Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin.

To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA) long alpha helix (LAH). Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants

Halfvortices in flat nanomagnets

We discuss a new type of topological defect in XY systems where the O(2) symmetry is broken in the presence of a boundary. Of particular interest is the appearance of such defects in nanomagnets with a planar geometry. They are manifested as kinks of magnetization along the edge and can be viewed as halfvortices with winding numbers \pm 1/2. We argue that halfvortices play a role equally important to that of ordinary vortices in the statics and dynamics of flat nanomagnets. Domain walls found in experiments and numerical simulations are composite objects containing two or more of these elementary defects. We also discuss a closely related system: the two-dimensional smectic liquid crystal films with planar boundary condition.Comment: 7 pages, 8 figures, To appear as a chapter in Les Houches summer school on Quantum Magnetis

Contamination levels assessment of potential toxic metals in road dust deposited in different types of urban environment

A total of 42 samples of road dust were collected along ring road, city centre, city side, and freeway in Urumqi, China. Total concentrations of Cd, Cr, Cu, Ni, Pb, Mn, Be, Co, Zn, and U were determined by using the inductively coupled plasma-mass spectrometry in order to assess and to compare road dust contamination levels of metals among the four roads. The results show that, among the four categories of roads, mean concentrations of Co and U vary little. City centre locations show strong enrichments of Cd, Cu, Pb, and Be. Along the ring road, the highest mean concentrations were found for Cr, Ni, Mn, and Co. However, the highest concentrations of Zn and U were found along the freeway. The cluster analysis shows that three main groups can be distinguished. Every group may be associated with different main sources and concentrations of the metals. The results of contamination assessment reveal that, among all of the potential toxic metals, Cd, Cu, and Zn pollution were obviously heavier with moderate or high contamination indices for most road dust samples, while Cr, Ni, and Pb contamination were lower along the four categories of roads. Compared with the city side, Cd, Cu, Pb, Ni, and Zn contamination were heavier along the ring road, the city centre, and the freeway with high traffic density. Low Pb contamination or no contamination in all the road dust samples may be related to the increasing usage of lead-free petrol

Heavy metal induced ecological risk in the city of Urumqi, NW China

A total of 169 samples of road dust collected in the city of Urumqi, capital of the Xinjiang Uygur Autonomous Region in northwest China, were analyzed by method of inductively coupled plasma-mass spectrometry for 10 elements (i.e., Cd, Cr, Cu, Ni, Pb, Mn, Be, Co, Zn, and U). The possible sources of metals are identified with multivariate analysis such as correlation analysis, principal component analysis, and cluster analysis. Besides, enrichment factors are used to quantitatively evaluate the influences of human activities on heavy metal concentrations. Moreover, the potential ecological risk index is applied to evaluating the ecological risk of heavy metal pollutants. The results indicate that: (1) the concentrations of the heavy metals involved were much higher in urban areas than the background values, except those of Co and U. Mn, U, and Co are mainly of natural origin; Cu, Pb, Zn, and Cr are mainly of traffic sources and are partly of industrial sources; Ni and Be are mainly the results of industrial activities, such as machine shops, firepower plants, tire and rubber factories, cement factories, and textile mills and are partly of the traffic sources; (2) with high "toxic-response" factor and high concentration, Cd has more serious influences on the environment than other heavy metals. Therefore, commercial and industrial areas are usually characterized by higher potential ecological risk when compared with residential areas and new developing urban areas. The results of this study could be helpful for the management of environment in industrial areas

Microwave assisted heterogeneous catalysis: effects of varying oxygen concentrations on the oxidative coupling of methane

The oxidative coupling of methane was investigated over alumina supported La2O3/CeO2 catalysts under microwave dielectric heating conditions at different oxygen concentrations. It was observed that, at a given temperature using microwave heating, selectivities for both ethane and ethylene were notably higher when oxygen was absent than that in oxygen/methane mixtures. The differences were attributed to the localised heating of microwave radiation resulting in temperature inhomogeneity in the catalyst bed. A simplified model was used to estimate the temperature inhomogeneity; the temperature at the centre of the catalyst bed was 85 °C greater than that at the periphery when the catalyst was heated by microwaves in a gas mixture with an oxygen concentration of 12.5% (v/v), and the temperature difference was estimated to be 168 °C in the absence of oxygen

Validating child vaccination status in a demographic surveillance system using data from a clinical cohort study: evidence from rural South Africa

<p><b>Background:</b> Childhood vaccination coverage can be estimated from a range of sources. This study aims to validate vaccination data from a longitudinal population-based demographic surveillance system (DSS) against data from a clinical cohort study.</p> <p><b>Methods:</b> The sample includes 821 children in the Vertical Transmission cohort Study (VTS), who were born between December 2001 and April 2005, and were matched to the Africa Centre DSS, in northern KwaZulu-Natal. Vaccination information in the surveillance was collected retrospectively, using standardized questionnaires during bi-annual household visits, when the child was 12 to 23 months of age. DSS vaccination information was based on extraction from a vaccination card or, if the card was not available, on maternal recall. In the VTS, vaccination data was collected at scheduled maternal and child clinic visits when a study nurse administered child vaccinations. We estimated the sensitivity of the surveillance in detecting vaccinations conducted as part of the VTS during these clinic visits.</p> <p><b>Results:</b> Vaccination data in matched children in the DSS was based on the vaccination card in about two-thirds of the cases and on maternal recall in about one-third. The sensitivity of the vaccination variables in the surveillance was high for all vaccines based on either information from a South African Road-to-Health (RTH) card (0.94-0.97) or maternal recall (0.94-0.98). Addition of maternal recall to the RTH card information had little effect on the sensitivity of the surveillance variable (0.95-0.97). The estimates of sensitivity did not vary significantly, when we stratified the analyses by maternal antenatal HIV status. Addition of maternal recall of vaccination status of the child to the RTH card information significantly increased the proportion of children known to be vaccinated across all vaccines in the DSS.</p> <p><b>Conclusion:</b> Maternal recall performs well in identifying vaccinated children aged 12-23 months (both in HIV-infected and HIV-uninfected mothers), with sensitivity similar to information extracted from vaccination cards. Information based on both maternal recall and vaccination cards should be used if the aim is to use surveillance data to identify children who received a vaccination.</p&gt

