Sequential bottlenecks drive viral evolution in early acute Hepatitis C virus infection

Hepatitis C is a pandemic human RNA virus, which commonly causes chronic infection and liver disease. The characterization of viral populations that successfully initiate infection, and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design. A comprehensive and longitudinal analysis of the viral population was conducted in four subjects followed from very early acute infection to resolution of disease outcome. By means of next generation sequencing (NGS) and standard cloning/Sanger sequencing, genetic diversity and viral variants were quantified over the course of the infection at frequencies as low as 0.1%. Phylogenetic analysis of reassembled viral variants revealed acute infection was dominated by two sequential bottleneck events, irrespective of subsequent chronicity or clearance. The first bottleneck was associated with transmission, with one to two viral variants successfully establishing infection. The second occurred approximately 100 days post-infection, and was characterized by a decline in viral diversity. In the two subjects who developed chronic infection, this second bottleneck was followed by the emergence of a new viral population, which evolved from the founder variants via a selective sweep with fixation in a small number of mutated sites. The diversity at sites with non-synonymous mutation was higher in predicted cytotoxic T cell epitopes, suggesting immune-driven evolution. These results provide the first detailed analysis of early within-host evolution of HCV, indicating strong selective forces limit viral evolution in the acute phase of infection

The provision of nutritional advice and care for cancer patients: a UK national survey of healthcare professionals.

PURPOSE: People living with and beyond cancer often experience nutrition-related issues and should receive appropriate advice on nutrition that is consistent and evidence based. The aim of this study was to investigate current practice for the provision of nutritional care by healthcare professionals (HCPs) from a UK national survey produced by the National Institute for Health Research (NIHR) Cancer and Nutrition Collaboration. METHODS: An online survey sent to professional groups and networks included questions on discussing nutrition, providing information, awareness of guidelines, confidence in providing nutritional advice, training and strategies for improving nutritional management. RESULTS: There were 610 HCPs who responded including nurses (31%), dietitians (25%), doctors (31%) and speech and language therapists (9%). The majority of HCPs discusses nutrition (94%) and provides information on nutrition (77%). However, only 39% of HCPs reported being aware of nutritional guidelines, and just 20% were completely confident in providing nutritional advice. Awareness of guidelines varied between the different professional groups with most but not all dietitians reporting the greatest awareness of guidelines and GPs the least (p = 0.001). Those HCPs with a greater awareness of guidelines had received training (p = 0.001) and were more likely to report complete confidence in providing nutritional advice (p = 0.001). CONCLUSION: Whilst HCPs discuss nutrition with cancer patients and may provide information, many lack an awareness of guidelines and confidence in providing nutritional advice. To ensure consistency of practice and improvements in patient care, there is scope for enhancing the provision of appropriate nutrition education and training

Anisotropic exchange interaction of localized conduction-band electrons in semiconductor structures

The spin-orbit interaction in semiconductors is shown to result in an anisotropic contribution into the exchange Hamiltonian of a pair of localized conduction-band electrons. The anisotropic exchange interaction exists in semiconductor structures which are not symmetric with respect to spatial inversion, for instance in bulk zinc-blend semiconductors. The interaction has both symmetric and antisymmetric parts with respect to permutation of spin components. The antisymmetric (Dzyaloshinskii-Moriya) interaction is the strongest one. It contributes significantly into spin relaxation of localized electrons; in particular, it governs low-temperature spin relaxation in n-GaAs with the donor concentration near 10^16cm-3. The interaction must be allowed for in designing spintronic devices, especially spin-based quantum computers, where it may be a major source of decoherence and errors

Vortex dynamics and states of artificially layered superconducting films with correlated defects

Linear resistances and $IV$-characteristics have been measured over a wide range in the parameter space of the mixed phase of multilayered a-TaGe/Ge films. Three films with varying interlayer coupling and correlated defects oriented at an angle $\approx 25$ from the film normal were investigated. Experimental data were analyzed within vortex glass models and a second order phase transition from a resistive vortex liquid to a pinned glass phase. Various vortex phases including changes from three to two dimensional behavior depending on anisotropy have been identified. Careful analysis of $IV$-characteristics in the glass phases revealed a distinctive $T$ and $H$-dependence of the glass exponent $\mu$. The vortex dynamics in the Bose-glass phase does not follow the predicted behavior for excitations of vortex kinks or loops.Comment: 16 pages, 10 figures, 3 table

