Chiminey: Reliable Computing and Data Management Platform in the Cloud

The enabling of scientific experiments that are embarrassingly parallel, long running and data-intensive into a cloud-based execution environment is a desirable, though complex undertaking for many researchers. The management of such virtual environments is cumbersome and not necessarily within the core skill set for scientists and engineers. We present here Chiminey, a software platform that enables researchers to (i) run applications on both traditional high-performance computing and cloud-based computing infrastructures, (ii) handle failure during execution, (iii) curate and visualise execution outputs, (iv) share such data with collaborators or the public, and (v) search for publicly available data.Comment: Preprint, ICSE 201

The Influence of Genetics on Cystic Fibrosis Phenotypes

Technological advances in genetics have made feasible and affordable large studies to identify genetic variants that cause or modify a trait. Genetic studies have been carried out to assess variants in candidate genes, as well as polymorphisms throughout the genome, for their associations with heritable clinical outcomes of cystic fibrosis (CF), such as lung disease, meconium ileus, and CF-related diabetes. The candidate gene approach has identified some predicted relationships, while genome-wide surveys have identified several genes that would not have been obvious disease-modifying candidates, such as a methionine sulfoxide transferase gene that influences intestinal obstruction, or a region on chromosome 11 proximate to genes encoding a transcription factor and an apoptosis controller that associates with lung function. These unforeseen associations thus provide novel insight into disease pathophysiology, as well as suggesting new therapeutic strategies for CF

Early childhood lung function is a stronger predictor of adolescent lung function in cystic fibrosis than early Pseudomonas aeruginosa infection

Pseudomonas aeruginosa has been suggested as a major determinant of poor pulmonary outcomes in cystic fibrosis (CF), although other factors play a role. Our objective was to investigate the association of early childhood Pseudomonas infection on differences in lung function in adolescence with CF

A simple ionizing radiation spectrometer/dosimeter based on radiation sensing field effect transistors (RadFETs)

This paper reports on the processing steps in a silicon foundry leading to improved performance of the Radiation Sensing Field Effect Transistor (RadFET) and the use of multiple RadFETs in a handheld, battery operated, combination spectrometer/dosimeter

Classifying Severity of Cystic Fibrosis Lung Disease Using Longitudinal Pulmonary Function Data

Rationale: The study of genetic modifiers in cystic fibrosis (CF) lung disease requires rigorous phenotyping. One type of genetic association study design compares polymorphisms in patients at extremes of phenotype, requiring accurate classification of pulmonary disease at varying ages

The evolution of the ISOLDE control system

The ISOLDE on-line mass separator facility is operating on a Personal Computer based control system since spring 1992. Front End Computers accessing the hardware are controlled from consoles running Microsoft WindowsTM through a Novell NetWare4TM local area network. The control system is transparently integrated in the CERN wide office network and makes heavy use of the CERN standard office application programs to control and to document the running of the ISOLDE isotope separators. This paper recalls the architecture of the control system, shows its recent developments and gives some examples of its graphical user interface

Notes on a paper of Mess

These notes are a companion to the article "Lorentz spacetimes of constant curvature" by Geoffrey Mess, which was first written in 1990 but never published. Mess' paper will appear together with these notes in a forthcoming issue of Geometriae Dedicata.Comment: 26 page

Determining the Electronic Confinement of a Subsurface Metallic State

Dopant profiles in semiconductors are important for understanding nanoscale electronics. Highly conductive and extremely confined phosphorus doping profiles in silicon, known as Si:P δ-layers, are of particular interest for quantum computer applications, yet a quantitative measure of their electronic profile has been lacking. Using resonantly enhanced photoemission spectroscopy, we reveal the real-space breadth of the Si:P δ-layer occupied states and gain a rare view into the nature of the confined orbitals. We find that the occupied valley-split states of the δ-layer, the so-called 1Γ and 2Γ, are exceptionally confined with an electronic profile of a mere 0.40 to 0.52 nm at full width at half-maximum, a result that is in excellent agreement with density functional theory calculations. Furthermore, the bulk-like Si 3pz orbital from which the occupied states are derived is sufficiently confined to lose most of its pz-like character, explaining the strikingly large valley splitting observed for the 1Γ and 2Γ states

Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice.

Background: P. aeruginosa is one of the top three causes of opportunistic human bacterial infections. The remarkable variability in the clinical outcomes of this infection is thought to be associated with genetic predisposition. However, the genes underlying host susceptibility to P. aeruginosa infection are still largely unknown. Results: As a step towards mapping these genes, we applied a genome wide linkage analysis approach to a mouse model. A large F2 intercross population, obtained by mating P. aeruginosa-resistant C3H/HeOuJ, and susceptible A/J mice, was used for quantitative trait locus (QTL) mapping. The F2 progenies were challenged with a P. aeruginosa clinical strain and monitored for the survival time up to 7 days post-infection, as a disease phenotype associated trait. Selected phenotypic extremes of the F2 distribution were genotyped with high-density single nucleotide polymorphic (SNP) markers, and subsequently QTL analysis was performed. A significant locus was mapped on chromosome 6 and was named P. aeruginosa infection resistance locus 1 (Pairl1). The most promising candidate genes, including Dok1, Tacr1, Cd207, Clec4f, Gp9, Gata2, Foxp1, are related to pathogen sensing, neutrophils and macrophages recruitment and inflammatory processes. Conclusions: We propose a set of genes involved in the pathogenesis of P. aeruginosa infection that may be explored to complement human studie