Hellinger Distance Trees for Imbalanced Streams

Classifiers trained on data sets possessing an imbalanced class distribution are known to exhibit poor generalisation performance. This is known as the imbalanced learning problem. The problem becomes particularly acute when we consider incremental classifiers operating on imbalanced data streams, especially when the learning objective is rare class identification. As accuracy may provide a misleading impression of performance on imbalanced data, existing stream classifiers based on accuracy can suffer poor minority class performance on imbalanced streams, with the result being low minority class recall rates. In this paper we address this deficiency by proposing the use of the Hellinger distance measure, as a very fast decision tree split criterion. We demonstrate that by using Hellinger a statistically significant improvement in recall rates on imbalanced data streams can be achieved, with an acceptable increase in the false positive rate.Comment: 6 Pages, 2 figures, to be published in Proceedings 22nd International Conference on Pattern Recognition (ICPR) 201

Ab-Initio Calculation of the Metal-Insulator Transition in Sodium rings and chains and in mixed Sodium-Lithium systems

We study how the Mott metal-insulator transition (MIT) is influenced when we deal with electrons with different angular momenta. For lithium we found an essential effect when we include $p$-orbitals in the description of the Hilbert space. We apply quantum-chemical methods to sodium rings and chains in order to investigate the analogue of a MIT, and how it is influenced by periodic and open boundaries. By changing the interatomic distance we analyse the character of the many-body wavefunction and the charge gap. In the second part we mimic a behaviour found in the ionic Hubbard model, where a transition from a band to a Mott insulator occurs. For that purpose we perform calculations for mixed sodium-lithium rings. In addition, we examine the question of bond alternation for the pure sodium system and the mixed sodium-lithium system, in order to determine under which conditions a Peierls distortion occurs.Comment: 8 pages, 7 figures, accepted Eur. J. Phys.

Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kB signaling pathway

Mathematical modelling offers a variety of useful techniques to help in understanding the intrinsic behaviour of complex signal transduction networks. From the system engineering point of view, the dynamics of metabolic and signal transduction models can always be described by nonlinear ordinary differential equations (ODEs) following mass balance principles. Based on the state-space formulation, many methods from the area of automatic control can conveniently be applied to the modelling, analysis and design of cell networks. In the present study, dynamic sensitivity analysis is performed on a model of the IB-NF-B signal pathway system. Univariate analysis of the Euclidean-form overall sensitivities shows that only 8 out of the 64 parameters in the model have major influence on the nuclear NF-B oscillations. The sensitivity matrix is then used to address correlation analysis, identifiability assessment and measurement set selection within the framework of least squares estimation and multivariate analysis. It is shown that certain pairs of parameters are exactly or highly correlated to each other in terms of their effects on the measured variables. The experimental design strategy provides guidance on which proteins should best be considered for measurement such that the unknown parameters can be estimated with the best statistical precision. The whole analysis scheme we describe provides efficient parameter estimation techniques for complex cell networks

Absolute quantification of the host-to-parasite DNA ratio in Theileria parva-infected lymphocyte cell lines

Theileria parva is a tick-transmitted intracellular apicomplexan pathogen of cattle in sub-Saharan Africa that causes East Coast fever (ECF). ECF is an acute fatal disease that kills over one million cattle annually, imposing a tremendous burden on African small-holder cattle farmers. The pathology and level of T. parva infections in its wildlife host, African buffalo (Syncerus caffer), and in cattle are distinct. We have developed an absolute quantification method based on quantitative PCR (qPCR) in which recombinant plasmids containing single copy genes specific to the parasite (apical membrane antigen 1 gene, ama1) or the host (hypoxanthine phosphoribosyltransferase 1, hprt1) are used as the quantification reference standards. Our study shows that T. parva and bovine cells are present in similar numbers in T. parva-infected lymphocyte cell lines and that consequently, due to its much smaller genome size, T. parva DNA comprises between 0.9% and 3% of the total DNA samples extracted from these lines. This absolute quantification assay of parasite and host genome copy number in a sample provides a simple and reliable method of assessing T. parva load in infected bovine lymphocytes, and is accurate over a wide range of host-to-parasite DNA ratios. Knowledge of the proportion of target DNA in a sample, as enabled by this method, is essential for efficient high-throughput genome sequencing applications for a variety of intracellular pathogens. This assay will also be very useful in future studies of interactions of distinct host-T. parva stocks and to fully characterize the dynamics of ECF infection in the field

