Review of statistical methods for disease mapping

Cancer poses an undeniable burden to the health and wellbeing of the Australian community. In a recent report commissioned by the Australian Institute for Health and Welfare(AIHW, 2010), one in every two Australians on average will be diagnosed with cancer by the age of 85, making cancer the second leading cause of death in 2007, preceded only by cardiovascular disease. Despite modest decreases in standardised combined cancer mortality over the past few decades, in part due to increased funding and access to screening programs, cancer remains a significant economic burden. In 2010, all cancers accounted for an estimated 19% of the country's total burden of disease, equating to approximately $3:8 billion in direct health system costs (Cancer Council Australia, 2011). Furthermore, there remains established socio-economic and other demographic inequalities in cancer incidence and survival, for example, by indigenous status and rurality. Therefore, in the interests of the nation's health and economic management, there is an immediate need to devise data-driven strategies to not only understand the socio-economic drivers of cancer but also facilitate the implementation of cost-effective resource allocation for cancer management...

Fine-mapping identifies multiple prostate cancer risk loci on 5p15 some associating with TERT expression

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease.

A dynamic mapping of the UK's creative industries

This paper argues that, despite its strengths, the UK Department of Culture, Media and Sport (DCMS) classification of the creative industries contains inconsistencies which need to be addressed to make it fully fit for purpose. It presents an improved methodology which retains the strengths of the DCMS's approach while addressing its deficiencies. We focus on creative intensity: the proportion of total employment within an industry that is engaged in creative occupations.

From vision to reality : views of primary school principals on inclusive education in New South Wales, Australia

This paper discusses the findings of a research study that used semi-structured interviews to explore the views of primary school principals on inclusive education in New South Wales, Australia. Content analysis of the transcript data indicates that principals’ attitudes towards inclusive education and their success in engineering inclusive practices within their school are significantly affected by their own conception of what “inclusion” means, as well as the characteristics of the school community, and the attitudes and capacity of staff. In what follows, we present two parallel conversations that arose from the interview data to illustrate the main conceptual divisions existing between our participants’ conceptions of inclusion. First, we discuss the act of “being inclusive” which was perceived mainly as an issue of culture and pedagogy. Second, we consider the mechanics of “including,” which reflected a more instrumentalist position based on perceptions of individual student deficit, the level of support they may require and the amount of funding they can attract.

Towards persistent indoor appearance-based localization, mapping and navigation using CAT-Graph

The challenge of persistent appearance-based navigation and mapping is to develop an autonomous robotic vision system that can simultaneously localize, map and navigate over the lifetime of the robot. However, the computation time and memory requirements of current appearance-based methods typically scale not only with the size of the environment but also with the operation time of the platform; also, repeated revisits to locations will develop multiple competing representations which reduce recall performance. In this paper we present a solution to the persistent localization, mapping and global path planning problem in the context of a delivery robot in an office environment over a one-week period. Using a graphical appearance-based SLAM algorithm, CAT-Graph, we demonstrate constant time and memory loop closure detection with minimal degradation during repeated revisits to locations, along with topological path planning that improves over time without using a global metric representation. We compare the localization performance of CAT-Graph to openFABMAP, an appearance-only SLAM algorithm, and the path planning performance to occupancy-grid based metric SLAM. We discuss the limitations of the algorithm with regard to environment change over time and illustrate how the topological graph representation can be coupled with local movement behaviors for persistent autonomous robot navigation.

Perception of Brownfield Sites : Myth or Reality?

The scarcity of large parcels of land in well-serviced areas is one motivator for redeveloping industrial or commercial property that is abandoned or underused and often environmentally contaminated – so-called brownfield land. Poor industrial waste disposal practices caused by industrial activities including gas works, factories, railway land and waste tips have contributed to many instances of contaminated land identified as brownfield sites. It is estimated there are between 10,000 and 160,000 brownfield sites in Australia, with Queensland accounting for around 4000 of these.