Simultaneous quantification of 12 different nucleotides and nucleosides released from renal epithelium and in human urine samples using ion-pair reversed-phase HPLC

Nucleotides and nucleosides are not only involved in cellular metabolism but also act extracellularly via P1 and P2 receptors, to elicit a wide variety of physiological and pathophysiological responses through paracrine and autocrine signalling pathways. For the first time, we have used an ion-pair reversed-phase high-performance liquid chromatography ultraviolet (UV)-coupled method to rapidly and simultaneously quantify 12 different nucleotides and nucleosides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, adenosine, uridine triphosphate, uridine diphosphate, uridine monophosphate, uridine, guanosine triphosphate, guanosine diphosphate, guanosine monophosphate, guanosine): (1) released from a mouse renal cell line (M1 cortical collecting duct) and (2) in human biological samples (i.e., urine). To facilitate analysis of urine samples, a solid-phase extraction step was incorporated (overall recovery rate ? 98 %). All samples were analyzed following injection (100 ?l) into a Synergi Polar-RP 80 Å (250 × 4.6 mm) reversed-phase column with a particle size of 10 ?m, protected with a guard column. A gradient elution profile was run with a mobile phase (phosphate buffer plus ion-pairing agent tetrabutylammonium hydrogen sulfate; pH 6) in 2-30 % acetonitrile (v/v) for 35 min (including equilibration time) at 1 ml min(-1) flow rate. Eluted compounds were detected by UV absorbance at 254 nm and quantified using standard curves for nucleotide and nucleoside mixtures of known concentration. Following validation (specificity, linearity, limits of detection and quantitation, system precision, accuracy, and intermediate precision parameters), this protocol was successfully and reproducibly used to quantify picomolar to nanomolar concentrations of nucleosides and nucleotides in isotonic and hypotonic cell buffers that transiently bathed M1 cells, and urine samples from normal subjects and overactive bladder patients

Photoluminescence study on coarsening of self-assembled InAlAs quantum dots on GaAs (001)

Red-emission at similar to 640 nm from self-assembled In0.55Al0.45As/Al0.5Ga0.5As quantum dots grown on GaAs substrate by molecular beam epitaxy (MBE) has been demonstrated. We obtained a double-peak structure of photoluminescence (PL) spectra from quantum dots. An atomic force micrograph (AFM) image for uncapped sample also shows a bimodal distribution of dot sizes. From the temperature and excitation intensity dependence of PL spectra, we found that the double-peak structure of PL spectra from quantum dots was strongly correlated to the two predominant quantum dot families. Taking into account quantum-size effect on the peak energy, we propose that the high (low) energy peak results from a smaller (larger) dot family, and this result is identical with the statistical distribution of dot lateral size from the AFM image

GdxSi grown with mass-analyzed low energy dual ion beam epitaxy technique

Semiconducting gadolinium silicide GdxSi samples were prepared by mass-analyzed low-energy dual ion beam epitaxy technique. Auger electron spectroscopy depth profiles indicate that the gadolinium ions are implanted into the single-crystal silicon substrate and formed 20 nm thick GdxSi film. X-ray double-crystal diffraction measurement shows that there is no new phase formed. The XPS spectra show that one type of silicon peaks whose binding energy is between that of silicide and silicon dioxide, and the gadolinium peak of binding energy is between that of metal Gd and Gd2O3. All of these results indicate that an amorphous semiconductor is formed. (C) 2002 Elsevier Science B.V. All rights reserved

Spatial distribution and contamination assessment of heavy metals in urban road dusts from Urumqi, NW China

This study reports the spatial distribution pattern and degree of heavy metal pollution (Cd, Cr, Cu, Ni, Pb, Mn, Be, Co, Zn and U) in 169 urban road dust samples from urban area of Urumqi city. The spatial distribution pattern shows that Cu, Pb, Cr and Zn have similar patterns of spatial distribution. Their hot-spot areas were mainly associated with main roads where high traffic density was identified. Ni and Mn show similar spatial distributions coinciding with the industrial areas, while the spatial distribution patterns of Co and U show hot-spot areas were mainly located in the sides of the urban area where the road dust was significantly influenced by natural soils. The spatial distributions of Be and Cd were very different from other metals. The geo-accumulation index suggests that road dust in Urumqi city was uncontaminated to moderately contaminated with Cd, Cu, Ni, Pb, Mn, Be, Zn and U. The integrated pollution index shows IPIs of all road dust samples were higher than 1, suggesting that the road dust quality of Urumqi city has clearly been polluted by anthropogenic emission of heavy metals. Moreover, the spatial distribution pattern of IPIs also shows several distribution trends in the studied region. (C) 2009 Elsevier B.V. All rights reserved