Sequencing of idiopathic pulmonary fibrosis-related genes reveals independent single gene associations

BACKGROUND: Previous studies investigating a genetic basis for idiopathic pulmonary fibrosis (IPF) have focused on resequencing single genes in IPF kindreds or cohorts to determine the genetic contributions to IPF. None has investigated interactions among the candidate genes. OBJECTIVE: To compare the frequencies and interactions of mutations in six IPF-associated genes in a cohort of 132 individuals with IPF with those of a disease-control cohort of 192 individuals with chronic obstructive pulmonary disease (COPD) and the population represented in the Exome Variant Server. METHODS: We resequenced the genes encoding surfactant proteins A2 (SFTPA2), and C (SFTPC), the ATP binding cassette member A3 (ABCA3), telomerase (TERT), thyroid transcription factor (NKX2-1) and mucin 5B (MUC5B) and compared the collapsed frequencies of rare (minor allele frequency <1%), computationally predicted deleterious variants in each cohort. We also genotyped a common MUC5B promoter variant that is over-represented in individuals with IPF. RESULTS: We found 15 mutations in 14 individuals (11%) in the IPF cohort: (SFTPA2 (n=1), SFTPC (n=5), ABCA3 (n=4) and TERT (n=5)). No individual with IPF had two different mutations, but one individual with IPF was homozygous for p.E292V, the most common ABCA3 disease-causing variant. We did not detect an interaction between any of the mutations and the MUC5B promoter variant. CONCLUSIONS: Rare mutations in SFTPA2, SFTPC and TERT are collectively over-represented in individuals with IPF. Genetic analysis and counselling should be considered as part of the IPF evaluation

Initiating e-learning by stealth, participation and consultation in a late majority institution

The extent to which opportunities afforded by e-learning are embraced by an institution can depend in large measure on whether it is perceived as enabling and transformative or as a major and disruptive distraction. Most case studies focus on the former. This paper describes how e-learning was introduced into the latter environment. The sensitivity of competing pressures in a research intensive university substantially influenced the manner in which e-learning was promoted. This paper tells that story, from initial stealth to eventual university acknowledgement of the relevance of e-learning specifically to its own context

AffecTech- an affect-aware interactive AV Artwork

New developments in real-time computing and body-worn sensor technology allow us to explore not just visible gestures using inertial sensors, but also invisible changes in an individual’s physiological state using bio-sensors (Kim & André 2008). This creates an opportunity for a more intimate interaction between the observer and technology-based art (Gonsalves 2008). We present a technical overview of the AffecTech system; a bio-signal based interactive audio- visual installation commissioned as part of the pre-ISEA symposium in November 2008. Observers were invited to sit on one of 2 sensor-enhanced chairs (Coghlan & Knapp 2008), which transmitted physiological data about the occupant to a central control system. This data was used to control and modulate interactive visuals, live video feeds and a surround sound score, with events and interactions dependent on the observers’ affective/emotional state and the disparity or similarity between the bio-signals of the chairs occupants. This technical overview is followed by an examination of the outcomes of the project, from both the artistic and technical viewpoints, with recommendations for modification in future implementations

A unique 3D nitrogen-doped carbon composite as high-performance oxygen reduction catalyst

The synthesis and properties of an oxygen reduction catalyst based on a unique 3-dimensional (3D) nitrogen doped (N-doped) carbon composite are described. The composite material is synthesised via a two-step hydrothermal and pyrolysis method using bio-source low-cost materials of galactose and melamine. Firstly, the use of iron salts and galactose to hydrothermally produceiron oxide (Fe₂O₃) magnetic nanoparticle clusters embedded carbon spheres. Secondly, magnetic nanoparticles diffused out of the carbon sphere when pyrolysed in the presence of melamine as nitrogen precursor. Interestingly, many of these nanoparticles, as catalyst-grown carbon nanotubes (CNTs), resulted in the formation of N-doped CNTs and N-doped carbon spheres under the decomposition of carbon and a nitrogen environment. The composite material consists of integrated N-doped carbon microspheres and CNTs show high ORR activity through a predominantly four-electron pathway.Ramesh Karunagaran, Tran Thanh Tung, Cameron Shearer, Diana Tran, Campbell Coghlan, Christian Doonan, and Dusan Losi

A City in Common: A Framework to Orchestrate Large-scale Citizen Engagement around Urban Issues

Citizen sensing is an approach that develops and uses lightweight technologies with local communities to collect, share and act upon data. In doing so it enables them to become more aware of how they can tackle local issues. We report here on the development and uptake of the 'City- Commons Framework for Citizen Sensing', a conceptual model that builds on Participatory Action Research with the aim of playing an integrating role: outlining the processes and mechanisms for ensuring sensing technologies are co-designed by citizens to address their concerns. At the heart of the framework is the idea of a city commons: a pool of community-managed resources. We discuss how the framework was used by communities in Bristol to measure and monitor the problem of damp housing

Neonatal abstinence syndrome.

