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

"Dark Matter" in Accretion Disks

Using Spitzer Space Telescope photometric observations of the eclipsing, interacting binary WZ Sge, we have discovered that the accretion disk is far more complex than previously believed. Our 4.5 and 8 micron time series observations reveal that the well known gaseous accretion disk is surrounded by an asymmetric disk of dusty material with a radius approximately 15 times larger than the gaseous disk. This dust ring contains only a small amount of mass and is completely invisible at optical and near-IR wavelengths, hence consisting of "dark matter". We have produced a model dust ring using 1 micron spherical particles with a density of 3 g/cm$^3$ and with a temperature profile ranging from 700-1500K. Our discovery about the accretion disk structure and the presence of a larger, outer dust ring have great relevance for accretion disks in general, including those in other interacting binary systems, pre-main sequence stars, and active galaxies.Comment: 34 pages, 8 figures (3 in color). Accepted to Ap

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

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