Aspect oriented business process modeling with precedence

Complexity is a major concern which is aimed to be overcome by people through modeling. One way of reducing complexity is separation of concerns, e.g. separation of business process from applications. One sort of concerns are cross-cutting concerns i.e. concerns which are scattered and tangled through one of several models. In business process management, examples of such concerns are security and privacy policies. To deal with these cross-cutting concerns, the aspect orientated approach was introduced in the software development area and recently also in the business process management area. The work presented in this paper elaborates on aspect oriented process modelling. It extends earlier work by defining a mechanism for capturing multiple concerns and specifying a precedence order according to which they should be handled in a process. A formal syntax of the notation is presented precisely capturing the extended concepts and mechanisms. Finally, the relevant of the approach is demonstrated through a case study.

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.

Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript

Abstract Genome-wide association studies (GWAS) have identified more than 30 prostate cancer (PrCa) susceptibility loci. One of these (rs2735839) is located close to a plausible candidate susceptibility gene, KLK3, which encodes prostate-specific antigen (PSA). PSA is widely used as a biomarker for PrCa detection and disease monitoring. To refine the association between PrCa and variants in this region, we used genotyping data from a two-stage GWAS using samples from the UK and Australia, and the Cancer Genetic Markers of Susceptibility (CGEMS) study. Genotypes were imputed for 197 and 312 single nucleotide polymorphisms (SNPs) from HapMap2 and the 1000 Genome Project, respectively. The most significant association with PrCa was with a previously unidentified SNP, rs17632542 (combined P = 3.9 × 10−22). This association was confirmed by direct genotyping in three stages of the UK/Australian GWAS, involving 10,405 cases and 10,681 controls (combined P = 1.9 × 10−34). rs17632542 is also shown to be associated with PSA levels and it is a non-synonymous coding SNP (Ile179Thr) in KLK3. Using molecular dynamic simulation, we showed evidence that this variant has the potential to introduce alterations in the protein or affect RNA splicing. We propose that rs17632542 may directly influence PrCa risk.

Operational semantics of aspects in business process management

Aspect orientation is an important approach to address complexity of cross-cutting concerns in Information Systems. This approach encapsulates these concerns separately and compose them to the main module when needed. Although there a different works which shows how this separation should be performed in process models, the composition of them is an open area. In this paper, we demonstrate the semantics of a service which enables this composition. The result can also be used as a blueprint to implement the service to support aspect orientation in Business Process Management area.

Dynamic weaving of aspects for business process management systems

Reducing complexity in Information Systems is a main concern in both research and industry. One strategy for reducing complexity is separation of concerns. This strategy advocates separating various concerns, like security and privacy, from the main concern. It results in less complex, easily maintainable, and more reusable Information Systems. Separation of concerns is addressed through the Aspect Oriented paradigm. This paradigm has been well researched and implemented in programming, where languages such as AspectJ have been developed. However, the rsearch on aspect orientation for Business Process Management is still at its beginning. While some efforts have been made proposing Aspect Oriented Business Process Modelling, it has not yet been investigated how to enact such process models in a Workflow Management System. In this paper, we define a set of requirements that specifies the execution of aspect oriented business process models. We create a Coloured Petri Net specification for the semantics of so-called Aspect Service that fulfils these requirements. Such a service extends the capability of a Workflow Management System with support for execution of aspect oriented business process models. The design specification of the Aspect Service is also inspected through state space analysis.

Two dicot-infecting mastreviruses (family Geminiviridae) occur in Pakistan

Most mastreviruses (family Geminiviridae) infect monocotyledonous hosts and are transmitted by leafhopper vectors. Only two mastrevirus species, Tobacco yellow dwarf virus from Australia and Bean yellow dwarf virus (BeYDV) from South Africa, have been identified whose members infect dicotyledonous plants. We have identified two distinct mastreviruses in chickpea stunt disease (CSD)-affected chickpea originating from Pakistan. The first is an isolate of BeYDV, previously only known to occur in South Africa. The second is a member of a new species with the BeYDV isolates as its closest relatives. A PCR-based diagnostic test was developed to differentiate these two virus species. Our results show that BeYDV plays no role in the etiology of CSD in Pakistan, while the second virus occurs widely in chickpea across Pakistan. A genomic clone of the new virus was infectious to chickpea (Cicer arietinum L.) and induced symptoms typical of CSD. We propose the use of the name Chickpea chlorotic dwarf Pakistan virus for the new species. The significance of these findings with respect to our understanding of the evolution, origin and geographic spread of dicot-infecting mastreviruses is discussed. © 2008 Springer-Verlag.

A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease

Genome-wide association studies (GWAS) have identified multiple common genetic variants associated with an increased risk of prostate cancer (PrCa), but these explain less than one-third of the heritability. To identify further susceptibility alleles, we conducted a meta-analysis of four GWAS including 5953 cases of aggressive PrCa and 11 463 controls (men without PrCa). We computed association tests for approximately 2.6 million SNPs and followed up the most significant SNPs by genotyping 49 121 samples in 29 studies through the international PRACTICAL and BPC3 consortia. We not only confirmed the association of a PrCa susceptibility locus, rs11672691 on chromosome 19, but also showed an association with aggressive PrCa [odds ratio = 1.12 (95% confidence interval 1.03-1.21), P = 1.4 × 10(-8)]. This report describes a genetic variant which is associated with aggressive PrCa, which is a type of PrCa associated with a poorer prognosis.