A 12 month review of infants admitted with neonatal abstinence syndrome to a neonatal intensive care unit was undertaken. The relationship of maternal drug abuse to symptoms, the effectiveness of pharmacologic agents in controlling symptoms and the length of inpatient stay were investigated. A retrospective review of maternal and infant records was performed. Those infants with a serial Finnegan score greater than 8 were treated. Pharmacologic treatment was oral morphine sulphate (0.2 mg 4-6 hourly), phenobarbitone (3-7 mgs/kg/day), or combination of the above. 43 infants were admitted to the hospital during the year. The average maternal age was 24.6 years, (18-34 years). Drug use volunteered by the mothers was methadone alone in 6 cases, methadone and benzodiazepines in 14, methadone and heroin and benzodiazepines in 7, methadone and heroin in 10, heroin alone in 2, and other multiple drug use including oral morphine sulphate, dothiepin and cannabis in 4. Average gestational age was 40.3 (35-42 weeks). The average birthweight was 2.81 kgs (1.89-3.91 kgs). Time to onset of withdrawal symptoms was 2.8 (1-13) days. The duration of pharmacologic treatment (oral morphine sulphate and/or phenobarbitone) was 21.8 (1-62) days. The total hospital stay for the 43 infants was 1,011 days. This study confirms that polydrug abuse is the commonest type of drug abuse in Dublin. The duration of withdrawal symptoms is loosely related to drug type, but increasing duration of symptoms is noted for infants exposed to benzodiazepines. Our experience would favour the use of morphine sulphate to treat pure opiate withdrawal symptoms. Over the 12-month period, there was an average occupancy of 3 beds per day in the paediatric department

Dilemmas in doing insider research in professional education

This article explores the dilemmas I encountered when researching social work education in England as an insider researcher who was simultaneously employed as an educator in the host institution. This was an ethnographic project deploying multiple methods and generating rich case study material which informed the student textbook Becoming a Social Worker the four-year period of the project. First, ethical dilemmas emerged around informed consent and confidentiality when conducting surveys of students and reading their portfolios. Second, professional dilemmas stemmed from the ways in which my roles as a researcher, academic tutor, social worker and former practice educator converged and collided. Third, political dilemmas pertained to the potential for the project to crystallize and convey conflicts among stakeholders in the university and community. Since the majority of research in social work education is conducted by insiders, we have a vital interest in making sense of such complexity

Why highly expressed proteins evolve slowly

Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we hypothesize that selection to reduce the burden of protein misfolding will favor protein sequences with increased robustness to translational missense errors. Pressure for translational robustness increases with expression level and constrains sequence evolution. Using several sequenced yeast genomes, global expression and protein abundance data, and sets of paralogs traceable to an ancient whole-genome duplication in yeast, we rule out several confounding effects and show that expression level explains roughly half the variation in Saccharomyces cerevisiae protein evolutionary rates. We examine causes for expression's dominant role and find that genome-wide tests favor the translational robustness explanation over existing hypotheses that invoke constraints on function or translational efficiency. Our results suggest that proteins evolve at rates largely unrelated to their functions, and can explain why highly expressed proteins evolve slowly across the tree of life.Comment: 40 pages, 3 figures, with supporting informatio

On the statistical mechanics of prion diseases

We simulate a two-dimensional, lattice based, protein-level statistical mechanical model for prion diseases (e.g., Mad Cow disease) with concommitant prion protein misfolding and aggregation. Our simulations lead us to the hypothesis that the observed broad incubation time distribution in epidemiological data reflect fluctuation dominated growth seeded by a few nanometer scale aggregates, while much narrower incubation time distributions for innoculated lab animals arise from statistical self averaging. We model `species barriers' to prion infection and assess a related treatment protocol.Comment: 5 Pages, 3 eps figures (submitted to Physical Review Letters

Non-perturbative dynamics of hot non-Abelian gauge fields: beyond leading log approximation

Many aspects of high-temperature gauge theories, such as the electroweak baryon number violation rate, color conductivity, and the hard gluon damping rate, have previously been understood only at leading logarithmic order (that is, neglecting effects suppressed only by an inverse logarithm of the gauge coupling). We discuss how to systematically go beyond leading logarithmic order in the analysis of physical quantities. Specifically, we extend to next-to-leading-log order (NLLO) the simple leading-log effective theory due to Bodeker that describes non-perturbative color physics in hot non-Abelian plasmas. A suitable scaling analysis is used to show that no new operators enter the effective theory at next-to-leading-log order. However, a NLLO calculation of the color conductivity is required, and we report the resulting value. Our NLLO result for the color conductivity can be trivially combined with previous numerical work by G. Moore to yield a NLLO result for the hot electroweak baryon number violation rate.Comment: 20 pages, 1 figur