A collaborative approach to embedding academic literacies in first year grant projects

This paper describes the collaborative approach that Academic Language and Learning developers are using as part of a university’s First Year Experience project. This project draws on the idea of a third generation approach which utilises a bottom-up and top-down institutional framework. Intrinsic to this framework at UTS is a small grant scheme devised to support academics in designing curricula which facilitate first year students’ transition. However, smooth transition can be affected by the academic and linguistic capital of the increasingly diverse student population. This has provided the opportunity for ALL developers to become active participants in the small grant scheme and to work collaboratively with academics on the seamless integration of domain specific academic literacy. Two case studies of FYE grants illustrate the parameters and benefits of such an approach and how it may enable a discursive space to support sustainable practice

Prevalence of HCV NS3 pre-treatment resistance associated amino acid variants within a Scottish cohort

Background: Protease inhibitors (PI) including boceprevir, telaprevir and simeprevir have revolutionised HCV genotype 1 treatment since their introduction. A number of pre-treatment resistance associated amino acid variants (RAVs) and polymorphisms have been associated with reduced response to treatment. Objectives: We measured the prevalence of RAVs/polymorphisms in a PI treatment-naïve HCV genotype 1 Scottish cohort using Sanger sequencing. Study design: Chronically infected, treatment-naïve, HCV genotype 1 patients (n = 146) attending NHS Greater Glasgow and Clyde clinics were investigated for RAVs/polymorphisms to the PIs boceprevir, telaprevir and simeprevir. The NS3/4A region was amplified by nested polymerase chain reaction. The 1.4 kb amplified product was sequenced using an ABI 3710XL DNA sequencer. Sequence analysis was performed using web-based ReCall (beta 2.10). Amino acid positions 36, 41, 43, 54, 55, 80, 109, 122, 155, 156, 168 and 170 were analysed for RAVs/polymorphisms. Results: Overall, 23.29% (34/146) of patients had an RAV or polymorphism detected. Overall, 13.69% (20/146) of patients had HCV virus that contained the Q8 K polymorphism. Other RAVs detected were: V36 M 0.70% (1/146), V36L 0.70% (1/146), T54S 6.85% (10/146), V55A 3.42% (5/146) and V/I170A 0.68% (1/146). Four patients had dual combinations of mutations (T54S + V36L; T54S + V55A and 2 patients with T54S + Q80K). Conclusions: Q80K was the most prevalent baseline polymorphism detected in the Scottish cohort. Simeprevir treatment is not recommended in patients infected with the Q80K genotype 1a variant. This highlights the need for baseline sequencing prior to administration of this drug in this population

Differential introgression reveals candidate genes for selection across a spruce (Picea sitchensis × P. glauca) hybrid zone

Differential patterns of introgression between species across ecological gradients provide a fine-scale depiction of extrinsic and intrinsic factors that contribute to the maintenance of species barriers and adaptation across heterogeneous environments. Introgression was examined for 721 individuals collected from the ecological transition zone spanning maritime to continental climates within the Picea sitchensis–Picea glauca contact zone using a panel of 268 candidate gene single nucleotide polymorphisms. Geographic clines showed a strong spatial relationship between allele frequencies and both distance from the ocean along major rivers and mean annual precipitation, indicating a strong role for environmental selection. Interspecific patterns of differentiation using outlier tests revealed three candidate genes that may be targets of long-term divergent selection between the parental species, although contemporary genomic clines within the hybrid zone suggested neutral patterns of introgression for these genes. This study provides a fine-scale analysis of locus-specific introgression, identifying a suite of candidate loci that may be targets of extrinsic or intrinsic selection, with broad application in understanding local adaptation to climate

Surface activation for low temperature wafer fusion bonding by radicals produced in an oxygen discharge

