783 research outputs found

    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

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    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

    Particle Acceleration at Relativistic Shocks

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    I review the current status of Fermi acceleration theory at relativistic shocks. I first discuss the relativistic shock jump conditions, then describe the non-relativistic Fermi mechanism and the differences introduced by relativistic flows. I present numerical calculations of the accelerated particle spectrum, and examine the maximum energy attainable by this process. I briefly consider the minimum energy for Fermi acceleration, and a possible electron pre-acceleration mechanism.Comment: 17 pages, 4 figures. To appear in "Relativistic Flows in Astrophysics", A.W. Guthmann, M. Georganopoulos, A. Marcowith and K. Manolokou, eds., Lecture Notes in Pysics, Springer Verla

    Information Invariance and Quantum Probabilities

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    We consider probabilistic theories in which the most elementary system, a two-dimensional system, contains one bit of information. The bit is assumed to be contained in any complete set of mutually complementary measurements. The requirement of invariance of the information under a continuous change of the set of mutually complementary measurements uniquely singles out a measure of information, which is quadratic in probabilities. The assumption which gives the same scaling of the number of degrees of freedom with the dimension as in quantum theory follows essentially from the assumption that all physical states of a higher dimensional system are those and only those from which one can post-select physical states of two-dimensional systems. The requirement that no more than one bit of information (as quantified by the quadratic measure) is contained in all possible post-selected two-dimensional systems is equivalent to the positivity of density operator in quantum theory.Comment: 8 pages, 1 figure. This article is dedicated to Pekka Lahti on the occasion of his 60th birthday. Found. Phys. (2009

    Graviton Resonances in E+ E- -> MU+ MU- at Linear Colliders with Beamstrahlung and ISR Effects

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    Electromagnetic radiation emitted by the colliding beams is expected to play an important role at the next generation of high energy e^+ e^- linear collider(s). Focusing on the simplest process e+e- -> mu+ mu-, we show that radiative effects like initial state radiation (ISR) and beamstrahlung can lead to greatly-enhanced signals for resonant graviton modes of the Randall-Sundrum model.Comment: 20 pages Latex, 7 eps figure

    Equilibration processes in the Warm-Hot Intergalactic Medium

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    The Warm-Hot Intergalactic Medium (WHIM) is thought to contribute about 40-50 % to the baryonic budget at the present evolution stage of the universe. The observed large scale structure is likely to be due to gravitational growth of density fluctuations in the post-inflation era. The evolving cosmic web is governed by non-linear gravitational growth of the initially weak density fluctuations in the dark energy dominated cosmology. Non-linear structure formation, accretion and merging processes, star forming and AGN activity produce gas shocks in the WHIM. Shock waves are converting a fraction of the gravitation power to thermal and non-thermal emission of baryonic/leptonic matter. They provide the most likely way to power the luminous matter in the WHIM. The plasma shocks in the WHIM are expected to be collisionless. Collisionless shocks produce a highly non-equilibrium state with anisotropic temperatures and a large differences in ion and electron temperatures. We discuss the ion and electron heating by the collisionless shocks and then review the plasma processes responsible for the Coulomb equilibration and collisional ionisation equilibrium of oxygen ions in the WHIM. MHD-turbulence produced by the strong collisionless shocks could provide a sizeable non-thermal contribution to the observed Doppler parameter of the UV line spectra of the WHIM.Comment: 13 pages, 4 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 8; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke

    Factorizing the hard and soft spectator scattering contributions for the nucleon form factor F_1 at large Q^2

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    We investigate the soft spectator scattering contribution for the FF F1F_{1}. We focus our attention on factorization of the hard-collinear scale QΛ\sim Q\Lambda corresponding to transition from SCET-I to SCET-II. We compute the leading order jet functions and find that the convolution integrals over the soft fractions are logarithmically divergent. This divergency is the consequence of the boost invariance and does not depend on the model of the soft correlation function describing the soft spectator quarks. Using as example a two-loop diagram we demonstrated that such a divergency corresponds to the overlap of the soft and collinear regions. As a result one obtains large rapidity logarithm which must be included in the correct factorization formalism. We conclude that a consistent description of the factorization for F1F_{1} implies the end-point collinear divergencies in the hard and soft spectator contributions, i.e. convolution integrals with respect to collinear fractions are not well-defined. Such scenario can only be realized when the twist-3 nucleon distribution amplitude has specific end-point behavior which differs from one expected from the evolution of the nucleon distribution amplitude. Such behavior leads to the violation of the collinear factorization for the hard spectator scattering contribution. We suggest that the soft spectator scattering and chiral symmetry breaking provide the mechanism responsible for the violation of collinear factorization in case of form factor F1F_{1}.Comment: 25 pages, 6 figures, text is improved, few typos corrected, one figure added, statement about end-point behavior of the nucleon DA is formulated more accuratel