A snapshot of radiation therapy techniques and technology in Queensland : an aid to mapping undergraduate curriculum

Introduction: Undergraduate students studying the Bachelor of Radiation Therapy at Queensland University of Technology (QUT) attend clinical placements in a number of department sites across Queensland. To ensure that the curriculum prepares students for the most common treatments and current techniques in use in these departments, a curriculum matching exercise was performed. Methods: A cross-sectional census was performed on a pre-determined “Snapshot” date in 2012. This was undertaken by the clinical education staff in each department who used a standardized proforma to count the number of patients as well as prescription, equipment, and technique data for a list of tumour site categories. This information was combined into aggregate anonymized data. Results: All 12 Queensland radiation therapy clinical sites participated in the Snapshot data collection exercise to produce a comprehensive overview of clinical practice on the chosen day. A total of 59 different tumour sites were treated on the chosen day and as expected the most common treatment sites were prostate and breast, comprising 46% of patients treated. Data analysis also indicated that intensity-modulated radiotherapy (IMRT) use is relatively high with 19.6% of patients receiving IMRT treatment on the chosen day. Both IMRT and image-guided radiotherapy (IGRT) indications matched recommendations from the evidence. Conclusion: The Snapshot method proved to be a feasible and efficient method of gathering useful

Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses

Historical information can be used, in addition to pedigree, traits and genotypes, to map quantitative trait locus (QTL) in general populations via maximum likelihood estimation of variance components. This analysis is known as linkage disequilibrium (LD) and linkage mapping, because it exploits both linkage in families and LD at the population level. The search for QTL in the wild population of Soay sheep on St. Kilda is a proof of principle. We analysed the data from a previous study and confirmed some of the QTLs reported. The most striking result was the confirmation of a QTL affecting birth weight that had been reported using association tests but not when using linkage-based analyses. Copyright © Cambridge University Press 2010.

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

Mapping of multiple quantitative trait loci affecting bovine spongiform encephalopathy

A whole-genome scan was conducted to map quantitative trait loci (QTL) for BSE resistance or susceptibility. Cows from four half-sib families were included and 173 microsatellite markers were used to construct a 2835-cM (Kosambi) linkage map covering 29 autosomes and the pseudoautosomal region of the sex chromosome. Interval mapping by linear regression was applied and extended to a multiple-QTL analysis approach that used identified QTL on other chromosomes as cofactors to increase mapping power. In the multiple-QTL analysis, two genome-wide significant QTL (BTA17 and X/Y ps) and four genome-wide suggestive QTL (BTA1, 6, 13, and 19) were revealed. The QTL identified here using linkage analysis do not overlap with regions previously identified using TDT analysis. One factor that may explain the disparity between the results is that a more extensive data set was used in the present study. Furthermore, methodological differences between TDT and linkage analyses may affect the power of these approaches.

Principals, Teachers, and Student's Perception of the Information and Communication Technology in Kuwait Secondary Schools (Rhetoric and reality)

ICT integration has been advocated to provide opportunities to improve students’ achievement and engagement through transforming the educational setting. A valuable tool that contributes in enhancing and developing students’ cognitive skills for lifelong learning, ICT integration has introduced a new educational philosophy, shifting the role of students into a more central position in the pedagogical processes. Kuwait, as with many other countries, has recently planned ICT integration to develop its citizen’s capacities. This study sought to capture the principals’, teachers’, and students’ perceptions of ICT integration in pedagogical activities, as well as how ICT is being used for learning and teaching activities in three ICT leading Kuwaiti secondary schools. Interviews with principals, teachers, and students were conducted, along with an open-ended questionnaire for the teachers, researcher observations, and document analysis. The findings revealed that ICT integration in Kuwait needed to be reinforced to accomplish the ICT integration objectives. A call for further support for teachers, and a reconsideration of the ICT integration strategies were also recommended.

