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.

Mathematical model of counter flow v-grove solar air collector

Double-pass counter flow v-grove collector is considered one of the most efficient solar air-collectors. In this design of the collector, the inlet air initially flows at the top part of the collector and changes direction once it reaches the end of the collector and flows below the collector to the outlet. A mathematical model is developed for this type of collector and simulation is carried out using MATLAB programme. The simulation results were verified with three distinguished research results and it was found that the simulation has the ability to predict the performance of the air collector accurately as proven by the comparison of experimental data with simulation. The difference between the predicted and experimental results is, at maximum, approximately 7% which is within the acceptable limit considering some uncertainties in the input parameter values to allow comparison. A parametric study was performed and it was found that solar radiation, inlet air temperature, flow rate and length has a significant effect on the efficiency of the air collector. Additionally, the results are compared with single flow V-groove collector.

A systematic approach for selecting lean strategies and assessing leanness in manufacturing organizations

Lean strategies have been developed to eliminate or reduce manufacturing waste and thus improve operational efficiency in manufacturing processes. However, implementing lean strategies requires a large amount of resources and, in practice, manufacturers encounter difficulties in selecting appropriate lean strategies within their resource constraints. There is currently no systematic methodology available for selecting appropriate lean strategies within a manufacturer's resource constraints. In the lean transformation process, it is also critical to measure the current and desired leanness levels in order to clearly evaluate lean implementation efforts. Despite the fact that many lean strategies are utilized to reduce or eliminate manufacturing waste, little effort has been directed towards properly assessing the leanness of manufacturing organizations. In practice, a single or specific group of metrics (either qualitative or quantitative) will only partially measure the overall leanness. Existing leanness assessment methodologies do not offer a comprehensive evaluation method, integrating both quantitative and qualitative lean measures into a single quantitative value for measuring the overall leanness of an organization. This research aims to develop mathematical models and a systematic methodology for selecting appropriate lean strategies and evaluating the leanness levels in manufacturing organizations. Mathematical models were formulated and a methodology was developed for selecting appropriate lean strategies within manufacturers' limited amount of available resources to reduce their identified wastes. A leanness assessment model was developed by using the fuzzy concept to assess the leanness level and to recommend an optimum leanness value for a manufacturing organization. In the proposed leanness assessment model, both quantitative and qualitative input factors have been taken into account. Based on program developed in MATLAB and C#, a decision support tool (DST) was developed for decision makers to select lean strategies and evaluate the leanness value based on the proposed models and methodology hence sustain the lean implementation efforts. A case study was conducted to demonstrate the effectiveness of these proposed models and methodology. Case study results suggested that out of 10 wastes identified, the case organization (ABC Limited) is able to improve a maximum of six wastes from the selected workstation within their resource limitations. The selected wastes are: unnecessary motion, setup time, unnecessary transportation, inappropriate processing, work in process and raw material inventory and suggested lean strategies are: 5S, Just-In-Time, Kanban System, the Visual Management System (VMS), Cellular Manufacturing, Standard Work Process using method-time measurement (MTM), and Single Minute Exchange of Die (SMED). From the suggested lean strategies, the impact of 5S was demonstrated by measuring the leanness level of two different situations in ABC. After that, MTM was suggested as a standard work process for further improvement of the current leanness value. The initial status of the organization showed a leanness value of 0.12. By applying 5S, the leanness level significantly improved to reach 0.19 and the simulation of MTM as a standard work method shows the leanness value could be improved to 0.31. The optimum leanness value of ABC was calculated to be 0.64. These leanness values provided a quantitative indication of the impacts of improvement initiatives in terms of the overall leanness level to the case organization. Sensitivity analsysis and a t-test were also performed to validate the model proposed. This research advances the current knowledge base by developing mathematical models and methodologies to overcome lean strategy selection and leanness assessment problems. By selecting appropriate lean strategies, a manufacturer can better prioritize implementation efforts and resources to maximize the benefits of implementing lean strategies in their organization. The leanness index is used to evaluate an organization's current (before lean implementation) leanness state against the state after lean implementation and to establish benchmarking (the optimum leanness state). Hence, this research provides a continuous improvement tool for a lean manufacturing organization.

Dynamic weaving in aspect oriented business process management

Reducing complexity in Information Systems is an important topic in both research and industry. One strategy to deal with complexity is separation of concerns, which results in less complex, easily maintainable and more reusable systems. Separation of concerns can be addressed through the Aspect Oriented paradigm. Although this paradigm has been well researched in programming, it is still at the preliminary stage in the area of Business Process Management. While some efforts have been made to extend business process modelling with aspect oriented capability, it has not yet been investigated how aspect oriented business process models should be executed at runtime. In this paper, we propose a generic solution to support execution of aspect oriented business process models based on the principle behind dynamic weaving of aspects. This solution is formally specified using Coloured Petri Nets. The resulting formal specification serves as the blueprint to the implementation of a service module in the framework of a state-of-the-art Business Process Management System. Using this developed artefact, a case study is performed in which two simplified processes from real business in the domain of banking are modelled and executed in an aspect oriented manner. Through this case study, we also demonstrate that adoption of aspect oriented modularization increases the reusability while reducing the complexity of business process models in practice.

