Universal Oligonucleotide Microarray for Sub-Typing of Influenza A Virus

A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1–H13, H15, H16) and neuraminidase (N1–N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus

First results from recent JET experiments in Hydrogen and Hydrogen-Deuterium plasmas

The hydrogen campaign completed at JET in 2016 has demonstrated isotope ratio control in JET-ILW using gas puffing and pellets for fuelling, Neutral Beam Injection alone or in combination, with D/H spectroscopy as a diagnostic. The plasma properties such as confinement, L-H threshold, density limit depend on the isotope composition. The L-H transition power increases with the hydrogen concentration with a wide plateau in the range 0.2<nH/(nD+nH)<0.8. Energy confinement is significantly lower in hydrogen than in comparable deuterium ELMy H-mode plasmas, suggesting an isotope mass scaling that is stronger than in IPB98(y,2). In L-mode, the isotope dependence of confinement is weaker. The H-mode density limit in hydrogen is up to 35% lower than in heuterium, whilst it is found to be higher in L-mode. The lower ion mass leads to reduced tungsten sputtering in hydrogen plasmas. During the campaign, the nD/(nD+nH) ratio dropped to ~1% in only a few discharges after the last deliberate introduction of deuterium, although it was seen to rise again to ~2% with several seconds of exposure of the divertor tiles to ~10MW of auxiliary heating. Several ICRH scenarios were also tested in hydrogen plasmas

Automodel Solutions of Biberman-Holstein Equation for Stark Broadening of Spectral Lines

The accuracy of approximate automodel solutions for the Green&rsquo;s function of the Biberman-Holstein equation for the Stark broadening of spectral lines is analyzed using the distributed computing. The high accuracy of automodel solutions in a wide range of parameters of the problem is shown

Self-Similar Solutions in the Theory of Nonstationary Radiative Transfer in Spectral Lines in Plasmas and Gases

Radiative transfer (RT) in spectral lines in plasmas and gases under complete redistribution of the photon frequency in the emission-absorption act is known as a superdiffusion transport characterized by the irreducibility of the integral (in the space coordinates) equation for the atomic excitation density to a diffusion-type differential equation. The dominant role of distant rare flights (Lévy flights, introduced by Mandelbrot for trajectories generated by the Lévy stable distribution) is well known and is used to construct approximate analytic solutions in the theory of stationary RT (the escape probability method is the best example). In the theory of nonstationary RT, progress based on similar principles has been made recently. This includes approximate self-similar solutions for the Green’s function (i) at an infinite velocity of carriers (no retardation effects) to cover the Biberman–Holstein equation for various spectral line shapes; (ii) for a finite fixed velocity of carriers to cover a wide class of superdiffusion equations dominated by Lévy walks with rests; (iii) verification of the accuracy of above solutions by comparison with direct numerical solutions obtained using distributed computing. The article provides an overview of the above results with an emphasis on the role of distant rare flights in the discovery of nonstationary self-similar solutions

The Presence of the Internalin Gene in Natural Atypically Hemolytic Listeria innocua Strains Suggests Descent from L. monocytogenes

The atypical hemolytic Listeria innocua strains PRL/NW 15B95 and J1-023 were previously shown to contain gene clusters analogous to the pathogenicity island (LIPI-1) present in the related foodborne gram-positive facultative intracellular pathogen Listeria monocytogenes, which causes listeriosis. LIPI-1 includes the hemolysin gene, thus explaining the hemolytic activity of the atypical L. innocua strains. No other L. monocytogenes-specific virulence genes were found to be present. In order to investigate whether any other specific L. monocytogenes genes could be identified, a global approach using a Listeria biodiversity DNA array was applied. According to the hybridization results, the isolates were defined as L. innocua strains containing LIPI-1. Surprisingly, evidence for the presence of the L. monocytogenes-specific inlA gene, previously thought to be absent, was obtained. The inlA gene codes for the InlA protein which enables bacterial entry into some nonprofessional phagocytic cells. PCR and sequence analysis of this region revealed that the flanking genes of the inlA gene at the upstream, 5′-end region were similar to genes found in L. monocytogenes serotype 4b isolates, whereas the organization of the downstream, 3′-end region was similar to that typical of L. innocua. Sequencing of the inlA region identified a small stretch reminiscent of the inlB gene of L. monocytogenes. The presence of two clusters of L. monocytogenes-specific genes makes it unlikely that PRL/NW 15B95 and J1-023 are L. innocua strains altered by horizontal transfer. It is more likely that they are distinct relics of the evolution of L. innocua from an ancestral L. monocytogenes, as postulated by others

Strength of the Hubbard potential and its modification by breathing distortion in BaBiO3

BaBiO3 compound is known as an archetype example of a three-dimensional Holstein model with the realization of the charge-density wave state at half filling and the superconducting state when doped. Although many works are devoted to the study the electron-phonon interaction in BaBiO3, the influence of the electron-electron Hubbard interaction on the electronic structure in this system is still under investigation. In our work, we obtain analytical expression for the screened Coulomb potential, and along with the basis of ab initio-computed maximally localized Wannier orbitals, we quantitatively estimate the magnitude of the effective on-site Hubbard potential scrutinizing the effects of distortion of the crystal lattice. We show that a proper inclusion of the electron-electron interactions into the Holstein model significantly lowers the value of the underlying electron-phonon coupling. Finally, we find that the amplitudes of the repulsive electron-electron potential and its attractive counterpart mediated by the electron-phonon coupling are rather comparable. This may open a way for a realization of the intermediate phase of BaBiO3 in terms of the Holstein-Hubbard model