively affect clinician behaviour change. Despite an increase in clinicians’ knowledge scores, our implementation strategy did not, however, significantly change clinician behaviour intentions for all three bowel management practices. Further research is required to explore the influence of opinion leaders and organizational culture on clinicians’ behaviour intentions related to bowel management for intensive care patients

The Earth System Grid Federation: Delivering globally accessible petascale data for CMIP5

The fifth Coupled Model Intercomparison Project (CMIP5) will involve the global production and analysis of petabytes of data. The Program for Climate Model Diagnosis and Intercomparison (PCMDI), with responsibility for archival for CMIP5, has established the global “Earth System Grid Federation” (ESGF) of data producers and data archives to support CMIP5. ESGF will provide a set of globally synchronised views of globally distributed data – including some large cache replicants which will be persisted for (at least) decades. Here we describe the archive requirements and key aspects of the resulting architecture. ESGF will stress international networks, as well as the data archives themselves – but significantly less than would have been the case of a centralised archive. Developing and deploying the ESGF has exploited good will and best efforts, but future developments are likely to require more formalised architecture and management

G-LiHT: Goddard's LiDAR, Hyperspectral and Thermal Airborne Imager

Scientists at NASA's Goddard Space Flight Center have developed an ultra-portable, low-cost, multi-sensor remote sensing system for studying the form and function of terrestrial ecosystems. G-LiHT integrates two LIDARs, a 905 nanometer single beam profiler and 1550 nm scanner, with a narrowband (1.5 nanometers) VNIR imaging spectrometer and a broadband (8-14 micrometers) thermal imager. The small footprint (approximately 12 centimeters) LIDAR data and approximately 1 meter ground resolution imagery are advantageous for high resolution applications such as the delineation of canopy crowns, characterization of canopy gaps, and the identification of sparse, low-stature vegetation, which is difficult to detect from space-based instruments and large-footprint LiDAR. The hyperspectral and thermal imagery can be used to characterize species composition, variations in biophysical variables (e.g., photosynthetic pigments), surface temperature, and responses to environmental stressors (e.g., heat, moisture loss). Additionally, the combination of LIDAR optical, and thermal data from G-LiHT is being used to assess forest health by sensing differences in foliage density, photosynthetic pigments, and transpiration. Low operating costs (approximately $1 ha) have allowed us to evaluate seasonal differences in LiDAR, passive optical and thermal data, which provides insight into year-round observations from space. Canopy characteristics and tree allometry (e.g., crown height:width, canopy:ground reflectance) derived from G-LiHT data are being used to generate realistic scenes for radiative transfer models, which in turn are being used to improve instrument design and ensure continuity between LiDAR instruments. G-LiHT has been installed and tested in aircraft with fuselage viewports and in a custom wing-mounted pod that allows G-LiHT to be flown on any Cessna 206, a common aircraft in use throughout the world. G-LiHT is currently being used for forest biomass and growth estimation in the CONUS and Mexico in support of NASA's Carbon Monitoring System (CMS) and AMIGA-Carb (AMerican Icesat Glas Assessment of Carbon). For NASA's CMS, wall-to-wall G-LiHT data have been acquired over intensive study sites with historic LiDAR datasets, dense inventory data, stem maps and flux tower observations. For AMIGA-Carb, G-LiHT transects have been acquired over ICESat tracks and USDA-FS inventory plots throughout the CONUS, and similar data will be acquired in Mexico during 2013. This talk will highlight recent science results from continental-scale transects landscape-scale deployments of G-LiHT, as well as seasonal forest dynamics from repeat pass G-LiHT acquisitions

Analysis of 983 civilian blast and ballistic casualties and the generation of a template of injury burden : an observational study

Funding: The work was supported in part by a grant to LM from School of Medicine, University of St Andrews.Background Terrorism and armed conflict cause blast and ballistic casualties that are unusual in civilian practice. The immediate surgical response to mass casualty events, with civilians injured by these mechanisms, has not been systematically characterised. Standardising an approach to reacting to these events is challenging but is essential to optimise preparation for them. We aimed to quantify and assesses the surgical response to blast and ballistic injuries managed in a world-class trauma unit paradigm. Methods This was an observational study conducted at the UK-led military Medical Treatment Facility, Camp Bastion, Afghanistan from original theatre log-book entries between Nov 5, 2009, and Sept 21, 2014; a total of 10,891 consecutive surgical cases prospectively gathered by surgical teams were catalogued. Patients with combatant status/wearing body-armour to various degrees including interpreters were excluded from the study. Civilian casualties that underwent primary trauma surgery for blast and ballistic injuries were included (n=983). Surgical activity was analysed as a rate per 100 casualties, and patients were grouped according to adult vs. paediatric and ballistic vs. blast injury mechanisms to aid comparison. Findings The three most common surgical procedures for civilian blast injuries were debridement, amputation, and laparotomy. For civilian ballistic injuries, these were debridement, laparotomy and vascular procedures. Blast injuries generated more amputations in both adults and children compared to ballistic injuries. Blast injuries generated more removal of fragmentation material compared to ballistics injuries amongst adult casualties. Ballistic injuries lead to more chest drain insertions in adults. As a rate per 100 casualties, adults injured by blast underwent significantly more debridement (63·5); temporary skeletal stabilisation (13·2) and vascular procedures (12·8) compared to children (43·4, z=4·026, p=0·00007; 5·7, z=2·230, p=0·022; 4·9, z=2·468, p=0·014). Adults injured by ballistics underwent significantly more debridement (63·4); chest drain (12·3) and temporary skeletal fixation procedures (11·4) compared to children (50·0, z=2·058, p=0.040, p<0·05; 2·9, z=2·283, p=0.0230; 2·9, z=2·131, p=0.034 respectively). By comparison, children injured by ballistics underwent significantly more removal of fragmentation and ballistic materials (20·6) when compared to adults (7·7, z=−3·234; p=0.001). Interpretation This is the first evidence-based, template of the immediate response required to manage civilians injured by blast and ballistic mechanisms. The template presented can be applied to similar conflict zones and to prepare for terror attacks on urban populations.Publisher PDFPeer reviewe

Spectral Bio-indicator Simulations for Tracking Photosynthetic Activities in a Corn Field

Accurate assessment of vegetation canopy optical properties plays a critical role in monitoring natural and managed ecosystems under environmental changes. In this context, radiative transfer (RT) models simulating vegetation canopy reflectance have been demonstrated to be a powerful tool for understanding and estimating spectral bio-indicators. In this study, two narrow band spectroradiometers were utilized to acquire observations over corn canopies for two summers. These in situ spectral data were then used to validate a two-layer Markov chain-based canopy reflectance model for simulating the Photochemical Reflectance Index (PRI), which has been widely used in recent vegetation photosynthetic light use efficiency (LUE) studies. The in situ PRI derived from narrow band hyperspectral reflectance exhibited clear responses to: 1) viewing geometry which affects the asset of light environment; and 2) seasonal variation corresponding to the growth stage. The RT model (ACRM) successfully simulated the responses to the variable viewing geometry. The best simulations were obtained when the model was set to run in the two layer mode using the sunlit leaves as the upper layer and shaded leaves as the lower layer. Simulated PRI values yielded much better correlations to in situ observations when the cornfield was dominated by green foliage during the early growth, vegetative and reproductive stages (r = 0.78 to 0.86) than in the later senescent stage (r = 0.65). Further sensitivity analyses were conducted to show the important influences of leaf area index (LAI) and the sunlit/shaded ratio on PRI observations