Estimating numbers of infectious units from serial dilution assays

The paper concerns the design and analysis of serial dilution assays to estimate the infectivity of a sample of tissue when it is assumed that the sample contains a finite number of indivisible infectious units such that a subsample will be infectious if it contains one or more of these units. The aim of the study is to estimate the number of infectious units in the original sample. The standard approach to the analysis of data from such a study is based on the assumption of independence of aliquots both at the same dilution level and at different dilution levels, so that the numbers of infectious units in the aliquots follow independent Poisson distributions. An alternative approach is based on calculation of the expected value of the total number of samples tested that are not infectious. We derive the likelihood for the data on the basis of the discrete number of infectious units, enabling calculation of the maximum likelihood estimate and likelihood-based confidence intervals. We use the exact probabilities that are obtained to compare the maximum likelihood estimate with those given by the other methods in terms of bias and standard error and to compare the coverage of the confidence intervals. We show that the methods have very similar properties and conclude that for practical use the method that is based on the Poisson assumption is to be recommended, since it can be implemented by using standard statistical software. Finally we consider the design of serial dilution assays, concluding that it is important that neither the dilution factor nor the number of samples that remain untested should be too large.

Active-control trials with binary data: a comparison of methods for testing superiority or non-inferiority using the odds ratio

This paper considers methods for testing for superiority or non-inferiority in active-control trials with binary data, when the relative treatment effect is expressed as an odds ratio. Three asymptotic tests for the log-odds ratio based on the unconditional binary likelihood are presented, namely the likelihood ratio, Wald and score tests. All three tests can be implemented straightforwardly in standard statistical software packages, as can the corresponding confidence intervals. Simulations indicate that the three alternatives are similar in terms of the Type I error, with values close to the nominal level. However, when the non-inferiority margin becomes large, the score test slightly exceeds the nominal level. In general, the highest power is obtained from the score test, although all three tests are similar and the observed differences in power are not of practical importance. Copyright (C) 2007 John Wiley & Sons, Ltd.

Parametric accelerated failure time models with random effects and an application to kidney transplant survival

Accelerated failure time models with a shared random component are described, and are used to evaluate the effect of explanatory factors and different transplant centres on survival times following kidney transplantation. Different combinations of the distribution of the random effects and baseline hazard function are considered and the fit of such models to the transplant data is critically assessed. A mixture model that combines short- and long-term components of a hazard function is then developed, which provides a more flexible model for the hazard function. The model can incorporate different explanatory variables and random effects in each component. The model is straightforward to fit using standard statistical software, and is shown to be a good fit to the transplant data. Copyright (C) 2004 John Wiley Sons, Ltd.

abctools: an R package for tuning approximate Bayesian computation analyses

Approximate Bayesian computation (ABC) is a popular family of algorithms which perform approximate parameter inference when numerical evaluation of the likelihood function is not possible but data can be simulated from the model. They return a sample of parameter values which produce simulations close to the observed dataset. A standard approach is to reduce the simulated and observed datasets to vectors of summary statistics and accept when the difference between these is below a specified threshold. ABC can also be adapted to perform model choice. In this article, we present a new software package for R, abctools which provides methods for tuning ABC algorithms. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold. We provide several illustrations of these routines on applications taken from the ABC literature.

A three-dimensional magnetometer for motion sensing of a balloon-carried atmospheric measurement package

An instrument is described which carries three orthogonal geomagnetic field sensors on a standard meteorological balloon package, to sense rapid motion and position changes during ascent through the atmosphere. Because of the finite data bandwidth available over the UHF radio link, a burst sampling strategy is adopted. Bursts of 9s of measurements at 3.6Hz are interleaved with periods of slow data telemetry lasting 25s. Calculation of the variability in each channel is used to determine position changes, a method robust to periods of poor radio signals. During three balloon ascents, variability was found repeatedly at similar altitudes, simultaneously in each of three orthogonal sensors carried. This variability is attributed to atmospheric motions. It is found that the vertical sensor is least prone to stray motions, and that the use of two horizontal sensors provides no additional information over a single horizontal sensor

