Association between prostinogen (KLK15) genetic variants and prostate cancer risk and aggressiveness in Australia and a meta-analysis of GWAS data

Background: Kallikrein 15 (KLK15)/Prostinogen is a plausible candidate for prostate cancer susceptibility. Elevated KLK15 expression has been reported in prostate cancer and it has been described as an unfavorable prognostic marker for the disease. Objectives: We performed a comprehensive analysis of association of variants in the KLK15 gene with prostate cancer risk and aggressiveness by genotyping tagSNPs, as well as putative functional SNPs identified by extensive bioinformatics analysis. Methods and Data Sources: Twelve out of 22 SNPs, selected on the basis of linkage disequilibrium pattern, were analyzed in an Australian sample of 1,011 histologically verified prostate cancer cases and 1,405 ethnically matched controls. Replication was sought from two existing genome wide association studies (GWAS): the Cancer Genetic Markers of Susceptibility (CGEMS) project and a UK GWAS study. Results: Two KLK15 SNPs, rs2659053 and rs3745522, showed evidence of association (p, 0.05) but were not present on the GWAS platforms. KLK15 SNP rs2659056 was found to be associated with prostate cancer aggressiveness and showed evidence of association in a replication cohort of 5,051 patients from the UK, Australia, and the CGEMS dataset of US samples. A highly significant association with Gleason score was observed when the data was combined from these three studies with an Odds Ratio (OR) of 0.85 (95% CI = 0.77-0.93; p = 2.7610 24). The rs2659056 SNP is predicted to alter binding of the RORalpha transcription factor, which has a role in the control of cell growth and differentiation and has been suggested to control the metastatic behavior of prostate cancer cells. Conclusions: Our findings suggest a role for KLK15 genetic variation in the etiology of prostate cancer among men of European ancestry, although further studies in very large sample sets are necessary to confirm effect sizes.

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.

Persistence of multiple genetic lineages within intra-host populations of Ross River virus

We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances

The implementation of sustainable housing through mutual benefits to key stakeholders

Among the Australian general public, there are increasing concerns about environmental issues. Accordingly, sustainability in the housing industry is also becoming a priority on the development agenda. However, putting the principles of ecological sustainability into practice within social and economic development requires intensive involvement of major stakeholders such as governments, developers, builders, consumers and a range of other professionals. Establishing a sustainable value entails asymmetric life-cycle returns, making it important for major stakeholders to appreciate the benefits of this new agenda not only for the individual businesses but also for other supply chain partners. This context warrants the study to promote collective benefits for key stakeholders by establishing a mutual-benefit framework for sustainable housing implementation. A research was carried out in the hope to establish a mutual-benefit framework by investigating challenges of achieving benefits (CABs) from sustainable housing development in a multi-stakeholder context. In the research work reported in this article, a comparative questionnaire study was first conducted among seven stakeholder groups in the Australian housing industry, to examine the importance and inter-relationships of CABs. In-depth interviews then furthered the survey findings with a focus on stakeholder diversity. The synthesized findings of the survey and interview study lead to the identification of 12 critical mutual-benefit factors and their mutual influence. Based on such a platform, a systematic framework is developed with the aid of Interpretive Structural Modelling (ISM), to identify the patterns of stakeholder benefit materialisation, suggest the priority of critical factors and provide related stakeholder-specific action guide for sustainable housing implementation.

Correlation-based damage detection for complicated truss bridges using multi-layer genetic algorithms

The study presents a multi-layer genetic algorithm (GA) approach using correlation-based methods to facilitate damage determination for through-truss bridge structures. To begin, the structure’s damage-suspicious elements are divided into several groups. In the first GA layer, the damage is initially optimised for all groups using correlation objective function. In the second layer, the groups are combined to larger groups and the optimisation starts over at the normalised point of the first layer result. Then the identification process repeats until reaching the final layer where one group includes all structural elements and only minor optimisations are required to fine tune the final result. Several damage scenarios on a complicated through-truss bridge example are nominated to address the proposed approach’s effectiveness. Structural modal strain energy has been employed as the variable vector in the correlation function for damage determination. Simulations and comparison with the traditional single-layer optimisation shows that the proposed approach is efficient and feasible for complicated truss bridge structures when the measurement noise is taken into account.

Genetic algorithms to schedule container transfers at multimodal terminals

Optimising the container transfer schedule at the multimodal terminals is known to be NP-hard, which implies that the best solution becomes computationally infeasible as problem sizes increase. Genetic Algorithm (GA) techniques are used to reduce container handling/transfer times and ships' time at the port by speeding up handling operations. The GA is chosen due to the relatively good results that have been reported even with the simplest GA implementations to obtain near-optimal solutions in reasonable time. Also discussed, is the application of the model to assess the consequences of increased scheduled throughput time as well as different strategies such as the alternative plant layouts, storage policies and number of yard machines. A real data set used for the solution and subsequent sensitivity analysis is applied to the alternative plant layouts, storage policies and number of yard machines.

Supply chain management systems benefits : the expectation-confirmation theory perspective

Organizations adopt a Supply Chain Management System (SCMS) expecting benefits to the organization and its functions. However, organizations are facing mounting challenges to realizing benefits through SCMS. Studies suggest a growing dissatisfaction among client organizations due to an increasing gap between expectations and realization of SCMS benefits. Further, reflecting the Enterprise System studies such as Seddon et al. (2010), SCMS benefits are also expected to flow to the organization throughout its lifecycle rather than being realized all at once. This research therefore proposes to derive a lifecycle-wide understanding of SCMS benefits and realization to derive a benefit expectation management framework to attain the full potential of an SCMS. The primary research question of this study is: How can client organizations better manage their benefit expectations of SCM systems? The specific research goals of the current study include: (1) to better understand the misalignment of received and expected benefits of SCM systems; (2) to identify the key factors influencing SCM system expectations and to develop a framework to manage SCMS benefits; (3) to explore how organizational satisfaction is influenced by the lack of SCMS benefit confirmation; and (4) to explore how to improve the realization of SCM system benefits. Expectation-Confirmation Theory (ECT) provides the theoretical underpinning for this study. ECT has been widely used in the consumer behavior literature to study customer satisfaction, post-purchase behavior and service marketing in general. Recently, ECT has been extended into Information Systems (IS) research focusing on individual user satisfaction and IS continuance. However, only a handful of studies have employed ECT to study organizational satisfaction on large-scale IS. The current study will enrich the research stream by extending ECT into organizational-level analysis and verifying the preliminary findings of relevant works by Staples et al. (2002), Nevo and Chan (2007) and Nevo and Wade (2007). Moreover, this study will go further trying to operationalize the constructs of ECT into the context of SCMS. The empirical findings of the study commence with a content analysis, through which 41 vendor reports and academic reports are analyzed yielding sixty expected benefits of SCMS. Then, the expected benefits are compared with the benefits realized at a case organization in the Fast Moving Consumer Goods industry sector that had implemented a SAP Supply Chain Management System seven years earlier. The study develops an SCMS Benefit Expectation Management (SCMS-BEM) Framework. The comparison of benefit expectations and confirmations highlights that, while certain benefits are realized earlier in the lifecycle, other benefits could take almost a decade to realize. Further analysis and discussion on how the developed SCMS-BEM Framework influences ECT when applied in SCMS was also conducted. It is recommended that when establishing their expectations of the SCMS, clients should remember that confirmation of these expectations will have a long lifecycle, as shown in the different time periods in the SCMS-BEM Framework. Moreover, the SCMS-BEM Framework will allow organizations to maintain high levels of satisfaction through careful mitigation and confirming expectations based on the lifecycle phase. In addition, the study reveals that different stakeholder groups have different expectations of the same SCMS. The perspective of multiple stakeholders has significant implications for the application of ECT in the SCMS context. When forming expectations of the SCMS, the collection of organizational benefits of SCMS should represent the perceptions of all stakeholder groups. The same mechanism should be employed in the measurements of received SCMS benefits. Moreover, for SCMS, there exists interdependence of the satisfaction among the various stakeholders. The satisfaction of decision-makers or the authorized staff is not only driven by their own expectation confirmation level, it is also influenced by the confirmation level of other stakeholders‘ expectations in the organization. Satisfaction from any one particular stakeholder group can not reflect the true satisfaction of the client organization. Furthermore, it is inferred from the SCMS-BEM Framework that organizations should place emphasis on the viewpoints of the operational and management staff when evaluating the benefits of SCMS in the short and middle term. At the same time, organizations should be placing more attention on the perspectives of strategic staff when evaluating the performance of the SCMS in the long term.

