Microarray-Based Sketches of the HERV Transcriptome Landscape

Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects

C-BORD : les conteneurs de fret maritimeau peigne fin neutronique

L’inspection des conteneurs de fret maritime est un enjeu critique pour le commerce et la protection des personnes afin de détecter rapidement les matières dangereuses ou illicites (sources radioactives, drogues, etc.) éventuellement transportées. Le projet C-BORD (Effective Container Inspection at BORDer Control Points), piloté par le CEA dans le cadre du programme Horizon 2020, aide les douanes européennes à relever ce défi logistique et technique en combinant plusieurs méthodes d’analyses non-intrusives

Monte Carlo parametric studies of neutron interrogation with the Associated Particle Technique for cargo container inspections

The detection of Special Nuclear Materials (SNM) by neutron interrogation is extensively studied by Monte Carlo simulation at the Nuclear Measurement Laboratory of CEA Cadarache (French Alternative Energies and Atomic Energy Commission). The active inspection system is based on the Associated Particle Technique (APT). Fissions induced by tagged neutrons (i.e. correlated to an alpha particle in the DT neutron generator) in SNM produce high multiplicity coincidences which are detected with fast plastic scintillators. At least three particles are detected in a short time window following the alpha detection, whereas nonnuclear materials mainly produce single events, or pairs due to (n,2n) and (n,n’γ) reactions. To study the performances of an industrial cargo container inspection system, Monte Carlo simulations are performed with the MCNP-PoliMi transport code, which records for each neutron history the relevant information: reaction types, position and time of interactions, energy deposits, secondary particles, etc. The output files are post-processed with a specific tool developed with ROOT data analysis software. Particles not correlated with an alpha particle (random background), counting statistics, and time-energy resolutions of the data acquisition system are taken into account in the numerical model. Various matrix compositions, suspicious items, SNM shielding and positions inside the container, are simulated to assess the performances and limitations of an industrial system

POLITRANI, A New Toolkit to Simulate Organic Scintillator Pulses

International audience3He shortage has provoked a renewed interest for organic scintillation detectors (good neutron detection efficiency) with neutron-gamma discrimination capability. Pulse Shape Discrimination (PSD) with plastic scintillators has recently shown important progresses and raises a great interest as plastic detectors are not toxic and not inflammable contrary to liquid scintillation detectors. In this context, the French Atomic and Renewable Energy Commission (CEA), within the FP7 European project SCINTILLA, is studying the possibility to produce large size plastic scintillators as candidates for 3He tube replacements together with the related FPGA electronics. To support the design of plastic scintillators with enhanced neutron-gamma discrimination power, software based on ROOT data analysis software was developed to couple photon-neutron transport with MCNP PoliMi and optical photon tracking in the scintillator with Litrani. This new tool called “POLITRANI” allows to build realistic electronic pulses delivered by radiation detectors, and thus to study PSD sensitivity to various factors such as plastic shape, size, coating, scintillation decay time for neutrons vs. gamma rays, and radiation scattering in the detector. Parameters of the FPGA-based electronics can also be investigated, such as sampling frequency, trigger, and length of the integration gate

Prompt gamma neutron activation analysis of toxic elements in radioactive waste packages

The French Alternative Energies and Atomic Energy Commission (CEA) and National Radioactive Waste Management Agency (ANDRA) are conducting an R&D program to improve the characterization of long-lived and medium activity (LL-MA) radioactive waste packages. In particular, the amount of toxic elements present in radioactive waste packages must be assessed before they can be accepted in repository facilities in order to avoid pollution of underground water reserves. To this aim, the Nuclear Measurement Laboratory of CEA-Cadarache has started to study the performances of Prompt Gamma Neutron Activation Analysis (PGNAA) for elements showing large capture cross sections such as mercury, cadmium, boron, and chromium. This paper reports a comparison between Monte Carlo calculations performed with the MCNPX computer code using the ENDF/B-VII.0 library and experimental gamma rays measured in the REGAIN PGNAA cell with small samples of nickel, lead, cadmium, arsenic, antimony, chromium, magnesium, zinc, boron, and lithium to verify the validity of a numerical model and gamma-ray production data. The measurement of a ∼20kg test sample of concrete containing toxic elements has also been performed, in collaboration with Forschungszentrum Jülich, to validate the model in view of future performance studies for dense and large LL-MA waste packages

