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.

Power network in loop : a paradigm for real-time simulation and hardware testing

This paper discusses a new paradigm of real-time simulation of power systems in which equipment can be interfaced with a real-time digital simulator. In this scheme, one part of a power system can be simulated by using a real-time simulator; while the other part is implemeneted as a physical system. The only interface of the physical system with the computer-based simulator is through data-acquisition system. The physical system is driven by a voltage-source converter (VSC)that mimics the power system simulated in the real-time simulator. In this papar, the VSC operates in a voltage-control mode to track the point of common coupling voltage signal supplied by the digital simulator. This type of splitting a network in two parts and running a real-time simulation with a physical system in parallel is called a power network in loop here. this opens up the possibility of study of interconnection o f one or several distributed generators to a complex power network. The proposed implementation is verified through simulation studies using PSCAD/EMTDC and through hardware implementation on a TMS320G2812 DSP.

Markov modelling of the IEEE 802.11 DCF for real-time applications with periodic traffic

Popular wireless network standards, such as IEEE 802.11/15/16, are increasingly adopted in real-time control systems. However, they are not designed for real-time applications. Therefore, the performance of such wireless networks needs to be carefully evaluated before the systems are implemented and deployed. While efforts have been made to model general wireless networks with completely random traffic generation, there is a lack of theoretical investigations into the modelling of wireless networks with periodic real-time traffic. Considering the widely used IEEE 802.11 standard, with the focus on its distributed coordination function (DCF), for soft-real-time control applications, this paper develops an analytical Markov model to quantitatively evaluate the network quality-of-service (QoS) performance in periodic real-time traffic environments. Performance indices to be evaluated include throughput capacity, transmission delay and packet loss ratio, which are crucial for real-time QoS guarantee in real-time control applications. They are derived under the critical real-time traffic condition, which is formally defined in this paper to characterize the marginal satisfaction of real-time performance constraints.

Real-time simulation for power systems based on parallel computing - an empirical study

Abstract Computer simulation is a versatile and commonly used tool for the design and evaluation of systems with different degrees of complexity. Power distribution systems and electric railway network are areas for which computer simulations are being heavily applied. A dominant factor in evaluating the performance of a software simulator is its processing time, especially in the cases of real-time simulation. Parallel processing provides a viable mean to reduce the computing time and is therefore suitable for building real-time simulators. In this paper, we present different issues related to solving the power distribution system with parallel computing based on a multiple-CPU server and we will concentrate, in particular, on the speedup performance of such an approach.

Connecting people and resource consumption in real time

The authors currently engage in two projects to improve human-computer interaction (HCI) designs that can help conserve resources. The projects explore motivation and persuasion strategies relevant to ubiquitous computing systems that bring real-time consumption data into the homes and hands of residents in Brisbane, Australia. The first project seeks to increase understanding among university staff of the tangible and negative effects that excessive printing has on the workplace and local environment. The second project seeks to shift attitudes toward domestic energy conservation through software and hardware that monitor real-time, in situ electricity consumption in homes across Queensland. The insights drawn from these projects will help develop resource consumption user archetypes, providing a framework linking people to differing interface design requirements.

V2V/V2I augmented maps : state-of-the-art and contribution to real-time crash risk assessment

A number of advanced driver assistance systems (ADAS) are currently being released on the market, providing safety functions to the drivers such as collision avoidance, adaptive cruise control or enhanced night-vision. These systems however are inherently limited by their sensory range: they cannot gather information from outside this range, also called their “perceptive horizon”. Cooperative systems are a developing research avenue that aims at providing extended safety and comfort functionalities by introducing vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) wireless communications to the road actors. This paper presents the problematic of cooperative systems, their advantages and contributions to road safety and exposes some limitations related to market penetration, sensors accuracy and communications scalability. It explains the issues of how to implement extended perception, a central contribution of cooperative systems. The initial steps of an evaluation of data fusion architectures for extended perception are exposed.

Genetic Diversity of Rice Tungro Spherical Virus in Tungro-Endemic Provinces of the Philippines and Indonesia

The two adjacent genes of coat protein 1 and 2 of rice tungro spherical virus (RTSV) were amplified from total RNA extracts of serologically indistinguishable field isolates from the Philippines and Indonesia, using reverse transcriptase polymerase chain reaction (RT-PCR). Digestion with HindIII and BstYI restriction endonucleases differentiated the amplified DNA products into eight distinct coat protein genotypes. These genotypes were then used as indicators of virus diversity in the field. Inter- and intra-site diversities were determined over three cropping seasons. At each of the sites surveyed, one or two main genotypes prevailed together with other related minor or mixed genotypes that did not replace the main genotype over the sampling time. The cluster of genotypes found at the Philippines sites was significantly different from the one at the Indonesia sites, suggesting geographic isolation for virus populations. Phylogenetic studies based on the nucleotide sequences of 38 selected isolates confirm the spatial distribution of RTSV virus populations but show that gene flow may occur between populations. Under the present conditions, rice varieties do not seem to exert selective pressure on the virus populations. Based on the selective constraints in the coat protein amino acid sequences and the virus genetic composition per site, a negative selection model followed by random-sampling events due to vector transmissions is proposed to explain the inter-site diversity observed

A synthesizable hardware evolutionary algorithm design for unmanned aerial system real-time path planning

The main objective of this paper is to detail the development of a feasible hardware design based on Evolutionary Algorithms (EAs) to determine flight path planning for Unmanned Aerial Vehicles (UAVs) navigating terrain with obstacle boundaries. The design architecture includes the hardware implementation of Light Detection And Ranging (LiDAR) terrain and EA population memories within the hardware, as well as the EA search and evaluation algorithms used in the optimizing stage of path planning. A synthesisable Very-high-speed integrated circuit Hardware Description Language (VHDL) implementation of the design was developed, for realisation on a Field Programmable Gate Array (FPGA) platform. Simulation results show significant speedup compared with an equivalent software implementation written in C++, suggesting that the present approach is well suited for UAV real-time path planning applications.

A criminological analysis : using real-time monitoring to gather data on online predators

The Internet presents a constantly evolving frontier for criminology and policing, especially in relation to online predators – paedophiles operating within the Internet for safer access to children, child pornography and networking opportunities with other online predators. The goals of this qualitative study are to undertake behavioural research – identify personality types and archetypes of online predators and compare and contrast them with behavioural profiles and other psychological research on offline paedophiles and sex offenders. It is also an endeavour to gather intelligence on the technological utilisation of online predators and conduct observational research on the social structures of online predator communities. These goals were achieved through the covert monitoring and logging of public activity within four Internet Relay Chat(rooms) (IRC) themed around child sexual abuse and which were located on the Undernet network. Five days of monitoring was conducted on these four chatrooms between Wednesday 1 to Sunday 5 April 2009; this raw data was collated and analysed. The analysis identified four personality types – the gentleman predator, the sadist, the businessman and the pretender – and eight archetypes consisting of the groomers, dealers, negotiators, roleplayers, networkers, chat requestors, posters and travellers. The characteristics and traits of these personality types and archetypes, which were extracted from the literature dealing with offline paedophiles and sex offenders, are detailed and contrasted against the online sexual predators identified within the chatrooms, revealing many similarities and interesting differences particularly with the businessman and pretender personality types. These personality types and archetypes were illustrated by selecting users who displayed the appropriate characteristics and tracking them through the four chatrooms, revealing intelligence data on the use of proxies servers – especially via the Tor software – and other security strategies such as Undernet’s host masking service. Name and age changes, which is used as a potential sexual grooming tactic was also revealed through the use of Analyst’s Notebook software and information on ISP information revealed the likelihood that many online predators were not using any safety mechanism and relying on the anonymity of the Internet. The activities of these online predators were analysed, especially in regards to child sexual grooming and the ‘posting’ of child pornography, which revealed a few of the methods in which online predators utilised new Internet technologies to sexually groom and abuse children – using technologies such as instant messengers, webcams and microphones – as well as store and disseminate illegal materials on image sharing websites and peer-to-peer software such as Gigatribe. Analysis of the social structures of the chatrooms was also carried out and the community functions and characteristics of each chatroom explored. The findings of this research have indicated several opportunities for further research. As a result of this research, recommendations are given on policy, prevention and response strategies with regards to online predators.