The 1998 tax reform proposal fringe benefits tax and nonprofit organisations

Fringe Benefits Tax (FBT) is a tax payable by employers on the value of certain fringe benefits that have been provided to their employees or to associates of those employees. It was introduced on 1 July 1986 to improve the equity of the taxation system because non-salary and wage benefits were escaping the taxation base. FBT ensures that tax is paid on those fringe benefits provided in place of, or in addition to, salary or wages of employees.

Benefits and challenges of using restorative justice approaches for victims of crime committed by adults: An exploration of theory and evidence

Book Abstract: Current experimentations with approaches to restorative justice for adult offenders represents a compelling new direction in the criminal justice system. This book examines the values and challenges of restorative justice for adult offenders, victims and communities. The discussion is situated within current debate, available research, and the international literature. In canvassing the structure, content, and delivery of key Australian and New Zealand restorative justice programs for adult offenders, the distinguished authors offer critical analysis of the emergence and impact of program developements for practitioners and professionals. This collection brings together stimulating and informed articles by experienced practitioners, leading academics and new researchers in the field. It also offers valuable insights into emerging restorative justice practice for adult offenders and provides a real alternative to the adversarial justice system.

Energy-efficient virtual machine placement in data centers by genetic algorithm

Server consolidation using virtualization technology has become an important technology to improve the energy efficiency of data centers. Virtual machine placement is the key in the server consolidation. In the past few years, many approaches to the virtual machine placement have been proposed. However, existing virtual machine placement approaches to the virtual machine placement problem consider the energy consumption by physical machines in a data center only, but do not consider the energy consumption in communication network in the data center. However, the energy consumption in the communication network in a data center is not trivial, and therefore should be considered in the virtual machine placement in order to make the data center more energy-efficient. In this paper, we propose a genetic algorithm for a new virtual machine placement problem that considers the energy consumption in both the servers and the communication network in the data center. Experimental results show that the genetic algorithm performs well when tackling test problems of different kinds, and scales up well when the problem size increases.

The benefits of tree-based models for stock selection

The identification of the primary drivers of stock returns has been of great interest to both financial practitioners and academics alike for many decades. Influenced by classical financial theories such as the CAPM (Sharp, 1964; Lintner, 1965) and APT (Ross, 1976), a linear relationship is conventionally assumed between company characteristics as derived from their financial accounts and forward returns. Whilst this assumption may be a fair approximation to the underlying structural relationship, it is often adopted for the purpose of convenience. It is actually quite rare that the assumptions of distributional normality and a linear relationship are explicitly assessed in advance even though this information would help to inform the appropriate choice of modelling technique. Non-linear models have nevertheless been applied successfully to the task of stock selection in the past (Sorensen et al, 2000). However, their take-up by the investment community has been limited despite the fact that researchers in other fields have found them to be a useful way to express knowledge and aid decision-making...

Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci : a conservation alert?

Genetic variation at allozyme and mitochondrial DNA loci was investigated in the Australian lungfish, Neoceratodus forsteri Krefft 1870. Tissue samples for genetic analysis were taken non-lethally from 278 individuals representing two spatially distinct endemic populations (Mary and Burnett rivers), as well as one population thought to be derived from an anthropogenic translocation in the 1890's (Brisbane river). Two of 24 allozyme loci resolved from muscle tissue were polymorphic. Mitochondrial DNA nucleotide sequence diversity estimated across 2,235 base pairs in each of 40 individuals ranged between 0.000423 and 0.001470 per river. Low genetic variation at allozyme and mitochondrial loci could be attributed to population bottlenecks, possibly induced by Pleistocene aridity. Limited genetic differentiation was detected among rivers using nuclear and mitochondrial markers suggesting that admixture may have occurred between the endemic Mary and Burnett populations during periods of low sea level when the drainages may have converged before reaching the ocean. Genetic data was consistent with the explanation that lungfish were introduced to the Brisbane river from the Mary river. Further research using more variable genetic loci is needed before the conservation status of populations can be determined, particularly as anthropogenic demands on lungfish habitat are increasing. In the interim we recommend a management strategy aimed at conserving existing genetic variation within and between rivers.

