Visualization of predictive distributions for discrete spatial-temporal log Cox processes approximated with MCMC

An important aspect of decision support systems involves applying sophisticated and flexible statistical models to real datasets and communicating these results to decision makers in interpretable ways. An important class of problem is the modelling of incidence such as fire, disease etc. Models of incidence known as point processes or Cox processes are particularly challenging as they are ‘doubly stochastic’ i.e. obtaining the probability mass function of incidents requires two integrals to be evaluated. Existing approaches to the problem either use simple models that obtain predictions using plug-in point estimates and do not distinguish between Cox processes and density estimation but do use sophisticated 3D visualization for interpretation. Alternatively other work employs sophisticated non-parametric Bayesian Cox process models, but do not use visualization to render interpretable complex spatial temporal forecasts. The contribution here is to fill this gap by inferring predictive distributions of Gaussian-log Cox processes and rendering them using state of the art 3D visualization techniques. This requires performing inference on an approximation of the model on a discretized grid of large scale and adapting an existing spatial-diurnal kernel to the log Gaussian Cox process context.

GPU accelerated MCMC for modelling terrorist activity

The use of graphical processing unit (GPU) parallel processing is becoming a part of mainstream statistical practice. The reliance of Bayesian statistics on Markov Chain Monte Carlo (MCMC) methods makes the applicability of parallel processing not immediately obvious. It is illustrated that there are substantial gains in improved computational time for MCMC and other methods of evaluation by computing the likelihood using GPU parallel processing. Examples use data from the Global Terrorism Database to model terrorist activity in Colombia from 2000 through 2010 and a likelihood based on the explicit convolution of two negative-binomial processes. Results show decreases in computational time by a factor of over 200. Factors influencing these improvements and guidelines for programming parallel implementations of the likelihood are discussed.

Automated surface sampling of lipids from worn contact lenses coupled with tandem mass spectrometry

The deposition of biological material (biofouling) onto polymeric contact lenses is thought to be a major contributor to lens discomfort and hence discontinuation of wear. We describe a method to characterize lipid deposits directly from worn contact lenses utilizing liquid extraction surface analysis coupled to tandem mass spectrometry (LESA-MS/MS). This technique effected facile and reproducible extraction of lipids from the contact lens surfaces and identified lipid molecular species representing all major classes present in human tear film. Our data show that LESA-MS/MS is a rapid and comprehensive technique for the characterization of lipid-related biofouling on polymer surfaces.

Image-guided sampling reveals increased stroma and lower glandular complexity in mammographically dense breast tissue

Mammographic density (MD) adjusted for age and body mass index (BMI) is a strong heritable breast cancer risk factor; however, its biological basis remains elusive. Previous studies assessed MD-associated histology using random sampling approaches, despite evidence that high and low MD areas exist within a breast and are negatively correlated with respect to one another. We have used an image-guided approach to sample high and low MD tissues from within individual breasts to examine the relationship between histology and degree of MD. Image-guided sampling was performed using two different methodologies on mastectomy tissues (n = 12): (1) sampling of high and low MD regions within a slice guided by bright (high MD) and dark (low MD) areas in a slice X-ray film; (2) sampling of high and low MD regions within a whole breast using a stereotactically guided vacuum-assisted core biopsy technique. Pairwise analysis accounting for potential confounders (i.e. age, BMI, menopausal status, etc.) provides appropriate power for analysis despite the small sample size. High MD tissues had higher stromal (P = 0.002) and lower fat (P = 0.002) compositions, but no evidence of difference in glandular areas (P = 0.084) compared to low MD tissues from the same breast. High MD regions had higher relative gland counts (P = 0.023), and a preponderance of Type I lobules in high MD compared to low MD regions was observed in 58% of subjects (n = 7), but did not achieve significance. These findings clarify the histologic nature of high MD tissue and support hypotheses regarding the biophysical impact of dense connective tissue on mammary malignancy. They also provide important terms of reference for ongoing analyses of the underlying genetics of MD.