Geometry‐specified troposphere decorrelation for subcentimeter real‐time kinematic solutions over long baselines

Real‐time kinematic (RTK) GPS techniques have been extensively developed for applications including surveying, structural monitoring, and machine automation. Limitations of the existing RTK techniques that hinder their applications for geodynamics purposes are twofold: (1) the achievable RTK accuracy is on the level of a few centimeters and the uncertainty of vertical component is 1.5–2 times worse than those of horizontal components and (2) the RTK position uncertainty grows in proportional to the base‐torover distances. The key limiting factor behind the problems is the significant effect of residual tropospheric errors on the positioning solutions, especially on the highly correlated height component. This paper develops the geometry‐specified troposphere decorrelation strategy to achieve the subcentimeter kinematic positioning accuracy in all three components. The key is to set up a relative zenith tropospheric delay (RZTD) parameter to absorb the residual tropospheric effects and to solve the established model as an ill‐posed problem using the regularization method. In order to compute a reasonable regularization parameter to obtain an optimal regularized solution, the covariance matrix of positional parameters estimated without the RZTD parameter, which is characterized by observation geometry, is used to replace the quadratic matrix of their “true” values. As a result, the regularization parameter is adaptively computed with variation of observation geometry. The experiment results show that new method can efficiently alleviate the model’s ill condition and stabilize the solution from a single data epoch. Compared to the results from the conventional least squares method, the new method can improve the longrange RTK solution precision from several centimeters to the subcentimeter in all components. More significantly, the precision of the height component is even higher. Several geosciences applications that require subcentimeter real‐time solutions can largely benefit from the proposed approach, such as monitoring of earthquakes and large dams in real‐time, high‐precision GPS leveling and refinement of the vertical datum. In addition, the high‐resolution RZTD solutions can contribute to effective recovery of tropospheric slant path delays in order to establish a 4‐D troposphere tomography.

Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis

In total, 782 Escherichia coli strains originating from various host sources have been analyzed in this study by using a highly discriminatory single-nucleotide polymorphism (SNP) approach. A set of eight SNPs, with a discrimination value (Simpson's index of diversity [D]) of 0.96, was determined using the Minimum SNPs software, based on sequences of housekeeping genes from the E. coli multilocus sequence typing (MLST) database. Allele-specific real-time PCR was used to screen 114 E. coli isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coli isolates using eight high-D SNPs resolved the isolates into 74 SNP profiles. The data obtained suggest that SNP typing is a promising approach for the discrimination of host-specific groups and allows for the identification of human-specific E. coli in environmental samples. However, a more diverse E. coli collection is required to determine animal- and environment-specific E. coli SNP profiles due to the abundance of human E. coli strains (56%) in the MLST database.

Textures of optical flow for real-time anomaly detection in crowds

Automated visual surveillance of crowds is a rapidly growing area of research. In this paper we focus on motion representation for the purpose of abnormality detection in crowded scenes. We propose a novel visual representation called textures of optical flow. The proposed representation measures the uniformity of a flow field in order to detect anomalous objects such as bicycles, vehicles and skateboarders; and can be combined with spatial information to detect other forms of abnormality. We demonstrate that the proposed approach outperforms state-of-the-art anomaly detection algorithms on a large, publicly-available dataset.