Single nucleotide polymorphism (SNP) - genotyping of Community Acquired Methicillin-Resistant Staphylococcus aureus, including the subtyping of PVL toxin producers using Real-Time PCR

Staphylococcus aureus is a common pathogen that causes a variety of infections including soft tissue infections, impetigo, septicemia toxic shock and scalded skin syndrome. Traditionally, Methicillin-Resistant Staphylococcus aureus (MRSA) was considered a Hospital-Acquired (HA) infection. It is now recognised that the frequency of infections with MRSA is increasing in the community, and that these infections are not originating from hospital environments. A 2007 report by the Centers for Disease Control and Prevention (CDC) stated that Staphylococcus aureus is the most important cause of serious and fatal infections in the USA. Community-Acquired MRSA (CA-MRSA) are genetically diverse and distinct, meaning they are able to be identified and tracked by way of genotyping. Genotyping of MRSA using Single nucleotide polymorphisms (SNPs) is a rapid and robust method for monitoring MRSA, specifically ST93 (Queensland Clone) dissemination in the community. It has been shown that a large proportion of CA-MRSA infections in Queensland and New South Wales are caused by ST93. The rationale for this project was that SNP analysis of MLST genes is a rapid and cost-effective method for genotyping and monitoring MRSA dissemination in the community. In this study, 16 different sequence types (ST) were identified with 41% of isolates identified as ST93 making it the predominate clone. Males and Females were infected equally with an average patient age of 45yrs. Phenotypically, all of the ST93 had an identical antimicrobial resistance pattern. They were resistant to the β-lactams – Penicillin, Flu(di)cloxacillin and Cephalothin but sensitive to all other antibiotics tested. Virulence factors play an important role in allowing S. aureus to cause disease by way of colonising, replication and damage to the host. One virulence factor of particular interest is the toxin Panton-Valentine leukocidin (PVL), which is composed of two separate proteins encoded by two adjacent genes. PVL positive CA-MRSA are shown to cause recurrent, chronic or severe skin and soft tissue infections. As a result, it is important that PVL positive CA-MRSA is genotyped and tracked. Especially now that CA-MRSA infections are more prevalent than HA-MRSA infections and are now deemed endemic in Australia. 98% of all isolates in this study tested positive for the PVL toxin gene. This study showed that PVL is present in many different community based ST, not just ST93, which were all PVL positive. With this toxin becoming entrenched in CA-MRSA, genotyping would provide more accurate data and a way of tracking the dissemination. PVL gene can be sub-typed using an allele-specific Real-Time PCR (RT-PCR) followed by High resolution meltanalysis. This allows the identification of PVL subtypes within the CA-MRSA population and allow the tracking of these clones in the community.

Multiple camera management using wide baseline matching

Camera calibration information is required in order for multiple camera networks to deliver more than the sum of many single camera systems. Methods exist for manually calibrating cameras with high accuracy. Manually calibrating networks with many cameras is, however, time consuming, expensive and impractical for networks that undergo frequent change. For this reason, automatic calibration techniques have been vigorously researched in recent years. Fully automatic calibration methods depend on the ability to automatically find point correspondences between overlapping views. In typical camera networks, cameras are placed far apart to maximise coverage. This is referred to as a wide base-line scenario. Finding sufficient correspondences for camera calibration in wide base-line scenarios presents a significant challenge. This thesis focuses on developing more effective and efficient techniques for finding correspondences in uncalibrated, wide baseline, multiple-camera scenarios. The project consists of two major areas of work. The first is the development of more effective and efficient view covariant local feature extractors. The second area involves finding methods to extract scene information using the information contained in a limited set of matched affine features. Several novel affine adaptation techniques for salient features have been developed. A method is presented for efficiently computing the discrete scale space primal sketch of local image features. A scale selection method was implemented that makes use of the primal sketch. The primal sketch-based scale selection method has several advantages over the existing methods. It allows greater freedom in how the scale space is sampled, enables more accurate scale selection, is more effective at combining different functions for spatial position and scale selection, and leads to greater computational efficiency. Existing affine adaptation methods make use of the second moment matrix to estimate the local affine shape of local image features. In this thesis, it is shown that the Hessian matrix can be used in a similar way to estimate local feature shape. The Hessian matrix is effective for estimating the shape of blob-like structures, but is less effective for corner structures. It is simpler to compute than the second moment matrix, leading to a significant reduction in computational cost. A wide baseline dense correspondence extraction system, called WiDense, is presented in this thesis. It allows the extraction of large numbers of additional accurate correspondences, given only a few initial putative correspondences. It consists of the following algorithms: An affine region alignment algorithm that ensures accurate alignment between matched features; A method for extracting more matches in the vicinity of a matched pair of affine features, using the alignment information contained in the match; An algorithm for extracting large numbers of highly accurate point correspondences from an aligned pair of feature regions. Experiments show that the correspondences generated by the WiDense system improves the success rate of computing the epipolar geometry of very widely separated views. This new method is successful in many cases where the features produced by the best wide baseline matching algorithms are insufficient for computing the scene geometry.

