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.

Implementing a Pattern and Structure Mathematics Awareness Program (PASMAP) in kindergarten

This paper provides an interim report of a large empirical evaluation study in progress. An intervention was implemented to evaluate the effectiveness of the Pattern and Structure Mathematical Awareness Program (PASMAP) on Kindergarten students’ mathematical development. Four large schools (two from Sydney and two from Brisbane), 16 teachers and their 316 students participated in the first phase of a 2-year longitudinal study. Eight of 16 classes implemented the PASMAP program over three school terms. This paper provides an overview of key aspects of the intervention, and preliminary analysis of the impact of PASMAP on students’ representation, abstraction and generalisation of mathematical ideas.

Population ageing in a globalizing labour market : implications for older workers

This article concerns the changing nature of the relationship between age and the labour market. Global demographic, economic and technological changes potentially pose major challenges for older workers trying to maintain a secure attachment to the labour market. Recent public policy has responded by defining concepts such as 'active ageing' which encourage older workers to participate fully within society, including maintaining workforce participation. Older workers' ability to secure quality work within a volatile labour market is considered. While activation approaches are currently popular among policymakers, the notion that older workers will easily avoid a diminution of their employment prospects is challenged.

Household type and structure, time-use pattern, and trip-chaining behavior

In order to examine time allocation patterns within household-level trip-chaining, simultaneous doubly-censored Tobit models are applied to model time-use behavior within the context of household activity participation. Using the entire sample and a sub-sample of worker households from Tucson's Household Travel Survey, two sets of models are developed to better understand the phenomena of trip-chaining behavior among five types of households: single non-worker households, single worker households, couple non-worker households, couple one-worker households, and couple two-worker households. Durations of out-of-home subsistence, maintenance, and discretionary activities within trip chains are examined. Factors found to be associated with trip-chaining behavior include intra-household interactions with the household types and their structure and household head attributes.

Impact of embeddedness in co-ethnic & non co-ethnic networks on business performance : evidence from Chinese immigrant entrepreneurs in Australia

This paper investigates the research question ‘What is the effect of co-ethnic and non coethnic networking on business performance in Chinese immigrant businesses?’ The research will discuss key themes such as the extent to which Chinese immigrant entrepreneurs are embedded in co-ethnic and non co-ethnic networks and the affect of embeddedness on business performance, such as the entrepreneur’s satisfaction and business growth. Research on immigrant entrepreneurship has emerged as an important new area of inquiry within the field of entrepreneurship. The increased importance of the subject is due in part to major immigrant receiving countries, such as Australia, the United States and Canada, experiencing a high growth rate in their immigrant population. Reflecting on the existing research on immigrant entrepreneurship, it was decided to investigate the role of embeddedness on entrepreneurial business performance. This research seeks to identify the impact of embeddedness in co-ethnic and non co-ethnic networks on business performance of Chinese immigrant entrepreneurs in Australia. Chinese immigrant restaurant entrepreneurs in southeast Queensland, Australia were studied. The result expands on existing research on immigrant entrepreneurship, since the majority of immigrant entrepreneurship studies have been conducted on the United States and Canada immigrant experiences, but few have been conducted in the Australian immigrant entrepreneur context. This thesis also adds empirical testing to a research area with little empirical testing. The results indicated that embeddedness in the co-ethnic network is positively related to business performance measured by both growth and satisfaction. Embeddedness in the non co-ethnic network of the Chinese immigrant entrepreneurs in Australia did not show a similar pattern in accordance with studies conducted in the United States and Canada. This result is interesting and creates the opportunity for future research employing a comparative study.

Population-based survival estimates for childhood cancer in Australia during the period 1997–2006

Background: This study provides the latest available relative survival data for Australian childhood cancer patients. Methods: Data from the population-based Australian Paediatric Cancer Registry were used to describe relative survival outcomes using the period method for 11 903 children diagnosed with cancer between 1983 and 2006 and prevalent at any time between 1997 and 2006. Results: The overall relative survival was 90.4% after 1 year, 79.5% after 5 years and 74.7% after 20 years. Where information onstage at diagnosis was available (lymphomas, neuroblastoma, renal tumours and rhabdomyosarcomas), survival was significantly poorer for more-advanced stage. Survival was lower among infants compared with other children for those diagnosed with leukaemia, tumours of the central nervous system and renal tumours but higher for neuroblastoma. Recent improvements in overall childhood cancer survival over time are mainly because of improvements among leukaemia patients. Conclusion: The high and improving survival prognosis for children diagnosed with cancer in Australia is consistent with various international estimates. However, a 5-year survival estimate of 79% still means that many children who are diagnosed with cancer will die within 5 years, whereas others have long-term health morbidities and complications associated with their treatments. It is hoped that continued developments in treatment protocols will result in further improvements in survival.

