Accelerated HIV testing for PMTCT in maternity and labour wards is vital to capture mothers at a critical point in the programme at district level

TORONTO AIDS Conference 200

Taxonomic study of entomopathogenic nematodes (Nematoda : Steinernematidae, Heterorhabditidae) from Benin

A study on the biodiversity of entomopathogenic nematodes was conducted during 2010 and 2011 in South Benin. Soil samples from eight sites production of annual and perennial crops were analysed. We obtained 13.21 % of positive soil samples out of 280. We here report on the identification of six of these isolates. Molecular, morphometrical and morphological observations classified the isolates within the genus Heterorhabditis ; one isolate was conspecific with H. indica and two other isolates with H. sonorensis. More information is needed for effective identification of the remaining three isolates. Phylogenic analysis based on sequences of ITS regions of rDNA grouped our isolates with H. sonorensis and H. taysearae with bootstrap support values of 94 and 99 % in Maximum Parsimony and Neighbour Joining trees, respectively. Morphological characters of the infective juveniles and males did not correspond to those of H. taysearae, but were close to H. sonorensis. In contrast, the female of the H. sonorensis populations did show some minor differences with the originally described one. No progeny was obtained from the crossbreeding of Beninese isolates and H. taysearae. Crossing with an isolate of H. sonorensis would have been more conclusive, but no isolates were available even for specimen’s morphological comparison.Keywords : Survey, identification, Molecular, cross-hybridization, Heterorhabditis.Etude taxonomique desnematodes entomopathogenes (Nematoda : Steinernematidae, Heterorhabditidae) du BeninUne étude diagnostique réalisée sur les nématodes entomopathogènes (NEP) en 2010 et 2011 dans le Sud- Bénin sur huit sites de production de cultures annuelles et pérennes a conduit à 13,21 % d’échantillons de sols positifs sur 280. Le présent travail a porté sur l’identification de six des isolats de NEP extraits. Les études moléculaires, morphologiques, morphométriques et d’hybridation effectuées utilisant les stades développementaux des nématodes ont révélé un isolat d’H. indica, deux d’H. sonorensis. Pour les autres isolats, des informations complémentaires sont nécessaires pour une identification complète. Le séquençage et l’analyse phylogénétique de la région interspécifique de l’ADN ribosomal ont groupé nos isolats avec H. sonorensis et H. Taysearae dans les arbres de parcimonie maximale et de Neighbour Joining avec les supports respectifs 94 et 99 %. Les caractères morphologiques des juvéniles infectieux et des mâles ne correspondent pas à ceux de la première description d’H. taysearae, mais sont proches d’H. sonorensis. Cependant, certaines femelles avec bouchon copulatoire ne correspondent pas à H. sonorensis. Nos isolats n’ont pas été féconds avec H. taysearae. Un croisement avec H. sonorensis population type serait plus concluant, mais il n’y avait aucun isolat disponible dans la base de gènes.Mots-clés : Etude, identification, moléculaire, hybridation-croisée, Heterorhabditis

Radiation-Hydrodynamics with MPI-AMRVAC: Flux-Limited Diffusion

Radiation controls the dynamics and energetics of many astrophysical environments. To capture the coupling between the radiation and matter, however, is often a physically complex and computationally expensive endeavour. We develop a numerical tool to perform radiation-hydrodynamics simulations in various configurations at an affordable cost. We build upon the finite volume code MPI-AMRVAC to solve the equations of hydrodynamics on multi-dimensional adaptive meshes and introduce a new module to handle the coupling with radiation. A non-equilibrium, flux-limiting diffusion approximation is used to close the radiation momentum and energy equations. The time-dependent radiation energy equation is then solved within a flexible framework, accounting fully for radiation forces and work terms and further allowing the user to adopt a variety of descriptions for the radiation-matter interaction terms (the 'opacities'). We validate the radiation module on a set of standard testcases for which different terms of the radiative energy equation predominate. As a preliminary application to a scientific case, we calculate spherically symmetric models of the radiation-driven and optically thick supersonic outflows from massive Wolf-Rayet stars. This also demonstrates our code's flexibility, as the illustrated simulation combines opacities typically used in static stellar structure models with a parametrised form for the enhanced line-opacity expected in supersonic flows. This new module provides a convenient and versatile tool to perform multi-dimensional and high resolution radiative-hydrodynamics simulations in optically thick environments with the MPI-AMRVAC code. The code is ready to be used for a variety of astrophysical applications, where a first target for us will be multi-dimensional simulations of stellar outflows from Wolf-Rayet stars.Comment: 14 pages, 10 figures Submitted to A&