A novel high voltage pulsed power supply based on low voltage switch-capacitor units

This paper presents a high voltage pulsed power system based on low voltage switch-capacitor units connected to a current source for several applications such as plasma systems. A modified positive buck-boost converter topology is used to utilize the current source concept and a series of low voltage switch-capacitor units is connected to the current source in order to provide high voltage with high voltage stress (dv/dt) as demanded by loads. This pulsed power converter is flexible in terms of energy control, in that the stored energy in the current source can be adjusted by changing the current magnitude to significantly improve the efficiency of various systems with different requirements. Output voltage magnitude and stress (dv/dt) can be controlled by a proper selection of components and control algorithm to turn on and off switching devices.

Applying SVMs and weight-based factor analysis to unsupervised adaptation for speaker verification

This paper presents an extended study on the implementation of support vector machine(SVM) based speaker verification in systems that employ continuous progressive model adaptation using the weight-based factor analysis model. The weight-based factor analysis model compensates for session variations in unsupervised scenarios by incorporating trial confidence measures in the general statistics used in the inter-session variability modelling process. Employing weight-based factor analysis in Gaussian mixture models (GMM) was recently found to provide significant performance gains to unsupervised classification. Further improvements in performance were found through the integration of SVM-based classification in the system by means of GMM supervectors. This study focuses particularly on the way in which a client is represented in the SVM kernel space using single and multiple target supervectors. Experimental results indicate that training client SVMs using a single target supervector maximises performance while exhibiting a certain robustness to the inclusion of impostor training data in the model. Furthermore, the inclusion of low-scoring target trials in the adaptation process is investigated where they were found to significantly aid performance.

Performance optimization for parallel processing on a multiple-CPU server

Symmetric multi-processor (SMP) systems, or multiple-CPU servers, are suitable for implementing parallel algorithms because they employ dedicated communication devices to enhance the inter-processor communication bandwidth, so that a better performance can be obtained. However, the cost for a multiple-CPU server is high and therefore, the server is usually shared among many users. The work-load due to other users will certainly affect the performance of the parallel programs so it is desirable to derive a method to optimize parallel programs under different loading conditions. In this paper, we present a simple method, which can be applied in SPMD type parallel programs, to improve the speedup by controlling the number of threads within the programs.

Parallel solution for railway power network simulation

The Streaming SIMD extension (SSE) is a special feature that is available in the Intel Pentium III and P4 classes of microprocessors. As its name implies, SSE enables the execution of SIMD (Single Instruction Multiple Data) operations upon 32-bit floating-point data therefore, performance of floating-point algorithms can be improved. In electrified railway system simulation, the computation involves the solving of a huge set of simultaneous linear equations, which represent the electrical characteristic of the railway network at a particular time-step and a fast solution for the equations is desirable in order to simulate the system in real-time. In this paper, we present how SSE is being applied to the railway network simulation.

Mobile communication in power distribution application

This paper investigates how to interface the wireless application protocol (WAP) architecture to the SCADA system running distributed network protocol (DNP) in a power process plant. DNP is a well-developed protocol to be applied in the supervisory control and data acquisition (SCADA) system but the system control centre and remote terminal units (RTUs) are presently connected through a local area network. The conditions in a process plant are harsh and the site is remote. Resources for data communication are difficult to obtain under these conditions, thus, a wireless channel communication through a mobile phone is practical and efficient in a process plant environment. The mobile communication industries and the public have a strong interest in the WAP technology application in mobile phone networks and the WAP application programming interface (API) in power industry applications is one area that requires extensive investigation.

Excess length of stay due to central line–associated bloodstream infection in intensive care units in Argentina, Brazil, and Mexico

Objective.To estimate the excess length of stay in an intensive care unit (ICU) due to a central line–associated bloodstream infection (CLABSI), using a multistate model that accounts for the timing of infection. Design.A cohort of 3,560 patients followed up for 36,806 days in ICUs. Setting.Eleven ICUs in 3 Latin American countries: Argentina, Brazil, and Mexico. Patients.All patients admitted to the ICU during a defined time period with a central line in place for more than 24 hours. Results.The average excess length of stay due to a CLABSI increased in 10 of 11 ICUs and varied from −1.23 days to 4.69 days. A reduction in length of stay in Mexico was probably caused by an increased risk of death due to CLABSI, leading to shorter times to death. Adjusting for patient age and Average Severity of Illness Score tended to increase the estimated excess length of stays due to CLABSI. Conclusions.CLABSIs are associated with an excess length of ICU stay. The average excess length of stay varies between ICUs, most likely because of the case‐mix of admissions and differences in the ways that hospitals deal with infections.