Lifestyle factors associated concurrently and prospectively with co-morbid cardiovascular disease in a population-based cohort of colorectal cancer survivors

Aims To assess self-reported lifetime prevalence of cardiovascular disease (CVD) among colorectal cancer survivors, and examine the cross-sectional and prospective associations of lifestyle factors with co-morbid CVD. Methods Colorectal cancer survivors were recruited (n = 1966). Data were collected at approximately 5, 12, 24 and 36 months post-diagnosis. Cross-sectional findings included six CVD categories (hypercholesterolaemia, hypertension, diabetes, heart failure, kidney disease and ischaemic heart disease (IHD)) at 5 months post-diagnosis. Longitudinal outcomes included the probability of developing (de novo) co-morbid CVD by 36 months post-diagnosis. Lifestyle factors included body mass index, physical activity, television (TV) viewing, alcohol consumption and smoking. Results Co-morbid CVD prevalence at 5 months post-diagnosis was 59%, and 16% of participants with no known CVD at the baseline reported de novo CVD by 36 months. Obesity at the baseline predicted de novo hypertension (odds ratio [OR] = 2.20, 95% confidence intervals [CI] = 1.09, 4.45) and de novo diabetes (OR = 6.55, 95% CI = 2.19, 19.53). Participants watching >4 h of TV/d at the baseline (compared with <2 h/d) were more likely to develop ischaemic heart disease by 36 months (OR = 5.51, 95% CI = 1.86, 16.34). Conclusion Overweight colorectal cancer survivors were more likely to suffer from co-morbid CVD. Interventions focusing on weight management and other modifiable lifestyle factors may reduce functional decline and improve survival.

Genetic resources in wild and cultured stocks of the Asian mud crab, Scylla paramamosain

The mud crab (Scylla spp.) aquaculture industry has expanded rapidly in recent years in many countries in the Indo - West Pacific (IWP) region as an alternative to marine shrimp culture because of significant disease outbreaks and associated failures of many shrimp culture industries in the region. Currently, practices used to produce and manage breeding crabs in hatcheries may compromise levels of genetic diversity, ultimately compromising growth rates, disease resistance and stock productivity. Therefore, to avoid “genetic pollution” and its harmful effects and to promote further development of mud crab aquaculture and fisheries in a sustainable way, a greater understanding of the genetic attributes of wild and cultured mud crab stocks is required. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations for multiple purposes including for commercial production, recreation and conservation and to increase profitability and sustainability of newly emerging crab culture industries. Phylogeographic patterns and the genetic structure of Asian mud crab populations across the IWP were assessed to determine if they were concordant with those of other widespread taxa possessing pelagic larvae of relatively long duration. A 597 bp fragment of the mitochondrial DNA COI gene was amplified and screened for variation in a total of 297 individuals of S. paramamosain from six sampling sites across the species’ natural geographical distribution in the IWP and 36 unique haplotypes were identified. Haplotype diversities per site ranged from 0.516 to 0.879. Nucleotide diversity estimates among haplotypes were 0.11% – 0.48%. Maximum divergence observed among S. paramamosain samples was 1.533% and samples formed essentially a single monophyletic group as no obvious clades were related to geographical location of sites. A weak positive relationship was observed however, between genetic distance and geographical distance among sites. Microsatellite markers were then used to assess contemporary gene flow and population structure in Asian mud crab populations sampled across their natural distribution in the IWP. Eight microsatellite loci were screened in sampled S. paramamosain populations and all showed high allelic diversity at all loci in sampled populations. In total, 344 individuals were analysed, and 304 microsatellite alleles were found across the 8 loci. The mean number of alleles per locus at each site ranged from 20.75 to 28.25. Mean allelic richness per site varied from 17.2 to 18.9. All sites showed high levels of heterozygosity as average expected heterozygosities for all loci ranged from 0.917 – 0.953 while mean observed heterozygosity ranged from 0.916 – 0.959. Allele diversities were similar at all sites and across all loci. The results did not show any evidence for major differences in allele frequencies among sites and patterns of allele frequencies were very similar in all populations across all loci. Estimates of population differentiation (FST) were relatively low and most probably largely reflect intra – individual variation for very highly variable loci. Results from nDNA analysis showed evidence for only very limited population genetic structure among sampled S. paramamosain, and a positive and significant association for genetic and geographical distance among sample sites. Microsatellite markers were then employed to determine if adequate levels of genetic diversity has been captured in crab hatcheries for the breeding cycle. The results showed that all microsatellite loci were polymorphic in hatchery samples. Culture populations were in general, highly genetically depauperate, compared with comparable wild populations, with only 3 to 8 alleles recorded for the same loci set per population. In contrast, very high numbers of alleles per locus were found in reference wild S. paramamosain populations, which ranged from 18 to 46 alleles per locus per population. In general, this translates into a 3 to 10 fold decline in mean allelic richness per locus in all culture stocks compared with wild reference counterparts. Furthermore, most loci in all cultured S. paramamosain samples showed departures from HWE equilibrium. Allele frequencies were very different in culture samples from that present in comparable wild reference samples and this in particular, was reflected in a large decline in allele diversity per locus. The pattern observed was best explained by significant impacts of breeding practices employed in hatcheries rather than natural differentiation among wild populations used as the source of brood stock. Recognition of current problems and management strategies for the species both for the medium and long-term development of the new culture industry are discussed. The priority research to be undertaken over the medium term for S. paramamosain should be to close the life cycle fully to allow individuals to be bred on demand and their offspring equalised to control broodstock reproductive contributions. Establishing a broodstock register and pedigree mating system will be required before any selection program is implemented. This will ensure that sufficient genetic variation will be available to allow genetic gains to be sustainably achieved in a future stock improvement program. A fundamental starting point to improve hatchery practices will be to encourage farmers and hatchery managers to spawn more females in their hatcheries as it will increase background genetic diversity in culture stocks. Combining crablet cohorts from multiple hatcheries into a single cohort for supply to farmers or rotation of breeding females regularly in hatcheries will help to address immediate genetic diversity problems in culture stocks. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations more efficiently. Over the long-term, application of data on genetic diversity in wild and cultured stocks of Asian mud crab will contribute to development of sustainable and productive culture industries in Vietnam and other countries in the IWP and can contribute towards conservation of wild genetic resources.

Dynamics of pattern writing and erasure in photorefractive lithium niobate for data storage applications

The present rate of technological advance continues to place significant demands on data storage devices. The sheer amount of digital data being generated each year along with consumer expectations, fuels these demands. At present, most digital data is stored magnetically, in the form of hard disk drives or on magnetic tape. The increase in areal density (AD) of magnetic hard disk drives over the past 50 years has been of the order of 100 million times, and current devices are storing data at ADs of the order of hundreds of gigabits per square inch. However, it has been known for some time that the progress in this form of data storage is approaching fundamental limits. The main limitation relates to the lower size limit that an individual bit can have for stable storage. Various techniques for overcoming these fundamental limits are currently the focus of considerable research effort. Most attempt to improve current data storage methods, or modify these slightly for higher density storage. Alternatively, three dimensional optical data storage is a promising field for the information storage needs of the future, offering very high density, high speed memory. There are two ways in which data may be recorded in a three dimensional optical medium; either bit-by-bit (similar in principle to an optical disc medium such as CD or DVD) or by using pages of bit data. Bit-by-bit techniques for three dimensional storage offer high density but are inherently slow due to the serial nature of data access. Page-based techniques, where a two-dimensional page of data bits is written in one write operation, can offer significantly higher data rates, due to their parallel nature. Holographic Data Storage (HDS) is one such page-oriented optical memory technique. This field of research has been active for several decades, but with few commercial products presently available. Another page-oriented optical memory technique involves recording pages of data as phase masks in a photorefractive medium. A photorefractive material is one by which the refractive index can be modified by light of the appropriate wavelength and intensity, and this property can be used to store information in these materials. In phase mask storage, two dimensional pages of data are recorded into a photorefractive crystal, as refractive index changes in the medium. A low-intensity readout beam propagating through the medium will have its intensity profile modified by these refractive index changes and a CCD camera can be used to monitor the readout beam, and thus read the stored data. The main aim of this research was to investigate data storage using phase masks in the photorefractive crystal, lithium niobate (LiNbO3). Firstly the experimental methods for storing the two dimensional pages of data (a set of vertical stripes of varying lengths) in the medium are presented. The laser beam used for writing, whose intensity profile is modified by an amplitudemask which contains a pattern of the information to be stored, illuminates the lithium niobate crystal and the photorefractive effect causes the patterns to be stored as refractive index changes in the medium. These patterns are read out non-destructively using a low intensity probe beam and a CCD camera. A common complication of information storage in photorefractive crystals is the issue of destructive readout. This is a problem particularly for holographic data storage, where the readout beam should be at the same wavelength as the beam used for writing. Since the charge carriers in the medium are still sensitive to the read light field, the readout beam erases the stored information. A method to avoid this is by using thermal fixing. Here the photorefractive medium is heated to temperatures above 150�C; this process forms an ionic grating in the medium. This ionic grating is insensitive to the readout beam and therefore the information is not erased during readout. A non-contact method for determining temperature change in a lithium niobate crystal is presented in this thesis. The temperature-dependent birefringent properties of the medium cause intensity oscillations to be observed for a beam propagating through the medium during a change in temperature. It is shown that each oscillation corresponds to a particular temperature change, and by counting the number of oscillations observed, the temperature change of the medium can be deduced. The presented technique for measuring temperature change could easily be applied to a situation where thermal fixing of data in a photorefractive medium is required. Furthermore, by using an expanded beam and monitoring the intensity oscillations over a wide region, it is shown that the temperature in various locations of the crystal can be monitored simultaneously. This technique could be used to deduce temperature gradients in the medium. It is shown that the three dimensional nature of the recording medium causes interesting degradation effects to occur when the patterns are written for a longer-than-optimal time. This degradation results in the splitting of the vertical stripes in the data pattern, and for long writing exposure times this process can result in the complete deterioration of the information in the medium. It is shown in that simply by using incoherent illumination, the original pattern can be recovered from the degraded state. The reason for the recovery is that the refractive index changes causing the degradation are of a smaller magnitude since they are induced by the write field components scattered from the written structures. During incoherent erasure, the lower magnitude refractive index changes are neutralised first, allowing the original pattern to be recovered. The degradation process is shown to be reversed during the recovery process, and a simple relationship is found relating the time at which particular features appear during degradation and recovery. A further outcome of this work is that the minimum stripe width of 30 ìm is required for accurate storage and recovery of the information in the medium, any size smaller than this results in incomplete recovery. The degradation and recovery process could be applied to an application in image scrambling or cryptography for optical information storage. A two dimensional numerical model based on the finite-difference beam propagation method (FD-BPM) is presented and used to gain insight into the pattern storage process. The model shows that the degradation of the patterns is due to the complicated path taken by the write beam as it propagates through the crystal, and in particular the scattering of this beam from the induced refractive index structures in the medium. The model indicates that the highest quality pattern storage would be achieved with a thin 0.5 mm medium; however this type of medium would also remove the degradation property of the patterns and the subsequent recovery process. To overcome the simplistic treatment of the refractive index change in the FD-BPM model, a fully three dimensional photorefractive model developed by Devaux is presented. This model shows significant insight into the pattern storage, particularly for the degradation and recovery process, and confirms the theory that the recovery of the degraded patterns is possible since the refractive index changes responsible for the degradation are of a smaller magnitude. Finally, detailed analysis of the pattern formation and degradation dynamics for periodic patterns of various periodicities is presented. It is shown that stripe widths in the write beam of greater than 150 ìm result in the formation of different types of refractive index changes, compared with the stripes of smaller widths. As a result, it is shown that the pattern storage method discussed in this thesis has an upper feature size limit of 150 ìm, for accurate and reliable pattern storage.

