Knowledge discovery and data mining in biological databases

The new technologies for Knowledge Discovery from Databases (KDD) and data mining promise to bring new insights into a voluminous growing amount of biological data. KDD technology is complementary to laboratory experimentation and helps speed up biological research. This article contains an introduction to KDD, a review of data mining tools, and their biological applications. We discuss the domain concepts related to biological data and databases, as well as current KDD and data mining developments in biology.

Numerical modelling of single-layer folding: clarification of an issue regarding the possible effect of computer codes and the influence of initial irregularities

The influence of initial perturbation geometry and material propel-ties on final fold geometry has been investigated using finite-difference (FLAC) and finite-element (MARC) numerical models. Previous studies using these two different codes reported very different folding behaviour although the material properties, boundary conditions and initial perturbation geometries were similar. The current results establish that the discrepancy was not due to the different computer codes but due to the different strain rates employed in the two previous studies (i.e. 10(-6) s(-1) in the FLAC models and 10(-14) s(-1) in the MARC models). As a result, different parts of the elasto-viscous rheological field were bring investigated. For the same material properties, strain rate and boundary conditions, the present results using the two different codes are consistent. A transition in Folding behaviour, from a situation where the geometry of initial perturbation determines final fold shape to a situation where material properties control the final geometry, is produced using both models. This transition takes place with increasing strain rate, decreasing elastic moduli or increasing viscosity (reflecting in each case the increasing influence of the elastic component in the Maxwell elastoviscous rheology). The transition described here is mechanically feasible but is associated with very high stresses in the competent layer (on the order of GPa), which is improbable under natural conditions. (C) 2000 Elsevier Science Ltd. All rights reserved.

Integrating attribute and space characteristics in choropleth display and spatial data mining

This paper develops an interactive approach for exploratory spatial data analysis. Measures of attribute similarity and spatial proximity are combined in a clustering model to support the identification of patterns in spatial information. Relationships between the developed clustering approach, spatial data mining and choropleth display are discussed. Analysis of property crime rates in Brisbane, Australia is presented. A surprising finding in this research is that there are substantial inconsistencies in standard choropleth display options found in two widely used commercial geographical information systems, both in terms of definition and performance. The comparative results demonstrate the usefulness and appeal of the developed approach in a geographical information system environment for exploratory spatial data analysis.

Simultaneous X-ray imaging of plant root growth and water uptake in thin-slab systems

Direct and simultaneous observation of root growth and plant water uptake is difficult because soils are opaque. X-ray imaging techniques such as projection radiography or Computer Tomography (CT) offer a partial alternative to such limitations. Nevertheless, there is a trade-off between resolution, large field-of-view and 3-dimensionality: With the current state of the technology, it is possible to have any two. In this study, we used X-ray transmission through thin-slab systems to monitor transient saturation fields that develop around roots as plants grow. Although restricted to 2-dimensions, this approach offers a large field-of-view together with high spatial and dynamic resolutions. To illustrate the potential of this technology, we grew peas in 1 cm thick containers filled with soil and imaged them at regular intervals. The dynamics of both the root growth and the water content field that developed around the roots could be conveniently monitored. Compared to other techniques such as X-ray CT, our system is relatively inexpensive and easy to implement. It can potentially be applied to study many agronomic problems, such as issues related to the impact of soil constraints (physical, chemical or biological) on root development.

Computer technology - A political player in social policy processes

The absence of considerations of technology in policy studies reinforces the popular notion that technology is a neutral tool, Through an analysis of the role played by computers in the policy processes of Australia's Department of Social Security, this paper argues that computers are political players in policy processes, Findings indicate that computers make aspects of the social domain knowable and therefore governable, The use of computers makes previously infeasible policies possible, Computers also operate as bureaucrats and as agents of client surveillance. Increased policy change, reduced discretion and increasingly targeted and complex policies can be attributed to the use of computer technology, If policy processes are to be adequately understood and analysed, then the role of technology in those processes must be considered.