Observational Constraints on Chaplygin Quartessence: Background Results

We derive the constraints set by several experiments on the quartessence Chaplygin model (QCM). In this scenario, a single fluid component drives the Universe from a nonrelativistic matter-dominated phase to an accelerated expansion phase behaving, first, like dark matter and in a more recent epoch like dark energy. We consider current data from SNIa experiments, statistics of gravitational lensing, FR IIb radio galaxies, and x-ray gas mass fraction in galaxy clusters. We investigate the constraints from this data set on flat Chaplygin quartessence cosmologies. The observables considered here are dependent essentially on the background geometry, and not on the specific form of the QCM fluctuations. We obtain the confidence region on the two parameters of the model from a combined analysis of all the above tests. We find that the best-fit occurs close to the $\Lambda$CDM limit ($\alpha=0$). The standard Chaplygin quartessence ($\alpha=1$) is also allowed by the data, but only at the $\sim2\sigma$ level.Comment: Replaced to match the published version, references update

Large-scale Bright Fronts in the Solar Corona: A Review of "EIT waves"

``EIT waves" are large-scale coronal bright fronts (CBFs) that were first observed in 195 \AA\ images obtained using the Extreme-ultraviolet Imaging Telescope (EIT) onboard the \emph{Solar and Heliospheric Observatory (SOHO)}. Commonly called ``EIT waves", CBFs typically appear as diffuse fronts that propagate pseudo-radially across the solar disk at velocities of 100--700 km s$^{-1}$ with front widths of 50-100 Mm. As their speed is greater than the quiet coronal sound speed ($c_s\leq$200 km s$^{-1}$) and comparable to the local Alfv\'{e}n speed ($v_A\leq$1000 km s$^{-1}$), they were initially interpreted as fast-mode magnetoacoustic waves ($v_{f}=(c_s^2 + v_A^2)^{1/2}$). Their propagation is now known to be modified by regions where the magnetosonic sound speed varies, such as active regions and coronal holes, but there is also evidence for stationary CBFs at coronal hole boundaries. The latter has led to the suggestion that they may be a manifestation of a processes such as Joule heating or magnetic reconnection, rather than a wave-related phenomena. While the general morphological and kinematic properties of CBFs and their association with coronal mass ejections have now been well described, there are many questions regarding their excitation and propagation. In particular, the theoretical interpretation of these enigmatic events as magnetohydrodynamic waves or due to changes in magnetic topology remains the topic of much debate.Comment: 34 pages, 19 figure

An Extreme Solar Event of 20 January 2005: Properties of the Flare and the Origin of Energetic Particles

The extreme solar and SEP event of 20 January 2005 is analyzed from two perspectives. Firstly, we study features of the main phase of the flare, when the strongest emissions from microwaves up to 200 MeV gamma-rays were observed. Secondly, we relate our results to a long-standing controversy on the origin of SEPs arriving at Earth, i.e., acceleration in flares, or shocks ahead of CMEs. All emissions from microwaves up to 2.22 MeV line gamma-rays during the main flare phase originated within a compact structure located just above sunspot umbrae. A huge radio burst with a frequency maximum at 30 GHz was observed, indicating the presence of a large number of energetic electrons in strong magnetic fields. Thus, protons and electrons responsible for flare emissions during its main phase were accelerated within the magnetic field of the active region. The leading, impulsive parts of the GLE, and highest-energy gamma-rays identified with pi^0-decay emission, are similar and correspond in time. The origin of the pi^0-decay gamma-rays is argued to be the same as that of lower energy emissions. We estimate the sky-plane speed of the CME to be 2000-2600 km/s, i.e., high, but of the same order as preceding non-GLE-related CMEs from the same active region. Hence, the flare itself rather than the CME appears to determine the extreme nature of this event. We conclude that the acceleration, at least, to sub-relativistic energies, of electrons and protons, responsible for both the flare emissions and the leading spike of SEP/GLE by 07 UT, are likely to have occurred simultaneously within the flare region. We do not rule out a probable contribution from particles accelerated in the CME-driven shock for the leading GLE spike, which seemed to dominate later on.Comment: 34 pages, 14 Postscript figures. Solar Physics, accepted. A typo corrected. The original publication is available at http://www.springerlink.co

On the Nature and Genesis of EUV Waves: A Synthesis of Observations from SOHO, STEREO, SDO, and Hinode

A major, albeit serendipitous, discovery of the SOlar and Heliospheric Observatory mission was the observation by the Extreme Ultraviolet Telescope (EIT) of large-scale Extreme Ultraviolet (EUV) intensity fronts propagating over a significant fraction of the Sun's surface. These so-called EIT or EUV waves are associated with eruptive phenomena and have been studied intensely. However, their wave nature has been challenged by non-wave (or pseudo-wave) interpretations and the subject remains under debate. A string of recent solar missions has provided a wealth of detailed EUV observations of these waves bringing us closer to resolving their nature. With this review, we gather the current state-of-art knowledge in the field and synthesize it into a picture of an EUV wave driven by the lateral expansion of the CME. This picture can account for both wave and pseudo-wave interpretations of the observations, thus resolving the controversy over the nature of EUV waves to a large degree but not completely. We close with a discussion of several remaining open questions in the field of EUV waves research.Comment: Solar Physics, Special Issue "The Sun in 360",2012, accepted for publicatio