Fine-mapping identifies multiple prostate cancer risk loci on 5p15 some associating with TERT expression

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease.

Risky driving behavior among university students and staff in the Sultanate of Oman

Background: There is a well developed literature on research investigating the relationship between various driving behaviours and road crash involvement. However, this research has predominantly been conducted in developed economies dominated by western types of cultural environments. To date no research has been published that has empirically investigated this relationship within the context of the emerging economies such as Oman. Objective: The present study aims to investigate driving behaviour as indexed in the Driving Behaviour Questionnaire (DBQ) among a group of Omani university students and staff. Methods: A convenience non-probability self- selection sampling approach was utilized with Omani university students and staff. Results: A total of 1003 Omani students (n= 632) and staff (n=371) participated in the survey. Factor analysis of the BDQ revealed four main factors that were errors, speeding violation, lapses and aggressive violation. In the multivariate logistic backward regression analysis, the following factors were identified as significant predictors of being involved in causing at least one crash: driving experience, history of offences and two DBQ components i.e. errors and aggressive violation. Conclusion: This study indicates that errors and aggressive violation of the traffic regulations as well as history of having traffic offences are major risk factors for road traffic crashes among the sample. While previous international research has demonstrated that speeding is a primary cause of crashing, in the current context, the results indicate that an array of factors is associated with crashes. Further research using more rigorous methodology is warranted to inform the development of road safety countermeasures in Oman that improves overall traffic safety culture.