Prevalence of depressive symptoms as elicited by Patient Health Questionnaire (PHQ-9) among medical trainees in Oman

Background Despite the increasing recognition that medical training tends to coincide with markedly high levels of stress and distress, there is a dearth of validated measures that are capable of gauging the prevalence of depressive symptoms among medical residents in the Arab/Islamic part of the world. Objective The aim of the present study is two-fold. First is to examine the diagnostic validity of the Patient Health Questionnaire (PHQ-9) using an Omani medical resident population in order to establish a cut-off point. Second is to compare gender, age, and residency level among Omani Medical residents who report current depressive symptomatology versus those who report as non-depressed according to PHQ-9 cut-off threshold. Results A total of 132 residents (42 males and 90 females) consented to participate in this study. The cut-off score of 12 on the PHQ-9 revealed a sensitivity of 80.6% and a specificity of 94.0%. The rate of depression, as elicited by PHQ-9, was 11.4%. The role of gender, age, and residency level was not significant in endorsing depression. Conclusion This study indicated that PHQ-9 is a reliable measure among this cross-cultural population. More studies employing robust methodology are needed to confirm this finding.

Temperature redistribution modelling during intermittent microwave convective heating

Microwave power is used for heating and drying processes because of its faster and volumetric heating capability. Non-uniform temperature distribution during microwave application is a major drawback of these processes. Intermittent application of microwave potentially reduces the impact of non-uniformity and improves energy efficiency by redistributing the temperature. However, temperature re-distribution during intermittent microwave heating has not been investigated adequately. Consequently, in this study, a coupled electromagnetic with heat and mass transfer model was developed using the finite element method embedded in COMSOL-Multyphysics software. Particularly, the temperature redistribution due to intermittent heating was investigated. A series of experiments were performed to validate the simulation. The test specimen was an apple and the temperature distribution was closely monitored by a TIC (Thermal Imaging Camera). The simulated temperature profile matched closely with thermal images obtained from experiments.

Mathematical modelling of counter flow v-grove solar air collector

Double-pass counter flow v-grove collector is considered one of the most efficient solar air-collectors. In this design of the collector, the inlet air initially flows at the top part of the collector and changes direction once it reaches the end of the collector and flows below the collector to the outlet. A mathematical model is developed for this type of collector and simulation is carried out using MATLAB programme. The simulation results were verified with three distinguished research results and it was found that the simulation has the ability to predict the performance of the air collector accurately as proven by the comparison of experimental data with simulation. The difference between the predicted and experimental results is, at maximum, approximately 7% which is within the acceptable limit considering some uncertainties in the input parameter values to allow comparison. A parametric study was performed and it was found that solar radiation, inlet air temperature, flow rate and length have a significant effect on the efficiency of the air collector. Additionally, the results are compared with single flow V-groove collector.

A time-based quantitative approach for selecting lean strategies for manufacturing organisations

Lean strategies have been developed to eliminate or reduce waste and thus improve operational efficiency in a manufacturing environment. However, in practice, manufacturers encounter difficulties to select appropriate lean strategies within their resource constraints and to quantitatively evaluate the perceived value of manufacturing waste reduction. This paper presents a methodology developed to quantitatively evaluate the contribution of lean strategies selected to reduce manufacturing wastes within the manufacturers’ resource (time) constraints. A mathematical model has been developed for evaluating the perceived value of lean strategies to manufacturing waste reduction and a step-by-step methodology is provided for selecting appropriate lean strategies to improve the manufacturing performance within their resource constraints. A computer program is developed in MATLAB for finding the optimum solution. With the help of a case study, the proposed methodology and developed model has been validated. A ‘lean strategy-wastes’ correlation matrix has been proposed to establish the relationship between the manufacturing wastes and lean strategies. Using the correlation matrix and applying the proposed methodology and developed mathematical model, authors came out with optimised perceived value of reduction of a manufacturer's wastes by implementing appropriate lean strategies within a manufacturer's resources constraints. Results also demonstrate that the perceived value of reduction of manufacturing wastes can significantly be changed based on policies and product strategy taken by a manufacturer. The proposed methodology can also be used in dynamic situations by changing the input in the programme developed in MATLAB. By identifying appropriate lean strategies for specific manufacturing wastes, a manufacturer can better prioritise implementation efforts and resources to maximise the success of implementing lean strategies in their organisation.

Collagen biosynthesis in cultured rat testicular Sertoli and peritubular myoid cells

The incorporation of 3H-proline into protein was regarded as a measure of total protein synthesis and the incorporation into hydroxyproline as indicative of collagen synthesis. Relative collagen synthesis (expressed as percent of total protein synthesized) by Sertoli and peritubular myoid cells cultured from 20-22 day old rat testis was estimated. In both secreted and cellular pools, relative collagen synthesis by Sertoli cells was significantly greater than by peritubular myoid cells. Coculture of Sertoli and myoid cells resulted in a significant increase in relative collagen synthesis when compared to monocultures of each cell type. Addition of serum to peritubular myoid cells resulted in a stronger stimulation of relative collagen production. Sertoli cell extracellular matrix inhibited relative collagen synthesis by peritubular myoid cells in the presence or absence of serum. Radioactivity into hydroxyproline as corrected per cellular DNA also showed similar results. Immunolocalization studies confirmed that both cell types synthesize type I and type IV collagens. These results indicate that stimulation of collagen synthesis observed in Sertoli-myoid cell cocultures is due to humoral interactions, rather than extracellular matrix, and Sertoli cell extracellular matrix regulates serum-induced increase in collagen synthesis by peritubular myoid cells.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent