Computational method for reducing variance with Affymetrix microarrays

BACKGROUND: Affymetrix microarrays are used by many laboratories to generate gene expression profiles. Generally, only large differences (> 1.7-fold) between conditions have been reported. Computational methods to reduce inter-array variability might be of value when attempting to detect smaller differences. We examined whether inter-array variability could be reduced by using data based on the Affymetrix algorithm for pairwise comparisons between arrays (ratio method) rather than data based on the algorithm for analysis of individual arrays (signal method). Six HG-U95A arrays that probed mRNA from young (21–31 yr old) human muscle were compared with six arrays that probed mRNA from older (62–77 yr old) muscle. RESULTS: Differences in mean expression levels of young and old subjects were small, rarely > 1.5-fold. The mean within-group coefficient of variation for 4629 mRNAs expressed in muscle was 20% according to the ratio method and 25% according to the signal method. The ratio method yielded more differences according to t-tests (124 vs. 98 differences at P < 0.01), rank sum tests (107 vs. 85 differences at P < 0.01), and the Significance Analysis of Microarrays method (124 vs. 56 differences with false detection rate < 20%; 20 vs. 0 differences with false detection rate < 5%). The ratio method also improved consistency between results of the initial scan and results of the antibody-enhanced scan. CONCLUSION: The ratio method reduces inter-array variance and thereby enhances statistical power

Pre-service and In-services Teachers Perspectives on Academic Success: More than Just A Grade

Students are constantly bombarded with messages about academic success and the importance of getting good grades. However, definitions of academic success are more complex than a letter grade. Many indicators to define academic success extend primarily from students’ perspectives and ignore how teachers’ definitions of success. This is an oversight as teachers’ perspectives on academic success shape their students’ perspectives on academic success for years to come, and thus represent an important voice to be included in the messaging around academic success. Thus, in this study we were interested in pre-service and in-service teachers’ definitions of academic success, and how they converge or diverge with indicators outlined in current research. We found that teachers have multiple perspectives on academic success, highlighting the complexity of this construct. Moreover, many of their definitions converged with researchers; however, teachers’ definitions were more varied and diverse. Our findings highlight the multidimensional nature of academic success. In closing, we identify various implications for schools and provide suggestions for future research and practice

Predicting the coefficient of thermal expansion for textile composites based on a unit cell approach

The study focuses on unit cell FE modelling to predict coefficients of thermal expansion (CTEs) for sheared fabric laminates. Shear, as a dominant deformation mode in textile composites forming, introduces high degrees of anisotropy in both elasticity and thermal expansion. The unit cell predictions are based on realistic fibre architecture and measured material properties of constituent fibre and resin. Under the multi-scale framework, the unit cell predictions are part of the essential input data for locally varied material definitions. These definitions are used to model structural components to predict shape distortion. The FE model gives predictions close to the experimental data, when the boundary conditions are correlated to the coupon size. Nesting is an influential factor for CTEs. For true material representation, in-plane periodicity and nesting have been considered

Predicting the coefficient of thermal expansion for textile composites based on a unit cell approach

The study focuses on unit cell FE modelling to predict coefficients of thermal expansion (CTEs) for sheared fabric laminates. Shear, as a dominant deformation mode in textile composites forming, introduces high degrees of anisotropy in both elasticity and thermal expansion. The unit cell predictions are based on realistic fibre architecture and measured material properties of constituent fibre and resin. Under the multi-scale framework, the unit cell predictions are part of the essential input data for locally varied material definitions. These definitions are used to model structural components to predict shape distortion. The FE model gives predictions close to the experimental data, when the boundary conditions are correlated to the coupon size. Nesting is an influential factor for CTEs. For true material representation, in-plane periodicity and nesting have been considered

Black carbon physical and optical properties across northern India during pre-monsoon and monsoon seasons

