Evolution of foot-and-mouth disease virus intra-sample sequence diversity during serial transmission in bovine hosts

RNA virus populations within samples are highly heterogeneous, containing a large number of minority sequence variants which can potentially be transmitted to other susceptible hosts. Consequently, consensus genome sequences provide an incomplete picture of the within- and between-host viral evolutionary dynamics during transmission. Foot-and-mouth disease virus (FMDV) is an RNA virus that can spread from primary sites of replication, via the systemic circulation, to found distinct sites of local infection at epithelial surfaces. Viral evolution in these different tissues occurs independently, each of them potentially providing a source of virus to seed subsequent transmission events. This study employed the Illumina Genome Analyzer platform to sequence 18 FMDV samples collected from a chain of sequentially infected cattle. These data generated snap-shots of the evolving viral population structures within different animals and tissues. Analyses of the mutation spectra revealed polymorphisms at frequencies >0.5% at between 21 and 146 sites across the genome for these samples, while 13 sites acquired mutations in excess of consensus frequency (50%). Analysis of polymorphism frequency revealed that a number of minority variants were transmitted during host-to-host infection events, while the size of the intra-host founder populations appeared to be smaller. These data indicate that viral population complexity is influenced by small intra-host bottlenecks and relatively large inter-host bottlenecks. The dynamics of minority variants are consistent with the actions of genetic drift rather than strong selection. These results provide novel insights into the evolution of FMDV that can be applied to reconstruct both intra- and inter-host transmission routes

Individual addressing and state readout of trapped ions utilizing rf- micromotion

A new scheme for the individual addressing of ions in a trap is described that does not rely on light beams tightly focused onto only one ion. The scheme utilizes ion micromotion that may be induced in a linear trap by dc offset potentials. Thus coupling an individual ion to the globally applied light fields corresponds to a mere switching of voltages on a suitable set of compensation electrodes. The proposed scheme is especially suitable for miniaturized rf (Paul) traps with typical dimensions of about 20-40 microns.Comment: 3 pages, 5 figure

Spatial variability in mass change of glaciers in the Everest region, central Himalaya, between 2000 and 2015

The mass balance of the majority of Himalayan glaciers is currently negative, and has been for several decades. Region wide averaging of mass change estimates has masked any catchment or glacier scale variability in glacier recession, thus the role of a number of glaciological processes in glacier wastage remains poorly understood. In this study, we quantify surface lowering and mass loss rates for the ablation areas of 32 glaciers in different catchments across the Everest region, and specifically examine the role of glacial lakes in glacier mass change. We then assess how future ice loss is likely to differ depending on glacier hypsometry. Spatially variable ice loss is observed within and between the Dudh Koshi and Tama Koshi catchments and glaciers that flow onto the Tibetan Plateau. Surface lowering rates on glaciers flowing onto the Tibetan Plateau are 54 and 19 % greater than those flowing southward into the Dudh Koshi and Tama Koshi catchments, respectively. Surface lowering rates of up to −3.78 ± 0.26 m a-1 occurred on some lacustrine terminating glaciers, although glaciers with small lakes showed rates of lowering comparable with those that terminate on land. We suggest that such a range reflects glacial lakes at different stages of development, and that rates of mass loss are likely to increase as glacial lakes expand and deep water calving begins to occur. Hypsometric data reveal a coincidence of the altitude of maximum surface lowering and the main glacier hypsometry in the Dudh Koshi catchment, thus a large volume of ice is readily available for melt. Should predicted CMIP5 RCP 4.5 scenario warming (0.9–2.3 °C by 2100) occur in the study area, 19–30, 17–50 and 14–37 % increases in the total glacierised area below the Equilibrium Line Altitude will occur in the Dudh Koshi and Tama Koshi catchments, and on the Tibetan Plateau. Comparison of our data with a conceptual model of Himalayan glacier shrinkage confirms the presence of three distinct process regimes, with all glaciers in our sample now in a state of accelerating mass loss and meltwater storage

Mobile radio propagation prediction using ray tracing methods

The basic problem is to solve the two-dimensional scalar Helmholtz equation for a point source (the antenna) situated in the vicinity of an array of scatterers (such as the houses and any other relevant objects in 1 square km of urban environment). The wavelength is a few centimeters and the houses a few metres across, so there are three disparate length scales in the problem. The question posed by BT concerned ray counting on the assumptions that: (i) rays were subject to a reflection coefficient of about 0.5 when bouncing off a house wall and (ii) that diffraction at corners reduced their energy by 90%. The quantity of particular interest was the number of rays that need to be accounted for at any particular point in order for those neglected to only contribute 10% of the field at that point; a secondary question concerned the use of rays to predict regions where the field was less than 1% of that in the region directly illuminated by the antenna. The progress made in answering these two questions is described in the next two sections and possibly useful representations of the solution of the Helmholtz equations in terms other than rays are given in the final section

Towards Bedmap Himalayas: development of an airborne ice-sounding radar for glacier thickness surveys in High-Mountain Asia

The thickness of glaciers in High-Mountain Asia (HMA) is critical in determining when the ice reserve will be lost as these glaciers thin but is remarkably poorly known because very few measurements have been made. Through a series of ground-based and airborne field tests, we have adapted a low-frequency ice-penetrating radar developed originally for Antarctic over-snow surveys, for deployment as a helicopter-borne system to increase the number of measurements. The manoeuvrability provided by helicopters and the ability of our system to detect glacier beds through thick, dirty, temperate ice makes it well suited to increase greatly the sample of measurements available for calibrating ice thickness models on the regional and global scale. The Bedmap Himalayas radar-survey system can reduce the uncertainty in present-day ice volumes and therefore in projections of when HMA's river catchments will lose this hydrological buffer against drought

First-principles study of stability and vibrational properties of tetragonal PbTiO_3

A first-principles study of the vibrational modes of PbTiO_3 in the ferroelectric tetragonal phase has been performed at all the main symmetry points of the Brillouin zone (BZ). The calculations use the local-density approximation and ultrasoft pseudopotentials with a plane-wave basis, and reproduce well the available experimental information on the modes at the Gamma point, including the LO-TO splittings. The work was motivated in part by a previously reported transition to an orthorhombic phase at low temperatures [(J. Kobayashi, Y. Uesu, and Y. Sakemi, Phys. Rev. B {\bf 28}, 3866 (1983)]. We show that a linear coupling of orthorhombic strain to one of the modes at Gamma plays a role in the discussion of the possibility of this phase transition. However, no mechanical instabilities (soft modes) are found, either at Gamma or at any of the other high-symmetry points of the BZ.Comment: 8 pages, two-column style with 3 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#ag_pbt