Non-parametric Bayesian modelling of digital gene expression data

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A common limitation in experiments using these technologies is the low number or even absence of biological replicates, which complicates the statistical analysis of digital gene expression data. Analysis of this type of data has often been based on modified tests originally devised for analysing microarrays; both these and even de novo methods for the analysis of RNA-seq data are plagued by the common problem of low replication. We propose a novel, non-parametric Bayesian approach for the analysis of digital gene expression data. We begin with a hierarchical model for modelling over-dispersed count data and a blocked Gibbs sampling algorithm for inferring the posterior distribution of model parameters conditional on these counts. The algorithm compensates for the problem of low numbers of biological replicates by clustering together genes with tag counts that are likely sampled from a common distribution and using this augmented sample for estimating the parameters of this distribution. The number of clusters is not decided a priori, but it is inferred along with the remaining model parameters. We demonstrate the ability of this approach to model biological data with high fidelity by applying the algorithm on a public dataset obtained from cancerous and non-cancerous neural tissues

Perspective Transformation Amongst Student Interns

This case study is an attempt to understand the impact of an International Service-Learning (ISL) experience on changing the world view or perspectives of 25 student participants in a three month internship to East Africa through a large Canadian research intensive university in response to the HIV/AIDS crisis. Using Kiely’s (2004) model of emerging global consciousness and a post-colonial lens, findings indicate that participants’ ‘common sense’ assumptions are disrupted and that they experience complex, ambiguous and varied shifts in their world view. The study identifies some of the experiences and contexts that contribute to perspective transformation and highlights the significance of self-reflexivity and mitigating asymmetrical power relationships in the process. Importantly, this study provides some evidence that participants in the ISL program have been able to persist up to six years after the internship experience, to translate their new world view into meaningful action in the face of dominant hegemonic Canadian values

Wave chaos in rapidly rotating stars

Effects of rapid stellar rotation on acoustic oscillation modes are poorly understood. We study the dynamics of acoustic rays in rotating polytropic stars and show using quantum chaos concepts that the eigenfrequency spectrum is a superposition of regular frequency patterns and an irregular frequency subset respectively associated with near-integrable and chaotic phase space regions. This opens new perspectives for rapidly rotating star seismology and also provides a new and potentially observable manifestation of wave chaos in a large scale natural system.Comment: 5 pages, 3 figures; accepted for publication in Phys. Rev.

Global shallow water magnetohydrodynamic waves in the solar tachocline

We derive analytical solutions and dispersion relations of global magnetic Poincar\'e (magneto-gravity) and magnetic Rossby waves in the approximation of shallow water magnetohydrodynamics. The solutions are obtained in a rotating spherical coordinate system for strongly and weakly stable stratification separately in the presence of toroidal magnetic field. In both cases magnetic Rossby waves split into fast and slow magnetic Rossby modes. In the case of strongly stable stratification (valid in the radiative part of the tachocline) all waves are slightly affected by the layer thickness and the toroidal magnetic field, while in the case of weakly stable stratification (valid in the upper overshoot layer of the tachocline) magnetic Poincar\'e and fast magnetic Rossby waves are found to be concentrated near the solar equator, leading to equatorially trapped waves. However, slow magnetic Rossby waves tend to concentrate near the poles, leading to polar trapped waves. The frequencies of all waves are smaller in the upper weakly stable stratification region than in the lower strongly stable stratification one

Introduction: youth entrepreneurship in sub-Saharan Africa

Introduction: youth entrepreneurship in sub-Saharan Afric

Dispersion of relative importance values contributes to the ranking uncertainty: sensitivity analysis of Multiple Criteria Decision-Making methods

Multiple Criteria Decision-Making (MCDM) methods are widely used in research and industrial applications. These methods rely heavily on expert perceptions and are often sensitive to the assumptions made. The reliability and robustness of MCDM analysis can be further tested and verified by a computer simulation and sensitivity analysis. In order to address this, five different MCDM approaches, including Weighted Sum Model (WSM), Weighted Product Model (WPM), revised Analytic Hierarchy Process (rAHP), Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) and COmplex PRoportional ASsessment (COPRAS) are explored in the paper. Real data of the case study for assessing housing affordability are used for testing the robustness of alternative ranking and finding the most sensitive criteria to the change of criterion weight. We identify the most critical criteria for any and best ranking alternatives. The paper highlights the significance of sensitivity analysis in assessing the robustness and reliability of MCDM outcomes. Furthermore, randomly generated and model-based data sets are used to establish relationship between the dispersion of relative importance values of alternatives and ranking uncertainty. Our findings demonstrate that the dispersion of relative importance values of alternatives correlate with the Euclidian distances of aggregated values. We conclude that the dispersion of relative importance values contributes directly to the ranking uncertainty and can be used as a measure for finding critical criteria

Introduction. Safe and inclusive cities: contesting violence

Introduction. Safe and inclusive cities: contesting violenc

Data base management system analysis and performance testing with respect to NASA requirements

Several candidate Data Base Management Systems (DBM's) that could support the NASA End-to-End Data System's Integrated Data Base Management System (IDBMS) Project, later rescoped and renamed the Packet Management System (PMS) were evaluated. The candidate DBMS systems which had to run on the Digital Equipment Corporation VAX 11/780 computer system were ORACLE, SEED and RIM. Oracle and RIM are both based on the relational data base model while SEED employs a CODASYL network approach. A single data base application which managed stratospheric temperature profiles was studied. The primary reasons for using this application were an insufficient volume of available PMS-like data, a mandate to use actual rather than simulated data, and the abundance of available temperature profile data

Heterogeneous uptake of the C1 to C4 organic acids on a swelling clay mineral

Mineral aerosol is of interest due to its physiochemical impacts on the Earth's atmosphere. However, adsorbed organics could influence the chemical and physical properties of atmospheric mineral particles and alter their impact on the biosphere and climate. In this work, the heterogeneous uptake of a series of small organic acids on the swelling clay, Na-montmorillonite, was studied at 212 K as a function of relative humidity (RH), organic acid pressure and clay mass. A high vacuum chamber equipped with a quadrupole mass spectrometer and a transmission Fourier transform infrared spectrometer was used to detect the gas and condensed phases, respectively. Our results show that while the initial uptake efficiency was found to be independent of organic acid pressure, it increased linearly with increasing clay mass. Thus, the small masses studied allow access to the entire surface area of the clay sample with minimal effects due to surface saturation. Additionally, results from this study show that the initial uptake efficiency for butanoic (butyric) acid on the clay increases by an order of magnitude as the RH is raised from 0% to 45% RH at 212 K while the initial uptake efficiency of formic, acetic and propanoic (propionic) acids increases only slightly at higher humidities. However, the initial uptake efficiency decreases significantly in a short amount of time due to surface saturation effects. Thus, although the initial uptake efficiencies are appropriate for initial times, the fact that the uptake efficiency will decrease over time as the surface saturates should be considered in atmospheric models. Surface saturation results in sub-monolayer coverage of organic acid on montmorillonite under dry conditions and relevant organic acid pressures that increases with increasing humidity for all organic acids studied. Additionally, the presence of large organic acids may slightly enhance the water content of the clay above 45% RH. Our results indicate that heterogeneous uptake of organic acids on swelling clay minerals provides an important irreversible heterogeneous sink for these species