Street computing : towards an integrated open data Application Programming Interface (API) for cities

This special issue of the Journal of Urban Technology brings together five articles that are based on presentations given at the Street Computing Workshop held on 24 November 2009 in Melbourne in conjunction with the Australian Computer- Human Interaction conference (OZCHI 2009). Our own article introduces the Street Computing vision and explores the potential, challenges, and foundations of this research trajectory. In order to do so, we first look at the currently available sources of information and discuss their link to existing research efforts. Section 2 then introduces the notion of Street Computing and our research approach in more detail. Section 3 looks beyond the core concept itself and summarizes related work in this field of interest. We conclude by introducing the papers that have been contributed to this special issue.

Designing a seasonality application to support urban agriculture practice

This position paper describes the work in progress towards the goal of building a technical prototype that enables users – those who have little or no knowledge and experience engaging in urban agriculture – to receive information personalised to their location and situation, and allow them to ask questions and share experiences with others. We describe the design process thus far, informed by a survey and a workshop with experts in the field, before concluding with the future direction of this work.

Utilising hospital data to inform product safety prioritisation : the application of RAPEX severity rankings in ICD-coded burn data

Background The implementation of the Australian Consumer Law in 2011 highlighted the need for better use of injury data to improve the effectiveness and responsiveness of product safety (PS) initiatives. In the PS system, resources are allocated to different priority issues using risk assessment tools. The rapid exchange of information (RAPEX) tool to prioritise hazards, developed by the European Commission, is currently being adopted in Australia. Injury data is required as a basic input to the RAPEX tool in the risk assessment process. One of the challenges in utilising injury data in the PS system is the complexity of translating detailed clinical coded data into broad categories such as those used in the RAPEX tool. Aims This study aims to translate hospital burns data into a simplified format by mapping the International Statistical Classification of Disease and Related Health Problems (Tenth Revision) Australian Modification (ICD-10-AM) burn codes into RAPEX severity rankings, using these rankings to identify priority areas in childhood product-related burns data. Methods ICD-10-AM burn codes were mapped into four levels of severity using the RAPEX guide table by assigning rankings from 1-4, in order of increasing severity. RAPEX rankings were determined by the thickness and surface area of the burn (BSA) with information extracted from the fourth character of T20-T30 codes for burn thickness, and the fourth and fifth characters of T31 codes for the BSA. Following the mapping process, secondary data analysis of 2008-2010 Queensland Hospital Admitted Patient Data Collection (QHAPDC) paediatric data was conducted to identify priority areas in product-related burns. Results The application of RAPEX rankings in QHAPDC burn data showed approximately 70% of paediatric burns in Queensland hospitals were categorised under RAPEX levels 1 and 2, 25% under RAPEX 3 and 4, with the remaining 5% unclassifiable. In the PS system, prioritisations are made to issues categorised under RAPEX levels 3 and 4. Analysis of external cause codes within these levels showed that flammable materials (for children aged 10-15yo) and hot substances (for children aged <2yo) were the most frequently identified products. Discussion and conclusions The mapping of ICD-10-AM burn codes into RAPEX rankings showed a favourable degree of compatibility between both classification systems, suggesting that ICD-10-AM coded burn data can be simplified to more effectively support PS initiatives. Additionally, the secondary data analysis showed that only 25% of all admitted burn cases in Queensland were severe enough to trigger a PS response.

Utilising hospital data to inform product safety prioritisation : the application of RAPEX severity rankings in ICD-coded Burn Data

