A Distance-Based Test of Association Between Paired Heterogeneous Genomic Data

Due to rapid technological advances, a wide range of different measurements can be obtained from a given biological sample including single nucleotide polymorphisms, copy number variation, gene expression levels, DNA methylation and proteomic profiles. Each of these distinct measurements provides the means to characterize a certain aspect of biological diversity, and a fundamental problem of broad interest concerns the discovery of shared patterns of variation across different data types. Such data types are heterogeneous in the sense that they represent measurements taken at very different scales or described by very different data structures. We propose a distance-based statistical test, the generalized RV (GRV) test, to assess whether there is a common and non-random pattern of variability between paired biological measurements obtained from the same random sample. The measurements enter the test through distance measures which can be chosen to capture particular aspects of the data. An approximate null distribution is proposed to compute p-values in closed-form and without the need to perform costly Monte Carlo permutation procedures. Compared to the classical Mantel test for association between distance matrices, the GRV test has been found to be more powerful in a number of simulation settings. We also report on an application of the GRV test to detect biological pathways in which genetic variability is associated to variation in gene expression levels in ovarian cancer samples, and present results obtained from two independent cohorts

Transport in higher dimensional phase spaces

We use a four dimensional symplectic mapping, the coupled cubic-quadratic map, to provide evidence of Arnol’d Diffusion in phase space. We use the method of frequency analysis for dynamical systems to demonstrate the existence of regular orbits, and show that these orbits enclose weakly chaotic orbits which escape in finite time around the tori. A new collocation method for frequency analysis is employed by adapting it to allow for higher precision results. Arbitrary precision numerics are used to obtain highly accurate orbits for long timescales, and the adapted frequency method is used to obtain highly accurate frequencies of the mapping. We review the method of frequency analysis, demonstrate its effectiveness and accuracy in determining frequencies and finding tori in simple systems and low-dimensional mappings, and extend the results to higher dimensions. In the four dimensional mapping, we find several regular orbits with irrational frequency ratios, indicating the existence of tori in the phase space, as well as interior orbits that escape around these tori.Physic

The Non-Abelian Wilson Loop as a Theory of Strings with Contact Interaction

We investigate a reformulation of Yang-Mills theory at the level of the expectation of the non-abelian Wilson loop using a string theory with non-standard interaction. We find that the path-ordering of the Wilson loop can be generated either from considering a worldsheet generalisation of a boundary theory or by introducing a gauge field onto the worldsheet. Only the gauge theory has the sufficient structure to accommodate the three gluon vertex of Yang-Mills theory in the string model. Supersymmetric analogues of these two models are also investigated which, specifically in the gauge theory model, can be made the basis of a realistic string model formulation of Yang-Mills theory coupled to spinors

Violence and horror : the anti-technology of subjectivity.

This thesis is about graphic representations of violence and subjectivity. Simply stated, the violence in many recent horror films is motivated by a nihilism resulting from frustration with the inadequacy of contemporary subjectivity. I want to explore the potential such representations have for providing a means of radically undermining the contemporary category of subjectivity. This subversion is due to what I call the inverted mirror stage effect in combination with a particular dislocation of the audience that is associated with the spectacle of violence displayed in contemporary, or postmodern, horror films. My theoretical approach is a cultural materialist psychoanalytic one that facilitates the traversal of the gap between individual and society by focusing attention not merely on society as a product of individuals, or vice versa, but instead upon the dynamic interaction of the two. Also, this essay draws upon the work of several feminist film theorists, including Carol J. Clover, Judith Halberstam, and Laura Mulvey

The Iconicity of Chainsaws from the Backyard to the BBQ

The chainsaw in American popular culture and especially in the Texas Chain Saw Massacre motion pictur

Long-Term Effects of an Invasive Shore Crab on Cape Cod, Massachusetts

Invasive species can cause dramatic changes in the structure of intertidal communities. In some systems, however, abundance or impacts of invaders may peak 10–20 years after invasion and decline thereafter. Hemigrapsus sanguineus (Asian Shore Crab) has been established at Sandwich, MA, on the north side of Cape Cod, since the mid-1990s. This study documented population dynamics of the Asian Shore Crab and 3 species of prey or competitors (Carcinus maenas [Green Crab], Mytilus edulis [Blue Mussel], and Littorina littorea [Common Periwinkle]) over 10 years. An additional goal of the study was to determine whether population growth of the Asian Shore Crab has slowed since its initial establishment. Density of the Asian Shore Crab increased over time, with no evidence of a density-dependent decrease in per capita growth rates. Concurrently, density of the Green Crab and the Blue Mussel declined, but there was no significant temporal trend in density of the Common Periwinkle. If observations at Sandwich are representative of sites north of Cape Cod, populations of the Asian Shore Crab are growing rapidly, and dramatic changes in community structure may be widespread

CYCLICAL CONCENTRATION AND CONSOLIDATION IN BIOTECH R&D: A NEO-SCHUMPETERIAN MODEL

Over the past fifteen years, the agricultural biotechnology industry has exhibited cyclical behavior in concentration and consolidation. This paper provides a theoretical model of endogenous R&D, in which industry concentration exhibits cyclical behavior. The model also generates additional testable hypotheses, and policy implications.Industrial Organization, Research and Development/Tech Change/Emerging Technologies,

Investigating the clinical use of structured light plethysmography to assess lung function in children with neuromuscular disorders

BackgroundChildren and young people with neuromuscular disorders (NMD), such as Duchenne Muscular Dystrophy (DMD), develop progressive respiratory muscles weakness and pulmonary restriction. Pulmonary function monitoring of the decline in lung function allows for timely intervention with cough assist techniques and nocturnal non-invasive ventilation (NIV). NMD may find the measurement of lung function difficult using current techniques. Structured Light Plethysmography (SLP) has been proposed as a novel, non-contact, self-calibrating, non-invasive method of assessing lung function. The overarching aim of this study was to investigate the use of SLP as a novel method for monitoring respiratory function in children with neuromuscular disease.MethodsSLP thoraco-abdominal (TA) displacement was correlated with forced vital capacity measurements recorded by spirometry and the repeatability of the measurements with both methods examined. SLP tidal breathing parameters were investigated to assess the range and repeatability of regional right and left side TA displacement and rib cage and abdominal wall displacement.ResultsThe comparison of the FVC measured with SLP and with spirometry, while having good correlation (R = 0.78) had poor measurement agreement (95% limits of agreement: -1.2 to 1.2L) The mean relative contribution of right and left TA displacement in healthy controls was 50:50 with a narrow range. Repeatability of this measure with SLP was found to be good in healthy controls and moderate in NMD children with/without scoliosis but with a wider range. The majority of the control group displayed a predominant rib cage displacement during tidal breathing and those who displayed predominant abdominal wall displacement showed displacement of both regions close to 50:50 with similar results for the rib cage and abdomen. In comparison, children with NMD have a more variable contribution for all of these parameters. In addition, SLP was able to detect a reduction in abdominal contribution to TA displacement with age in the DMD group and detect paradoxical breathing in children with NMD. Using SLP tracings during tidal breathing we were able to identify three specific patterns of breathing amongst healthy individuals and in children with NMD.ConclusionsSLP is a novel method for measuring lung function that requires limited patient cooperation and may be especially useful in children with neuromuscular disorders. Measuring the relative contributions of the right and left chest wall and chest versus abdominal movements allows a more detailed assessment