Perspex machine X: software development

The Perspex Machine arose from the unification of computation with geometry. We now report significant redevelopment of both a partial C compiler that generates perspex programs and of a Graphical User Interface (GUI). The compiler is constructed with standard compiler-generator tools and produces both an explicit parse tree for C and an Abstract Syntax Tree (AST) that is better suited to code generation. The GUI uses a hash table and a simpler software architecture to achieve an order of magnitude speed up in processing and, consequently, an order of magnitude increase in the number of perspexes that can be manipulated in real time (now 6,000). Two perspex-machine simulators are provided, one using trans-floating-point arithmetic and the other using transrational arithmetic. All of the software described here is available on the world wide web. The compiler generates code in the neural model of the perspex. At each branch point it uses a jumper to return control to the main fibre. This has the effect of pruning out an exponentially increasing number of branching fibres, thereby greatly increasing the efficiency of perspex programs as measured by the number of neurons required to implement an algorithm. The jumpers are placed at unit distance from the main fibre and form a geometrical structure analogous to a myelin sheath in a biological neuron. Both the perspex jumper-sheath and the biological myelin-sheath share the computational function of preventing cross-over of signals to neurons that lie close to an axon. This is an example of convergence driven by similar geometrical and computational constraints in perspex and biological neurons.

Measurements and modelling of airflows in houses using passive sampling and HAM software

Passive samplers have been predominantly used to monitor environmental conditions in single volumes. However, measurements using a calibrated passive sampler- Solid Phase Microextraction (SPME) fibre, in three houses with cold pitched roof, successfully demonstrated the potential of the SPME fibre as a device for monitoring air movement in two volumes. The roofs monitored were pitched at 15° - 30° with insulation thickness varying between 200-300 mm on the ceiling. For effective analysis, two constant sources of volatile organic compounds were diffused steadily in the house. Emission rates and air movement from the house to the roof was predicted using developed algorithms. The airflow rates which were calibrated against conventional tracer gas techniques were introduced into a HAM software package to predict the effects of air movement on other varying parameters. On average it was shown from the in situ measurements that about 20-30% of air entering the three houses left through gaps and cracks in the ceiling into the roof. Although these field measurements focus on the airflows, it is associated with energy benefits such that; if these flows are reduced then significantly energy losses would also be reduced (as modelled) consequently improving the energy efficiency of the house. Other results illustrated that condensation formation risks were dependent on the airtightness of the building envelopes including configurations of their roof constructions.

Practical neural networks in a computer control package

This paper deals with the integration of radial basis function (RBF) networks into the industrial software control package Connoisseur. The paper shows the improved modelling capabilities offered by RBF networks within the Connoisseur environment compared to linear modelling techniques such as recursive least squares. The paper also goes on to mention the way this improved modelling capability, obtained through the RBF networks will be utilised within Connoisseur.

The impact of Group Intelligence software on enquiry-based learning

Despite the increasing use of groupware technologies in education, there is little evidence of their impact, especially within an enquiry-based learning (EBL) context. In this paper, we examine the use of a commercial standard Group Intelligence software called GroupSystems®ThinkTank. To date, ThinkTank has been adopted mainly in the USA and supports teams in generating ideas, categorising, prioritising, voting and multi-criteria decision-making and automatically generates a report at the end of each session. The software was used by students carrying out an EBL project, set by employers, for a full academic year. The criteria for assessing the impact of ThinkTank on student learning were those of creativity, participation, productivity, engagement and understanding. Data was collected throughout the year using a combination of interviews and questionnaires, and written feedback from employers. The overall findings show an increase in levels of productivity and creativity, evidence of a deeper understanding of their work but some variation in attitudes towards participation in the early stages of the project.

Assessing the performance of a building integrated BP c-Si PV system

In this study, the performance, yield and characteristics of a 16 year old photovoltaic (PV) system installation have been investigated. The technology, BP Saturn modules which were steel-blue polycrystalline silicon cells are no longer in production. A bespoke monitoring system has been designed to monitor the characteristics of 6 refurbished strings, of 18 modules connected in series. The total output of the system is configured to 6.5 kWp (series to parallel configuration). In addition to experimental results, the performance ratio (PR) of known values was simulated using PVSyst, a simulation software package. From calculations using experimental values, the PV system showed approximately 10% inferior power outputs to what would have been expected as standard test conditions. However, efficiency values in comparison to standard test conditions and the performance ratio (w75% from PVSyst simulations) over the past decade have remained practically the same. This output though very relevant to the possible performance and stability of aging cells, requires additional parametric studies to develop a more robust argument. The result presented in this paper is part of an on-going investigation into PV system aging effects.