Sampling Methods for Exploring Between Subject Variability in Cardiac Electrophysiology Experiments

Between-subject and within-subject variability is ubiquitous in biology and physiology and understanding and dealing with this is one of the biggest challenges in medicine. At the same time it is difficult to investigate this variability by experiments alone. A recent modelling and simulation approach, known as population of models (POM), allows this exploration to take place by building a mathematical model consisting of multiple parameter sets calibrated against experimental data. However, finding such sets within a high-dimensional parameter space of complex electrophysiological models is computationally challenging. By placing the POM approach within a statistical framework, we develop a novel and efficient algorithm based on sequential Monte Carlo (SMC). We compare the SMC approach with Latin hypercube sampling (LHS), a method commonly adopted in the literature for obtaining the POM, in terms of efficiency and output variability in the presence of a drug block through an in-depth investigation via the Beeler-Reuter cardiac electrophysiological model. We show improved efficiency via SMC and that it produces similar responses to LHS when making out-of-sample predictions in the presence of a simulated drug block.

A comparison of mark-recapture distance-sampling methods applied to aerial surveys of eastern grey kangaroos

Aerial surveys of kangaroos (Macropus spp.) in Queensland are used to make economically important judgements on the levels of viable commercial harvest. Previous analysis methods for aerial kangaroo surveys have used both mark-recapture methodologies and conventional distance-sampling analyses. Conventional distance sampling has the disadvantage that detection is assumed to be perfect on the transect line, while mark-recapture methods are notoriously sensitive to problems with unmodelled heterogeneity in capture probabilities. We introduce three methodologies for combining together mark-recapture and distance-sampling data, aimed at exploiting the strengths of both methodologies and overcoming the weaknesses. Of these methods, two are based on the assumption of full independence between observers in the mark-recapture component, and this appears to introduce more bias in density estimation than it resolves through allowing uncertain trackline detection. Both of these methods give lower density estimates than conventional distance sampling, indicating a clear failure of the independence assumption. The third method, termed point independence, appears to perform very well, giving credible density estimates and good properties in terms of goodness-of-fit and percentage coefficient of variation. Estimated densities of eastern grey kangaroos range from 21 to 36 individuals km-2, with estimated coefficients of variation between 11% and 14% and estimated trackline detection probabilities primarily between 0.7 and 0.9.

Assessment of sampling methods to estimate horseshoe crab (Limulus polyphemus L.) egg density in Delaware Bay

Each spring horseshoe crabs (Limulus polyphemus L.) emerge from Delaware Bay to spawn and deposit their eggs on the foreshore of sandy beaches (Shuster and Botton, 1985; Smith et al., 2002a). From mid-May to early June, migratory shorebirds stopover in Delaware Bay and forage heavily on horseshoe crab eggs that have been transported up onto the beach (Botton et al., 1994; Burger et al., 1997; Tsipoura and Burger, 1999). Thus, estimating the quantity of horseshoe crab eggs in Delaware Bay beaches can be useful for monitoring spawning activity and assessing the amount of forage available to migratory shorebirds.

Development of sampling methods for Raman analysis of solid dosage forms of therapeutic and illicit drugs

The results of a study aimed at determining the most important experimental parameters for automated, quantitative analysis of solid dosage form pharmaceuticals (seized and model 'ecstasy' tablets) are reported. Data obtained with a macro-Raman spectrometer were complemented by micro-Raman measurements, which gave information on particle size and provided excellent data for developing statistical models of the sampling errors associated with collecting data as a series of grid points on the tablets' surface. Spectra recorded at single points on the surface of seized MDMA-caffeine-lactose tablets with a Raman microscope (lambda(ex) = 785 nm, 3 mum diameter spot) were typically dominated by one or other of the three components, consistent with Raman mapping data which showed the drug and caffeine microcrystals were ca 40 mum in diameter. Spectra collected with a microscope from eight points on a 200 mum grid were combined and in the resultant spectra the average value of the Raman band intensity ratio used to quantify the MDMA: caffeine ratio, mu(r), was 1.19 with an unacceptably high standard deviation, sigma(r), of 1.20. In contrast, with a conventional macro-Raman system (150 mum spot diameter), combined eight grid point data gave mu(r) = 1.47 with sigma(r) = 0.16. A simple statistical model which could be used to predict sigma(r) under the various conditions used was developed. The model showed that the decrease in sigma(r) on moving to a 150 mum spot was too large to be due entirely to the increased spot diameter but was consistent with the increased sampling volume that arose from a combination of the larger spot size and depth of focus in the macroscopic system. With the macro-Raman system, combining 64 grid points (0.5 mm spacing and 1-2 s accumulation per point) to give a single averaged spectrum for a tablet was found to be a practical balance between minimizing sampling errors and keeping overhead times at an acceptable level. The effectiveness of this sampling strategy was also tested by quantitative analysis of a set of model ecstasy tablets prepared from MDEA-sorbitol (0-30% by mass MDEA). A simple univariate calibration model of averaged 64 point data had R-2 = 0.998 and an r.m.s. standard error of prediction of 1.1% whereas data obtained by sampling just four points on the same tablet showed deviations from the calibration of up to 5%.

