Perturbations of the CD8+ T-cell repertoire in CVID patients with complications

AbstractA higher chronic expansion of effector cytotoxic CD8+DR+ T-lymphocytes has been reported in common variable immunodeficiency (CVID) patients with complications such as splenomegaly, autoimmune disease and/or granulomatous disease. In order to document the features associated with this T cell activation involving the CD8+ T-compartment, we examined the diversity of the alpha/beta TCR repertoire of the patient's CD8+ T-lymphocytes using the qualitative analysis of the CDR3 lengths (Immunoscope).Ten CIVD patients were enrolled in this study, four without complications (Group 1), six with complications (Group 2). All patients exhibited non-gaussian altered CDR3 length distributions, albeit to different extent within the different Vβ families. CVID patients with activated CD8+ T-cells show a reduction of their TCR repertoire diversity which is more severe in patients with complications. Viral reactivations such as CMV are suspected to be part of the mechanisms underlying immunosenescence

A unified approach to robust estimation in finite population sampling

We argue that the conditional bias associated with a sample unit can be a useful measure of influence in finite population sampling. We use the conditional bias to derive robust estimators that are obtained by downweighting the most influential sample units. Under the model-based approach to inference, our proposed robust estimator is closely related to the well-known estimator of Chambers (1986). Under the design-based approach, it possesses the desirable feature of being applicable with most sampling designs used in practice. For stratified simple random sampling, it is essentially equivalent to the estimator of Kokic & Bell (1994). The proposed robust estimator depends on a tuning constant. In this paper, we propose a method for determining the tuning constant and show that the resulting estimator is consistent. Results from a simulation study suggest that our approach improves the efficiency of standard nonrobust estimators when the population contains units that may be influential if selected in the sample

SAT, a flexible and optimized Web application for SSR marker development

<p>Abstract</p> <p>Background</p> <p>Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process.</p> <p>Results</p> <p>SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries.</p> <p>SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis.</p> <p>Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow.</p> <p>Conclusion</p> <p>The SAT Web application is available at <url>http://sat.cirad.fr/sat</url>, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator <email>[email protected]</email> to request a login and password.</p

Análisis participativo de las dinámicas socio-ecológicas de la cuenca Perico-Manantiales

The socio-ecological system of the Jujuy Model Forest territory is analyzed within the framework of conceptual models, constructed using the participatory method PARDI (Problem, Actors, Resources, Dynamics, Interactions). Two principal models focus on water quality and availability in two areas: an upstream Catchment zone and a downstream Irrigation zone. Socio-ecological dynamics there are linked to diverse processes: social (population increase, immigration and urbanization), ecological (state of the upper basin and land use downstream) and economic (development models, prices and market fluctuations). Four complementary sub-models account for: pollution, erosion, sedimentation and deforestation, highlighting the central role of these processes for water quality and availability in the future. In the Catchment zone, water is first of all affected by the state of its sources (Rio Grande and Perico rivers, rainfall). The demand for drinking water to supply the municipalities and agricultural activities in the downstream zone put pressure on its availability. The water from the catchment basins also plays a central role in fishing, tourism, agriculture and livestock activities located nearby. In the Irrigation zone, water serves two main uses: as drinking (domestic) water for residents and as irrigation water, mainly in tobacco and sugarcane production. In both areas, water quality is decreasing because of pollution, classified as either solid (garbage), biological (sewage, animal waste) or chemical (agricultural inputs and industrial chemicals). In the long term, current dynamics can have strong impacts on public health, the desirability of the area for tourism and its economy. Local responses include: improvements to the efficiency of the irrigation system and other hydro-infrastructure, environmental awareness, and alternative development models adapted to a sustainable management. With a view to future planning, we identify decision rules that modify local actors’ practices in the context of climate change.Se analiza el sistema socio-ecológico conformado por el Bosque Modelo Jujuy en Argentina, a través de la construcción participativa de modelos conceptuales por el método PARDI (Problema, Actores, Dinámica e Interacciones). Dos modelos enfocados sobre la calidad y cantidad del agua representan dos zonas principales: la Zona de los Diques y la Zona de Riego. Las dinámicas socio-ecológicas allí son vinculados a diversos procesos sociales (aumento de la población, inmigración y urbanización), ecológicos (estado de la cuenca alta y uso de la tierra río abajo), y económicos (modelos de desarrollo, fluctuaciones de precios y mercados). Presentamos cuatro sub-modelos de: contaminación, erosión, sedimentación y deforestación, por el rol central de esos procesos en la calidad y disponibilidad del agua al futuro. En la zona de los diques, el agua depende primero del estado de sus fuentes (Río Grande, Río Perico, lluvias). La demanda de agua potable para las municipalidades y la producción agrícola en la zona abajo ejercen presión sobre la disponibilidad de agua. El agua de los diques, juega igualmente un rol central en las actividades de pesca, turismo, agricultura y ganado en su entorno. En la zona de riego, el agua está compartida entre agua potable y agua para riego, del tabaco y de la caña de azúcar principalmente. En ambos zonas, la calidad del agua está bajando a causa de su contaminación: solida (basura), biológica (cloacas, desechos de animales), y química (agroquímicos, químicos industriales). Al largo plazo, identificamos fuertes impactos potenciales de las dinámicas actuales sobre la salud pública, lo atractivo turístico de la zona y su economía. Varias respuestas se presentan: mejoras en la eficiencia del sistema de riego y otras infraestructuras hídricas; conciencia ambiental; modelos de desarrollo alternativos adaptados a un manejo sostenible. Para la planificación al futuro, identificamos las reglas de decisión que están modificando las prácticas de los actores en el contexto del cambio climático

