Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci

Objective: To perform a 1-stage meta-analysis of genome-wide association studies (GWAS) of multiple sclerosis (MS) susceptibility and to explore functional consequences of new susceptibility loci. Methods: We synthesized 7 MS GWAS. Each data set was imputed using HapMap phase II, and a per single nucleotide polymorphism (SNP) meta-analysis was performed across the 7 data sets. We explored RNA expression data using a quantitative trait analysis in peripheral blood mononuclear cells (PBMCs) of 228 subjects with demyelinating disease. Results: We meta-analyzed 2,529,394 unique SNPs in 5,545 cases and 12,153 controls. We identified 3 novel susceptibility alleles: rs170934T at 3p24.1 (odds ratio [OR], 1.17; p ¼ 1.6 � 10�8) near EOMES, rs2150702G in the second intron of MLANA on chromosome 9p24.1 (OR, 1.16; p ¼ 3.3 � 10�8), and rs6718520A in an intergenic region on chromosome 2p21, with THADA as the nearest flanking gene (OR, 1.17; p ¼ 3.4 � 10�8). The 3 new loci do not have a strong cis effect on RNA expression in PBMCs. Ten other susceptibility loci had a suggestive p < 1 � 10�6, some of these loci have evidence of association in other inflammatory diseases (ie, IL12B, TAGAP, PLEK, and ZMIZ1). Interpretation: We have performed a meta-analysis of GWAS in MS that more than doubles the size of previous gene discovery efforts and highlights 3 novel MS susceptibility loci. These and additional loci with suggestive evidence of association are excellent candidates for further investigations to refine and validate their role in the genetic architecture of MS.

Novel NOD2 haplotype strengthens the association between TLR4 Asp299gly and Crohnʼs disease in an Australian population

Background:: The first major Crohn's disease (CD) susceptibility gene, NOD2, implicates the innate intestinal immune system and other pattern recognition receptors in the pathogenesis of this chronic, debilitating disorder. These include the Toll‐like receptors, specifically TLR4 and TLR5. A variant in the TLR4 gene (A299G) has demonstrated variable association with CD. We aimed to investigate the relationship between TLR4 A299G and TLR5 N392ST, and an Australian inflammatory bowel disease cohort, and to explore the strength of association between TLR4 A299G and CD using global meta‐analysis. Methods:: Cases (CD = 619, ulcerative colitis = 300) and controls (n = 360) were genotyped for TLR4 A299G, TLR5 N392ST, and the 4 major NOD2 mutations. Data were interrogated for case‐control analysis prior to and after stratification by NOD2 genotype. Genotype–phenotype relationships were also sought. Meta‐analysis was conducted via RevMan. Results:: The TLR4 A299G variant allele showed a significant association with CD compared to controls (P = 0.04) and a novel NOD2 haplotype was identified which strengthened this (P = 0.003). Furthermore, we identified that TLR4 A299G was associated with CD limited to the colon (P = 0.02). In the presence of the novel NOD2 haplotype, TLR4 A299G was more strongly associated with colonic disease (P < 0.001) and nonstricturing disease (P = 0.009). A meta‐analysis of 11 CD cohorts identified a 1.5‐fold increase in risk for the variant TLR4 A299G allele (P < 0.00001). Conclusions:: TLR 4 A299G appears to be a significant risk factor for CD, in particular colonic, nonstricturing disease. Furthermore, we identified a novel NOD2 haplotype that strengthens the relationship between TLR4 A299G and these phenotypes.

Identification and simultaneous analysis of harmane, harmol, isovitexin and vitexin in Passiflora incarnata extracts with a novel HLPC method

A high performance liquid chromatographic method for the simultaneous analysis of two flavonoids (iso-vitexin and vitexin), and three indole alkaloids (harmane, harmine, and harmol) was developed. This method was then utilised to quantitate levels of these five constituents in methanolic extracts of Australian Passiflora incarnata. HPLC analysis was performed using a Waters™ Novapak C18 (150 × 4 mm, 4 μm) column, with a gradient solvent system of methanol-water-acetic acid. Detection was achieved by PDA UV (254 nm) and fluorescence (excitation 254 nm, emission 414 nm), utilising the external standard method to obtain quantification.

Simultaneous determination of aldrin, dieldrin, endrin, heptachlor, and p,p'-DDT in medicinal plant extracts using a novel high performance liquid chromatography method

A high performance liquid chromatographic method for the simultaneous determination of five organochlorine pesticides (aldrin, p,p’-DDT, dieldrin, endrin, and heptachlor) was developed. The method was used to determine the levels of these pesticides in medicinal plant samples. Analysis was carried out using a Merck LiChrospher 100 RP C18 (5 μm) column with a gradient solvent system of acetonitrile-water and PDA UV detection (224 nm). Quantification was carried out by the external standard method. The limit of detection for the utilized method was below the local legal limits (ANZFA) for similar plant materials for all 5 pesticides excepting endrin. Medicinal plant extracts were further analyzed by conventional GC-ECD and GC-NPD means using SPE and GPC cleanup as required.