Estimating Two-Stage Models for Genetic Influences on Alcohol, Tobacco or Drug Use Initiation and Dependence Vulnerability in Twin and Family Data

Genetic research on risk of alcohol, tobacco or drug dependence must make allowance for the partial overlap of risk-factors for initiation of use, and risk-factors for dependence or other outcomes in users. Except in the extreme cases where genetic and environmental risk-factors for initiation and dependence overlap completely or are uncorrelated, there is no consensus about how best to estimate the magnitude of genetic or environmental correlations between Initiation and Dependence in twin and family data. We explore by computer simulation the biases to estimates of genetic and environmental parameters caused by model misspecification when Initiation can only be defined as a binary variable. For plausible simulated parameter values, the two-stage genetic models that we consider yield estimates of genetic and environmental variances for Dependence that, although biased, are not very discrepant from the true values. However, estimates of genetic (or environmental) correlations between Initiation and Dependence may be seriously biased, and may differ markedly under different two-stage models. Such estimates may have little credibility unless external data favor selection of one particular model. These problems can be avoided if Initiation can be assessed as a multiple-category variable (e.g. never versus early-onset versus later onset user), with at least two categories measurable in users at risk for dependence. Under these conditions, under certain distributional assumptions., recovery of simulated genetic and environmental correlations becomes possible, Illustrative application of the model to Australian twin data on smoking confirmed substantial heritability of smoking persistence (42%) with minimal overlap with genetic influences on initiation.

The role of handouts, note-taking and overhead transparencies in veterinary science lectures

Objective To study student and staff views of the role and use of handouts, note-taking and overhead transparencies in veterinary science lectures at the University of Queensland Methods The Nominal Group Technique was used to help develop a questionnaire, which was completed by 351 students (a response rate of 84%) and 35 staff (76%) from the 5 years of the veterinary course. The data were analysed using the SAS statistical computer package. Results Staff and students held different views as to the frequency with which handouts should be used, their educational value, and whether they should be complete or partial. Fewer students than staff agreed that handouts discourage further reading in a subject. Almost all staff and students saw the central functions of note-taking to be provision of notes for subsequent revision and encoding information given by the lecturer. More students than staff however, considered that note-taking in lectures interferes with understanding. Staff and students held similar views as to the uses of overheads in lectures. Interestingly however, more staff than students agreed that overheads often contain too much information. Conclusion Both students and staff saw the central role of note-taking as providing a set of good notes for revision. Generally students preferred that this information be provided in the form of partial or complete handouts, while staff preferred students to take notes and to read outside lectures. Surprisingly, more staff than students felt that overhead transparencies often contained too much information. Note-taking, handouts and overhead transparencies need to be linked in a coherent educational strategy to promote effective learning.

Age and gender differences in objectively measured physical activity in youth

TROST. S. G., R. R. PATE, J. F. SALLIS, P. S. FREEDSON, W. C. TAYLOR, M. DOWDA, and J. SIRARD. Age and gender differences in objectively measured physical activity in youth. Med. Sci. Sports Ererc., Vol. 34, No. 2, pp. 350-355, 2002. Purpose: The purpose of this study was to evaluate age and gender differences in objectively measured physical activity (PA) in a population-based sample of students in grades 1-12. Methods: Participants (185 male, 190 female) wore a CSA 7164 accelerometer for 7 consecutive days. To examine age-related trends. students were grouped as follows: grades 1-3 (N = 90), grades 4-6 (N = 91), grades 7-9 (N = 96). and grades 10-12 (N = 92). Bouts of PA and minutes spent in moderate-to-vigorous PA (MVPA) and vigorous PA (VPA) were examined. Results: Daily MVPA and VPA exhibited a significant inverse relationship with grade level, with the largest differences occurring between grades 1d-3 and 4-6. Boys were more active than girls; however, for overall PA, the magnitudes of the gender differences were modest. Participation in continuous 20-min bouts of PA was low to nonexistent. Conclusion: Our results support the notion that PA declines rapidly during childhood and adolescence and that accelerometers are feasible alternatives to self-report methods in moderately sized population-level surveillance studies.