The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone

Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage : genome analysis and virulence mechanisms

Escherichia coli strains causing urinary tract infection (UTI) are increasingly recognized as belonging to specific clones. E. coli clone O25b:H4-ST131 has recently emerged globally as a leading multi-drug resistant pathogen causing urinary tract and bloodstream infections in hospitals and the community. While most molecular studies to date examine the mechanisms conferring multi-drug resistance in E. coli ST131, relatively little is known about their virulence potential. Here we examined E. coli ST131 clinical isolates from two geographically diverse collections, one representing the major pathogenic lineages causing UTI across the United Kingdom and a second representing UTI isolates from patients presenting at two large hospitals in Australia. We determined a draft genome sequence for one representative isolate, E. coli EC958, which produced CTX-M-15 extended-spectrum β-lactamase, CMY-23 type AmpC cephalosporinase and was resistant to ciprofloxacin. Comparative genome analysis indicated that EC958 encodes virulence genes commonly associated with uropathogenic E. coli (UPEC). The genome sequence of EC958 revealed a transposon insertion in the fimB gene encoding the activator of type 1 fimbriae, an important UPEC bladder colonization factor. We identified the same fimB transposon insertion in 59% of the ST131 UK isolates, as well as 71% of ST131 isolates from Australia, suggesting this mutation is common among E. coli ST131 strains. Insertional inactivation of fimB resulted in a phenotype resembling a slower off-to-on switching for type 1 fimbriae. Type 1 fimbriae expression could still be induced in fimB-null isolates; this correlated strongly with adherence to and invasion of human bladder cells and bladder colonisation in a mouse UTI model. We conclude that E. coli ST131 is a geographically widespread, antibiotic resistant clone that has the capacity to produce numerous virulence factors associated with UTI.

Whole-genome multiparametric screening to identify modulators of epithelial-to-mesenchymal transition

Metastasis accounts for the poor prognosis of the majority of solid tumors. The phenotypic transition of nonmotile epithelial tumor cells to migratory and invasive “mesenchymal” cells (epithelial-to-mesenchymal transition [EMT]) enables the transit of cancer cells from the primary tumor to distant sites. There is no single marker of EMT; rather, multiple measures are required to define cell state. Thus, the multiparametric capability of high-content screening is ideally suited for the comprehensive analysis of EMT regulators. The aim of this study was to generate a platform to systematically identify functional modulators of tumor cell plasticity using the bladder cancer cell line TSU-Pr1-B1 as a model system. A platform enabling the quantification of key EMT characteristics, cell morphology and mesenchymal intermediate filament vimentin, was developed using the fluorescent whole-cell-tracking reagent CMFDA and a fluorescent promoter reporter construct, respectively. The functional effect of genome-wide modulation of protein-coding genes and miRNAs coupled with those of a collection of small-molecule kinase inhibitors on EMT was assessed using the Target Activation Bioapplication integrated in the Cellomics ArrayScan platform. Data from each of the three screens were integrated to identify a cohort of targets that were subsequently examined in a validation assay using siRNA duplexes. Identification of established regulators of EMT supports the utility of this screening approach and indicated capacity to identify novel regulators of this plasticity program. Pathway analysis coupled with interrogation of cancer-related expression profile databases and other EMT-related screens provided key evidence to prioritize further experimental investigation into the molecular regulators of EMT in cancer cells.

Development of a new regulatory model for occupational health and safety in the New South Wales coal industry: an issues paper for the New South Wales Department of Mineral Resources

This paper addresses the regulatory issues arising in developing a new regulatory model for the New South Wales Coal Industry. As such, it identifies the relevant literature on this subject, the options available for reform, and the experience of Australian and key international bodies responsible for the development of regulatory standards in this area. In particular it: Identifies the main shortcomings in the existing regulatory approach; Identifies the potential roles/main strengths and weaknesses of different types of standards (eg specification, performance, process and systems-based rules) and potential “best practice’ combinations of standards; Examines the appropriateness of the current regulatory regime whereby the general OHS legislation (including the general duty provisions) applies to mining in addition to the large body of regulation which is specific to mining; Identifies the importance of, and possible means of addressing, issues of worker participation within the coal mining industry; Draws on the literature on what motivates companies and individuals for the purpose of recommending key provisions for inclusion in new legislation to provide appropriate personal and organisational incentives; Draws on the literature on major hazards facilities to suggest the appropriate roles for OHS management systems and safety reports or comparable approaches (eg mine safety management plans); Draws on the United Kingdom (UK) and United States of America (USA) experience of coal mine safety and its regulation for comparative purposes, and for insights as to what sort of regulation most effectively reduces work related injury and disease in coal mining; Examines the relevant roles of International Labour Organisation (ILO) Conventions; Examines the extent to which different regulatory regimes would be appropriate to open cut and underground coal mining; and Examines options for reform. This paper is focussed specifically on the issues identified above.