High resolution melt analysis : a novel method for studying the genetic relatedness of Pseudomonas aeruginosa isolates from clinical and environmental sources

A novel method was developed for studying the genetic relatedness of Pseudomonas aeruginosa isolates from clinical and environmental sources. This bacterium is ubiquitous in the natural environment and is an important pathogen known to infect Cystic Fibrosis (CF) patients. The transmission route of strains has not yet been defined; current theories include acquisition from an environmental source or through patient-to-patient spread. A highly discriminatory, bioinformatics based, DNA typing method was developed to investigate the relatedness of clinical and environmental isolates. This study found a similarity between the environmental and several CF clonal strains and also highlighted occurrence of environmental P. aeruginosa strains in CF infections.

Understanding requirements of novel healthcare information systems for management of advanced prostate cancer

Effective management of chronic diseases is a global health priority. A healthcare information system offers opportunities to address challenges of chronic disease management. However, the requirements of health information systems are often not well understood. The accuracy of requirements has a direct impact on the successful design and implementation of a health information system. Our research describes methods used to understand the requirements of health information systems for advanced prostate cancer management. The research conducted a survey to identify heterogeneous sources of clinical records. Our research showed that the General Practitioner was the common source of patient's clinical records (41%) followed by the Urologist (14%) and other clinicians (14%). Our research describes a method to identify diverse data sources and proposes a novel patient journey browser prototype that integrates disparate data sources.

Distributed low-power image processing in wireless sensor networks for intelligent video surveillance applications

Distributed Wireless Smart Camera (DWSC) network is a special type of Wireless Sensor Network (WSN) that processes captured images in a distributed manner. While image processing on DWSCs sees a great potential for growth, with its applications possessing a vast practical application domain such as security surveillance and health care, it suffers from tremendous constraints. In addition to the limitations of conventional WSNs, image processing on DWSCs requires more computational power, bandwidth and energy that presents significant challenges for large scale deployments. This dissertation has developed a number of algorithms that are highly scalable, portable, energy efficient and performance efficient, with considerations of practical constraints imposed by the hardware and the nature of WSN. More specifically, these algorithms tackle the problems of multi-object tracking and localisation in distributed wireless smart camera net- works and optimal camera configuration determination. Addressing the first problem of multi-object tracking and localisation requires solving a large array of sub-problems. The sub-problems that are discussed in this dissertation are calibration of internal parameters, multi-camera calibration for localisation and object handover for tracking. These topics have been covered extensively in computer vision literatures, however new algorithms must be invented to accommodate the various constraints introduced and required by the DWSC platform. A technique has been developed for the automatic calibration of low-cost cameras which are assumed to be restricted in their freedom of movement to either pan or tilt movements. Camera internal parameters, including focal length, principal point, lens distortion parameter and the angle and axis of rotation, can be recovered from a minimum set of two images of the camera, provided that the axis of rotation between the two images goes through the camera's optical centre and is parallel to either the vertical (panning) or horizontal (tilting) axis of the image. For object localisation, a novel approach has been developed for the calibration of a network of non-overlapping DWSCs in terms of their ground plane homographies, which can then be used for localising objects. In the proposed approach, a robot travels through the camera network while updating its position in a global coordinate frame, which it broadcasts to the cameras. The cameras use this, along with the image plane location of the robot, to compute a mapping from their image planes to the global coordinate frame. This is combined with an occupancy map generated by the robot during the mapping process to localised objects moving within the network. In addition, to deal with the problem of object handover between DWSCs of non-overlapping fields of view, a highly-scalable, distributed protocol has been designed. Cameras that follow the proposed protocol transmit object descriptions to a selected set of neighbours that are determined using a predictive forwarding strategy. The received descriptions are then matched at the subsequent camera on the object's path using a probability maximisation process with locally generated descriptions. The second problem of camera placement emerges naturally when these pervasive devices are put into real use. The locations, orientations, lens types etc. of the cameras must be chosen in a way that the utility of the network is maximised (e.g. maximum coverage) while user requirements are met. To deal with this, a statistical formulation of the problem of determining optimal camera configurations has been introduced and a Trans-Dimensional Simulated Annealing (TDSA) algorithm has been proposed to effectively solve the problem.