Evaluation of sampling methods for learning from imbalanced data

The problem of learning from imbalanced data is of critical importance in a large number of application domains and can be a bottleneck in the performance of various conventional learning methods that assume the data distribution to be balanced. The class imbalance problem corresponds to dealing with the situation where one class massively outnumbers the other. The imbalance between majority and minority would lead machine learning to be biased and produce unreliable outcomes if the imbalanced data is used directly. There has been increasing interest in this research area and a number of algorithms have been developed. However, independent evaluation of the algorithms is limited. This paper aims at evaluating the performance of five representative data sampling methods namely SMOTE, ADASYN, BorderlineSMOTE, SMOTETomek and RUSBoost that deal with class imbalance problems. A comparative study is conducted and the performance of each method is critically analysed in terms of assessment metrics. © 2013 Springer-Verlag.

Evaluating the efficiency of sampling methods in assessing soil macrofauna communities in arable systems

The soil fauna is often a neglected group in many large-scale studies of farmland biodiversity due to difficulties in extracting organisms efficiently from the soil. This study assesses the relative efficiency of the simple and cheap sampling method of handsorting against Berlese-Tullgren funnel and Winkler apparatus extraction. Soil cores were taken from grassy arable field margins and wheat fields in Cambridgeshire, UK, and the efficiencies of the three methods in assessing the abundances and species densities of soil macroinver-tebrates were compared. Handsorting in most cases was as efficient at extracting the majority of the soil macrofauna as the Berlese-Tullgren funnel and Winkler bag methods, although it underestimated the species densities of the woodlice and adult beetles. There were no obvious biases among the three methods for the particular vegetation types sampled and no significant differences in the size distributions of the earthworms and beetles. Proportionally fewer damaged earthworms were recorded in larger (25 x 25 cm) soil cores when compared with smaller ones (15 x 15 cm). Handsorting has many benefits, including targeted extraction, minimum disturbance to the habitat and shorter sampling periods and may be the most appropriate method for studies of farmland biodiversity when a high number of soil cores need to be sampled. (C) 2008 Elsevier Masson SAS. All rights reserved.

Comparison of Neck Skin Excision and Whole Carcass Rinse Sampling Methods for Microbiological Evaluation of Broiler Carcasses before and after Immersion Chilling

Sampling protocols for detecting Salmonella on poultry differ among various countries. In the United States, the U.S. Department of Agriculture Food Safety and Inspection Service dictates that whole broiler carcasses should be rinsed with 400 ml of 1% buffered peptone water, whereas in the European Union 25-g samples composed of neck skin from three carcasses are evaluated. The purpose of this study was to evaluate a whole carcass rinse (WCR) and a neck skin excision (NS) procedure for Salmonella and Escherichia coli isolation from the same broiler carcass. Carcasses were obtained from three broiler processing plants. The skin around the neck area was aseptically removed and bagged separately from the carcass, and microbiological analysis was performed. The corresponding carcass was bagged and a WCR sample was evaluated. No significant difference (alpha <= 0.05) in Salmonella prevalence was found between the samples processed by the two methods, but both procedures produced many false-negative Salmonella results. Prechill, 37% (66 carcasses), 28% (50 carcasses), and 51% (91 carcasses) of the 180 carcasses examined were positive for Salmonella by WCR, NS, and both procedures combined, respectively. Postchill, 3% (5 carcasses), 7% (12 carcasses), and 10% (17 carcasses) of the 177 carcasses examined were positive for Salmonella by the WCR, NS, and combination of both procedures, respectively. Prechill, E. coli plus coliform counts were 3.0 and 2.6 log CFU/ml by the WCR and NS methods, respectively. Postchill. E. coli plus coliform counts were 1.7 and 1.4 log CFU/ml by the WCR and NS methods, respectively.

The efficiency of improved ranked set sampling methods

Ranked set sampling is a desirable sampling technique where the ranking of the sample observations does not require the actual measurement. This thesis develops new ranked set sampling techniques and determines the sampling characteristics required to best estimate the required population parameters, such as mean and variance.

Comparing probability and non-probability sampling methods in ecstasy research : implications for the internet as a research tool

The usage of Ecstasy and related drug (ERD) has increasingly been the focus of epidemiological and other public health-related research. One of the more promising methods is the use of the Internet as a recruitment and survey tool.However, there remain methodological concerns and questions about representativeness. Three samples of ERD users in Melbourne, Australia surveyed in 2004 are compared in terms of a number of key demographic and drug use variables. The Internet, face-to-face, and probability
sampling methods appear to access similar but not identical groups of ERD users. Implications and limitations of the study are noted and future research is recommended.

Bats from Fazenda Intervales, Southeastern Brazil: species account and comparison between different sampling methods

Assessing the composition of an area's bat fauna is typically accomplished by using captures or by monitoring echolocation calls with bat detectors. The two methods may not provide the same data regarding species composition. Mist nets and harp traps may be biased towards sampling low flying species, and bat detectors biased towards detecting high intensity echolocators. A comparison of the bat fauna of Fazenda Intervales, southeastern Brazil, as revealed by mist nets and harp trap captures, checking roosts and by monitoring echolocation calls of flying bats illustrates this point. A total of 17 species of bats was sampled. Fourteen bat species were captured and the echolocation calls of 12 species were recorded, three of them not revealed by mist nets or harp traps. The different sampling methods provided different pictures of the bat fauna. Phyllostomid bats dominated the catches in mist nets, but in the field their echolocation calls were never detected. No single sampling approach provided a complete assessment of the bat fauna in the study area. In general, bats producing low intensity echolocation calls, such as phyllostomids, are more easily assessed by netting, and bats producing high intensity echolocation calls are better surveyed by bat detectors. The results demonstrate that a combined and varied approach to sampling is required for a complete assessment of the bat fauna of an area.