    Magnetic fields in supernova remnants and pulsar-wind nebulae

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    We review the observations of supernova remnants (SNRs) and pulsar-wind nebulae (PWNe) that give information on the strength and orientation of magnetic fields. Radio polarimetry gives the degree of order of magnetic fields, and the orientation of the ordered component. Many young shell supernova remnants show evidence for synchrotron X-ray emission. The spatial analysis of this emission suggests that magnetic fields are amplified by one to two orders of magnitude in strong shocks. Detection of several remnants in TeV gamma rays implies a lower limit on the magnetic-field strength (or a measurement, if the emission process is inverse-Compton upscattering of cosmic microwave background photons). Upper limits to GeV emission similarly provide lower limits on magnetic-field strengths. In the historical shell remnants, lower limits on B range from 25 to 1000 microGauss. Two remnants show variability of synchrotron X-ray emission with a timescale of years. If this timescale is the electron-acceleration or radiative loss timescale, magnetic fields of order 1 mG are also implied. In pulsar-wind nebulae, equipartition arguments and dynamical modeling can be used to infer magnetic-field strengths anywhere from about 5 microGauss to 1 mG. Polarized fractions are considerably higher than in SNRs, ranging to 50 or 60% in some cases; magnetic-field geometries often suggest a toroidal structure around the pulsar, but this is not universal. Viewing-angle effects undoubtedly play a role. MHD models of radio emission in shell SNRs show that different orientations of upstream magnetic field, and different assumptions about electron acceleration, predict different radio morphology. In the remnant of SN 1006, such comparisons imply a magnetic-field orientation connecting the bright limbs, with a non-negligible gradient of its strength across the remnant.Comment: 20 pages, 24 figures; to be published in SpSciRev. Minor wording change in Abstrac

    Charged-Particle Multiplicities in Charged-Current Neutrino-- and Anti-Neutrino--Nucleus Interactions

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    The CHORUS experiment, designed to search for νμντ\nu_{\mu}\to\nu_{\tau} oscillations, consists of a nuclear emulsion target and electronic detectors. In this paper, results on the production of charged particles in a small sample of charged-current neutrino-- and anti-neutrino--nucleus interactions at high energy are presented. For each event, the emission angle and the ionization features of the charged particles produced in the interaction are recorded, while the standard kinematic variables are reconstructed using the electronic detectors. The average multiplicities for charged tracks, the pseudo-rapidity distributions, the dispersion in the multiplicity of charged particles and the KNO scaling are studied in different kinematical regions. A study of quasi-elastic topologies performed for the first time in nuclear emulsions is also reported. The results are presented in a form suitable for use in the validation of Monte Carlo generators of neutrino--nucleus interactions.Comment: 17 pages, 5 figure

    Black Hole Spin via Continuum Fitting and the Role of Spin in Powering Transient Jets

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    The spins of ten stellar black holes have been measured using the continuum-fitting method. These black holes are located in two distinct classes of X-ray binary systems, one that is persistently X-ray bright and another that is transient. Both the persistent and transient black holes remain for long periods in a state where their spectra are dominated by a thermal accretion disk component. The spin of a black hole of known mass and distance can be measured by fitting this thermal continuum spectrum to the thin-disk model of Novikov and Thorne; the key fit parameter is the radius of the inner edge of the black hole's accretion disk. Strong observational and theoretical evidence links the inner-disk radius to the radius of the innermost stable circular orbit, which is trivially related to the dimensionless spin parameter a_* of the black hole (|a_*| < 1). The ten spins that have so far been measured by this continuum-fitting method range widely from a_* \approx 0 to a_* > 0.95. The robustness of the method is demonstrated by the dozens or hundreds of independent and consistent measurements of spin that have been obtained for several black holes, and through careful consideration of many sources of systematic error. Among the results discussed is a dichotomy between the transient and persistent black holes; the latter have higher spins and larger masses. Also discussed is recently discovered evidence in the transient sources for a correlation between the power of ballistic jets and black hole spin.Comment: 30 pages. Accepted for publication in Space Science Reviews. Also to appear in hard cover in the Space Sciences Series of ISSI "The Physics of Accretion onto Black Holes" (Springer Publisher). Changes to Sections 5.2, 6.1 and 7.4. Section 7.4 responds to Russell et al. 2013 (MNRAS, 431, 405) who find no evidence for a correlation between the power of ballistic jets and black hole spi
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