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

IoT focused VHF and UHF propagation study and comparisons

As the market for internet of things (IoT) is growing and due to Ofcom's decision to reassign parts of the very high frequency (VHF) spectrum in the UK for IoT use, a propagation study has been conducted using the newly released VHF spectrum and the currently commercially operated ultra-high frequency (UHF) spectrum, in order to compare and contrast the suitability of the VHF spectrum for IoT use. The authors conducted their study in a number of different environments (rural, suburban, urban and dense urban), with measurement equipment deployed in a manner suitable for a portable IoT use case. Results are presented in comparison to other propagation studies available in the literature and widely used propagation models such as the Hata model. Shadowing and noise are also measured and examined. It is found that current propagation models do not provide adequate predictions within the considered use case, but found it is possible to calculate log-distance based models that provide good predictions. Path-loss is found to be constantly lower at VHF than UHF, but radio frequency noise is consistently higher. The newly released spectrum is found to be suitable for IoT deployments in all the examined environments

Quasiparticle excitation in and around the vortex core of underdoped YBa_2Cu_4O_8 studied by site-selective NMR

We report a site-selective ^{17}O spin-lattice relaxation rate T_1^{-1} in the vortex state of underdoped YBa_2Cu_4O_8. We found that T_1^{-1} at the planar sites exhibits an unusual nonmonotonic NMR frequency dependence. In the region well outside the vortex core, T_1^{-1} cannot be simply explained by the density of states of the Doppler-shifted quasiparticles in the d-wave superconductor. Based on T_1^{-1} in the vortex core region, we establish strong evidence that the local density of states within the vortex core is strongly reduced.Comment: 5 pages, 3 figure

Templates for Convex Cone Problems with Applications to Sparse Signal Recovery

This paper develops a general framework for solving a variety of convex cone problems that frequently arise in signal processing, machine learning, statistics, and other fields. The approach works as follows: first, determine a conic formulation of the problem; second, determine its dual; third, apply smoothing; and fourth, solve using an optimal first-order method. A merit of this approach is its flexibility: for example, all compressed sensing problems can be solved via this approach. These include models with objective functionals such as the total-variation norm, ||Wx||_1 where W is arbitrary, or a combination thereof. In addition, the paper also introduces a number of technical contributions such as a novel continuation scheme, a novel approach for controlling the step size, and some new results showing that the smooth and unsmoothed problems are sometimes formally equivalent. Combined with our framework, these lead to novel, stable and computationally efficient algorithms. For instance, our general implementation is competitive with state-of-the-art methods for solving intensively studied problems such as the LASSO. Further, numerical experiments show that one can solve the Dantzig selector problem, for which no efficient large-scale solvers exist, in a few hundred iterations. Finally, the paper is accompanied with a software release. This software is not a single, monolithic solver; rather, it is a suite of programs and routines designed to serve as building blocks for constructing complete algorithms.Comment: The TFOCS software is available at http://tfocs.stanford.edu This version has updated reference

Large Angle CMB Fluctuations from Cosmic Strings with a Comological Constant

In this paper, we present results for large-angle CMB anisotropies generated from high resolution simulations of cosmic string networks in a range of flat FRW universes with a cosmological constant. Using an ensemble of all-sky maps, we compare with the COBE data to infer a normalization (or upper bound) on the string linear energy density $\mu$. For a flat matter-dominated model ($\Omega_{M}=1$) we find $G\mu/c^2 \approx 0.7\times 10^{-6}$, which is lower than previous constraints probably because of the more accurate inclusion of string small-scale structure. For a cosmological constant within an observationally acceptable range, we find a relatively weak dependence with $G\mu/c^2$ less than 10% higher.Comment: 5 pages, 5 figures; replaced with version to appear in Physical Review

The Ties that Double Bind Us: Career, Emotion and Narrative Coping in Difficult Working Relationships

This article examines through an autoethnographic account how career aspirations and constraints may lead individuals to endure emotionally aversive situations. It presents evidence that individuals in such situations engage in emotion‐focused coping through narrative, illustrated by the author’s autoethnographic narrative of a difficult working relationship which developed into a double bind situation. The paper suggests that narrative coping in response to a double bind can actually serve to reify and prolong such situations. The paper concludes that autoethnographic research does not lend itself to simple organisational solutions. Possible avenues for further research are outlined and discussed

A Bayesian analysis of pentaquark signals from CLAS data

We examine the results of two measurements by the CLAS collaboration, one of which claimed evidence for a $\Theta^{+}$ pentaquark, whilst the other found no such evidence. The unique feature of these two experiments was that they were performed with the same experimental setup. Using a Bayesian analysis we find that the results of the two experiments are in fact compatible with each other, but that the first measurement did not contain sufficient information to determine unambiguously the existence of a $\Theta^{+}$. Further, we suggest a means by which the existence of a new candidate particle can be tested in a rigorous manner.Comment: 5 pages, 3 figure

Magnetic Field Generation in Stars

Enormous progress has been made on observing stellar magnetism in stars from the main sequence through to compact objects. Recent data have thrown into sharper relief the vexed question of the origin of stellar magnetic fields, which remains one of the main unanswered questions in astrophysics. In this chapter we review recent work in this area of research. In particular, we look at the fossil field hypothesis which links magnetism in compact stars to magnetism in main sequence and pre-main sequence stars and we consider why its feasibility has now been questioned particularly in the context of highly magnetic white dwarfs. We also review the fossil versus dynamo debate in the context of neutron stars and the roles played by key physical processes such as buoyancy, helicity, and superfluid turbulence,in the generation and stability of neutron star fields. Independent information on the internal magnetic field of neutron stars will come from future gravitational wave detections. Thus we maybe at the dawn of a new era of exciting discoveries in compact star magnetism driven by the opening of a new, non-electromagnetic observational window. We also review recent advances in the theory and computation of magnetohydrodynamic turbulence as it applies to stellar magnetism and dynamo theory. These advances offer insight into the action of stellar dynamos as well as processes whichcontrol the diffusive magnetic flux transport in stars.Comment: 41 pages, 7 figures. Invited review chapter on on magnetic field generation in stars to appear in Space Science Reviews, Springe

Observation of exclusive DVCS in polarized electron beam asymmetry measurements

We report the first results of the beam spin asymmetry measured in the reaction e + p -> e + p + gamma at a beam energy of 4.25 GeV. A large asymmetry with a sin(phi) modulation is observed, as predicted for the interference term of Deeply Virtual Compton Scattering and the Bethe-Heitler process. The amplitude of this modulation is alpha = 0.202 +/- 0.028. In leading-order and leading-twist pQCD, the alpha is directly proportional to the imaginary part of the DVCS amplitude.Comment: 6 pages, 5 figure