The doctrine of command responsibility in the midst of war : legal fallacy or reflection of reality

The history of war is blighted with astonishing reminders of man’s ability to cast his sense of humanity aside and inflict unspeakable harm upon one another. The ruthless bombing of Dresden, the callousness of the Nazi concentration camps and the massacre of the Tutsis are but a few of the atrocities that have haunted our past. In response to these atrocities, society has imposed an ever-increasing number of laws and rules to regulate warfare. Amongst these is the doctrine of command responsibility. The doctrine of command responsibility states that a commander is criminally liable for the crimes of his subordinates if he knew or should have known of their crimes. This paper will examine whether the doctrine is an appropriate and realistic legal standard to hold commanders accountable to or whether the doctrine is more a reflection of social sentiment and legal rhetoric. If the doctrine, and indeed the law of war in general, is unrealistic then the law cannot fulfil its purpose - that is, the prevention of atrocities. Instead of being solely a reflection of moral authority and social sentiments the law must also be a tool that guides and shapes the decisions and actions of the military through the chaotic and brutal nature of war...

From movie screens to moving screens : mapping qualities of new urban interactions

Next generation screens of diverse dimensions such as the Pebble e-paper watch, Google’s Project Glass, Microsoft’s Kinect and IllumiRoom, and large-scale multi-touch screen surface areas, increasingly saturate and diversify the urban mediascape. This paper seeks to contribute to media architecture and interaction design theory by starting to critically examine how these different screen formats are creating a ubiquitous screen mediascape across the city. We introduce next generation personal, domestic, and public screens. The paper critically challenges conventional dichotomies such as local / global, online / offline, private / public, large / small, mobile / static, that have been created in the past to describe some of the qualities and characteristics of interfaces and their usage. More and more scholars recognise that the black and white nature of these dichotomies does not adequately represent the fluid and agile capabilities of many new screen interfaces. With this paper, we hope to illustrate the more nuanced ‘trans-scalar’ qualities of these new urban interactions, that is, ways in which they provide a range functionality, without being locked into either end of a scale.

Comparing cooperative and non-cooperative crash risk assessment

Cooperative Systems provide, through the multiplication of information sources over the road, a lot of potential to improve the assessment of the road risk describing a particular driving situation. In this paper, we compare the performance of a cooperative risk assessment approach against a non-cooperative approach; we used an advanced simulation framework, allowing for accurate and detailed, close-to-reality simulations. Risk is estimated, in both cases, with combinations of indicators based on the TTC. For the non-cooperative approach, vehicles are equipped only with an AAC-like forward-facing ranging sensor. On the other hand, for the cooperative approach, vehicles share information through 802.11p IVC and create an augmented map representing their environment; risk indicators are then extracted from this map. Our system shows that the cooperative risk assessment provides a systematic increase of forward warning to most of the vehicles involved in a freeway emergency braking scenario, compared to a non-cooperative system.

A pre-treatment verification tool for IMRT based on EPID measurements and a GEANT4 back projection application

The aim of this work is to develop software that is capable of back projecting primary fluence images obtained from EPID measurements through phantom and patient geometries in order to calculate 3D dose distributions. In the first instance, we aim to develop a tool for pretreatment verification in IMRT. In our approach, a Geant4 application is used to back project primary fluence values from each EPID pixel towards the source. Each beam is considered to be polyenergetic, with a spectrum obtained from Monte Carlo calculations for the LINAC in question. At each step of the ray tracing process, the energy differential fluence is corrected for attenuation and beam divergence. Subsequently, the TERMA is calculated and accumulated to an energy differential 3D TERMA distribution. This distribution is then convolved with monoenergetic point spread kernels, thus generating energy differential 3D dose distributions. The resulting dose distributions are accumulated to yield the total dose distribution, which can then be used for pre-treatment verification of IMRT plans. Preliminary results were obtained for a test EPID image comprised of 100 9 100 pixels of unity fluence. Back projection of this field into a 30 cm9 30 cm 9 30 cm water phantom was performed, with TERMA distributions obtained in approximately 10 min (running on a single core of a 3 GHz processor). Point spread kernels for monoenergetic photons in water were calculated using a separate Geant4 application. Following convolution and summation, the resulting 3D dose distribution produced familiar build-up and penumbral features. In order to validate the dose model we will use EPID images recorded without any attenuating material in the beam for a number of MLC defined square fields. The dose distributions in water will be calculated and compared to TPS predictions.