Magnetodielectric coupling of infrared phonons in single crystal Cu2_{2}OSeO3_{3}

Reflection and transmission as a function of temperature have been measured on a single crystal of the magnetoelectric ferrimagnetic compound Cu$_{2}$OSeO$_{3}$ utilizing light spanning the far infrared to the visible portions of the electromagnetic spectrum. The complex dielectric function and optical properties were obtained via Kramers-Kronig analysis and by fits to a Drude-Lortentz model. The fits of the infrared phonons show a magnetodielectric effect near the transition temperature ($T_{c}\sim 60$~K). Assignments to strong far infrared phonon modes have been made, especially those exhibiting anomalous behavior around the transition temperature

Epidemiology and fitness effects of wood mouse herpesvirus in a natural host population

Rodent gammaherpesviruses have become important models for understanding human herpesvirus diseases. In particular, interactions between murid herpesvirus 4 and Mus musculus (a non-natural host species) have been extensively studied under controlled laboratory conditions. However, several fundamental aspects of murine gammaherpesvirus biology are not well understood, including how these viruses are transmitted from host to host, and their impacts on host fitness under natural conditions. Here, we investigate the epidemiology of a gammaherpesvirus in free-living wood mice (Apodemus sylvaticus) and bank voles (Myodes glareolus) in a 2-year longitudinal study. Wood mouse herpesvirus (WMHV) was the only herpesvirus detected and occurred frequently in wood mice and also less commonly in bank voles. Strikingly, WMHV infection probability was highest in reproductively active, heavy male mice. Infection risk also showed a repeatable seasonal pattern, peaking in spring and declining through the summer. We show that this seasonal decline can be at least partly attributed to reduced recapture of WMHV-infected adults. These results suggest that male reproductive behaviours could provide an important natural route of transmission for these viruses. They also suggest that gammaherpesvirus infection may have significant detrimental effects in wild hosts, questioning the view that these viruses have limited impacts in natural, co-evolved host species

Experimental study of laser detected magnetic resonance based on atomic alignment

We present an experimental study of the spectra produced by optical/radio-frequency double resonance in which resonant linearly polarized laser light is used in the optical pumping and detection processes. We show that the experimental spectra obtained for cesium are in excellent agreement with a very general theoretical model developed in our group and we investigate the limitations of this model. Finally, the results are discussed in view of their use in the study of relaxation processes in aligned alkali vapors.Comment: 8 pages, 9 figures. Submitted to Phys. Rev. A. Related to physics/060523

Nitrogenase activity associated with codium species from New Zealand marine habitats

Nitrogenase activity, measured as acetylene reduction, was recorded at rates up to 1028 nmol.h \g * dry weight for Codium adhaerens (Cabr.) Ag. var. convolutum Dellow and Codium fragile (Sur.) Hariot subsp. tomentosoides (Van Goor) Silva collected from New Zealand habitats. In both species the ability to reduce acetylene is invariably associated with the presence of a heterocystous blue-green alga, Calothrix sp., epiphytic or embedded in the Codium thallus. A highly significant (P < 0.001) correlation between heterocyst frequency and nitrogenase activity was found. Nitrogenase and net photosynthesis of the Codium-Calothrix system have different steady-state responses to light intensity, and the kinetics of the two processes also differ in that nitrogenase is slow to respond to illumination or darkening. Glucose additions to Codium did not significantly increase nitrogenase activity. Nitrogenase is relatively insensitive to oxygen tension over the range 0-1.0 atm (0-1.033 kgf.cnT2) and still occurs at 1.5 atm (1.55 kgf.cm"2); this condition is unique in all nitrogenase systems thus far reported. Collectively these facts suggest that Calothrix is the agent primarily responsible for nitrogenase activity in these Codium species