Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

BACKGROUND: Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. RESULTS: We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC) in peripheral blood mononuclear cells); the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. CONCLUSION: Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting

Exploring the Quality of Life of People in North Eastern and Southern Thailand.

The assumption that development brings not only material prosperity but also a better overall quality of life lies at the heart of the development project. Against this, critics assert that development can undermine social cohesion and threaten cultural integrity. Rarely, however, is the impact of development on wellbeing rigourously analysed using empirical data. This is what the Wellbeing in Developing Countries Group at the University of Bath aims to do drawing on fieldwork carried out in four developing countries, which addresses the themes of resources, needs, agency and structure, and subjective Quality of life (QoL). The first phase of the QoL research in Thailand aimed to explore the categories and components of quality of life for people from different backgrounds and locations with the aim of developing methods for QoL assessment in the third phase of the WeD QoL research. The study presents data obtained from rural and peri-urban sites in Southern and Northeastern Thailand (two villages in Songkhla and three in Khon Kaen, Mukdaharn, and Roi-et). Participants were divided into six groups by gender and age, and were divided again by religion (Buddhist and Muslim) and wealth status in the South. Data collection was conducted between October and December 2004 using focus group discussions, semi-structured interviews, and the Person Generated Index. Content analysis was used for data analysis. The use of a qualitative approach enabled the gathering of empirical data that reflects the sources of difficulty and happiness in the lives of participants. Respondents identified 26 aspects to their quality of life, including family relations, health and longevity, income and having money, jobs, housing, education, debt, and so on. The results reveal clear similarities and differences in the role of traditions, religious beliefs, and values in the lives of people living in remote rural or peri-urban areas in Northeastern and Southern Thailand. These results, together with the findings from Peru, Ethiopia, and Bangladesh, will inform the rest of the WeD research and be used to develop measures to assess the quality of life of people living in developing countries

Apoptosis in the Nervous System in Experimental Allergic Encephalomyelitis

We report here for the first time the occurrence of apoptosis of cells in the spinal cord in experimental allergic encephalomyelitis (EAE), an autoimmune, T-cell-mediated demyelinating disease. Four different forms of EAE were studied in the Lewis rat: (i) acute EAE induced by inoculation with whole spinal cord and adjuvants; (ii) acute EAE induced by inoculation with myelin basic protein (MBP) and adjuvants; (iii) acute EAE induced by the passive transfer of MBP-sensitized spleen cells; (iv) chronic relapsing EAE induced by inoculation with whole spinal cord and adjuvants followed by treatment with low-dose cyclosporin A. Cells undergoing apoptosis were recognized at light and electron microscopy by the presence of either crescentic masses of condensed chromatin lying against the nuclear envelope or rounded masses of uniformly dense chromatin. They were found in both the white and grey matter of the spinal cord in all 4 forms of this disease. Although it was not possible to identify definitively the types of cells undergoing apoptosis, the size and location of some of the affected cells suggested that they were oligodendrocytes. As there is now a large body of evidence that T-cell-induced target cell death takes the form of apoptosis, it is attractive to hypothesize that oligodendrocyte apoptosis is occurring in EAE as a result of oligodendrocyte-directed T-cell cytotoxicity. However, other apoptotic cells were located within the myelin sheath, meninges and perivascular spaces and were clearly not oligodendrocytes but were most likely blood-derived mononuclear cells. The sparsity of their cytoplasm and the absence of phagocytosed material suggested that they were mainly lymphocytes rather than macrophages. Apoptosis has been shown to be involved in deleting autoreactive T-cells during the normal development of tolerance. Thus apoptotic deletion of myelin/oligodendrocyte-specific lymphocytes in the central nervous system in EAE might explain both the subsidence of inflammation and the acquisition of tolerance in this autoimmune disease

Determination of the Jet Energy Scale at the Collider Detector at Fermilab

A precise determination of the energy scale of jets at the Collider Detector at Fermilab at the Tevatron $p\bar{p}$ collider is described. Jets are used in many analyses to estimate the energies of partons resulting from the underlying physics process. Several correction factors are developed to estimate the original parton energy from the observed jet energy in the calorimeter. The jet energy response is compared between data and Monte Carlo simulation for various physics processes, and systematic uncertainties on the jet energy scale are determined. For jets with transverse momenta above 50 GeV the jet energy scale is determined with a 3% systematic uncertainty

An integrated dual process simulation model of alcohol use behaviours in individuals, with application to US population-level consumption, 1984–2012

