A mixture model-based approach to the clustering of microarray expression data

Motivation: This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of t distributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes. Results: The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets.

Woodstoves uncovered: a paediatric problem

Objectives: To document and describe the effects of woodstove burns in children. To identify how these accidents occur so that a prevention strategy can be devised. Design, Patients and Setting: Retrospective departmental database and case note review of all children with woodstove burns seen at the Burns Unit of a Tertiary Referral Children's Hospital between January 1997 and September 2001. Main outcome measures: Number and ages of children burned: circumstances of the accidents; injuries-sustained, treatment-required and long-term sequelae. Results. Eleven children, median age 1.0 year, sustained burns, usually to the hands, of varying thickness. Two children required skin grafting and five required scar therapy. Seven children intentionally placed their hands onto the Outside of the stove. In all children, burns occurred despite adult supervision Conclusions: Woodstoves area cause of burns in children. These injuries are associated with significant morbidity and financial costs. Through public education, woodstove burns can easily be prevented utilising simple safety measures. (C) 2002 Elsevier Science Ltd and ISBI All rights reserved.

On the Hamilton-Waterloo problem

The Hamilton-Waterloo problem asks for a 2-factorisation of K-v in which r of the 2-factors consist of cycles of lengths a(1), a(2),..., a(1) and the remaining s 2-factors consist of cycles of lengths b(1), b(2),..., b(u) (where necessarily Sigma(i)(=1)(t) a(i) = Sigma(j)(=1)(u) b(j) = v). In thus paper we consider the Hamilton-Waterloo problem in the case a(i) = m, 1 less than or equal to i less than or equal to t and b(j) = n, 1 less than or equal to j less than or equal to u. We obtain some general constructions, and apply these to obtain results for (m, n) is an element of {(4, 6)1(4, 8), (4, 16), (8, 16), (3, 5), (3, 15), (5, 15)}.

The three-way intersection problem for latin squares

The set of integers k for which there exist three latin squares of order n having precisely k cells identical, with their remaining n(2) - k cells different in all three latin squares, denoted by I-3[n], is determined here for all orders n. In particular, it is shown that I-3[n] = {0,...,n(2) - 15} {n(2) - 12,n(2) - 9,n(2)} for n greater than or equal to 8. (C) 2002 Elsevier Science B.V. All rights reserved.

An Analytic Simplification for the Reconstruction Problem of Electrical Impedance Tomography

This paper introduces a new reconstruction algorithm for electrical impedance tomography. The algorithm assumes that there are two separate regions of conductivity. These regions are represented as eccentric circles. This new algorithm then solves for the location of the eccentric circles. Due to the simple geometry of the forward problem, an analytic technique using conformal mapping and separation of variables has been employed. (C) 2002 John Wiley Sons, Inc.

A subset-oriented algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries

Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at http://www.imb.uq.edu.au/groups/smythe/tran), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search. (C) 2002 Elsevier Science Ltd. All rights reserved.

The GP problem: quantifying gene-to-phenotype relationships

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.

Couple communication and female problem drinking: A behavioral observation study

Couples with alcohol and relationship problems often report poor communication, yet little is known about the communication of maritally distressed couples in which the woman abuses alcohol (MDWA couples). Compared with maritally distressed couples without alcohol problems (MDNA) and couples with neither problem (NDNA), MDWA couples showed a distinctive pattern of negative communication. Similar to MDNA men, MDWA men spoke negatively to their partners but listened positively to their partners much like NDNA men. MDWA women listened negatively, much as MDNA women did, but spoke positively, like NDNA women did. The interactions of MDWA couples can be characterized as a male-demand-female-withdraw pattern, which is a gender reversal of the female-demand-male-withdraw pattern often observed in MDNA couples.