Black carbon (BC) is known to have major impacts on both climate and human health and is therefore of global importance, particularly in regions close to large populations that have strong sources. The size-resolved mixing state of BC-containing particles was characterised using a single-particle soot photometer (SP2). The study focusses on the Indo-Gangetic Plain (IGP) during the pre-monsoon and monsoon seasons. Data presented are from the UK Facility for Airborne Atmospheric Measurements BAe-146 research aircraft that performed flights during the pre-monsoon (11 and 12 June) and monsoon (30 June to 11 July) seasons of 2016. Over the IGP, BC mass concentrations were greater (1.95 µg m−3) compared to north-west India (1.50 µg m−3) and north-east India (0.70 µg m−3) during the pre-monsoon season. Across northern India, two distinct BC modes were recorded; a mode of small BC particles (core diameter <0.16 µm and coating thickness <50 nm) and a mode of moderately coated BC (core diameter <0.22 µm and coating thickness of 50–200 nm). The IGP and north-east India locations exhibited moderately coated black carbon particles with enhanced coating thicknesses, core sizes, mass absorption cross sections, and scattering enhancement values compared to much lower values present in the north-west. The coating thickness and mass absorption cross section increased with altitude (13 %) compared to those in the boundary layer. As the monsoon arrived across the region, mass concentration of BC decreased over the central IGP and north-east locations (38 % and 28 % respectively), whereas for the north-west location BC properties remained relatively consistent. Post-monsoon onset, the coating thickness, core size, mass absorption cross section, and scattering enhancement values were all greatest over the central IGP much like the pre-monsoon season but were considerably reduced over both north-east and north-west India. Increases in mass absorption cross section through the atmospheric column were still present during the monsoon for the north-west and central IGP locations, but less so over the north-east due to lack of long-range transport aerosol aloft. Across the Indo-Gangetic Plain and north-east India during the pre-monsoon and monsoon seasons, solid-fuel (wood burning) emissions form the greatest proportion of BC with moderately coated particles. However, as the monsoon develops in the north-east there was a switch to small uncoated BC particles indicative of traffic emissions, but the solid-fuel emissions remained in the IGP into the monsoon. For both seasons in the north-west, traffic emissions form the greatest proportion of BC particles. Our findings will prove important for greater understanding of the BC physical and optical properties, with important consequences for the atmospheric radiative forcing of BC-containing particles. The findings will also help constrain the regional aerosol models for a variety of applications such as space-based remote sensing, chemistry transport modelling, air quality, and BC source and emission inventories

Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine

BACKGROUND: The mouse C57BL/6 (C57) and DBA/2J (DBA) inbred strains differ substantially in many aspects of their response to drugs of abuse. The development of microarray analyses represents a genome-wide method for measuring differences across strains, focusing on expression differences. In the current study, we carried out microarray analysis in C57 and DBA mice in the nucleus accumbens of drug-naïve and morphine-treated animals. RESULTS: We identified mRNAs with altered expression between the two strains. We validated the mRNA expression changes of several such mRNAs, including Gnb1, which has been observed to be regulated by several drugs of abuse. In addition, we validated alterations in the enzyme activity of one mRNA product, catechol-O-methyltransferase (Comt). Data mining of expression and behavioral data indicates that both Gnb1 and Comt expression correlate with aspects of drug response in C57/DBA recombinant inbred strains. Pathway analysis was carried out to identify pathways showing significant alterations as a result of treatment and/or due to strain differences. These analyses identified axon guidance genes, particularly the semaphorins, as showing altered expression in the presence of morphine, and plasticity genes as showing altered expression across strains. Pathway analysis of genes showing strain by treatment interaction suggest that the phosphatidylinositol signaling pathway may represent an important difference between the strains as related to morphine exposure. CONCLUSION: mRNAs with differing expression between the two strains could potentially contribute to strain-specific responses to drugs of abuse. One such mRNA is Comt and we hypothesize that altered expression of Comt may represent a potential mechanism for regulating the effect of, and response to, multiple substances of abuse. Similarly, a role for Gnb1 in responses to multiple drugs of abuse is supported by expression data from our study and from other studies. Finally, the data support a role for semaphorin signaling in morphine effects, and indicate that altered expression of genes involved in phosphatidylinositol signaling and plasticity might also affect the altered drug responses in the two strains

