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

Stability and renormalization of Yang-Mills theory with Background Field Method: a regularization independent proof

In this paper the stability and the renormalizability of Yang-Mills theory in the Background Field Gauge are studied. By means of Ward Identities of Background gauge invariance and Slavnov-Taylor Identities the stability of the classical model is proved and, in a regularization independent way, its renormalizability is verified. A prescription on how to build the counterterms is given and the possible anomalies which may appear for Ward Identities and for Slavnov-Taylor Identities are shown.Comment: 25 pages, Latex 2.09, no figure

Hospitality, Culture and Regeneration: Urban decay, entrepreneurship and the "ruin" bars of Budapest

This paper considers the relationships between hospitality, culture and urban regeneration through an examination of rom (ruin) venues, which operate in dilapidated buildings in Budapest, Hungary. The paper reviews previous work on culture and urban regeneration in order to locate the role of hospitality within emerging debates. It subsequently interrogates the evolution of the rom phenomenon and demonstrates how, in this context, hospitality thrives because of social and physical decay in urban locations, how operators and entrepreneurs exploit conflicts among various actors involved in regeneration, and how hospitality may be mobilised purposefully in the regeneration process. The paper demonstrates how networked entrepreneurship maintains these operations and how various forms of cultural production are entangled and mobilised in the venues’ hospitality propositions

νd→μ−Δ++n\nu d \to \mu^- \Delta^{++} n Reaction and Axial Vector N−ΔN-\Delta Coupling

The reaction $\nu d \to \mu^- \Delta^{++} n$ is studied in the region of low $q^2$ to investigate the effect of deuteron structure and width of the $\Delta$ resonance on the differential cross section. The results are used to extract the axial vector $N-\Delta$ coupling $C^{A}_5$ from the experimental data on this reaction. The possibility to determine this coupling from electroweak interaction experiments with high intensity electron accelerators is discussed.Comment: 14 pages, REVTEX, 5 figure

Magnetic Reconnection in Extreme Astrophysical Environments

Magnetic reconnection is a basic plasma process of dramatic rearrangement of magnetic topology, often leading to a violent release of magnetic energy. It is important in magnetic fusion and in space and solar physics --- areas that have so far provided the context for most of reconnection research. Importantly, these environments consist just of electrons and ions and the dissipated energy always stays with the plasma. In contrast, in this paper I introduce a new direction of research, motivated by several important problems in high-energy astrophysics --- reconnection in high energy density (HED) radiative plasmas, where radiation pressure and radiative cooling become dominant factors in the pressure and energy balance. I identify the key processes distinguishing HED reconnection: special-relativistic effects; radiative effects (radiative cooling, radiation pressure, and Compton resistivity); and, at the most extreme end, QED effects, including pair creation. I then discuss the main astrophysical applications --- situations with magnetar-strength fields (exceeding the quantum critical field of about 4 x 10^13 G): giant SGR flares and magnetically-powered central engines and jets of GRBs. Here, magnetic energy density is so high that its dissipation heats the plasma to MeV temperatures. Electron-positron pairs are then copiously produced, making the reconnection layer highly collisional and dressing it in a thick pair coat that traps radiation. The pressure is dominated by radiation and pairs. Yet, radiation diffusion across the layer may be faster than the global Alfv\'en transit time; then, radiative cooling governs the thermodynamics and reconnection becomes a radiative transfer problem, greatly affected by the ultra-strong magnetic field. This overall picture is very different from our traditional picture of reconnection and thus represents a new frontier in reconnection research.Comment: Accepted to Space Science Reviews (special issue on magnetic reconnection). Article is based on an invited review talk at the Yosemite-2010 Workshop on Magnetic Reconnection (Yosemite NP, CA, USA; February 8-12, 2010). 30 pages, no figure

Cassini UVIS Observations of the Io Plasma Torus. IV. Modeling Temporal and Azimuthal Variability

In this fourth paper in a series, we present a model of the remarkable temporal and azimuthal variability of the Io plasma torus observed during the Cassini encounter with Jupiter. Over a period of three months, the Cassini Ultraviolet Imaging Spectrograph (UVIS) observed a dramatic variation in the average torus composition. Superimposed on this long-term variation, is a 10.07-hour periodicity caused by an azimuthal variation in plasma composition subcorotating relative to System III longitude. Quite surprisingly, the amplitude of the azimuthal variation appears to be modulated at the beat frequency between the System III period and the observed 10.07-hour period. Previously, we have successfully modeled the months-long compositional change by supposing a factor of three increase in the amount of material supplied to Io's extended neutral clouds. Here, we extend our torus chemistry model to include an azimuthal dimension. We postulate the existence of two azimuthal variations in the number of super-thermal electrons in the torus: a primary variation that subcorotates with a period of 10.07 hours and a secondary variation that remains fixed in System III longitude. Using these two hot electron variations, our model can reproduce the observed temporal and azimuthal variations observed by Cassini UVIS.Comment: Revised 24 August 2007 Accepted by Icarus, 50 pages, 2 Tables, 8 figure

An efficient algorithm to calculate intrinsic thermoelectric parameters based on Landauer approach

The Landauer approach provides a conceptually simple way to calculate the intrinsic thermoelectric (TE) parameters of materials from the ballistic to the diffusive transport regime. This method relies on the calculation of the number of propagating modes and the scattering rate for each mode. The modes are calculated from the energy dispersion (E(k)) of the materials which require heavy computation and often supply energy relation on sparse momentum (k) grids. Here an efficient method to calculate the distribution of modes (DOM) from a given E(k) relationship is presented. The main features of this algorithm are, (i) its ability to work on sparse dispersion data, and (ii) creation of an energy grid for the DOM that is almost independent of the dispersion data therefore allowing for efficient and fast calculation of TE parameters. The inclusion of scattering effects is also straight forward. The effect of k-grid sparsity on the compute time for DOM and on the sensitivity of the calculated TE results are provided. The algorithm calculates the TE parameters within 5% accuracy when the K-grid sparsity is increased up to 60% for all the dimensions (3D, 2D and 1D). The time taken for the DOM calculation is strongly influenced by the transverse K density (K perpendicular to transport direction) but is almost independent of the transport K density (along the transport direction). The DOM and TE results from the algorithm are bench-marked with, (i) analytical calculations for parabolic bands, and (ii) realistic electronic and phonon results for $Bi_{2}Te_{3}$.Comment: 16 Figures, 3 Tables, submitted to Journal of Computational electronic