Differential analysis of biological networks

In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling and control networks are subject to some degree of localised re-wiring. Being able to detect disrupted interaction patterns induced by the presence or progression of the disease can lead to the discovery of novel molecular diagnostic and prognostic signatures. Currently there is a lack of scalable statistical procedures for two-network comparisons aimed at detecting localised topological differences. We propose the dGHD algorithm, a methodology for detecting differential interaction patterns in two-network comparisons. The algorithm relies on a statistic, the Generalised Hamming Distance (GHD), for assessing the degree of topological difference between networks and evaluating its statistical significance. dGHD builds on a non-parametric permutation testing framework but achieves computationally efficiency through an asymptotic normal approximation. We show that the GHD is able to detect more subtle topological differences compared to a standard Hamming distance between networks. This results in the dGHD algorithm achieving high performance in simulation studies as measured by sensitivity and specificity. An application to the problem of detecting differential DNA co-methylation subnetworks associated to ovarian cancer demonstrates the potential benefits of the proposed methodology for discovering network-derived biomarkers associated with a trait of interest

Universal corner contributions to entanglement negativity

It has been realised that corners in entangling surfaces can induce new universal contributions to the entanglement entropy and R\'enyi entropy. In this paper we study universal corner contributions to entanglement negativity in three- and four-dimensional CFTs using both field theory and holographic techniques. We focus on the quantity $\chi$ defined by the ratio of the universal part of the entanglement negativity over that of the entanglement entropy, which may characterise the amount of distillable entanglement. We find that for most of the examples $\chi$ takes bigger values for singular entangling regions, which may suggest increase in distillable entanglement. However, there also exist counterexamples where distillable entanglement decreases for singular surfaces. We also explore the behaviour of $\chi$ as the coupling varies and observe that for singular entangling surfaces, the amount of distillable entanglement is mostly largest for free theories, while counterexample exists for free Dirac fermion in three dimensions. For holographic CFTs described by higher derivative gravity, $\chi$ may increase or decrease, depending on the sign of the relevant parameters. Our results may reveal a more profound connection between geometry and distillable entanglement.Comment: 28 pages, 5 figure

Steps in modular specifications for concurrent modules

© 2015 Published by Elsevier B.V.The specification of a concurrent program module is a difficult problem. The specifications must be strong enough to enable reasoning about the intended clients without reference to the underlying module implementation. We survey a range of verification techniques for specifying concurrent modules, in particular highlighting four key concepts: auxiliary state, interference abstraction, resource ownership and atomicity. We show how these concepts combine to provide powerful approaches to specifying concurrent modules

Controlling the polarisation correlation of photon pairs from a charge-tuneable quantum dot

Correlation between the rectilinear polarisations of the photons emitted from the biexciton decay in a single quantum dot is investigated in a device which allows the charge-state of the dot to be controlled. Optimising emission from the neutral exciton states maximises the operating efficiency of the biexciton decay. This is important for single dot applications such as a triggered source of entangled photons. As the bias on the device is reduced correlation between the two photons is found to fall dramatically as emission from the negatively charged exciton becomes significant. Lifetime measurements demonstrate that electronic spin-scattering is the likely cause.Comment: 3 figure

Asian Americans respond less favorably to excitement (vs. calm)-focused physicians compared to European Americans

OBJECTIVES: Despite being considered a model minority, Asian Americans report worse health care encounters than do European Americans. This may be due to affective mismatches between Asian American patients and their European American physicians. We predicted that because Asian Americans value excitement (vs. calm) less than European Americans, they will respond less favorably to excitement-focused (vs. calm) physicians. METHOD: In Study 1, 198 European American, Chinese American, and Hong Kong Chinese community adults read a medical scenario and indicated their preference for an excitement-focused versus calm-focused physician. In Study 2, 81 European American and Asian American community college students listened to recommendations made by an excitement-focused or calm-focused physician in a video, and later attempted to recall the recommendations. In Study 3, 101 European American and Asian American middle-aged and older adults had multiple online encounters with an excitement-focused or calm-focused physician and then evaluated their physicians\u27 trustworthiness, competence, and knowledge. RESULTS: As predicted, Hong Kong Chinese preferred excitement-focused physicians less than European Americans, with Chinese Americans falling in the middle (Study 1). Similarly, Asian Americans remembered health information delivered by an excitement-focused physician less well than did European Americans (Study 2). Finally, Asian Americans evaluated an excitement-focused physician less positively than did European Americans (Study 3). CONCLUSIONS: These findings suggest that while physicians who promote and emphasize excitement states may be effective with European Americans, they may be less so with Asian Americans and other ethnic minorities who value different affective states

Judges and judging in the Court of Final Appeal: a statistical picture

The authors provide a unique perspective on how the Court of Final Appeal has operated from 1997 to 2010. The study tracks the rising caseload in the Court, considers the statistical profile of the new system of judges and notes the greater attention being paid by the final court to public law cases.published_or_final_versio

Inversion of exciton level splitting in quantum dots

The demonstration of degeneracy of exciton spin states is an important step toward the production of entangled photon pairs from the biexciton cascade. We measure the fine structure of exciton and biexciton states for a large number of single InAs quantum dots in a GaAs matrix; the energetic splitting of the horizontally and vertically polarized components of the exciton doublet is shown to decrease as the exciton confinement decreases, crucially passing through zero and changing sign. Thermal annealing is shown to reduce the exciton confinement, thereby increasing the number of dots with splitting close to zero

Automatic Feature Detection and Age Classification of Human Faces in Digital Images

This invention includes a four step process for automatically finding facial images of a human face in an electronically digitized image (for example, taken by a video-camera) and classifying the age of the person (associated with the face) into an age category

Modular termination verification for non-blocking concurrency

© Springer-Verlag Berlin Heidelberg 2016.We present Total-TaDA, a program logic for verifying the total correctness of concurrent programs: that such programs both terminate and produce the correct result. With Total-TaDA, we can specify constraints on a thread’s concurrent environment that are necessary to guarantee termination. This allows us to verify total correctness for nonblocking algorithms, e.g. a counter and a stack. Our specifications can express lock- and wait-freedom. More generally, they can express that one operation cannot impede the progress of another, a new non-blocking property we call non-impedance. Moreover, our approach is modular. We can verify the operations of a module independently, and build up modules on top of each other