Mutation analysis of the CDKN2A promoter in Australian melanoma families

Approximately 50% of all melanoma families worldwide show linkage to 9p21-22, but only about half of these have been shown to contain germ line CDKN2A mutations. It has been hypothesized that a proportion of these families carry mutations in the noncoding regions of CDKN2A. Several Canadian families have been reported to carry a mutation in the 5' UTR, at position -34 relative to the start site, which gives rise to a novel AUG translation initiation codon that markedly decreases translation from the wild-type AUG (Liu et al., 1999). Haplotype sharing in these Canadian families suggested that this mutation is of British origin. We sequenced 1,327 base pairs (bp) of CDKN2A, making up 1,116 bp of the 5' UTR and promoter, all of exon 1, and 61 bp of intron 1, in at least one melanoma case from 110 Australian families with three or more affected members known not to carry mutations within the p16 coding region. In addition, 431 bp upstream of the start codon was sequenced in an additional 253 affected probands from two-case melanoma families for which the CDKN2A mutation status was unknown. Several known polymorphisms at positions -33, -191, -493, and -735 were detected, in addition to four novel variants at positions 120, -252, -347, and -981 relative to the start codon. One of the probands from a two-case family was found to have the previously reported Q50R mutation. No family member was found to carry the mutation at position -34 or any other disease-associated mutation. For further investigation of noncoding CDKN2A mutations that may affect transcription, allele-specific expression analysis was carried out in 31 of the families with at least three affected members who showed either complete or "indeterminate" 9p haplotype sharing without CDKN2A exonic mutations. Reverse transcription polymerase chain reaction and automated sequencing showed expression of both CDKN2A alleles in all family members tested. The lack of CDKN2A promoter mutations and the absence of transcriptional silencing in the germ line of this cohort of families suggest that mutations in the promoter and 5' UTR play a very limited role in melanoma predisposition.

Utility of COI, CAD and morphological data for resolving relationships within the genus Sarcophaga (sensu lato) (Diptera: Sarcophagidae) : a preliminary study

Currently there are ~3000 known species of Sarcophagidae (Diptera), which are classified into 173 genera in three subfamilies. Almost 25% of sarcophagids belong to the genus Sarcophaga (sensu lato) however little is known about the validity of, and relationships between the ~150 (or more) subgenera of Sarcophaga s.l. In this preliminary study, we evaluated the usefulness of three sources of data for resolving relationships between 35 species from 14 Sarcophaga s.l. subgenera: the mitochondrial COI barcode region, ~800. bp of the nuclear gene CAD, and 110 morphological characters. Bayesian, maximum likelihood (ML) and maximum parsimony (MP) analyses were performed on the combined dataset. Much of the tree was only supported by the Bayesian and ML analyses, with the MP tree poorly resolved. The genus Sarcophaga s.l. was resolved as monophyletic in both the Bayesian and ML analyses and strong support was obtained at the species-level. Notably, the only subgenus consistently resolved as monophyletic was Liopygia. The monophyly of and relationships between the remaining Sarcophaga s.l. subgenera sampled remain questionable. We suggest that future phylogenetic studies on the genus Sarcophaga s.l. use combined datasets for analyses. We also advocate the use of additional data and a range of inference strategies to assist with resolving relationships within Sarcophaga s.l.

Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of 'Golden Delicious', SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.

Nonlinear effects of ionization on surface waves on a plasma-metal interface

Nonlinear effects associated with density modulation caused by wave-induced ionization in magnetized plasmas were studied. The ionizing surface waves propagate at the interface between the plasma and a metallic surface. It is shown that the ionization nonlinearity can be important for typical experimental conditions.

The robustness of mine water accounting over a range of operating contexts and commodities

Communicating the mining industry’s water use is fundamental to maintaining its social license to operate but the majority of corporate reporting schemes list indicators. The Minerals Council of Australia’s Water Accounting Framework was designed to assist the minerals industry obtain consistency in its accounting method and in the definitions of terms used in water reporting. The significance of this paper is that it shows that the framework has been designed to be sufficiently robust to describe any mining/mineral related operation. The Water Accounting Framework was applied across four operations over three countries producing four commodities. The advantages of the framework were then evident through the presentation of the reports. The contextual statement of the framework was able to explain contrasting reuse efficiencies. The Input-Output statements showed that evaporation was a significant loss for most of the operations in the study which highlights a weakness of reporting schemes that focus on discharge volumes. The framework method promotes data reconciliation which proved the presence of flows that two operations in the study had neglected to provide. Whilst there are many advantages of the framework, the major points are that the reporting statements of the framework, when presented together, can better enable the public to understand water interactions at a site-level and allows for valid comparisons between sites, regardless of locale and commodity. With mining being a global industry, these advantages are best realised if there was international adoption of the framework.

