The robust selection of predictive genes via a simple classifier

Identifying genes that direct the mechanism of a disease from expression data is extremely useful in understanding how that mechanism works. This in turn may lead to better diagnoses and potentially can lead to a cure for that disease. This task becomes extremely challenging when the data are characterised by only a small number of samples and a high number of dimensions, as it is often the case with gene expression data. Motivated by this challenge, we present a general framework that focuses on simplicity and data perturbation. These are the keys for the robust identification of the most predictive features in such data. Within this framework, we propose a simple selective na¨ıve Bayes classifier discovered using a global search technique, and combine it with data perturbation to increase its robustness to small sample sizes. An extensive validation of the method was carried out using two applied datasets from the field of microarrays and a simulated dataset, all confounded by small sample sizes and high dimensionality. The method has been shown capable of identifying genes previously confirmed or associated with prostate cancer and viral infections

From Golden Spirals to Constant Slope Surfaces

In this paper, we find all constant slope surfaces in the Euclidean 3-space, namely those surfaces for which the position vector of a point of the surface makes constant angle with the normal at the surface in that point. These surfaces could be thought as the bi-dimensional analogue of the generalized helices. Some pictures are drawn by using the parametric equations we found.Comment: 11 pages, 8 figure

The supercluster--void network III. The correlation function as a geometrical statistic

We investigate properties of the correlation function of clusters of galaxies using geometrical models. On small scales the correlation function depends on the shape and the size of superclusters. On large scales it describes the geometry of the distribution of superclusters. If superclusters are distributed randomly then the correlation function on large scales is featureless. If superclusters and voids have a tendency to form a regular lattice then the correlation function on large scales has quasi-regularly spaced maxima and minima of decaying amplitude; i.e., it is oscillating. The period of oscillations is equal to the step size of the grid of the lattice. We calculate the power spectrum for our models and compare the geometrical information of the correlation function with other statistics. We find that geometric properties (the regularity of the distribution of clusters on large scales) are better quantified by the correlation function. We also analyse errors in the correlation function and the power spectrum by generating random realizations of models and finding the scatter of these realizations.Comment: MNRAS LaTex style, 12 pages, 7 PostScript figures embedded, accepted by MNRA

Consensus clustering and functional interpretation of gene-expression data

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas

Progression and assessment in foreign languages at Key Stage 2

The teaching of primary languages has been increasing steadily, in response to the future entitlement for all Key Stage 2 (KS2) pupils aged 7-11 to learn a foreign language by 2010. However, there remain concerns about progression both within KS2 and through to secondary school and about how learners' progress is assessed. This paper presents findings on the issues of progression and assessment taken from case studies which formed part of a project funded by the then Department for Education and Skills (DfES), now the Department for Children, Schools and Families (DCSF). This project set out to evaluate 19 local authority (LA) Pathfinders in England that were piloting the introduction of foreign language learning at KS2 between 2003 and 2005. Findings revealed that there was inconsistency between schools, even within each LA Pathfinder, in the use of schemes of work and that assessment was generally underdeveloped in the majority of the Pathfinders. In order to set these findings in context, this paper examines the issues of progression and assessment in foreign language learning in England. Finally, it investigates the challenges English primary schools face in terms of progression and assessment in the light of the new entitlement and discusses implications for the future. Managing progression, both within KS2 and through to secondary school at KS3 (ages 11-14), is one of the key factors in determining the overall success of starting languages in primary school

Influence of qubit displacements on quantum logic operations in a silicon-based quantum computer with constant interaction

The errors caused by qubit displacements from their prescribed locations in an ensemble of spin chains are estimated analytically and calculated numerically for a quantum computer based on phosphorus donors in silicon. We show that it is possible to polarize (initialize) the nuclear spins even with displaced qubits by using Controlled NOT gates between the electron and nuclear spins of the same phosphorus atom. However, a Controlled NOT gate between the displaced electron spins is implemented with large error because of the exponential dependence of exchange interaction constant on the distance between the qubits. If quantum computation is implemented on an ensemble of many spin chains, the errors can be small if the number of chains with displaced qubits is small

A Catalog of Very Isolated Galaxies from the SDSS Data Release 1

We present a new catalog of isolated galaxies obtained through an automated systematic search. These 2980 isolated galaxies were found in approximately 2099 sq deg of sky in the Sloan Digital Sky Survey Data Release 1 (SDSS DR1) photometry. The selection algorithm, implementing a variation on the criteria developed by Karachentseva in 1973, proved to be very efficient and fast. This catalog will be useful for studies of the general galaxy characteristics. Here we report on our results.Comment: 67 pages, which includes 14 figures. Accepted for publication by A

Effect of gut active carbohydrates on plasma IgG concentrations in piglets and calves

Improving immune status in neonates is crucial to health and production. Gut active carbohydrates (GAC) have been associated with increasing immunoglobin levels and immonucompetence development in mammals. The objective of the following studies was to evaluate whether GAC (mannan-oligosaccharides) applied orally to progeny immediately following parturition, improved blood plasma immunoglobulin (Ig) type G concentrations in piglets and calves. Three trials were conducted comparing control groups with those receiving GAC orally. The first two trials used piglets that were monitored for blood IgG at 2 days of age and for changes in body weight (BW), and the third trial monitored calf IgG from birth to 21 days of age. Piglets in the experimental group received 0.75 g GAC in 10 ml saline at birth and 24 h of age. The calf trial compared the control group against calves that received 22.5 g GAC mixed into 4.5 l of colostrum (to give 5 g/l) in the first 24 h after parturition. Blood serum samples were taken at 2 days post partum in piglets, and at several time points from 6 h to 21 days of age in calves, and were analysed for IgG levels by radial immunodiffusion. In the first piglet trial, significantly higher levels (32%) of IgG were observed for piglets fed GAC (P < 0.001), and in the second, IgG concentration was elevated by 23% (P < 0.01) and BW increased by 9% (P = 0.023) with GAC supplementation. Significant improvements for calves were recorded at all time points in those fed GAC (P < 0.05), with an increase in serum IgG observed after the first day, which was maintained throughout the sampling period, resulting in a difference of 39% at the end of the trial (21 d). These findings form a basis for further studies, which are required to investigate possible modes of action involved in enhancing blood immunoglobulin concentrations in young animals, and the longer-term effects this may have on the development of the immune respons

Environmental Enhancement of Loose Groups around Rich Clusters of Galaxies

We have studied the properties of Las Campanas Loose Groups in the neighbourhood of rich (Abell, APM and X-ray) clusters of galaxies. These loose groups show strong evidence of segregation measured in terms of the group richness and the group velocity dispersion: loose groups in the neighbourhood of a rich cluster are typically 2.5 times more massive and 1.6 times more luminous than groups on average, and these loose groups havevelocity dispersions 1.3 times larger than groups on average. This is evidence that the large-scale gravitational field causing the formation of rich clusters enhances the evolution of neighbouring poor systems, a phenomenon recently established in numerical simulations of group and cluster formation

Non-Riemannian Gravity and the Einstein-Proca System

We argue that all Einstein-Maxwell or Einstein-Proca solutions to general relativity may be used to construct a large class of solutions (involving torsion and non-metricity) to theories of non-Riemannian gravitation that have been recently discussed in the literature.Comment: 9 pages Plain Tex (No Figures), Letter to Editor Classical and Quantum Gravit