Cathodoluminescence Applied to the Microcharacterization of Mineral Materials: A Present Status in Experimentation and Interpretation

Experimentation and interpretation of cathodoluminescence (CL) microscopy and spectroscopy applied to the microcharacterization of material minerals are reviewed. The origins of the intrinsic (host lattice) and extrinsic (impurities) luminescence emissions in crystals are briefly discussed. Merits and limitations of the available techniques are illustrated. CL emission changes as a function of the incident electron dose are illustrated for the case of natural quartz and sphalerite (ZnS) crystals. These effects are discussed in terms of the development of bulk charging, production of heat, diffusion of impurities, and creation of lattice defects induced by the incident ionizing particles. Although CL emission is mostly extrinsic in origin there is no general rule for identifying the nature of impurities from the CL emission spectra of minerals. However there is potential for using CL spectroscopy for trace element analysis as presented for the case of minerals containing rare-earth luminescent ions. The CL emission is a signature of the crystal-chemistry properties of minerals and hence contains potential genetic information. Some of the applications of CL emissions in the geosciences are summarized

Relationship between pp65 antigenemia levels and real-time quantitative DNA PCR for Human Cytomegalovirus (HCMV) management in immunocompromised patients

<p>Abstract</p> <p>Background</p> <p>Quantitative real-time PCR assays, which are more rapid and practical than pp65 antigenemia determination, are progressively becoming the preferred method for monitoring Human Cytomegalovirus (HCMV) reactivation. However, the relationship between HCMV DNA and antigenemia levels is still under investigation. The aim of this study was to analyse the relationship between HCMV DNA and pp65 antigenemia levels in order to identify clinically useful threshold values for the management of patients.</p> <p>Methods</p> <p>475 consecutive samples from 156 immunosuppressed patients were tested for HCMV by pp65 antigenemia and Real-time PCR assay.</p> <p>Results </p> <p>136 out of 475 consecutive samples derived from 48 patients showed evidence of HCMV infection. HCMV DNA was detected in 106 samples, pp65 antigen in 3, and both markers in 27. pp65 antigen detection was associated with higher HCMV DNA levels. The cut-off HCMV DNA level that best predicted pp65 antigenemia in this series of samples was 11,500 copies/ml, but different threshold levels could be observed for specific groups of patients. HCMV disease was observed in 5 out of 48 patients with active HCMV infection. The presence of clinical symptoms was associated with positive pp65 and with higher antigenemia levels. Higher HCMV DNA load at the onset of viral replication was correlated to the development of clinical symptoms.</p> <p>Conclusion</p> <p>Both pp65 antigenemia and HCMV DNA load can be useful for the prospective monitoring of immunocompromised subjects. Specific cut-off levels capable of triggering preemptive antiviral treatment should be determined in accordance to the type of test used and the characteristics of patients and prospectively validated.</p

Genotype 1 hepatitis C virus envelope features that determine antiviral response assessed through optimal covariance networks

The poor response to the combined antiviral therapy of pegylated alfa-interferon and ribavarin for hepatitis C virus (HCV) infection may be linked to mutations in the viral envelope gene E1E2 (env), which can result in escape from the immune response and higher efficacy of viral entry. Mutations that result in failure of therapy most likely require compensatory mutations to achieve sufficient change in envelope structure and function. Compensatory mutations were investigated by determining positions in the E1E2 gene where amino acids (aa) covaried across groups of individuals. We assessed networks of covarying positions in E1E2 sequences that differentiated sustained virological response (SVR) from non-response (NR) in 43 genotype 1a (17 SVR), and 49 genotype 1b (25 SVR) chronically HCV-infected individuals. Binary integer programming over covariance networks was used to extract aa combinations that differed between response groups. Genotype 1a E1E2 sequences exhibited higher degrees of covariance and clustered into 3 main groups while 1b sequences exhibited no clustering. Between 5 and 9 aa pairs were required to separate SVR from NR in each genotype. aa in hypervariable region 1 were 6 times more likely than chance to occur in the optimal networks. The pair 531-626 (EI) appeared frequently in the optimal networks and was present in 6 of 9 NR in one of the 1a clusters. The most frequent pairs representing SVR were 431-481 (EE), 500-522 (QA) in 1a, and 407-434 (AQ) in 1b. Optimal networks based on covarying aa pairs in HCV envelope can indicate features that are associated with failure or success to antiviral therapy

Evolutionary history of hepatitis C virus genotype 5a in France, a multicenter ANRS study