Introduction The Theory of Planned Behaviour (TPB) describes how attitudes, norms and perceived behavioural control guide health behaviour, including alcohol consumption. Dual Process Theories (DPT) suggest that alongside these reasoned pathways, behaviour is influenced by automatic processes that are determined by the frequency of engagement in the health behaviour in the past. We present a computational model integrating TPB and DPT to determine drinking decisions for simulated individuals. We explore whether this model can reproduce historical patterns in US population alcohol use and simulate a hypothetical scenario, “Dry January”, to demonstrate the utility of the model for appraising the impact of policy interventions on population alcohol use. Method Constructs from the TPB pathway were computed using equations from an existing individual-level dynamic simulation model of alcohol use. The DPT pathway was initialised by simulating individuals’ past drinking using data from a large US survey. Individuals in the model were from a US population microsimulation that accounts for births, deaths and migration (1984–2015). On each modelled day, for each individual, we calculated standard drinks consumed using the TPB or DPT pathway. In each year we computed total population alcohol use prevalence, frequency and quantity. The model was calibrated to alcohol use data from the Behavioral Risk Factor Surveillance System (1984–2004). Results The model was a good fit to prevalence and frequency but a poorer fit to quantity of alcohol consumption, particularly in males. Simulating Dry January in each year led to a small to moderate reduction in annual population drinking. Conclusion This study provides further evidence, at the whole population level, that a combination of reasoned and implicit processes are important for alcohol use. Alcohol misuse interventions should target both processes. The integrated TPB-DPT simulation model is a useful tool for estimating changes in alcohol consumption following hypothetical population interventions

Role of electromagnetically induced transparency in resonant four-wave-mixing schemes.

Published versio

Training in the Conduct of Population-Based Multi-Site and Multi-Disciplinary Studies: the Cancer Research Network’s Scholars Program

Expanding research capacity of large research networks within health care delivery systems requires strategically training both embedded and external investigators in necessary skills for this purpose. Researchers new to these settings frequently lack the skills and specialized knowledge conducive to multi-site and multi-disciplinary research set in delivery systems. This report describes the goals and components of the Cancer Research Network (CRN) Scholars Program, a 26-month training program developed to increase the capacity for cancer research conducted within the network’s participating sites, its progression from training embedded investigators to a mix of internal and external investigators, and the content evolution of the training program. The CRN Scholars program was launched in 2007 to assist junior investigators from member sites develop independent and sustainable research programs within the CRN. Resulting from CRN’s increased emphasis on promoting external collaborations, the 2013 Scholars program began recruiting junior investigators from external institutions committed to conducting delivery system science. Based on involvement of this broader population and feedback from prior Scholar cohorts, the program has honed its focus on specific opportunities and issues encountered in conducting cancer research within health care delivery systems. Efficiency and effectiveness of working within networks is accelerated by strategic and mentored navigation of these networks. Investing in training programs specific to these settings provides the opportunity to improve multi-disciplinary and multi-institutional collaboration, particularly for early-stage investigators. Aspects of the CRN Scholars Program may help inform others considering developing similar programs to expand delivery system research or within large, multi-disciplinary research networks

Avalanche Dynamics in Evolution, Growth, and Depinning Models

The dynamics of complex systems in nature often occurs in terms of punctuations, or avalanches, rather than following a smooth, gradual path. A comprehensive theory of avalanche dynamics in models of growth, interface depinning, and evolution is presented. Specifically, we include the Bak-Sneppen evolution model, the Sneppen interface depinning model, the Zaitsev flux creep model, invasion percolation, and several other depinning models into a unified treatment encompassing a large class of far from equilibrium processes. The formation of fractal structures, the appearance of $1/f$ noise, diffusion with anomalous Hurst exponents, Levy flights, and punctuated equilibria can all be related to the same underlying avalanche dynamics. This dynamics can be represented as a fractal in $d$ spatial plus one temporal dimension. We develop a scaling theory that relates many of the critical exponents in this broad category of extremal models, representing different universality classes, to two basic exponents characterizing the fractal attractor. The exact equations and the derived set of scaling relations are consistent with numerical simulations of the above mentioned models.Comment: 27 pages in revtex, no figures included. Figures or hard copy of the manuscript supplied on reques

Active Galactic Nuclei at the Crossroads of Astrophysics

Over the last five decades, AGN studies have produced a number of spectacular examples of synergies and multifaceted approaches in astrophysics. The field of AGN research now spans the entire spectral range and covers more than twelve orders of magnitude in the spatial and temporal domains. The next generation of astrophysical facilities will open up new possibilities for AGN studies, especially in the areas of high-resolution and high-fidelity imaging and spectroscopy of nuclear regions in the X-ray, optical, and radio bands. These studies will address in detail a number of critical issues in AGN research such as processes in the immediate vicinity of supermassive black holes, physical conditions of broad-line and narrow-line regions, formation and evolution of accretion disks and relativistic outflows, and the connection between nuclear activity and galaxy evolution.Comment: 16 pages, 5 figures; review contribution; "Exploring the Cosmic Frontier: Astrophysical Instruments for the 21st Century", ESO Astrophysical Symposia Serie

Neutral-Current Four-Fermion Production in e+e- Interactions at LEP

Neutral-current four-fermion production, e+e- -> ffff is studied in 0.7/fb of data collected with the L3 detector at LEP at centre-of-mass energies root(s)=183-209GeV. Four final states are considered: qqvv, qqll, llll and llvv, where l denotes either an electron or a muon. Their cross sections are measured and found to agree with the Standard Model predictions. In addition, the e+e- -> Zgamma* -> ffff process is studied and its total cross section at the average centre-of-mass energy 196.6GeV is found to be 0.29 +/- 0.05 +/- 0.03 pb, where the first uncertainty is statistical and the second systematic, in agreement with the Standard Model prediction of 0.22 pb. Finally, the mass spectra of the qqll final states are analysed to search for the possible production of a new neutral heavy particle, for which no evidence is found