The long and short of it: branch lengths and the problem of placing the New Zealand short-tailed bat.

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous–Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

The Long and Short of It: Branch Lengths and the Problem of Placing the New Zealand Short-Tailed Bat, Mystacina

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha

Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

Room-temperature tilted-target sputtering deposition of highly transparent and low sheet resistance Al doped ZnO electrodes

Target-tilted room temperature sputtering of aluminium doped zinc oxide (AZO) provides transparent conducting electrodes with sheet resistances of <10 Ω □-1 and average transmittance in the visible region of up to 84%. The properties of the AZO electrode are found to be strongly dependent on the target-tilting angle and film thickness. The AZO electrodes showed comparable performance to commercial indium tin oxide (ITO) electrodes in organic photovoltaic (OPV) devices. OPV devices containing a bulk heterojunction active layer comprised of poly(3-n-hexylthiophene) (P3HT):phenyl-C61-butyric acid methyl ester (PCBM) and an AZO transparent conducting electrode had a power conversion efficiency (PCE) of up to 2.5% with those containing ITO giving a PCE of 2.6%. These results demonstrate that AZO films are a good alternative to ITO for transparent conducting electrodes.

The effect of thermal radiation on the natural convection boundary layer flow over a wavy horizontal surface

In this article, natural convection boundary layer flow is investigated over a semi-infinite horizontal wavy surface. Such an irregular (wavy) surface is used to exchange heat with an external radiating fluid which obeys Rosseland diffusion approximation. The boundary layer equations are cast into dimensionless form by introducing appropriate scaling. Primitive variable formulations (PVF) and stream function formulations (SFF) are independently used to transform the boundary layer equations into convenient form. The equations obtained from the former formulations are integrated numerically via implicit finite difference iterative scheme whereas equations obtained from lateral formulations are simulated through Keller-box scheme. To validate the results, solutions produced by above two methods are compared graphically. The main parameters: thermal radiation parameter and amplitude of the wavy surface are discussed categorically in terms of shear stress and rate of heat transfer. It is found that wavy surface increases heat transfer rate compared to the smooth wall. Thus optimum heat transfer is accomplished when irregular surface is considered. It is also established that high amplitude of the wavy surface in the boundary layer leads to separation of fluid from the plate.

Automatic ICD-10 classification of cancers from free-text death certificates

Objective Death certificates provide an invaluable source for cancer mortality statistics; however, this value can only be realised if accurate, quantitative data can be extracted from certificates – an aim hampered by both the volume and variable nature of certificates written in natural language. This paper proposes an automatic classification system for identifying cancer related causes of death from death certificates. Methods Detailed features, including terms, n-grams and SNOMED CT concepts were extracted from a collection of 447,336 death certificates. These features were used to train Support Vector Machine classifiers (one classifier for each cancer type). The classifiers were deployed in a cascaded architecture: the first level identified the presence of cancer (i.e., binary cancer/nocancer) and the second level identified the type of cancer (according to the ICD-10 classification system). A held-out test set was used to evaluate the effectiveness of the classifiers according to precision, recall and F-measure. In addition, detailed feature analysis was performed to reveal the characteristics of a successful cancer classification model. Results The system was highly effective at identifying cancer as the underlying cause of death (F-measure 0.94). The system was also effective at determining the type of cancer for common cancers (F-measure 0.7). Rare cancers, for which there was little training data, were difficult to classify accurately (F-measure 0.12). Factors influencing performance were the amount of training data and certain ambiguous cancers (e.g., those in the stomach region). The feature analysis revealed a combination of features were important for cancer type classification, with SNOMED CT concept and oncology specific morphology features proving the most valuable. Conclusion The system proposed in this study provides automatic identification and characterisation of cancers from large collections of free-text death certificates. This allows organisations such as Cancer Registries to monitor and report on cancer mortality in a timely and accurate manner. In addition, the methods and findings are generally applicable beyond cancer classification and to other sources of medical text besides death certificates.