Background The implementation of the Australian Consumer Law in 2011 highlighted the need for better use of injury data to improve the effectiveness and responsiveness of product safety (PS) initiatives. In the PS system, resources are allocated to different priority issues using risk assessment tools. The rapid exchange of information (RAPEX) tool to prioritise hazards, developed by the European Commission, is currently being adopted in Australia. Injury data is required as a basic input to the RAPEX tool in the risk assessment process. One of the challenges in utilising injury data in the PS system is the complexity of translating detailed clinical coded data into broad categories such as those used in the RAPEX tool. Aims This study aims to translate hospital burns data into a simplified format by mapping the International Statistical Classification of Disease and Related Health Problems (Tenth Revision) Australian Modification (ICD-10-AM) burn codes into RAPEX severity rankings, using these rankings to identify priority areas in childhood product-related burns data. Methods ICD-10-AM burn codes were mapped into four levels of severity using the RAPEX guide table by assigning rankings from 1-4, in order of increasing severity. RAPEX rankings were determined by the thickness and surface area of the burn (BSA) with information extracted from the fourth character of T20-T30 codes for burn thickness, and the fourth and fifth characters of T31 codes for the BSA. Following the mapping process, secondary data analysis of 2008-2010 Queensland Hospital Admitted Patient Data Collection (QHAPDC) paediatric data was conducted to identify priority areas in product-related burns. Results The application of RAPEX rankings in QHAPDC burn data showed approximately 70% of paediatric burns in Queensland hospitals were categorised under RAPEX levels 1 and 2, 25% under RAPEX 3 and 4, with the remaining 5% unclassifiable. In the PS system, prioritisations are made to issues categorised under RAPEX levels 3 and 4. Analysis of external cause codes within these levels showed that flammable materials (for children aged 10-15yo) and hot substances (for children aged <2yo) were the most frequently identified products. Discussion and conclusions The mapping of ICD-10-AM burn codes into RAPEX rankings showed a favourable degree of compatibility between both classification systems, suggesting that ICD-10-AM coded burn data can be simplified to more effectively support PS initiatives. Additionally, the secondary data analysis showed that only 25% of all admitted burn cases in Queensland were severe enough to trigger a PS response.

Shrinkage empirical likelihood estimator in longitudinal analysis with time-dependent covariates-application to modeling the health of Filipino children

The method of generalized estimating equations (GEE) is a popular tool for analysing longitudinal (panel) data. Often, the covariates collected are time-dependent in nature, for example, age, relapse status, monthly income. When using GEE to analyse longitudinal data with time-dependent covariates, crucial assumptions about the covariates are necessary for valid inferences to be drawn. When those assumptions do not hold or cannot be verified, Pepe and Anderson (1994, Communications in Statistics, Simulations and Computation 23, 939–951) advocated using an independence working correlation assumption in the GEE model as a robust approach. However, using GEE with the independence correlation assumption may lead to significant efficiency loss (Fitzmaurice, 1995, Biometrics 51, 309–317). In this article, we propose a method that extracts additional information from the estimating equations that are excluded by the independence assumption. The method always includes the estimating equations under the independence assumption and the contribution from the remaining estimating equations is weighted according to the likelihood of each equation being a consistent estimating equation and the information it carries. We apply the method to a longitudinal study of the health of a group of Filipino children.

Modelling of ellipsoidal nanowires : control and application

The properties of ellipsoidal nanowires are yet to be examined. They have likely applications in sensing, solar cells, microelectronics and cloaking devices. Little is known of the qualities that ellipse nanowires exhibit as we vary the aspect ratio with different dielectric materials and how varying these attributes affects plasmon coupling and propagation. It is known that the distance a plasmon can travel is further if it is supported by a thicker circular nanowire, while thinner nanowires are expected to be able to increase QD coupling. Ellipsoidal nanowires may be a good compromise due to their ability to have both thin and thick dimensions. Furthermore it has been shown that the plasmon resonances along the main axis of an ellipsoidal particle is governed by the relative aspect ratio of the ellipsoid, which may lead to further control of the plasmon. Research was done by the use of COMSOL Multiphysics by looking at the fundamental plasmon mode supported by an ellipsoidal nanowire and then studying this mode for various geometrical parameters, materials and illumination wavelength. Accordingly it was found that ellipsoidal nanowires exhibit a minimum for the wavenumber and a maximum for the propagation distance at roughly the same dimensions - Highlighting that there is an aspect ratio for which there is poor coupling but low loss. Here we investigate these and related attributes.

