Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

HIV-1 set-point viral load—the approximately stable value of viraemia in the first years of chronic infection—is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%–43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical “Brownian motion” model and another model (“Ornstein–Uhlenbeck”) that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%–43%) is consistent with other studies based on regression of viral load in donor–recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation

Pyrolysis Gas Composition for a Phenolic Impregnated Carbon Ablator Heatshield

Published physical properties of phenolic impregnated carbon ablator (PICA) are compiled, and the composition of the pyrolysis gases that form at high temperatures internal to a heatshield is investigated. A link between the composition of the solid resin, and the composition of the pyrolysis gases created is provided. This link, combined with a detailed investigation into a reacting pyrolysis gas mixture, allows a consistent, and thorough description of many of the physical phenomena occurring in a PICA heatshield, and their implications, to be presented

Model Driven Engineering and Dependability Analyses: The Topcased Approach

International audienceModel Driven Engineering approaches are widely promoted to overcome difficulties to design, validate and maintain large complex systems. They present interesting dependability characteristics especially in terms of prevention of design faults and validation of design correctness. However industrial needs, practices and applicable standards impose constraints on the dependability activities to perform and justify. Therefore it is necessary to analyze how a complete dependability and safety process can be integrated with model-driven approaches within a seamless global process: which dependability activities are naturally covered or facilitated by model-driven approaches, and which additional activities are needed with which support. This paper presents the results of a study aiming at the establishment of requirements to model-driven engineering methods and tools, to support dependability analyses

Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level Relationships

Background Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. Results The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. Conclusions The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect. As such, these data are likely inappropriate for investigating such ancient relationships

Cisplatin in combination with Phenethyl Isothiocyanate (PEITC), a potential new therapeutic strategy for malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is a very aggressive form of cancer with a poor diagnosis and prognosis. The first line treatment for MPM is a combination of cisplatin and Pemetrexed, which displayed limited efficacy and severe side effects. The naturally occurring compound phenethyl isothiocyanate (PEITC) previously showed interesting anti-tumor properties on several cancer cell lines. We thus aim at evaluating PEITC used alone or in combination with cisplatin in order to improve MPM treatment. Nine MPM cell lines and primary mesothelial cells (PMC), co-cultured or not with M2 macrophages present in MPM microenvironment, were used to assess PEITC and cisplatin anti-tumor properties. Compounds were used alone or in combination. Both PEITC and cisplatin were cytotoxic on MPM cells in a dose dependent manner. We herein showed that PEITC-induced cytotoxicity was due to the generation of reactive oxygen species. Moreover, we showed that cisplatin-PEITC combination allowed the potentialization of both compounds’ cytotoxic effects and prevented the emergence of resistant MPM cells. Interestingly, PMC were not sensitive to the combination. Finally, we showed that M2 macrophages did not alter the anti-tumor properties of the combination. Cisplatin-PEITC combination thus represents a promising strategy to induce a selective toxicity towards malignant cells.Iza Denis, Laurent Cellerin, Marc Gregoire and Christophe Blanquar

Integration of formal fault analysis in ASSERT: Case studies and lessons learnt

International audienceThe ASSERT European Integrated Project (Automated proof-based System and Software Engineering for Real-Time systems; EC FP6, IST-004033) has investigated, elaborated and experimented advanced methods based on the AltaRica language and support tool OCAS for architecture and fault approach propagation description analysis, and integrated in the complete ASSERT process. The paper describes lessons learnt from three case studies: safety critical spacecraft, autonomous deep exploration spacecraft, and civil aircraft

Characterization of proton irradiated 3D-DDTC pixel sensor prototypes fabricated at FBK

In this paper we discuss results relevant to 3D Double-Side Double Type Column (3D-DDTC) pixel sensors fabricated at FBK (Trento, Italy) and oriented to the ATLAS upgrade. Some assemblies of these sensors featuring different columnar electrode configurations (2, 3, or 4 columns per pixel) and coupled to the ATLAS FEI3 read-out chip were irradiated up to large proton fluences and tested in laboratory with radioactive sources. In spite of the non optimized columnar electrode overlap, sensors exhibit reasonably good charge collection properties up to an irradiation fluence of 2 x 10**15 neq/cm2, while requiring bias voltages in the order of 100 V. Sensor operation is further investigated by means of TCAD simulations which can effectively explain the basic mechanisms responsible for charge loss after irradiation.Comment: Preprint submitted to Nuclear Instruments and Methods A, 11 pages, 13 fig