Estimating local stream fish assemblage attributes: Sampling effort and efficiency at two spatial scales

As part of a wider study to develop an ecosystem-health monitoring program for wadeable streams of south-eastern Queensland, Australia, comparisons were made regarding the accuracy, precision and relative efficiency of single-pass backpack electrofishing and multiple-pass electrofishing plus supplementary seine netting to quantify fish assemblage attributes at two spatial scales (within discrete mesohabitat units and within stream reaches consisting of multiple mesohabitat units). The results demonstrate that multiple-pass electrofishing plus seine netting provide more accurate and precise estimates of fish species richness, assemblage composition and species relative abundances in comparison to single-pass electrofishing alone, and that intensive sampling of three mesohabitat units (equivalent to a riffle-run-pool sequence) is a more efficient sampling strategy to estimate reach-scale assemblage attributes than less intensive sampling over larger spatial scales. This intensive sampling protocol was sufficiently sensitive that relatively small differences in assemblage attributes (<20%) could be detected with a high statistical power (1-β > 0.95) and that relatively few stream reaches (<4) need be sampled to accurately estimate assemblage attributes close to the true population means. The merits and potential drawbacks of the intensive sampling strategy are discussed, and it is deemed to be suitable for a range of monitoring and bioassessment objectives.

The effect of preferential sampling on sampling variance

We examine some variations of standard probability designs that preferentially sample sites based on how easy they are to access. Preferential sampling designs deliver unbiased estimates of mean and sampling variance and will ease the burden of data collection but at what cost to our design efficiency? Preferential sampling has the potential to either increase or decrease sampling variance depending on the application. We carry out a simulation study to gauge what effect it will have when sampling Soil Organic Carbon (SOC) values in a large agricultural region in south-eastern Australia. Preferential sampling in this region can reduce the distance to travel by up to 16%. Our study is based on a dataset of predicted SOC values produced from a datamining exercise. We consider three designs and two ways to determine ease of access. The overall conclusion is that sampling performance deteriorates as the strength of preferential sampling increases, due to the fact the regions of high SOC are harder to access. So our designs are inadvertently targeting regions of low SOC value. The good news, however, is that Generalised Random Tessellation Stratification (GRTS) sampling designs are not as badly affected as others and GRTS remains an efficient design compared to competitors.

Computation of ECG signal features using MCMC modelling in software and FPGA reconfigurable hardware

Computational optimisation of clinically important electrocardiogram signal features, within a single heart beat, using a Markov-chain Monte Carlo (MCMC) method is undertaken. A detailed, efficient data-driven software implementation of an MCMC algorithm has been shown. Initially software parallelisation is explored and has been shown that despite the large amount of model parameter inter-dependency that parallelisation is possible. Also, an initial reconfigurable hardware approach is explored for future applicability to real-time computation on a portable ECG device, under continuous extended use.

Determining gas sampling timelines for estimating emissions in small chamber incubation experiments

A laboratory experiment was set up in small chambers for monitoring greenhouse gas emissions and determining the most suitable time for sampling. A six-treatment experiment was conducted, including a one week pre-incubation and a week for incubation. Timelines for sampling were 1, 2, 3, 6 and 24 hours after closing the lid of the incubation chambers. Variation in greenhouse gas fluxes was high due to the time of sampling. The rates of gas emissions increased in first three hours and decreased afterward. The rates of greenhouse gas emissions at 3 hours after closing lids was close to the mean for the 24-h period.

Combining passive sampling and toxicity testing for evaluation of mixtures of polar organic chemicals in sewage treatment plant effluent

Effluent from sewage treatment plants has been associated with a range of pollutant effects. Depending on the influent composition and treatment processes the effluent may contain a myriad of different chemicals which makes monitoring very complex. In this study we aimed to monitor relatively polar organic pollutant mixtures using a combination of passive sampling techniques and a set of biochemistry based assays covering acute bacterial toxicity (Microtox™), phytotoxicity (Max-I-PAM assay) and genotoxicity (umuC assay). The study showed that all of the assays were able to detect effects in the samples and allowed a comparison of the two plants as well as a comparison between the two sampling periods. Distinct improvements in water quality were observed in one of the plants as result of an upgrade to a UV disinfection system, which improved from 24× sample enrichment required to induce a 50% response in the Microtox™ assay to 84×, from 30× sample enrichment to induce a 50% reduction in photosynthetic yield to 125×, and the genotoxicity observed in the first sampling period was eliminated. Thus we propose that biochemical assay techniques in combination with time integrated passive sampling can substantially contribute to the monitoring of polar organic toxicants in STP effluents.

Recruiting, Sampling and Data Collection with Difficult Populations: Clients of Male Sex Workers.