Measurement, modelling and capacity analysis for novel, fixed multi-user single-antenna MIMO-OFDM system, in rural environments

High-speed broadband internet access is widely recognised as a catalyst to social and economic development. However, the provision of broadband Internet services with the existing solutions to rural population, scattered over an extensive geographical area, remains both an economic and technical challenge. As a feasible solution, the Commonwealth Scientific and Industrial Research Organization (CSIRO) proposed a highly spectrally efficient, innovative and cost-effective fixed wireless broadband access technology, which uses analogue TV frequency spectrum and Multi-User MIMO (MUMIMO) technology with Orthogonal-Frequency-Division-Multiplexing (OFDM). MIMO systems have emerged as a promising solution for the increasing demand of higher data rates, better quality of service, and higher network capacity. However, the performance of MIMO systems can be significantly affected by different types of propagation environments e.g., indoor, outdoor urban, or outdoor rural and operating frequencies. For instance, large spectral efficiencies associated with MIMO systems, which assume a rich scattering environment in urban environments, may not be valid for all propagation environments, such as outdoor rural environments, due to the presence of less scatterer densities. Since this is the first time a MU-MIMO-OFDM fixed broadband wireless access solution is deployed in a rural environment, questions from both theoretical and practical standpoints arise; For example, what capacity gains are available for the proposed solution under realistic rural propagation conditions?. Currently, no comprehensive channel measurement and capacity analysis results are available for MU-MIMO-OFDM fixed broadband wireless access systems which employ large scale multiple antennas at the Access Point (AP) and analogue TV frequency spectrum in rural environments. Moreover, according to the literature, no deterministic MU-MIMO channel models exist that define rural wireless channels by accounting for terrain effects. This thesis fills the aforementioned knowledge gaps with channel measurements, channel modeling and comprehensive capacity analysis for MU-MIMO-OFDM fixed wireless broadband access systems in rural environments. For the first time, channel measurements were conducted in a rural farmland near Smithton, Tasmania using CSIRO's broadband wireless access solution. A novel deterministic MU-MIMO-OFDM channel model, which can be used for accurate performance prediction of rural MUMIMO channels with dominant Line-of-Sight (LoS) paths, was developed under this research. Results show that the proposed solution can achieve 43.7 bits/s/Hz at a Signal-to- Noise Ratio (SNR) of 20 dB in rural environments. Based on channel measurement results, this thesis verifies that the deterministic channel model accurately predicts channel capacity in rural environments with a Root Mean Square (RMS) error of 0.18 bits/s/Hz. Moreover, this study presents a comprehensive capacity analysis of rural MU-MIMOOFDM channels using experimental, simulated and theoretical models. Based on the validated deterministic model, further investigations on channel capacity and the eects of capacity variation, with different user distribution angles (θ) around the AP, were analysed. For instance, when SNR = 20dB, the capacity increases from 15.5 bits/s/Hz to 43.7 bits/s/Hz as θ increases from 10° to 360°. Strategies to mitigate these capacity degradation effects are also presented by employing a suitable user grouping method. Outcomes of this thesis have already been used by CSIRO scientists to determine optimum user distribution angles around the AP, and are of great significance for researchers and MU-MUMO-OFDM system developers to understand the advantages and potential capacity gains of MU-MIMO systems in rural environments. Also, results of this study are useful to further improve the performance of MU-MIMO-OFDM systems in rural environments. Ultimately, this knowledge contribution will be useful in delivering efficient, cost-effective high-speed wireless broadband systems that are tailor-made for rural environments, thus, improving the quality of life and economic prosperity of rural populations.

Aligned poly(L-lactic-co-ε-caprolactone) electrospun microfibers and knitted structure: a novel composite scaffold for ligament tissue engineering

We developed a novel technique involving knitting and electrospinning to fabricate a composite scaffold for ligament tissue engineering. Knitted structures were coated with poly(L-lactic-co-e-caprolactone) (PLCL) and then placed onto a rotating cylinder and a PLCL solution was electrospun onto the structure. Highly aligned 2-μm-diameter microfibers covered the space between the stitches and adhered to the knitted scaffolds. The stress–strain tensile curves exhibited an initial toe region similar to the tensile behavior of ligaments. Composite scaffolds had an elastic modulus (150 ± 14 MPa) similar to the modulus of human ligaments. Biological evaluation showed that cells proliferated on the composite scaffolds and they spontaneously orientated along the direction of microfiber alignment. The microfiber architecture also induced a high level of extracellular matrix secretion, which was characterized by immunostaining. We found that cells produced collagen type I and type III, two main components found in ligaments. After 14 days of culture, collagen type III started to form a fibrous network. We fabricated a composite scaffold having the mechanical properties of the knitted structure and the morphological properties of the aligned microfibers. It is difficult to seed a highly macroporous structure with cells, however the technique we developed enabled an easy cell seeding due to presence of the microfiber layer. Therefore, these scaffolds presented attractive properties for a future use in bioreactors for ligament tissue engineering.

