Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

Objectives: CLEF is an MRC sponsored project in the E-Science programme that aims to establish methodologies and a technical infrastructure for the next generation of integrated clinical and bioscience research. Methods: The heart of the CLEF approach to this challenge is to design and develop a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies have been developed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. Results: This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows, pseudonymisation measures and additional monitoring policies that are currently being developed. Conclusion: Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research

Twin-free YBa2Cu3O7 films on (001) NdGaO3 showing isotropic electrical behaviour

Investigating the epitaxial nature of YBa2Cu3O7 films on NdGaO3 (001) by Rutherford backscattering (RBS) and X-ray diffraction (XRD) texture measurements we find that the films are almost single crystalline, in the sense that the a, b and c axes are uniquely defined with respect to those of NdGaO3. The crystalline perfection is, however, not reflected in the electrical properties of the films. Although we measure a Tc of 89.7 K, we did not observe the expected anisotropy in the resistivity. We interpret this to be due to Ga diffusion from the substrate into the film, which effectively blocks the chain conductivity

Broadening the Scope of Nanopublications

In this paper, we present an approach for extending the existing concept of nanopublications --- tiny entities of scientific results in RDF representation --- to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications.Comment: To appear in the Proceedings of the 10th Extended Semantic Web Conference (ESWC 2013

X-Ray Spectral Variability of PKS 2005-489 During the Spectacular November 1998 Flare

We report on monitoring of the BL Lac object PKS 2005-489 by the Rossi X-ray Timing Explorer (RXTE) in October-December 1998. During these months, the source underwent a spectacular flare; at its peak on November 10, its 2-10 keV flux was $3.33 \times 10^{-10} {\rm ~erg ~cm^{-2} ~s^{-1}}$, over 30 times brighter than in quiescence. During the rising phase, the X-ray spectrum of PKS 2005-489 hardened considerably, reaching $\alpha = 1.32~ (F_\nu \propto \nu^{-\alpha})$ near maximum. During the declining phase, the X-ray spectrum steepened rapidly, reaching $\alpha = 1.82$, then became somewhat harder towards the end of December ($\alpha \sim 1.6$). While such behavior has been seen before, the simplicity, magnitude and duration of this flare allowed us to study it in great detail. We argue that this flare was caused by either the injection of particles into the jet or {\it in situ} particle acceleration, and that the spectral steepening which followed the flare maximum was the result of synchrotron cooling. Contrary to other recently observed blazar flares (e.g., Mkn 501, 3C 279, PKS 2155-304), our results do not imply a major shift in the location of the synchrotron peak during this flare.Comment: ApJ Letters in press, 6 pages, 2 figures Corrected reference

Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

CLEF is an MRC sponsored project in the E-Science programme that aims to establish policies and infrastructure for the next generation of integrated clinical and bioscience research. One of the major goals of the project is to provide a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies are needed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows and pseudonymisation mechanisms that are currently being developed. Intended constraints and monitoring policies that will apply to research interrogation of the repository are also outlined. Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research

Efficient discontinuous finite difference meshes for 3-D Laplace-Fourier domain seismic wavefield modelling in acoustic media with embedded boundaries

Simulation of acoustic wave propagation in the Laplace?Fourier (LF) domain, with a spatially uniform mesh, can be computationally demanding especially in areas with large velocity contrasts. To improve efficiency and convergence, we use 3-D second- and fourth-order velocitypressure finite difference (FD) discontinuous meshes (DM). Our DM algorithm can use any spatial discretization ratio between meshes. We evaluate direct and iterative parallel solvers for computational speed, memory requirements and convergence. Benchmarks in realistic 3-D models and topographies show more efficient and stable results for DM with direct solvers than uniform mesh results with iterative solvers

Six questions on the construction of ontologies in biomedicine

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today

Using Insights from Psychology and Language to Improve How People Reason with Description Logics

Inspired by insights from theories of human reasoning and language, we propose additions to the Manchester OWL Syntax to improve comprehensibility. These additions cover: functional and inverse functional properties, negated conjunction, the definition of exceptions, and existential and universal restrictions. By means of an empirical study, we demonstrate the effectiveness of a number of these additions, in particular: the use of solely to clarify the uniqueness of the object in a functional property; the replacement of and with intersection in conjunction, which was particularly beneficial in negated conjunction; the use of except as a substitute for and not; and the replacement of some with including and only with noneOrOnly, which helped in certain situations to clarify the nature of these restrictions