Genotyping of enterococcus faecalis and enterococcus faecium isolates using a set of eight single nucleotide polymorphisms (SNPs)

A SNP genotyping method was developed for E. faecalis and E. faecium using the 'Minimum SNPs' program. SNP sets were interrogated using allele-specific real-time PCR. SNP-typing sub-divided clonal complexes 2 and 9 of E. faecalis and 17 of E. faecium, members of which cause the majority of nosocomial infections globally.

Empirical comparison of machine learning algorithms for image texture classification with application to vegetation management in power line corridors

This paper reports on the empirical comparison of seven machine learning algorithms in texture classification with application to vegetation management in power line corridors. Aiming at classifying tree species in power line corridors, object-based method is employed. Individual tree crowns are segmented as the basic classification units and three classic texture features are extracted as the input to the classification algorithms. Several widely used performance metrics are used to evaluate the classification algorithms. The experimental results demonstrate that the classification performance depends on the performance matrix, the characteristics of datasets and the feature used.

Semantic oscillations : encoding context and structure in complex valued holographic vectors

In computational linguistics, information retrieval and applied cognition, words and concepts are often represented as vectors in high dimensional spaces computed from a corpus of text. These high dimensional spaces are often referred to as Semantic Spaces. We describe a novel and efficient approach to computing these semantic spaces via the use of complex valued vector representations. We report on the practical implementation of the proposed method and some associated experiments. We also briefly discuss how the proposed system relates to previous theoretical work in Information Retrieval and Quantum Mechanics and how the notions of probability, logic and geometry are integrated within a single Hilbert space representation. In this sense the proposed system has more general application and gives rise to a variety of opportunities for future research.

Longitudinal investigation of wandering behavior in department of veterans affairs nursing home care units

Objectives To explore the extent of and factors associated with male residents who change wandering status post nursing home admission. Design Longitudinal design with secondary data analyses. Admissions over a 4-year period were examined using repeat assessments with the Minimum Data Set (MDS) to formulate a model understanding the development of wandering behavior. Setting One hundred thirty-four Veterans Administration (VA) nursing homes throughout the United States. Participants: Included 6673 residents admitted to VA nursing homes between October 2000 and October 2004. Measurements MDS variables (cognitive impairment, mood, behavior problems, activities of daily living and wandering) included ratings recorded at residents’ admission to the nursing home and a minimum of two other time points at quarterly intervals. Results The majority (86%) of the sample were classified as non wanderers at admission and most of these (94%) remained non wanderers until discharge or the end of the study. Fifty one per cent of the wanderers changed status to non wanderers with 6% of these residents fluctuating in status more than two times. Admission variables associated with an increased risk of changing status from non-wandering to wandering included older age, greater cognitive impairment, more socially inappropriate behavior, resisting care, easier distractibility, and needing less help with personal hygiene. Requiring assistance with locomotion and having three or more medical comorbidities were associated with a decreased chance of changing from non-wandering to wandering status. Conclusion A resident’s change from non-wandering to wandering status may reflect an undetected medical event that affects cognition, but spares mobility.

A virtual test assessment tool for second year signal processing students

The development and use of a virtual assessment tool for a signal processing unit is described. It allows students to take a test from anywhere using a web browser to connect to the university server that hosts the test. While student responses are of the multiple choice type, they have to work out problems to arrive at the answer to be entered. CGI programming is used to verify student identification information and record their scores as well as provide immediate feedback after the test is complete. The tool has been used at QUT for the past 3 years and student feedback is discussed. The virtual assessment tool is an efficient alternative to marking written assignment reports that can often take more hours than actual lecture hall contact from a lecturer or tutor. It is especially attractive for very large classes that are now the norm at many universities in the first two years.

A simple orientation robust transmit polarization signalling scheme

A special transmit polarization signalling scheme is presented to alleviate the power reduction as a result of polarization mismatch from random antenna orientations. This is particularly useful for hand held mobile terminals typically equipped with only a single linearly polarized antenna, since the average signal power is desensitized against receiver orientations. Numerical simulations also show adequate robustness against incorrect channel estimations.