Characterization of Uranium Ore Samples by HPGe Gamma-Ray Spectroscopy

International audienceGamma logging for uranium exploration is currently based on total counting with the Geiger–Müller gas detectors or NaI(Tl) scintillators. However, the total count rate interpretation in terms of uranium concentration may be impaired in case of roll fronts when the radioactive equilibrium of the natural 238 U radioactive chain is modified by the differential leaching of uranium and its daughter radioisotopes radium, radon, and so on. Indeed, in the case of secular equilibrium, more than 95% of gamma rays emitted by uranium ores come from 214 Pb and 214 Bi isotopes that are in the back end of the 238 U decay chain. These two isotopes might produce an intense gamma signal even when uranium is not present, or with a much smaller activity, in the ore. Therefore, gamma spectroscopy measurements of core samples are performed on the surface with HPGe detectors to directly characterize uranium activity from the 1001-keV gamma ray of 234 mPa that is at the beginning of the 238 U chain. However, due to the low intensity of this gamma ray, acquisitions of several hours are needed. In view to characterize uranium concentration within a few minutes, we propose a method using both the 92 keV gamma rays of 234 Th and 235 U and the 98.4-keV uranium X-ray. This last is due to uranium self-induced fluorescence caused by gamma rays of the uranium chain, mainly 214 Pb and 214 Bi. The gamma rays of 214 Pb and 214 Bi undergo scatterings in the sample leading to photons with energy in the 100-keV range that favor photoelectric interactions and, thus, fluorescence. The comparison of the uranium activity obtained with the 92- and 98.4-keV lines allows detecting a uranium heterogeneity in the ore. Indeed, in the case of uranium nugget, the 92-keV peak leads to underestimated uranium concentration due to the gamma self-absorption, but on the contrary, the 98.4-keV peak leads to an overestimation because of increased fluorescence. In order to test this new approach, tens of uranium..

Gamma-ray spectroscopy for the characterization of uranium contamination in nuclear decommissioning

International audienceDecommissioning is the last step in the life cycle of a nuclear facility. After the evacuation of the facility components, the remaining structures such as concrete walls and floors must be surveyed to ensure that no residual contamination remains. It is a costly and time consuming activity, for which CEA develops fast alpha and beta detection methods allowing a full scanning of very large areas (hundreds of thousands of square meters) in legacy uranium enrichment plants. To support these developments, we present here complementary high-resolution gamma-ray spectroscopy analyses of a contaminated area at the gaseous diffusion uranium enrichment facility UDG, currently under decommissioning at Pierrelatte nuclear plant, France. Long measurements are performed with a High-Purity Germanium (HPGe) detector on the contaminated surface, and in a clean area to assess the natural gamma background of the concrete ground. The surface activity of uranium is 16.6 ± 6.0 Bq.cm-2, mainly due to 234U and 238U, most of the uncertainty coming from the non-uniform distribution of the contamination on the ground. This measurements also allowed us estimating the uranium enrichment of the contamination, which amounts to (0.80 ± 0.13) % of 235U mass fraction, consistently with the range of the Low Enrichment Plant where this measure was performed. Eventually, the background spectrum allowed us to determine the mass fractions of natural uranium, thorium and potassium in the concrete ground, which respectively amount to 3.8 ± 0.2. ppmU (i.e. 3.8 mg of uranium per kg of concrete), 7.4 ± 0.7 ppmTh, and (2.6 ± 0.1) %K of potassium

Comparison between GEANT4 and MCNP for well logging applications

International audienceMCNP and GEANT4 are two reference Monte Carlo nuclear simulators, MCNP being the standard in the Oil & Gas nuclear logging industry. While performing a simulation benchmark of these two software for the purpose of “Cased Hole” wellbore evaluation, discrepancies between MCNP and GEANT4 were observed: computational experiments were performed first in a theoretical and simplified environment using spherical models, then in a more realistic “Open Hole” wellbore context with simplified logging tools. Results of this comparison show an excellent overall agreement for gamma-gamma physics and an acceptable agreement for neutron-neutron physics. However, the agreement for neutron-gamma physics is satisfactory only for certain lithologies and energy windows, but not acceptable for other operating conditions. These results need to be put in perspective with the current use of nuclear simulation in the logging industry. Indeed, wellbore evaluations rely on charts simulated with Monte Carlo codes in various contexts. In the case of radially heterogeneous environments such as “Cased Hole” wellbores, nuclear simulations are mandatory to precisely determine the radial sensitivity of logging tools via the so-called sensitivity functions. The feasibility of wellbore inversion relies on the physical validity of such sensitivity functions obtained from nuclear simulations. This MCNP vs. GEANT4 benchmark was conducted with the perspective to secure the physical fundamentals used for building the sensitivity functions of logging tools.Key words: Well logging / Monte-Carlo modeling / MCNP / GEANT4 / Gamma-Gamma / Neutron-Neutron / Neutron-Gamma / Sensitivity function / Nuclear logging probe

Passive and Active Correlation Techniques for the Detection of Nuclear Materials

International audienceIn the frame of the French trans-governmental R&D program against CBRN-E threats, CEA (French Alternative Energies and Atomic Energy Commission) is studying the detection of Special Nuclear Materials (SNM) by neutron interrogation with the Associated Particle Technique (APT). Coincidences including at least 3 fission neutrons or gamma rays induced by tagged neutrons are used to detect and distinguish SNM from benign materials in which lower multiplicity events of 1 or 2 particles are produced by (n,2n) or (n,n’ ) reactions. Coincidences are detected by fast plastic scintillators and correlated with tagged neutrons to improve the signal-to-noise ratio. Dedicated data acquisition electronics (DAQ) have been developed with independent FPGA cards associated with each detector, so that the acquisition window can be opened by any of the plastic scintillators. DAQ tests in passive mode are presented, in which acquisition is triggered by the sum signal of all detectors. The system time and energy calibrationand resolution are reported, as well as the qualification of numerical simulations thanks to experimental data acquired with simple setups using a source. Numerical studies for the design and performance of cargo container inspection are also performed with the MCNP-PoliMi computer code and the ROOT data analysis package. SNM detection in iron matrix is quite straightforward, but in organic matrix, data processing will need to combine more information to evidence SNM