A novel bioreactor for ligament tissue engineering

Bioreactors are defined as devices in which biological and/or biochemical processes develop under closely monitored and tightly controlled environmental and operating conditions (e.g. pH, temperature, mechanical conditions, nutrient supply and waste removal). In functional tissue engineering of musculoskeletal tissues, a bioreactor capable of controlling dynamic loading plays a determinant role. It has been shown that mechanical stretching promotes the expression of type I and III collagens, fibronectin, tenascin-C in cultured ligament fibroblasts (J.C.-H. Goh et al., Tissue Eng. 9 (2003), S31) and that human bone marrow mesenchymal stem cells (hBMMSC) – even in the absence of biochemical regulators – could be induced to differentiate into ligament-like fibroblast by the application of physiologically relevant cyclic strains (G. Vunjak-Novakovic et al., Ann. Rev. Biomed. Eng. 6 (2004), 131; H.A. Awad et al., Tissue Eng. 5 (1999), 267; R.G. Young et al., J. Orthop. Res. 16 (1998), 406). Different bioreactors are commercially available but they are too generic to be used for a given tissue, each tissue showing specific mechanical loading properties. In the case of ligament tissue engineering, the design of a bioreactor is still an open question. Our group proposes a bioreactor allowing cyclic traction–torsion on a scaffold seeded with stem cells.

A novel representation of bioacoustic events for content-based search in field audio data

Bioacoustic data can provide an important base for environmental monitoring. To explore a large amount of field recordings collected, an automated similarity search algorithm is presented in this paper. A region of an audio defined by frequency and time bounds is provided by a user; the content of the region is used to construct a query. In the retrieving process, our algorithm will automatically scan through recordings to search for similar regions. In detail, we present a feature extraction approach based on the visual content of vocalisations – in this case ridges, and develop a generic regional representation of vocalisations for indexing. Our feature extraction method works best for bird vocalisations showing ridge characteristics. The regional representation method allows the content of an arbitrary region of a continuous recording to be described in a compressed format.

Photovoltaic DC-DC module integrated converter for novel cascaded and bypass grid connection topologies - design and optimisation

Grid connected photovoltaic (PV) inverters fall into three broad categories - central, string and module integrated converters (MICs). MICs offer many advantages in performance and flexibility, but are at a cost disadvantage. Two alternative novel approaches proposed by the author - cascaded dc-dc MICs and bypass dc-dc MICs - integrate a simple non-isolated intelligent dc-dc converter with each PV module to provide the advantages of dc-ac MICs at a lower cost. A suitable universal 150 W 5 A dc-dc converter design is presented based on two interleaved MOSFET half bridges. Testing shows zero voltage switching (ZVS) keeps losses under 1 W for bi-directional power flows up to 15 W between two adjacent 12 V PV modules for the bypass application, and efficiencies over 94% for most of the operational power range for the cascaded converter application. Based on the experimental results, potential optimizations to further reduce losses are discussed.

Let's eat the captain! Thinking, feeling, doing : intercultural language learning through process drama

This research investigated the sustained use of process drama in a middle school foreign language classroom. The experience led to widespread learner engagement, a deeper contextualisation of the language as a socio-cultural practice, and a willingness to use the spoken and written language, regardless of limited proficiency. The drama required that language use be context and culture specific, contingent and multi-modal, which encouraged the beginner students to "mushfake" or improvise spoken and written text. Particularly important was the way the body was used through drama to express emotion, remember language and to illustrate the sociocultural context of its use.

Exercise-induced phosphorylation of the novel Akt substrates AS160 and filamin A in human skeletal muscle

Skeletal muscle contraction stimulates multiple signaling cascades that govern a variety of metabolic and transcriptional events. Akt/protein kinase B regulates metabolism and growth/muscle hypertrophy, but contraction effects on this target and its substrates are varied and may depend on the mode of the contractile stimulus. Accordingly, we determined the effects of endurance or resistance exercise on phosphorylation of Akt and downstream substrates in six trained cyclists who performed a single bout of endurance or resistance exercise separated by ?7 days. Muscle biopsies were taken from the vastus lateralis at rest and immediately after exercise. Akt Ser 473 phosphorylation was increased (1.8-fold; P = 0.011) after endurance but was unchanged after resistance exercise. Conversely, Akt Thr 308 phosphorylation was unaltered after either bout of exercise. Several exercise-responsive phosphoproteins were detected by immunoblot analysis with a phospho-Akt substrate antibody. pp160 and pp300 were identified as AS160 and filamin A, respectively, with increased phosphorylation (2.0- and 4.9-fold, respectively; P < 0.05) after endurance but not resistance exercise. In conclusion, AS160 and filamin A may provide an important link to mediate endurance exercise-induced bioeffects in skeletal muscle.