Although there are many potential new insights to be gained through advancing research on the clients of male sex workers, significant social, ethical and methodological challenges to accessing this population exist. This research project case explores our attempts to recruit a population that does not typically form a cohesive or coherent 'community' and often avoids self-identifying to mitigate the stigma attached to buying sex. We used an arms-length recruitment campaign that focussed on directing potential participants to our study website, which could in turn lead them to participate in an anonymous telephone interview. Barriers to reaching male sex-work clients, however, demanded the evolution of our recruitment strategy. New technologies are part of the solution to accessing a hard-to-reach population, but they only work if researchers engage responsively. We also show how we conducted an in-depth interview with a client and discuss the value of using secondary data.

‘True Blood’ the critical care story: An audit of blood sampling practice across three adult, paediatric and neonatal intensive care settings

Background Anaemia is common in critically ill patients, and has a significant negative impact on patients' recovery. Blood conservation strategies have been developed to reduce the incidence of iatrogenic anaemic caused by sampling for diagnostic testing. Objectives Describe practice and local guidelines in adult, paediatric and neonatal Australian intensive care units (ICUs) regarding blood sampling and conservation strategies. Methods Cross-sectional descriptive study, conducted July 2013 over one week in single adult, paediatric and neonatal ICUs in Brisbane. Data were collected on diagnostic blood samples obtained during the study period, including demographic and acuity data of patients. Institutional blood conservation practice and guidelines were compared against seven evidence-based recommendations. Results A total of 940 blood sampling episodes from 96 patients were examined across three sites. Arterial blood gas was the predominant reason for blood sampling in each unit, accounting for 82% of adult, 80% of paediatric and 47% of neonatal samples taken (p <. 0.001). Adult patients had significantly more median [IQR] samples per day in comparison to paediatrics and neonates (adults 5.0 [2.4]; paediatrics 2.3 [2.9]; neonatal 0.7 [2.7]), which significantly increased median [IQR] blood sampling costs per day (adults AUD$101.11 [54.71]; paediatrics AUD$41.55 [56.74]; neonatal AUD$8.13 [14.95]; p <. 0.001). The total volume of samples per day (median [IQR]) was also highest in adults (adults 22.3. mL [16.8]; paediatrics 5.0. mL [1.0]; neonates 0.16. mL [0.4]). There was little information about blood conservation strategies in the local clinical practice guidelines, with the adult and neonatal sites including none of the seven recommendations. Conclusions There was significant variation in blood sampling practice and conservation strategies between critical care settings. This has implications not only for anaemia but also infection control and healthcare costs.

Populations of models, experimental designs and coverage of parameter space by Latin Hypercube and Orthogonal Sampling

In this paper we have used simulations to make a conjecture about the coverage of a t-dimensional subspace of a d-dimensional parameter space of size n when performing k trials of Latin Hypercube sampling. This takes the form P(k,n,d,t) = 1 - e^(-k/n^(t-1)). We suggest that this coverage formula is independent of d and this allows us to make connections between building Populations of Models and Experimental Designs. We also show that Orthogonal sampling is superior to Latin Hypercube sampling in terms of allowing a more uniform coverage of the t-dimensional subspace at the sub-block size level. These ideas have particular relevance when attempting to perform uncertainty quantification and sensitivity analyses.

Ratcheting and wear behavior of Australian rail steel: Experimental investigation of material properties and sampling method

To The ratcheting behavior of high-strength rail steel (Australian Standard AS1085.1) is studied in this work for the purpose of predicting wear and damage to the rail surface. Historically, researchers have used circular test coupons obtained from the rail head to conduct cyclic load tests, but according to hardness profile data, considerable variation exists across the rail head section. For example, the induction-hardened rail (AS1085.1) shows high hardness (400-430 HV100) up to four-millimeters into the rail head’s surface, but then drops considerably beyond that. Given that cyclic test coupons five millimeters in diameter at the gauge area are usually taken from the rail sample, there is a high probability that the original surface properties of the rail do not apply across the entire test coupon and, therefore, data representing only average material properties are obtained. In the literature, disks (47 mm in diameter) for a twin-disk rolling contact test machine have been obtained directly from the rail sample and used to validate rolling contact fatigue wear models. The question arises: How accurate are such predictions? In this research paper, the effect of rail sampling position on the ratcheting behavior of AS1085.1 rail steel was investigated using rectangular shaped specimens. Uniaxial stress-controlled tests were conducted with samples obtained at four different depths to observe the ratcheting behaviour of each. Micro-hardness measurements of the test coupons were carried out to obtain a constitutive relationship to predict the effect of depth on the ratcheting behaviour of the rail material. This work ultimately assists the selection of valid material parameters for constitutive models in the study of rail surface ratcheting.