Imagining neighbourhood-based community : an autoethnography

This research is an autoethnographic investigation of consumption experiences, public and quasi-public spaces, and their relationship to community within an inner city neighbourhood. The research specifically focuses on the gentrifying inner city, where class-based processes of change can have implications for people’s abilities to remain within, or feel connected to place. However, the thesis draws on broader theories of the throwntogetherness of the contemporary city (e.g., Amin and Thrift, 2002; Massey 2005) to argue that the city is a space where place-based meanings cannot be seen to be fixed, and are instead better understood as events of place – based on ever shifting interrelations between the trajectories of people and things. This perspective argues the experience of belonging to community is not just born of a social encounter, but also draws on the physical and symbolic elements of the context in which it is situated. The thesis particularly explores the ways people construct identifications within this shifting urban environment. As such, consumption practices and spaces offer one important lens through which to explore the interplay of the physical, social and symbolic. Consumer research tells us that consumption practices can facilitate experiences in which identity-defining meaning can be generated and shared. Consumption spaces can also support different kinds of collective identification – as anchoring realms for specific cultural groups or exposure realms that enable individuals to share in the identification practices of others with limited risk (Aubert-Gamet & Cova, 1999). Furthermore, the consumption-based lifestyles that gentrifying inner city neighbourhoods both support and encourage can also mean that consumption practices may be a key reason that people are moving through public space. That is, consumption practices and spaces may provide a purpose for which – and spatial frame against which – our everyday interactions and connections with people and objects are undertaken within such neighbourhoods. The purpose of this investigation then was to delve into the subjectivities at the heart of identifying with places, using the lens of our consumption-based experiences within them. The enquiry describes individual and collective identifications and emotional connections, and explores how these arise within and through our experiences within public and quasi-public spaces. It then theorises these ‘imaginings’ as representative of an experience of community. To do so, it draws on theories of imagination and its relation to community. Theories of imagined community remind us that both the values and identities of community are held together by projections that create relational links out of objects and shared practices (e.g., Benedict Anderson, 2006; Urry, 2000). Drawing on broader theories of the processes of the imagination, this thesis suggests that an interplay between reflexivity and fantasy – which are products of the critical and the fascinated consciousness – plays a role in this imagining of community (e.g., Brann, 1991; Ricoeur, 1994). This thesis therefore seeks to explore how these processes of imagining are implicated within the construction of an experience of belonging to neighbourhood-based community through consumption practices and the public and quasi-public spaces that frame them. The key question of this thesis is how do an individual’s consumption practices work to construct an imagined presence of neighbourhood-based community? Given the focus on public and quasi-public spaces and our experiences within them, the research also asked how do experiences in the public and quasi-public spaces that frame these practices contribute to the construction of this imagined presence? This investigation of imagining community through consumption practices is based on my own experiences of moving to, and attempting to construct community connections within, an inner city neighbourhood in Melbourne, Australia. To do so, I adopted autoethnographic methodology. This is because autoethnography provides the methodological tools through which one can explore and make visible the subjectivities inherent within the lived experiences of interest to the thesis (Ellis, 2004). I describe imagining community through consumption as an extension of a placebased self. This self is manifest through personal identification in consumption spaces that operate as anchoring realms for specific cultural groups, as well as through a broader imagining of spaces, people, and practices as connected through experiences within realms of exposure. However, this is a process that oscillates through cycles of identification; these anchor one within place personally, but also disrupt those attachments. This instability can force one to question the orientation and motives of these imaginings, and reframe them according to different spaces and reference groups in ways that can also work to construct a more anonymous and, conversely, more achievable collective identification. All the while, the ‘I’ at the heart of this identification is in an ongoing process of negotiation, and similarly, the imagined community is never complete. That is, imagining community is a negotiation, with people and spaces – but mostly with the different identifications of the self. This thesis has been undertaken by publication, and thus the process of imagining community is explored and described through four papers. Of these, the first two focus on specific types of consumption spaces – a bar and a shopping centre – and consider the ways that anchoring and exposure within these spaces support the process of imagining community. The third paper examines the ways that the public and quasi-public spaces that make up the broader neighbourhood context are themselves throwntogether as a realm of exposure, and considers the ways this shapes my imaginings of this neighbourhood as community. The final paper develops a theory of imagined community, as a process of comparison and contrast with imagined others, to provide a summative conceptualisation of the first three papers. The first paper, chapter five, explores this process of comparison and contrast in relation to authenticity, which in itself is a subjective assessment of identity. This chapter was written as a direct response to the recent work of Zukin (2010), and draws on theories of authenticity as applied to personal and collective identification practices by consumer researchers Arnould and Price (2000). In this chapter, I describe how my assessments of the authenticity of my anchoring experiences within one specific consumption space, a neighbourhood bar, are evaluated in comparison to my observations of and affective reactions to the social practices of another group of residents in a different consumption space, the local shopping centre. Chapter five also provides an overview of the key sites and experiences that are considered in more detail in the following two chapters. In chapter six, I again draw on my experiences within the bar introduced in chapter five, this time to explore the process of developing a regular identity within a specific consumption space. Addressing the popular theory of the cafe or bar as third place (Oldenburg, 1999), this paper considers the purpose of developing anchored relationships with people within specific consumption spaces, and explores the different ways this may be achieved in an urban context where the mobilities and lifestyle practices of residents complicate the idea of a consumption space as an anchoring or third place. In doing so, this chapter also considers the manner in which this type of regular identification may be seen to be the beginning of the process of imagining community. In chapter seven, I consider the ways the broader public spaces of the neighbourhood work cumulatively to expose different aspects of its identity by following my everyday movements through the neighbourhood’s shopping centre and main street. Drawing on the theories of Urry (2000), Massey (2005), and Amin (2007, 2008), this chapter describes how these spaces operate as exposure realms, enabling the expression of different senses of the neighbourhood’s spaces, times, cultures, and identities through their physical, social, and symbolic elements. Yet they also enable them to be united: through habitual pathways, group practices of appropriation of space, and memory traces that construct connections between objects and experiences. This chapter describes this as a process of exposure to these different elements. Our imagination begins to expand the scope of the frames onto which it projects an imagined presence; it searches for patterns within the physical, social, and symbolic environment and draws connections between people and practices across spaces. As the final paper, chapter eight, deduces, it is in making these connections that one constructs the objects and shared practices of imagined community. This chapter describes this as an imagining of neighbourhood as a place-based extension of the self, and then explores the ways in which I drew on physical, social, and symbolic elements in an attempt to construct a fit between the neighbourhood’s offerings and my desires for place-based identity definition. This was as a cumulative but fragmented process, in which positive and negative experiences of interaction and identification with people and things were searched for their potential to operate as the objects and shared practices of imagined community. This chapter describes these connections as constructed through interplay between reflexivity and fantasy, as the imagination seeks balance between desires for experiences of belonging, and the complexities of constructing them within the throwntogether context of the contemporary city. The conclusion of the thesis describes the process of imagining community as a reflexive fantasy, that is, as a product of both the critical and fascinated consciousness (Ricoeur, 1994). It suggests that the fascinated consciousness imbues experiences with hope and desire, which the reflexive imagining can turn to disappointment and shame as it critically reflects on the reality of those fascinated projections. At the same time, the reflexive imagination also searches the practices of others for affirmation of those projections, effectively seeking to prove the reality of the fantasy of the imagined community.

Characterisation of candidate nuclear genes for species delineation in the genus Cherax

Understanding the evolutionary history and phylogenetic relationships between rare and common species is necessary for the effective management of rare species. The genus Cherax, a group of freshwater crayfish species, is of interest in this regard as a number of species are rare or have restricted distributions while other species are common and widespread. Here we describe the characterisation of three novel nuclear genes of the haemocyanin superfamily for phylogenetic reconstruction of the genus. All novel markers developed in this study amplified consistently in species from three divergent clades of the genus Cherax. The level of polymorphism found in these markers was consistently higher than that found in other nuclear genes previously used in invertebrate systematics, such as NaK ATP-ase. In combination, these markers will be useful to delineate phylogenetic relationships between rare and common Cherax species.