Individual difference predictors of change in career adaptability over time

Career adaptability is a psychosocial construct that reflects individuals' resources for managing career tasks and challenges. This study investigated the effects of demographic characteristics and three sets of individual difference variables (Big Five personality traits, core self-evaluations, and temporal focus) on changes over time in career adaptability and its dimensions (concern, control, curiosity, and confidence). Data came from 659 full-time employees in Australia who participated in two measurement waves six months apart. Results showed that age and future temporal focus predicted change in overall career adaptability. In addition, age, education, extraversion, neuroticism, openness to experience, core self-evaluations, and future temporal focus differentially predicted change over time in one or more of the four career adaptability dimensions. While the lagged effects found in this study were generally small, the findings suggest that certain individual difference characteristics predispose employees to experience change in career adaptability over time.

Indoor environments : design, productivity and health

In a typical large office block, by far the largest lifetime expense is the salaries of the workers - 84% for salaries compared with : office rent (14%), total energy (1%), and maintenance (1%). The key drive for business is therefore the maximisation of the productivity of the employees as this is the largest cost. Reducing total energy use by 50% will not produce the same financial return as 1% productivity improvement? The aim of the project which led to this review of the literature was to understand as far as possible the state of knowledge internationally about how the indoor environment of buildings does influence occupants and the impact this influence may have on the total cost of ownership of buildings. Therefore one of the main focus areas for the literature has been identifying whether there is a link between productivity and health of building occupants and the indoor environment. Productivity is both easy to define - the ratio of output to input - but at the same time very hard to measure in a relatively small environment where individual contributions can influence the results, in particular social interactions. Health impacts from a building environment are also difficult to measure well, as establishing casual links between the indoor environment and a particular health issue can be very difficult. All of those issues are canvassed in the literature reported here. Humans are surprisingly adaptive to different physical environments, but the workplace should not test the limits of human adaptability. Physiological models of stress, for example, accept that the body has a finite amount of adaptive energy available to cope with stress. The importance of, and this projects' focus on, the physical setting within the integrated system of high performance workplaces, means this literature survey explores research which has been undertaken on both physical and social aspects of the built environment. The literature has been largely classified in several different ways, according to the classification scheme shown below. There is still some inconsistency in the use of keywords, which is being addressed and greater uniformity will be developed for a CD version of this literature, enabling searching using this classification scheme.

How can Australia sustain middle-schooling education?

Middle schooling is a crucial area of education where adolescents experiencing physiological and psychological hanges require expert guidance. As more research evidence is provided about adolescent learning, teachers are considered pivotal to adolescents’ educational development. The two levels of implementing reform measures need to be targeted, that is, at the inservice and preservice teacher levels. This quantitative study employs a 40-item, five-part Likert scale survey to understand preservice teachers’ (n=142) perceptions of their confidence to teach in the middle school at the conclusion of their tertiary education. The survey instrument was developed from the literature with connections to the Queensland College of Teachers professional standards. Results indicated that they perceived themselves as capable of creating a positive classroom environment with seven items greater than 80%, except with behaviour management (<80% for two items) and they considered their pedagogical knowledge to be adequate (i.e., 7 out of 8 items >84%). Items associated with implementing middle schooling curriculum had varied responses (e.g., implementing literacy and numeracy were 74% while implementing learning with real-world connections was 91%). This information may assist coursework designers. For example, if significant percentages of preservice teachers indicate they believe they were not well prepared for assessment and reporting in the middle school then course designers can target these areas more effectively.

Humans, ‘things’ and space : costing hospital infection control interventions

Background: Previous attempts at costing infection control programmes have tended to focus on accounting costs rather than economic costs. For studies using economic costs, estimates tend to be quite crude and probably underestimate the true cost. One of the largest costs of any intervention is staff time, but this cost is difficult to quantify and has been largely ignored in previous attempts. Aim: To design and evaluate the costs of hospital-based infection control interventions or programmes. This article also discusses several issues to consider when costing interventions, and suggests strategies for overcoming these issues. Methods: Previous literature and techniques in both health economics and psychology are reviewed and synthesized. Findings: This article provides a set of generic, transferable costing guidelines. Key principles such as definition of study scope and focus on large costs, as well as pitfalls (e.g. overconfidence and uncertainty), are discussed. Conclusion: These new guidelines can be used by hospital staff and other researchers to cost their infection control programmes and interventions more accurately.