Kallikrein 14 is down-regulated by androgen receptor signalling and harbours genetic variation that is associated with prostate tumour aggressiveness

Kallikrein 14 (KLK14) has been proposed as a useful prognostic marker in prostate cancer, with expression reported to be associated with tumour characteristics such as higher stage and Gleason score. KLK14 tumour expression has also shown the potential to predict prostate cancer patients at risk of disease recurrence after radical prostatectomy. The KLKs are a remarkably hormone-responsive family of genes, although detailed studies of androgen regulation of KLK14 in prostate cancer have not been undertaken to date. Using in vitro studies, we have demonstrated that unlike many other prostatic KLK genes that are strictly androgen responsive, KLK14 is more broadly expressed and inversely androgen regulated in prostate cancer cells. Given these results and evidence that KLK14 may play a role in prostate cancer prognosis, we also investigated whether common genetic variants in the KLK14 locus are associated with risk and/or aggressiveness of prostate cancer in approximately 1200 prostate cancer cases and 1300 male controls. Of 41 single nucleotide polymorphisms assessed, three were associated with higher Gleason score (≥7): rs17728459 and rs4802765, both located upstream of KLK14, and rs35287116, which encodes a p.Gln33Arg substitution in the KLK14 signal peptide region. Our findings provide further support for KLK14 as a marker of prognosis in prostate cancer.

Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant

Maize streak virus (MSV) contributes significantly to the problem of extremely low African maize yields. Whilst a diverse range of MSV and MSV-like viruses are endemic in sub-Saharan Africa and neighbouring islands, only a single group of maize-adapted variants - MSV subtypes A1 -A6 - causes severe enough disease in maize to influence yields substantially. In order to assist in designing effective strategies to control MSV in maize, a large survey covering 155 locations was conducted to assess the diversity, distribution and genetic characteristics of the Ugandan MSV-A population. PCR-restriction fragment-length polymorphism analyses of 391 virus isolates identified 49 genetic variants. Sixty-two full-genome sequences were determined, 52 of which were detectably recombinant. All but two recombinants contained predominantly MSV-A1-like sequences. Of the ten distinct recombination events observed, seven involved inter-MSV-A subtype recombination and three involved intra-MSV-A1 recombination. One of the intra-MSV-A1 recombinants, designated MSV-A1 UgIII, accounted for >60% of all MSV infections sampled throughout Uganda. Although recombination may be an important factor in the emergence of novel geminivirus variants, it is demonstrated that its characteristics in MSV are quite different from those observed in related African cassava-infecting geminivirus species. © 2007 SGM.

Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates

Psittacine beak and feather disease (PBFD) has a broad host range and is widespread in wild and captive psittacine populations in Asia, Africa, the Americas, Europe and Australasia. Beak and feather disease circovirus (BFDV) is the causative agent. BFDV has an ~2 kb single stranded circular DNA genome encoding just two proteins (Rep and CP). In this study we provide support for demarcation of BFDV strains by phylogenetic analysis of 65 complete genomes from databases and 22 new BFDV sequences isolated from infected psittacines in South Africa. We propose 94% genome-wide sequence identity as a strain demarcation threshold, with isolates sharing > 94% identity belonging to the same strain, and strain subtypes sharing> 98% identity. Currently, BFDV diversity falls within 14 strains, with five highly divergent isolates from budgerigars probably representing a new species of circovirus with three strains (budgerigar circovirus; BCV-A, -B and -C). The geographical distribution of BFDV and BCV strains is strongly linked to the international trade in exotic birds; strains with more than one host are generally located in the same geographical area. Lastly, we examined BFDV and BCV sequences for evidence of recombination, and determined that recombination had occurred in most BFDV and BCV strains. We established that there were two globally significant recombination hotspots in the viral genome: the first is along the entire intergenic region and the second is in the C-terminal portion of the CP ORF. The implications of our results for the taxonomy and classification of circoviruses are discussed. © 2011 SGM.