PREDICTING THE COEFFICIENT OF THERMAL EXPANSION FOR TEXTILE COMPOSITES BASED ON A UNIT CELL APPROACH

ABSTRACT INTRODUCTION Shape distortion of composite components is a common problem in composites manufacturing. The major cause of shape distortion is anisotropic thermal expansion, which would impact not only on the manufacturing process but also the in-service performanc

MOCVD of ultra-thin PV solar cell devices using a pyrite based p-i-n structure

Ultra-thin photovoltaic (PV) devices were produced by atmospheric pressure metal organic chemical vapour deposition (AP-MOCVD) incorporating a highly absorbing intermediate sulphurised FeSₓ layer into a CdS/CdTe structure. X ray diffraction (XRD) confirmed a transitional phase change to pyrite FeS₂ after post growth sulphur (S) annealing of the FeSₓ layer between 400⁰C and 500⁰C. Devices using a superstrate configuration incorporating a sulphurised or non sulphurised FeSₓ layer were compared to p-n devices with only a CdS/CdTe structure. Devices with sulphurised FeSₓ layers performed least efficiently, even though pyrite fractions were present. Rutherford back scattering (RBS) confirmed deterioration of the CdS/FeSₓ interface due to S inter-diffusion during the annealing process

Antarctic Climate Change and the Environment: A Decadal Synopsis and Recommendations for Action

Scientific evidence is abundantly clear and convincing that due to the current trajectory of human-derived emissions of CO2 and other greenhouse gases, the atmosphere and ocean will continue to warm, the ocean will continue to acidify, atmospheric and ocean circulation patterns will be altered, the cryosphere will continue to lose ice in all forms, and sea level will rise

Continental threat: How many common carp (Cyprinus carpio) are there in Australia?

Common carp (Cyprinus carpio) are one of the world's most destructive vertebrate pests. In Australia, they dominate many aquatic ecosystems causing a severe threat to aquatic plants, invertebrates, water quality, native fish and social amenity. The Australian Government is considering release of cyprinid herpesvirus-3 (CyHV-3) as a control measure and consequently a robust, continental-scale estimate of the carp population and biomass is essential to inform planning and risk management. Here, we pioneer a novel model-based approach to provide the first estimate of carp density (no/ha) and biomass density (kg/ha) at river reach/waterbody, basin and continental scales. We built a spatial layer of rivers and waterbodies, classified aquatic habitats and calculated the area of each throughout the range of carp in Australia. We then developed a database of fishery-independent electrofishing catch-per-unit-effort (CPUE) for habitat types, containing catch information for 574,145 carp caught at 4831 sites. Eastern Australia accounted for 96% of carp biomass and 92% of the total available wetted habitat area (16,686 km2) was occupied. To correct these data for variable detection efficiencies, we used existing electrofishing data and undertook additional field experiments to establish relationships between relative and absolute abundances. We then scaled-up site-based estimates to habitat types to generate continental estimates. The number of carp was estimated at 199.2 M (95%Crl: 106 M to 357.6 M) for an ‘average’ hydrological scenario and 357.5 M (95%Crl: 178.9 M to 685.1 M) for a ‘wet’ hydrological scenario. In eastern Australia, these numbers correspond with biomasses of 205,774 t (95%Crl: 117,532–356,482 t) (average scenario) and 368,357 t (95%Crl: 184,234–705,630 t) (wet scenario). At a continental scale the total biomass was estimated at 215,456 t for an ‘average’ hydrological scenario. Perennial lowland rivers had the highest CPUE and greatest biomass density (up to 826 kg/ha) and the modelled biomass exceeded a density-impact threshold of 80–100 kg/ha in 54% of wetlands and 97% of stream area in large lowland rivers. The continental-scale biomass estimates provide a baseline for focusing national conservation strategies to reduce carp populations below thresholds needed to restore aquatic ecosystems at a range of spatial scales