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

Calibration and performance tests of the Very-Front-End electronics for the CMS electromagnetic calorimeter

The Very-Front-End electronics processing signals from photodetectors of the CMS electromagnetic calorimeter have been put through an extensive test programme to guarantee functionality and reliability. The final characteristics of the VFE boards designed for the calorimeter barrel and endcaps are presented. The results, which have been also verified during test beam at CERN, confirm the high quality of the boards production and show that the CMS detector specifications are reached

Performance of Glass Resistive Plate Chambers for a high granularity semi-digital calorimeter

A new design of highly granular hadronic calorimeter using Glass Resistive Plate Chambers (GRPCs) with embedded electronics has been proposed for the future International Linear Collider (ILC) experiments. It features a 2-bit threshold semi-digital read-out. Several GRPC prototypes with their electronics have been successfully built and tested in pion beams. The design of these detectors is presented along with the test results on efficiency, pad multiplicity, stability and reproducibility.Comment: 16 pages, 15 figure

Inner structure of the Puy de Dˆome volcano: cross-comparison of geophysical models (ERT, gravimetry, muon imaging)

International audienceMuon imaging of volcanoes and of geological structures in general is actively being developed by several groups in the world. It has the potential to provide 3-D density distributions with an accuracy of a few percent. At this stage of development, comparisons with established geophysical methods are useful to validate the method. An experiment has been carried out in 2011 and 2012 on a large trachytic dome, the Puy de Dˆome volcano, to perform such a comparison of muon imaging with gravimetric tomography and 2-D electrical resistivity tomography. Here, we present the preliminary results for the last two methods. North-south and east-west resistivity profiles allow us to model the resistivity distribution down to the base of the dome. The modelling of the Bouguer anomaly provides models for the density distribution within the dome that are directly comparable with the results from the muon imaging. Our ultimate goal is to derive a model of the dome using the joint interpretation of all sets of data

Air shower simulation for background estimation in muon tomography of volcanoes

International audienceOne of the main sources of background for the radiography of volcanoes using atmospheric muons comes from the accidental coincidences produced in the muon telescopes by charged particles belonging to the air shower generated by the primary cosmic ray. In order to quantify this background effect, Monte Carlo simulations of the showers and of the detector are developed by the TOMUVOL collaboration. As a first step, the atmospheric showers were simulated and investigated using two Monte Carlo packages, CORSIKA and GEANT4.We compared the results provided by the two programs for the muonic component of vertical proton-induced showers at three energies: 1, 10 and 100 TeV. We found that the spatial distribution and energy spectrum of the muons were in good agreement for the two codes

Construction and commissioning of a technological prototype of a high-granularity semi-digital hadronic calorimeter

A large prototype of 1.3m3 was designed and built as a demonstrator of the semi-digital hadronic calorimeter (SDHCAL) concept proposed for the future ILC experiments. The prototype is a sampling hadronic calorimeter of 48 units. Each unit is built of an active layer made of 1m2 Glass Resistive Plate Chamber(GRPC) detector placed inside a cassette whose walls are made of stainless steel. The cassette contains also the electronics used to read out the GRPC detector. The lateral granularity of the active layer is provided by the electronics pick-up pads of 1cm2 each. The cassettes are inserted into a self-supporting mechanical structure built also of stainless steel plates which, with the cassettes walls, play the role of the absorber. The prototype was designed to be very compact and important efforts were made to minimize the number of services cables to optimize the efficiency of the Particle Flow Algorithm techniques to be used in the future ILC experiments. The different components of the SDHCAL prototype were studied individually and strict criteria were applied for the final selection of these components. Basic calibration procedures were performed after the prototype assembling. The prototype is the first of a series of new-generation detectors equipped with a power-pulsing mode intended to reduce the power consumption of this highly granular detector. A dedicated acquisition system was developed to deal with the output of more than 440000 electronics channels in both trigger and triggerless modes. After its completion in 2011, the prototype was commissioned using cosmic rays and particles beams at CERN.Comment: 49 pages, 41 figure

First test of a power-pulsed electronics system on a GRPC detector in a 3-Tesla magnetic field

An important technological step towards the realization of an ultra-granular hadronic calorimeter to be used in the future International Linear Collider (ILC) experiments has been made. A 33X50 cm2 GRPC detector equipped with a power-pulsed electronics board offering a 1cm2 lateral segmentation was successfully tested in a 3-Tesla magnet operating at the H2 beam line of the CERN SPS. An important reduction of power consumption with no deterioration of the detector performance is obtained when the power-pulsing mode is applied. This important result shows that ultra-granular calorimeters for ILC experiments are not only an attractive but also a realistic option.Comment: 10 pages, 9 figure

High rate, fast timing Glass RPC for the high {\eta} CMS muon detectors

The HL-LHC phase is designed to increase by an order of magnitude the amount of data to be collected by the LHC experiments. To achieve this goal in a reasonable time scale the instantaneous luminosity would also increase by an order of magnitude up to $6.10^{34} cm^{-2} s^{-1}$ . The region of the forward muon spectrometer ($|{\eta}| > 1.6$) is not equipped with RPC stations. The increase of the expected particles rate up to $2 kHz/cm^{2}$ (including a safety factor 3) motivates the installation of RPC chambers to guarantee redundancy with the CSC chambers already present. The actual RPC technology of CMS cannot sustain the expected background level. The new technology that will be chosen should have a high rate capability and provides a good spatial and timing resolution. A new generation of Glass-RPC (GRPC) using low-resistivity (LR) glass is proposed to equip at least the two most far away of the four high ${\eta}$ muon stations of CMS. First the design of small size prototypes and studies of their performance in high-rate particles flux is presented. Then the proposed designs for large size chambers and their fast-timing electronic readout are examined and preliminary results are provided.Comment: 14 pages, 11 figures, Conference proceeding for the 2016 Resistive Plate Chambers and Related Detector