MOLECULAR IDENTIFICATION OF HETERODERA SPP., AN OVERVIEW OF FIFTEEN YEARS OF RESEARCH *

SUMMARY During the last 15 years, researchers have collected and characterised more than 40 species of nematodes from the genus Heterodera. The species were identified by sequencing the ITS-rRNA genes and by PCR-RFLP profiles; these tools remain the best available for identifying cyst-forming nematodes. By restricting the ITS amplicons with one or a combination of seven restriction enzymes (AluI, AvaI, Bsh1236I, BsuRI, CfoI, MvaI, and RsaI), researchers can distinguish most of the agriculturally important cyst nematode species from one another and from their sibling species. Species from the Avenae group can be differentiated from one another using the enzymes AluI, CfoI, HinfI, ItaI, PstI, RsaI, TaqI and Tru9I. However, in some cases, it is not possible to use sequences of ITS-rRNA genes and PCR-RFLPs in diagnostic work. In these cases, morphometric characteristics are better for differentiating these species. Intraspecific polymorphism in the ITS sequences can make identification even more difficult; here, more conclusive molecular identification tools are needed to diagnose some species. In the future, end-point PCR and semi-quantitative PCR (SYBR Green I) with species-specific primers (already developed for Heterodera glycines and H. schachtii) will be the likely choices for fast and reliable detection and quantification of cyst nematodes in samples

Scraping the Social? Issues in live social research

What makes scraping methodologically interesting for social and cultural research? This paper seeks to contribute to debates about digital social research by exploring how a ‘medium-specific’ technique for online data capture may be rendered analytically productive for social research. As a device that is currently being imported into social research, scraping has the capacity to re-structure social research, and this in at least two ways. Firstly, as a technique that is not native to social research, scraping risks to introduce ‘alien’ methodological assumptions into social research (such as an pre-occupation with freshness). Secondly, to scrape is to risk importing into our inquiry categories that are prevalent in the social practices enabled by the media: scraping makes available already formatted data for social research. Scraped data, and online social data more generally, tend to come with ‘external’ analytics already built-in. This circumstance is often approached as a ‘problem’ with online data capture, but we propose it may be turned into virtue, insofar as data formats that have currency in the areas under scrutiny may serve as a source of social data themselves. Scraping, we propose, makes it possible to render traffic between the object and process of social research analytically productive. It enables a form of ‘real-time’ social research, in which the formats and life cycles of online data may lend structure to the analytic objects and findings of social research. By way of a conclusion, we demonstrate this point in an exercise of online issue profiling, and more particularly, by relying on Twitter to profile the issue of ‘austerity’. Here we distinguish between two forms of real-time research, those dedicated to monitoring live content (which terms are current?) and those concerned with analysing the liveliness of issues (which topics are happening?)

Method and new tabulations for flux-weighted line opacity and radiation line force in supersonic media

In accelerating and supersonic media, the interaction of photons with spectral lines can be of ultimate importance. However, fully accounting for such line forces currently can only be done by specialised codes in 1-D steady-state flows. More general cases and higher dimensions require alternative approaches. We presented a comprehensive and fast method for computing the radiation line-force using tables of spectral line-strength distribution parameters, which can be applied in arbitrary (multi-D, time-dependent) simulations, including those accounting for the line-deshadowing instability, to compute the appropriate opacities. We assumed local thermodynamic equilibrium to compute a flux-weighted line opacity from $>4$ million spectral lines. We derived the spectral line strength and tabulated the corresponding line-distribution parameters for a range of input densities $\rho\in[10^{-20},10^{-10}]gcm^{-3}$ and temperatures $T\in[10^4,10^{4.7}]K$. We found that the variation of the line distribution parameters plays an essential role in setting the wind dynamics in our models. In our benchmark study, we also found a good overall agreement between the O-star mass-loss rates of our models and those derived from steady-state studies using more detailed radiative transfer. Our models reinforce that self-consistent variation of the line-distribution parameters is important for the dynamics of line-driven flows. Within a well-calibrated O-star regime, our results support the proposed methodology. In practice, utilising the provided tables, yielded a factor $>100$ speed-up in computational time compared to specialised 1-D model-atmosphere codes of line-driven winds, which constitutes an important step towards efficient multi-D simulations. We conclude that our method and tables are ready to be exploited in various radiation-hydrodynamic simulations where the line force is important

Radiation-hydrodynamics with MPI-AMRVAC: Flux-limited diffusion

Radiation controls the dynamics and energetics of many astrophysical environments. To capture the coupling between the radiation and matter, however, is often a physically complex and computationally expensive endeavor. Aims. We sought to develop a numerical tool to perform radiation-hydrodynamics simulations in various configurations at an affordable cost. Methods. We built upon the finite volume code MPI-AMRVAC to solve the equations of hydrodynamics on multi-dimensional adaptive meshes and introduce a new module to handle the coupling with radiation. A non-equilibrium, flux-limiting diffusion approximation was used to close the radiation momentum and energy equations. The time-dependent radiation energy equation was then solved within a flexible framework, fully accounting for radiation forces and work terms and further allowing the user to adopt a variety of descriptions for the radiation-matter interaction terms ("opacities"). Results. We validated the radiation module on a set of standard test cases for which different terms of the radiative energy equation predominate. As a preliminary application to a scientific case, we calculated spherically symmetric models of the radiation-driven and optically thick supersonic outflows from massive Wolf-Rayet stars. This also demonstrates our code's flexibility, as the illustrated simulation combines opacities typically used in static stellar structure models with a parametrized form for the enhanced line-opacity expected in supersonic flows. Conclusions. This new module provides a convenient and versatile tool for performing multi-dimensional and high-resolution radiative-hydrodynamics simulations in optically thick environments with the MPI-AMRVAC code. The code is ready to be used for a variety of astrophysical applications, where our first target is set to be multi-dimensional simulations of stellar outflows from Wolf-Rayet stars