Social Justice Impacts of the Resources Boom

Until the 1970s mining leases were issued by state governments subject to conditions that companies build or substantially finance local community infrastructure, including housing, streets, transport, schools, hospitals and recreation facilities. Townships and communities went hand in hand with mining development. However, in the past thirty years mining companies have moved progressively to an expeditionary strategy for natural resources extraction - operating a continuous production cycle of 12 hour shifts - increasingly reliant on non-resident, fly-in, fly-out or drive-in, drive-out (FIFO/DIDO) workers who typically work block rosters, reside in work camps adjacent to existing communities and travel large distances from their homes. This paper presents the key findings of our survey into the social impacts of this kind of mining development in Qld. Based on the results we argue that the social license to develop new mining projects is strong for projects requiring a 25% or less non-resident workforce, diminishes significantly thereafter and is very weak for projects planning to recruit a non-resident workforce in excess of 75%. This finding is significant because there are at least 67 new mining projects undergoing social impact assessment in Queensland, and many it appears are planning to hire significant proportions of non-resident workers. The paper considers the policy implications of this growing social justice issue concluding there is a clear need for national leadership in formulating a national policy framework for guiding socially responsible and sustainable mining development into the next millennium.

Emotional intelligence and job-demands resources model

Occupational stress research has consistently demonstrated negative effects for employees. Research also describes potential moderators of this relationship. While research has revealed some positive effects of emotional intelligence (EI) on employee adjustment, it has neglected investigation of their potential stress buffering effects. Based on the Job-Demand Resources model, it was predicted that higher trait emotional intelligence would act as a buffer to the potential negative effects of stressors on employee adjustment. Hierarchical multiple regression analyses with a sample of 306 nurses found no main effects of EI but revealed eight moderating effects. While some interactions support the buffering hypothesis, others revealed buffering for those with low EI. Findings are discussed in terms of theoretical and practical implications.

The flip side of fly-in-fly-out : the use of 457 visas by smaller firms in the Western Australian resources sector

The focus in this article is how the extensive use of fly-in fly-out (FIFO) working arrangements in the Western Australian resources sector has an impact directly and indirectly on smaller firms and their ability to recruit workers in remote locations. We argue that the growth of FIFO working arrangements has disadvantaged smaller resource-sector firms by increasing their employment costs and decreasing their ability to attract skilled workers. As a result, smaller resource-sector firms are recruiting skilled workers on 457 visas to secure their business stability and growth, despite the complexity, costs, and risks involved.

Multilingual lexical resources to detect cognates in non-aligned texts

The identification of cognates between two distinct languages has recently start- ed to attract the attention of NLP re- search, but there has been little research into using semantic evidence to detect cognates. The approach presented in this paper aims to detect English-French cog- nates within monolingual texts (texts that are not accompanied by aligned translat- ed equivalents), by integrating word shape similarity approaches with word sense disambiguation techniques in order to account for context. Our implementa- tion is based on BabelNet, a semantic network that incorporates a multilingual encyclopedic dictionary. Our approach is evaluated on two manually annotated da- tasets. The first one shows that across different types of natural text, our method can identify the cognates with an overall accuracy of 80%. The second one, con- sisting of control sentences with semi- cognates acting as either true cognates or false friends, shows that our method can identify 80% of semi-cognates acting as cognates but also identifies 75% of the semi-cognates acting as false friends.

Children's Literature Digital Resources Project

Children's Literature Digital Resources is a full text digital repository of Australian children’s literature from 1830 to 1945. Users can read online the complete texts of a selection of early Australian children’s literature, both popular and rare. Digitised items include children’s and young adult fiction, poetry, short stories, and picture books. Users can also read related full text critical articles that were digitised as part of the project.

Energy Efficiency Resources for Undergraduate Engineering Education: Final Report

This report presents the findings of an investigation of energy efficiency resources for undergraduate engineering education, undertaken by web-based research, conversations with educators, and a university survey. The investigation draws on the results of a number of previous investigations undertaken by the research team for NFEE related to energy efficiency education and presents the following findings and recommendations, as explained in greater detail in the body of the report. The findings suggest that even though certain EE concepts and principles have been identified by lecturers as being important there is little to no coverage of a number of these concepts in some programs/courses. Similarly, many topics relating to the most important EE workforce skills and significant shortages as identified in industry research, do not rate highly in terms of both perceived importance by lecturers, or coverage within existing courses. Overall, these findings suggest that despite growing awareness of the importance of EE in both industry and academia, the current depth and breadth of EE content in courses does not reflect this. It confirms that efforts in these areas can be better supported.