Introducing standardized protocols for anthropological measurement of virtual subadult crania using computed tomography

Objectives This study introduces and assesses the precision of a standardized protocol for anthropometric measurement of the juvenile cranium using three-dimensional surface rendered models, for implementation in forensic investigation or paleodemographic research. Materials and methods A subset of multi-slice computed tomography (MSCT) DICOM datasets (n=10) of modern Australian subadults (birth—10 years) was accessed from the “Skeletal Biology and Forensic Anthropology Virtual Osteological Database” (n>1200), obtained from retrospective clinical scans taken at Brisbane children hospitals (2009–2013). The capabilities of Geomagic Design X™ form the basis of this study; introducing standardized protocols using triangle surface mesh models to (i) ascertain linear dimensions using reference plane networks and (ii) calculate the area of complex regions of interest on the cranium. Results The protocols described in this paper demonstrate high levels of repeatability between five observers of varying anatomical expertise and software experience. Intra- and inter-observer error was indiscernible with total technical error of measurement (TEM) values ≤0.56 mm, constituting <0.33% relative error (rTEM) for linear measurements; and a TEM value of ≤12.89 mm2, equating to <1.18% (rTEM) of the total area of the anterior fontanelle and contiguous sutures. Conclusions Exploiting the advances of MSCT in routine clinical assessment, this paper assesses the application of this virtual approach to acquire highly reproducible morphometric data in a non-invasive manner for human identification and population studies in growth and development. The protocols and precision testing presented are imperative for the advancement of “virtual anthropology” into routine Australian medico-legal death investigation.

Distance education and the application of academagogy : a case study

The education sector has dramatically changed in the past half decade. In a time of globalisation of education and tightening budgets, various paradigm shifts and challenges have rapidly changed learning and teaching. These include: meeting student expectation for more engaging, more interactive learning experiences, the increased focus to deliver content online, and the complexities of fast-changing technologies. Rising to these challenges and responding to them is a complex and multi-faceted task. This paper discusses educational theories and issues and explores current educational practices in the context of teaching undergraduate students via distance education in the university context. A case study applies a framework drawn from engineering education using the learner-centric concept of academagogy. Results showed that academagogy actively empowers students to build effective learning, and engages facilitators in meaningful teaching and delivery methods.

De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

Background: Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. Methodology/Results: RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. Conclusions: The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant. © 2013 Nakasugi et al.

Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines

Forward genetic screens have identified numerous genes involved in development and metabolism, and remain a cornerstone of biological research. However, to locate a causal mutation, the practice of crossing to a polymorphic background to generate a mapping population can be problematic if the mutant phenotype is difficult to recognize in the hybrid F2 progeny, or dependent on parental specific traits. Here in a screen for leaf hyponasty mutants, we have performed a single backcross of an Ethane Methyl Sulphonate (EMS) generated hyponastic mutant to its parent. Whole genome deep sequencing of a bulked homozygous F2 population and analysis via the Next Generation EMS mutation mapping pipeline (NGM) unambiguously determined the causal mutation to be a single nucleotide polymorphisim (SNP) residing in HASTY, a previously characterized gene involved in microRNA biogenesis. We have evaluated the feasibility of this backcross approach using three additional SNP mapping pipelines; SHOREmap, the GATK pipeline, and the samtools pipeline. Although there was variance in the identification of EMS SNPs, all returned the same outcome in clearly identifying the causal mutation in HASTY. The simplicity of performing a single parental backcross and genome sequencing a small pool of segregating mutants has great promise for identifying mutations that may be difficult to map using conventional approaches.

Application of gene silencing in plants

Recent studies of gene silencing in plants have revealed two RNA-mediated epigenetic processes, RNA-directed RNA degradation and RNA-directed DNA methylation. These natural processes have provided new avenues for developing high-efficiency, high-throughput technology for gene suppression in plants.

Application of gene silencing in plants

Recent studies of gene silencing in plants have revealed two RNA-mediated epigenetic processes, RNA-directed RNA degradation and RNA-directed DNA methylation. These natural processes have provided new avenues for developing high-efficiency, high-throughput technology for gene suppression in plants.

Education of health professionals for preventing diabetic foot ulceration (Protocol)

This is the protocol for a review and there is no abstract. The objectives are as follows: To investigate the effects of educational interventions on the behaviour and clinical practice of health professionals, and subsequent patient outcomes related to prevention of foot ulceration in people with diabetes.

Intensive versus conventional glycaemic control for treating diabetic foot ulcers (Protocol)

This is the protocol for a review and there is no abstract. The objectives are as follows: To assess the effects of intensive glycaemic control compared to conventional control on the outcome of foot ulcers in patients with type 1 and type 2 diabetes.