A new method of exposing silicon/semiconductor wafers to a mixture of radicals is described, in which these species are generated in an oxygen-rich gas discharge confined between a concentric pair of annular mesh electrodes surrounding the wafers. This approach allows the wafer surfaces to be treated without damage from the energetic ions, strong electric fields, and high UV fluxes associated with direct treatment by exposure to gas discharge plasmas. The process is compared with direct oxygen plasma activation for its latitude with respect to treatment duration, effect on wafer surface roughness and bond strength. Wider process latitude and reduced surface roughening are obtained for treatment by radicals compared with direct plasma exposure. Comparative analysis of treated and untreated silicon surfaces by X-ray photoelectron spectroscopy indicate that traces of fluorine present on the wafer surface before treatment are removed with great efficiency by the process

Effects of Mismatch Strain and Substrate Surface Corrugation on Morphology of Supported Monolayer Graphene

Graphene monolayers supported on oxide substrates have been demonstrated with superior charge mobility and thermal transport for potential device applications. Morphological corrugation can strongly influence the transport properties of the supported graphene. In this paper, we theoretically analyze the morphological stability of a graphene monolayer on an oxide substrate, subject to van der Waals interactions and in-plane mismatch strains. First, we define the equilibrium separation and the interfacial adhesion energy as the two key parameters that characterize the van der Waals interaction between a flat monolayer and a flat substrate surface. By a perturbation analysis, a critical compressive mismatch strain is predicted, beyond which the graphene monolayer undergoes strain-induced instability, forming corrugations with increasing amplitude and decreasing wavelength on a perfectly flat surface. When the substrate surface is not perfectly flat, the morphology of graphene depends on both the amplitude and the wavelength of the surface corrugation. A transition from conformal (corrugated) to non-conformal (flat) morphology is predicted. The effects of substrate surface corrugation on the equilibrium mean thickness of the supported graphene and the interfacial adhesion energy are analyzed. Furthermore, by considering both the substrate surface corrugation and the mismatch strain, it is found that, while a tensile mismatch strain reduces the corrugation amplitude of graphene, a corrugated substrate surface promotes strain-induced instability under a compressive strain. These theoretical results suggest possible means to control the morphology of graphene monolayer on oxide substrates by surface patterning and strain engineering.Comment: 25 pages, 9 figures, submitted for review on March 3, 201

Combination of measurements and the BLUE method

The most accurate method to combine measurement from different experiments is to build a combined likelihood function and use it to perform the desired inference. This is not always possible for various reasons, hence approximate methods are often convenient. Among those, the best linear unbiased estimator (BLUE) is the most popular, allowing to take into account individual uncertainties and their correlations. The method is unbiased by construction if the true uncertainties and their correlations are known, but it may exhibit a bias if uncertainty estimates are used in place of the true ones, in particular if those estimated uncertainties depend on measured values. In those cases, an iterative application of the BLUE method may reduce the bias of the combined measurement.Comment: 10 pages, 4 figures, proceedings of the XIIth Quark Confinement and Hadron Spectrum conference, 28/8-2/9 2016, Tessaloniki, Greec

Selection for Improved Growth and Wood Density in Lodgepole Pine: Effects on Radial Patterns of Wood Variation

Changes in growth and wood density traits were investigated across annual rings of 12-year-old trees from four selected subpopulations in lodgepole pine (Pinus contorta Dougl. Ex Loud var. latifolia Engelm) based on X-ray densitometry profile data. Four subpopulations were constructed based on height growth and wood density as follows: 1) fast growth and high wood density (FH); 2) slow growth and high density (SH); 3) fast growth and low density (FL); and 4) slow growth and low density (SL). Annual ring density was initially high, declined with age until age 10, and then plateaued. Significant differences among subpopulations were found for ring density, earlywood and latewood densities, ring width, earlywood width, latewood proportion, and earlywood width after age 6. Wood density decreased less from the pith to the bark in both overall and earlywood densities in the FH subpopulation, resulting in denser, more homogeneous wood than in other subpopulations. This suggests that it may be possible to increase wood density and homogeneity in juvenile wood of this species by selecting FH families. Overall ring density may be better improved by selecting for earlywood and latewood components separately. The earliest age of which families combining fast growth and high wood density can be accurately identified is about 7 years