The effects of muscle fatigue on knee function during landing

The human knee acts as a sophisticated shock absorber during landing movements. The ability of the knee to perform this function in the real world is remarkable given that the context of the landing movement may vary widely between performances. For this reason, humans must be capable of rapidly adjusting the mechanical properties of the knee under impact load in order to satisfy many competing demands. However, the processes involved in regulating these properties in response to changing constraints remain poorly understood. In particular, the effects of muscle fatigue on knee function during step landing are yet to be fully explored. Fatigue of the knee muscles is significant for 2 reasons. First, it is thought to have detrimental effects on the ability of the knee to act as a shock absorber and is considered a risk factor for knee injury. Second, fatigue of knee muscles provides a unique opportunity to examine the mechanisms by which healthy individuals alter knee function. A review of the literature revealed that the effect of fatigue on knee function during landing has been assessed by comparing pre and postfatigue measurements, with fatigue induced by a voluntary exercise protocol. The information is limited by inconsistent results with key measures, such as knee stiffness, showing varying results following fatigue, including increased stiffness, decreased stiffness or failure to detect any change in some experiments. Further consideration of the literature questions the validity of the models used to induce and measure fatigue, as well as the pre-post study design, which may explain the lack of consensus in the results. These limitations cast doubt on the usefulness of the available information and identify a need to investigate alternative approaches. Based on the results of this review, the aims of this thesis were to: • evaluate the methodological procedures used in validation of a fatigue model • investigate the adaptation and regulation of post-impact knee mechanics during repeated step landings • use this new information to test the effects of fatigue on knee function during a step-landing task. To address the aims of the thesis, 3 related experiments were conducted that collected kinetic, kinematic and electromyographic data from 3 separate samples of healthy male participants. The methodologies involved optoelectronic motion capture (VICON), isokinetic dynamometry (System3 Pro, BIODEX) and wireless surface electromyography (Zerowire, Aurion, Italy). Fatigue indicators and knee function measures used in each experiment were derived from the data. Study 1 compared the validity and reliability of repetitive stepping and isokinetic contractions with respect to fatigue of the quadriceps and hamstrings. Fifteen participants performed 50 repetitions of each exercise twice in randomised order, over 4 sessions. Sessions were separated by a minimum of 1 week’s rest, to ensure full recovery. Validity and reliability depended on a complex interaction between the exercise protocol, the fatigue indicator, the individual and the muscle of interest. Nevertheless, differences between exercise protocols indicated that stepping was less effective in eliciting valid and reliable changes in peak power and spectral compression, compared with isokinetic exercise. A key finding was that fatigue progressed in a biphasic pattern during both exercises. The point separating the 2 phases, known as the transition point, demonstrated superior between-test reliability during the isokinetic protocol, compared with stepping. However, a correction factor should be used to accurately apply this technique to the study of fatigue during landing. Study 2 examined alterations in knee function during repeated landings, with a different sample (N =12) performing 60 consecutive step landing trials. Each landing trial was separated by 1-minute rest periods. The results provided new information in relation to the pre-post study design in the context of detecting adjustments in knee function during landing. First, participants significantly increased or decreased pre-impact muscle activity or post-impact mechanics despite environmental and task constraints remaining unchanged. This is the 1st study to demonstrate this effect in healthy individuals without external feedback on performance. Second, single-subject analysis was more effective in detecting alterations in knee function compared to group-level analysis. Finally, repeated landing trials did not reduce inter-trial variability of knee function in some participants, contrary to assumptions underpinning previous studies. The results of studies 1 and 2 were used to modify the design of Study 3 relative to previous research. These alterations included a modified isokinetic fatigue protocol, multiple pre-fatigue measurements and singlesubject analysis to detect fatigue-related changes in knee function. The study design incorporated new analytical approaches to investigate fatiguerelated alterations in knee function during landing. Participants (N = 16) were measured during multiple pre-fatigue baseline trial blocks prior to the fatigue model. A final block of landing trials was recorded once the participant met the operational fatigue definition that was identified in Study 1. The analysis revealed that the effects of fatigue in this context are heavily dependent on the compensatory response of the individual. A continuum of responses was observed within the sample for each knee function measure. Overall, preimpact preparation and post-impact mechanics of the knee were altered with highly individualised patterns. Moreover, participants used a range of active or passive pre-impact strategies to adapt post-impact mechanics in response to quadriceps fatigue. The unique patterns identified in the data represented an optimisation of knee function based on priorities of the individual. The findings of these studies explain the lack of consensus within the literature regarding the effects of fatigue on knee function during landing. First, functional fatigue protocols lack validity in inducing fatigue-related changes in mechanical output and spectral compression of surface electromyography (sEMG) signals, compared with isokinetic exercise. Second, fatigue-related changes in knee function during landing are confounded by inter-individual variation, which limits the sensitivity of group-level analysis. By addressing these limitations, the 3rd study demonstrated the efficacies of new experimental and analytical approaches to observe fatigue-related alterations in knee function during landing. Consequently, this thesis provides new perspectives into the effects of fatigue in knee function during landing. In conclusion: • The effects of fatigue on knee function during landing depend on the response of the individual, with considerable variation present between study participants, despite similar physical characteristics. • In healthy males, adaptation of pre-impact muscle activity and postimpact knee mechanics is unique to the individual and reflects their own optimisation of demands such as energy expenditure, joint stability, sensory information and loading of knee structures. • The results of these studies should guide future exploration of adaptations in knee function to fatigue. However, research in this area should continue with reduced emphasis on the directional response of the population and a greater focus on individual adaptations of knee function.