Web-based Tools for the Analysis of DNA Microarrays

End of project reportDNA microarrays are widely used for gene expression profiling. Raw data resulting from microarray experiments, however, tends to be very noisy and there are many sources of technical variation and bias. This raw data needs to be quality assessed and interactively preprocessed to minimise variation before statistical analysis in order to achieve meaningful result. Therefore microarray analysis requires a combination of visualisation and statistical tools, which vary depending on what microarray platform or experimental design is used.Bioconductor is an existing open source software project that attempts to facilitate analysis of genomic data. It is a collection of packages for the statistical programming language R. Bioconductor is particularly useful in analyzing microarray experiments. The problem is that the R programming language’s command line interface is intimidating to many users who do not have a strong background in computing. This often leads to a situation where biologists will resort to using commercial software which often uses antiquated and much less effective statistical techniques, as well as being expensively priced. This project aims to bridge this gap by providing a user friendly web-based interface to the cutting edge statistical techniques of Bioconductor

Prescission neutron multiplicity and fission probability from Langevin dynamics of nuclear fission

A theoretical model of one-body nuclear friction which was developed earlier, namely the chaos-weighted wall formula, is applied to a dynamical description of compound nuclear decay in the framework of the Langevin equation coupled with statistical evaporation of light particles and photons. We have used both the usual wall formula friction and its chaos-weighted version in the Langevin equation to calculate the fission probability and prescission neutron multiplicity for the compound nuclei $^{178}$W, $^{188}$Pt, $^{200}$Pb, $^{213}$Fr, $^{224}$Th, and $^{251}$Es. We have also obtained the contributions of the presaddle and postsaddle neutrons to the total prescission multiplicity. A detailed analysis of our results leads us to conclude that the chaos-weighted wall formula friction can adequately describe the fission dynamics in the presaddle region. This friction, however, turns out to be too weak to describe the postsaddle dynamics properly. This points to the need for a suitable explanation for the enhanced neutron emission in the postsaddle stage of nuclear fission.Comment: RevTex, 14 pages including 5 Postscript figures, results improved by using a different potential, conclusions remain unchanged, to appear in Phys. Rev.

Evidence of microscopic effects in fragment mass distribution in heavy ion induced fusion-fission reactions

Our measurements of variances ($\sigma_{m}^2$) in mass distributions of fission fragments from fusion-fission reactions of light projectiles (C, O and F) on deformed thorium targets exhibit a sharp anomalous increase with energy near the Coulomb barrier, in contrast to the smooth variation of $\sigma_{m}^2$ for the spherical bismuth target. This departure from expectation based on a statistical description is explained in terms of microscopic effects arising from the orientational dependence in the case of deformed thorium targets.Comment: Replaced with revised version, to appear in Phys. Lett.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H_2, CH) and triatomic (H_3, CH_2) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently

A study to assess the influence of interprofessional point of care simulation training on safety culture in the operating theatre environment of a university teaching hospital.

Interprofessional point of care or in situ simulation is used as a training tool in our operating theatre directorate with the aim of improving crisis behaviours. This study aimed to assess the impact of interprofessional point of care simulation on the safety culture of operating theatres. A validated Safety Attitude Questionnaire was administered to staff members before each simulation scenario and then re-administered to the same staff members after 6-12 months. Pre- and post-training Safety Attitude Questionnaire-Operating Room (SAQ-OR) scores were compared using paired sample t-tests. Analysis revealed a statistically significant perceived improvement in both safety (p < 0.001) and teamwork (p = 0.013) climate scores (components of safety culture) 6-12 months after interprofessional simulation training. A growing body of literature suggests that a positive safety culture is associated with improved patient outcomes. Our study supports the implementation of point of care simulation as a useful intervention to improve safety culture in theatres

A temporal and spatial study of invertebrate communities associated with hard-bottom habitats in the South Atlantic Bight