Morphological analysis of microcellular PP produced in a core-back injection process using chemical blowing agents and gas counter pressure

International audienceA complete experimental analysis of the microcellular injection process using Chemical Blowing Agents (CBA) with Gas Counter Pressure (GCP) and core-back expansion is presented. Three different types of polypropylene, neat and charged, were mixed with two different CBAs and injected into a plate mold with varying process parameters. First, an exhaustive cartographical mapping of the plate morphology is analyzed. In a second step, the relation between injection parameters and the resulting morphology is investigated. The results show that injection time affects the cellular structure. The formulation, especially the type of chemical foaming agent, controls the average bubble radius. Compared with classical injection process, the use of CBAs, combined to Gas Counter Pressure and core-back process, allows obtaining parts with good surface aspect, more homogeneous cellular structures and smaller bubble radiu

Understanding nitrogen transfer dynamics in a small agricultural catchment: Comparison of a distributed (TNT2) and a semi distributed (SWAT) modeling approaches

The coupling of an hydrological and a crop model is an efficient approach to study the impact of the interactions between agricultural practices and catchment physical characteristics on stream water quality. We analyzed the consequences of using different modeling approaches of the processes controlling the nitrogen (N) dynamics in a small agricultural catchment monitored for 15 years. Two agro-hydrological models were applied: the fully distributed model TNT2 and the semi-distributed SWAT model. Using the same input dataset, the calibration process aimed at reproducing the same annual water and N balance in both models, to compare the spatial and temporal variability of the main N processes. The models simulated different seasonal cycles for soil N. The main processes involved were N mineralization and denitrification. TNT2 simulated marked seasonal variations with a net increase of mineralization in autumn, after a transient immobilization phase due to the burying of the straw with low C:N ratio. SWAT predicted a steady humus mineralization with an increase when straws are buried and a decrease afterwards. Denitrification was mainly occuring in autumn in TNT2 because of the dynamics of N availability in soil and of the climatic and hydrological conditions. SWAT predicts denitrification in winter, when mineral N is available in soil layers. The spatial distribution of these two processes was different as well: less denitrification in bottom land and close to ditches in TNT2, as a result of N transfer dynamics. Both models simulate correctly global trend and inter-annual variability of N losses in small agricultural catchment when a sufficient amount data is available for calibration. However, N processes and their spatial interactions are simulated very differently, in particular soil mineralization and denitrification. The use of such tools for prediction must be considered with care, unless a proper calibration and validation of the different N processes is carried out

Polymer foaming with chemical blowing agents: Experiment and modeling

International audienceAn experimental and theoretical analysis of the polypropylene foaming process using three different chemical blowing agents (CBA) was performed. A simple experiment was designed to analyze the foaming process of polypropylene (PP)/CO2 system under two different pressure conditions. The expansion ratio and final foam structure was measured both by direct observation and from optical measurements and image analysis, showing a good agreement. A single bubble simulation based on relevant differential scanning calorimetry and thermo-gravimetrical analysis experiments, assuming each CBA particles as a nucleation site and accounting for gas diffusion in the surrounding polymer matrix has been built. The sensitivity of the model to physical and processing parameters has been tested. The calculation results are compared to the experiments and open the route to a simplified method for evaluating the efficiency of CBA