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Biomedical subjects

Andrew Hooker

Publications and source records attributed to Andrew Hooker.

4 recordsLinked to original sources

Simultaneous population optimal design for pharmacokinetic-pharmacodynamic experiments.

Multiple outputs or measurement types are commonly gathered in biological experiments. Often, these experiments are expensive (such as clinical drug trials) or require careful design to achieve the desired information content. Optimal experimental design protocols could help alleviate the cost and increase the accuracy of these experiments. In general, optimal design techniques ignore between-individual variability, but even work that incorporates it (population optimal design) has treated simultaneous multiple output experiments separately by computing the optimal design sequentially, first finding the optimal design for one output (eg, a pharmacokinetic [PK] measurement) and then determining the design for the second output (eg, a pharmacodynamic [PD] measurement). Theoretically, this procedure can lead to biased and imprecise results when the second model parameters are also included in the first model (as in PK-PD models). We present methods and tools for simultaneous population D-optimal experimental designs, which simultaneously compute the design of multiple output experiments, allowing for correlation between model parameters. We then apply these methods to simulated PK-PD experiments. We compare the new simultaneous designs to sequential designs that first compute the PK design, fix the PK parameters, and then compute the PD design in an experiment. We find that both population designs yield similar results in designs for low sample number experiments, with simultaneous designs being possibly superior in situations in which the number of samples is unevenly distributed between outputs. Simultaneous population D-optimality is a potentially useful tool in the emerging field of experimental design.

Computer Simulation↗

Automated identification of axonal growth cones in time-lapse image sequences.

The isolation and purification of axon guidance molecules has enabled in vitro studies of the effects of axon guidance molecule gradients on numerous neuronal cell types. In a typical experiment, cultured neurons are exposed to a chemotactic gradient and their growth is recorded by manual identification of the axon tip position from two or more micrographs. Detailed and statistically valid quantification of axon growth requires evaluation of a large number of neurons at closely spaced time points (e.g. using a time-lapse microscopy setup). However, manual tracing becomes increasingly impractical for recording axon growth as the number of time points and/or neurons increases. We present a software tool that automatically identifies and records the axon tip position in each phase-contrast image of a time-lapse series with minimal user involvement. The software outputs several quantitative measures of axon growth, and allows users to develop custom measurements. For, example analysis of growth velocity for a dissociated E13 mouse cortical neuron revealed frequent extension and retraction events with an average growth velocity of 0.05 +/- 0.14 microm/min. Comparison of software-identified axon tip positions with manually identified axon tip positions shows that the software's performance is indistinguishable from that of skilled human users.

Animals↗

POPED, a software for optimal experiment design in population kinetics.

Population kinetic analysis is the methodology used to quantify inter-subject variability in kinetic studies. It entails the collection of (possibly sparse) data from dynamic experiments in a group of subjects and their quantitative interpretation by means of a mathematical model. This methodology is widely used in the pharmaceutical industry (where it is termed "pharmacokinetic population analysis") and recently it is becoming increasingly used in other areas of biomedical research. Unlike traditional kinetic studies, where the number of subjects can be quite small, population kinetic studies require large numbers of subjects. It is, therefore, of great interest to design these studies in the most efficient manner possible, to maximize the information content provided by the data. In this paper we propose an algorithm and a computer program, POPED, for the optimal design of a population kinetic experiment. In particular, the number of samples for each subject and the design of the individual sampling strategies, i.e. the number and location of the time points at which the output variable is sampled, will be considered. Among the various criteria proposed in the literature, D and ED optimality are the ones implemented in our software program, since they are the most widely used. A brief description of the techniques employed to perform design optimization is given, together with some details on their actual implementation. Some examples are then presented to show the program usage and the results provided.

Algorithms↗

Quantitative magnetic resonance imaging analysis of neovasculature volume in carotid atherosclerotic plaque.

BACKGROUND: Neovasculature within atherosclerotic plaques is believed to be associated with infiltration of inflammatory cells and plaque destabilization. The aim of the present investigation was to determine whether the amount of neovasculature present in advanced carotid plaques can be noninvasively measured by dynamic, contrast-enhanced MRI. METHODS AND RESULTS: A total of 20 consecutive patients scheduled for carotid endarterectomy were recruited to participate in an MRI study. Images were obtained at 15-second intervals, and a gadolinium contrast agent was injected coincident with the second of 10 images in the sequence. The resulting image intensity within the plaque was tracked over time, and a kinetic model was used to estimate the fractional blood volume. For validation, matched sections from subsequent endarterectomy were stained with ULEX and CD-31 antibody to highlight microvessels. Finally, all microvessels within the matched sections were identified, and their total area was computed as a fraction of the plaque area. Results were obtained from 16 participants, which showed fractional blood volumes ranging from 2% to 41%. These levels were significantly higher than the histological measurements of fractional vascular area. Nevertheless, the 2 measurements were highly correlated, with a correlation coefficient of 0.80 (P<0.001). CONCLUSIONS: Dynamic contrast-enhanced MRI provides an indication of the extent of neovasculature within carotid atherosclerotic plaque. MRI therefore provides a means for prospectively studying the link between neovasculature and plaque vulnerability.

Blood Volume↗