Species composition, biomass, density, and diversity of benthic invertebrates from six bard-bottom areas were evaluated. Seasonal collections using a dredge, trawl, and suction and grab samplers yielded 432, 525, and 845 taxa, respectively. Based on collections wltb the different gear types, species composition of invertebrates was found to change bathymetrically. Inner- and mlddle-shelf sites were more similar to each other in terms of invertebrate species composition than they were to outer-shelf sites, regardless of season. Sites on the inner and outer shelf were grouped according to latitude; however, results suggest that depth is apparently a more important determinant of invertebrate species composition than either season or latitude. Sponges generally dominated dredge and trawl collections in terms of biomass. Generally, cnidarians, bryozoans, and sponges dominated at sites In terms of number of taxa collected. The most abundant smaller macrofauna collected in suction and grab samples were polychaetes, amphipods, and mollusks. Densities of the numerically dominant species changed botb seasonally and bathymetrically, with very few of these species restricted to a specific bathymetrlc zone. The high diversity of invertebrates from hard-bottom sites is attributed to the large number of rare species. No consistent seasonal changes in diversity or number of species were noted for individual stations or depth zones. In addition, H and its components showed no definite patterns related to depth or latitude. However, more species were collected at middle-shelf sites than at inner- or outer-shelf sites, which may be related to more stable bottom temperature or greater habitat complexity in that area. (PDF file contains 110 pages.

An evaporation-based model of thermal neutron induced ternary fission of plutonium

Ternary fission probabilities for thermal neutron induced fission of plutonium are analyzed within the framework of an evaporation-based model where the complexity of time-varying potentials, associated with the neck collapse, are included in a simplistic fashion. If the nuclear temperature at scission and the fission-neck-collapse time are assumed to be ~1.2 MeV and ~10^-22 s, respectively, then calculated relative probabilities of ternary-fission light-charged-particle emission follow the trends seen in the experimental data. The ability of this model to reproduce ternary fission probabilities spanning seven orders of magnitude for a wide range of light-particle charges and masses implies that ternary fission is caused by the coupling of an evaporation-like process with the rapid re-arrangement of the nuclear fluid following scission.Comment: 25 pages, 12 figures, accepted for publication in IJMP

Complete Fusion Enhancement and Suppression of Weakly Bound Nuclei at Near Barrier Energies

We consider the influence of breakup channels on the complete fusion of weakly bound systems in terms of dynamic polarization potentials. It is argued that the enhancement of the cross section at sub-barrier energies may be consistent with recent experimental observations that nucleon transfer, often leading to breakup, is dominant compared to direct breakup. The main trends of the experimental complete fusion cross section for $^{6,7}$Li + $^{209}$Bi are analyzed in the framework of the DPP approach.Comment: 12 pages, 2 figure

lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time

Background and Objective: Observational studies and experiments in medicine, pharmacology and agronomy are often concerned with assessing whether different methods/raters produce similar values over the time when measuring a quantitative variable. This article aims to describe the statistical package lcc, for are, that can be used to estimate the extent of agreement between two (or more) methods over the time, and illustrate the developed methodology using three real examples. Methods: The longitudinal concordance correlation, longitudinal Pearson correlation, and longitudinal accuracy functions can be estimated based on fixed effects and variance components of the mixed-effects regression model. Inference is made through bootstrap confidence intervals and diagnostic can be done via plots, and statistical tests. Results: The main features of the package are estimation and inference about the extent of agreement using numerical and graphical summaries. Moreover, our approach accommodates both balanced and unbalanced experimental designs or observational studies, and allows for different within-group error structures, while allowing for the inclusion of covariates in the linear predictor to control systematic variations in the response. All examples show that our methodology is flexible and can be applied to many different data types. Conclusions: The lcc package, available on the CRAN repository, proved to be a useful tool to describe the agreement between two or more methods over time, allowing the detection of changes in the extent of agreement. The inclusion of different structures for the variance-covariance matrices of random effects and residuals makes the package flexible for working with different types of databases