Development and validation of 'AutoRIF': Software for the automated analysis of radiation-induced foci

Copyright @ 2012 McVean et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.Background: The quantification of radiation-induced foci (RIF) to investigate the induction and subsequent repair of DNA double strands breaks is now commonplace. Over the last decade systems specific for the automatic quantification of RIF have been developed for this purpose, however to ask more mechanistic questions on the spatio-temporal aspects of RIF, an automated RIF analysis platform that also quantifies RIF size/volume and relative three-dimensional (3D) distribution of RIF within individual nuclei, is required. Results: A java-based image analysis system has been developed (AutoRIF) that quantifies the number, size/volume and relative nuclear locations of RIF within 3D nuclear volumes. Our approach identifies nuclei using the dynamic Otsu threshold and RIF by enhanced Laplacian filtering and maximum entropy thresholding steps and, has an application ‘batch optimisation’ process to ensure reproducible quantification of RIF. AutoRIF was validated by comparing output against manual quantification of the same 2D and 3D image stacks with results showing excellent concordance over a whole range of sample time points (and therefore range of total RIF/nucleus) after low-LET radiation exposure. Conclusions: This high-throughput automated RIF analysis system generates data with greater depth of information and reproducibility than that which can be achieved manually and may contribute toward the standardisation of RIF analysis. In particular, AutoRIF is a powerful tool for studying spatio-temporal relationships of RIF using a range of DNA damage response markers and can be run independently of other software, enabling most personal computers to perform image analysis. Future considerations for AutoRIF will likely include more complex algorithms that enable multiplex analysis for increasing combinations of cellular markers.This article is made available through the Brunel Open Access Publishing Fund

Patterns for renaming and stamping out object-oriented models.

Modern system engineering is supported by a families of modelling languages; each member of a specific family addresses a different aspect of the application domain. Constructing families of modelling languages is facilitated by the use of packages and templates. Packages are containers of modelling elements. Packages may be specialised and merged. Renamings may be applied to packages. Templates are parameteric packages. New packages are constructed by supplying arguments to a template. Packages and templates rely on the following underlying technology: specialisation; merging; renaming and stamping. Specialisation and merging have been described elsewhere; this paper defines mechanisms for renaming and stamping

A Strong X-Ray Burst from the Low Mass X-Ray Binary EXO0748-676

We have observed an unusually strong X-ray burst as a part of our regular eclipse timing observations of the low mass binary system EXO0748-676. The burst peak flux was 5.2x10^-8 ergs cm^-2 s^-1, approximately five times the normal peak X-ray burst flux observed from this source by RXTE. Spectral fits to the data strongly suggest that photospheric radius expansion occurred during the burst. In this Letter we examine the properties of this X-ray burst, which is the first example of a radius expansion burst from EXO0748-676 observed by RXTE. We find no evidence for coherent burst oscillations. Assuming that the peak burst luminosity is the Eddington luminosity for a 1.4 solar mass neutron star we derive a distance to EXO0748-676 of 7.7 kpc for a helium-dominated burst photosphere and 5.9 kpc for a hydrogen-dominated burst photosphere.Comment: 15 pages including 2 figures and 1 table. Accepted for publication in the Astrophysical Journa

Efficient calculation of the antiferromagnetic phase diagram of the 3D Hubbard model

The Dynamical Cluster Approximation with Betts clusters is used to calculate the antiferromagnetic phase diagram of the 3D Hubbard model at half filling. Betts clusters are a set of periodic clusters which best reflect the properties of the lattice in the thermodynamic limit and provide an optimal finite-size scaling as a function of cluster size. Using a systematic finite-size scaling as a function of cluster space-time dimensions, we calculate the antiferromagnetic phase diagram. Our results are qualitatively consistent with the results of Staudt et al. [Eur. Phys. J. B 17 411 (2000)], but require the use of much smaller clusters: 48 compared to 1000

Unified Band Theoretic Description of Electronic and Magnetic Properties of Vanadium Dioxide Phases

The debate about whether the insulating phases of vanadium dioxide (VO2) can be described by band theory or must be described by a theory of strong electron correlations remains unresolved even after decades of research. Energy-band calculations using hybrid exchange functionals or including self-energy corrections account for the insulating or metallic nature of different phases, but have not yet successfully accounted for the observed magnetic orderings. Strongly-correlated theories have had limited quantitative success. Here we report that, by using hard pseudopotentials and an optimized hybrid exchange functional, the energy gaps and magnetic orderings of both monoclinic VO2 phases and the metallic nature of the high-temperature rutile phase are consistent with available experimental data, obviating an explicit role for strong correlations. We also report a potential candidate for the newly-found metallic monoclinic phase and present a detailed magnetic structure of the M2 monoclinic phase