The epidemic history of HCV genotype 5a is poorly documented in France, where its prevalence is very low, except in a small central area, where it accounts for 14.2% of chronic hepatitis C cases. A Bayesian coalescent phylogenetic investigation based on the E1 envelope gene and a non-structural genomic segment (NS3/4) was carried out to trace the origin of this epidemic using a large sample of genotype 5a isolates collected throughout France. The dates of documented transmissions by blood transfusion were used to calibrate five nodes in the phylogeny. The results of the E1 gene analysis showed that the best-fitting population dynamic model was the expansion growth model under a relaxed molecular clock. The rate of nucleotide substitutions and time to the most recent common ancestors (tMRCA) of genotype 5a isolates were estimated. The divergence of all the French HCV genotype 5a strains included in this study was dated to 1939 [95% HPD: 1921–1956], and the tMRCA of isolates from central France was dated to 1954 [1942–1967], which is in agreement with epidemiological data. NS3/4 analysis provided similar estimates with strongly overlapping HPD values. Phylodynamic analyses give a plausible reconstruction of the evolutionary history of HCV genotype 5a in France, suggesting the concomitant roles of transfusion, iatrogenic route and intra-familial transmission in viral diffusion

Antiretroviral-naive and -treated HIV-1 patients can harbour more resistant viruses in CSF than in plasma

Objectives The neurological disorders in HIV-1-infected patients remain prevalent. The HIV-1 resistance in plasma and CSF was compared in patients with neurological disorders in a multicentre study. Methods Blood and CSF samples were collected at time of neurological disorders for 244 patients. The viral loads were >50 copies/mL in both compartments and bulk genotypic tests were realized. Results On 244 patients, 89 and 155 were antiretroviral (ARV) naive and ARV treated, respectively. In ARV-naive patients, detection of mutations in CSF and not in plasma were reported for the reverse transcriptase (RT) gene in 2/89 patients (2.2%) and for the protease gene in 1/89 patients (1.1%). In ARV-treated patients, 19/152 (12.5%) patients had HIV-1 mutations only in the CSF for the RT gene and 30/151 (19.8%) for the protease gene. Two mutations appeared statistically more prevalent in the CSF than in plasma: M41L (P = 0.0455) and T215Y (P = 0.0455). Conclusions In most cases, resistance mutations were present and similar in both studied compartments. However, in 3.4% of ARV-naive and 8.8% of ARV-treated patients, the virus was more resistant in CSF than in plasma. These results support the need for genotypic resistance testing when lumbar puncture is performe

The morphology of the enamel-dentine junction in Neanderthal molars: Gross morphology, non-metric traits, and temporal trends

This study explores the morphological differences between the enamel–dentine junction (EDJ) of maxillary and mandibular molars of Neanderthals (n = 150) and recent modern humans (n = 106), and between an earlier Neanderthal sample (consisting of Pre-Eemian and Eemian Neanderthals dating to before 115 ka) and a later Neanderthal sample (consisting of Post-Eemian Neanderthals dating to after 115 ka). The EDJ was visualised by segmenting microtomographic scans of each molar. A geometric morphometric methodology compared the positioning of the dentine horns, the shape of the marginal ridge between the dentine horns, and the shape of the cervix. We also examined the manifestation of non-metric traits at the EDJ including the crista obliqua, cusp 5, and post-paracone tubercle. Furthermore, we report on additional morphological features including centrally placed dentine horn tips and twinned dentine horns. Our results indicate that EDJ morphology can discriminate with a high degree of reliability between Neanderthals and recent modern humans at every molar position, and discriminate between the earlier and the later Neanderthal samples at every molar position, except for the M3 in shape space. The cervix in isolation can also discriminate between Neanderthals and recent modern humans, except at the M3 in form space, and is effective at discriminating between the earlier and the later Neanderthal samples, except at the M2/M2 in form space. In addition to demonstrating the taxonomic valence of the EDJ, our analysis reveals unique manifestations of dental traits in Neanderthals and expanded levels of trait variation that have implications for trait definitions and scoring

Detection by thermoluminescence of damages created by alpha desintegrations in radionuclear waste glass

International audienceStudy of thermo-stimulated luminescence of an a irradiated natural glass has revealed the formation of a structural defect that cannot be annealed thermally and is therefore cumulative. This phenomenon was again encountered and analysed in synthetic borosilicate glass to be used as radionuclear waste glass. To detect this structural modification, the thermoluminescence signal of an a irradiated sample is traced under certain conditions, Two peak characteristics of a previous a irradiation appear at 230 °C and 320 °C. Their intensity increases at each new experiment, although the a irradiation dose administered remains constant. In other words, despite the successive thermal emptyings, the glass keeps the trace of previous irradiations and consequently gives an increasing signal for constant doses. This study deals with a description of a physical phenomenon concerning the formation of defects within a irradiated glass matrices. This phenomenon was detected after a thermoluminescence (TL) analysis induced by a particles in natural glass (1,2) and it was systematically detected in synthetic horosili-care glass to be used as radionuclear waste glass. It should be remembered that during the fission reaction of uranium 235 in the centre of a nuclear plant, new nuclei and transuranic elements (neptu-nium, plutonium, americium) are generated. The former constitute the major part of nuclear waste, while the latter are long-life a emitters. After waste recycling to extract the uranium and plutonium (which is fissile and can be reused, mainly in fast-breeder reactors), a nitric solution remains containing 99.9% of fission products, 0.5% of generated plutonium and most of the neptunium and americium. Being co