Exploiting medical hierarchies for concept-based information retrieval

Search technologies are critical to enable clinical sta to rapidly and e ectively access patient information contained in free-text medical records. Medical search is challenging as terms in the query are often general but those in rel- evant documents are very speci c, leading to granularity mismatch. In this paper we propose to tackle granularity mismatch by exploiting subsumption relationships de ned in formal medical domain knowledge resources. In symbolic reasoning, a subsumption (or `is-a') relationship is a parent-child rela- tionship where one concept is a subset of another concept. Subsumed concepts are included in the retrieval function. In addition, we investigate a number of initial methods for combining weights of query concepts and those of subsumed concepts. Subsumption relationships were found to provide strong indication of relevant information; their inclusion in retrieval functions yields performance improvements. This result motivates the development of formal models of rela- tionships between medical concepts for retrieval purposes.

Developing a predictive contractor satisfaction model (CoSMo) for construction projects

Over the last few decades, construction project performance has been evaluated due to the increase of delays, cost overruns and quality failures. Growing numbers of disputes, inharmonious working environments, conflict, blame cultures, and mismatches of objectives among project teams have been found to be contributory factors to poor project performance. Performance measurement (PM) approaches have been developed to overcome these issues, however, the comprehensiveness of PM as an overall approach is still criticised in terms of the iron triangle; namely time, cost, and quality. PM has primarily focused on objective measures, however, continuous improvement requires the inclusion of subjective measures, particularly contractor satisfaction (Co-S). It is challenging to deal with the two different groups of large and small-medium contractor satisfaction as to date, Co-S has not been extensively defined, primarily in developing countries such as Malaysia. Therefore, a Co-S model is developed in this research which aims to fulfil the current needs in the construction industry by integrating performance measures to address large and small-medium contractor perceptions. The positivist paradigm used in the research was adhered to by reviewing relevant literature and evaluating expert discussions on the research topic. It yielded a basis for the contractor satisfaction model (CoSMo) development which consists of three elements: contractor satisfaction (Co-S) dimensions; contributory factors and characteristics (project and participant). Using valid questionnaire results from 136 contractors in Malaysia lead to the prediction of several key factors of contractor satisfaction and to an examination of the relationships between elements. The relationships were examined through a series of sequential statistical analyses, namely correlation, one-way analysis of variance (ANOVA), t-tests and multiple regression analysis (MRA). Forward and backward MRAs were used to develop Co-S mathematical models. Sixteen Co-S models were developed for both large and small-medium contractors. These determined that the large contractor Malaysian Co-S was most affected by the conciseness of project scope and quality of the project brief. Contrastingly, Co-S for small-medium contractors was strongly affected by the efficiency of risk control in a project. The results of the research provide empirical evidence in support of the notion that appropriate communication systems in projects negatively contributes to large Co-S with respect to cost and profitability. The uniqueness of several Co-S predictors was also identified through a series of analyses on small-medium contractors. These contractors appear to be less satisfied than large contractors when participants lack effectiveness in timely authoritative decision-making and communication between project team members. Interestingly, the empirical results show that effective project health and safety measures are influencing factors in satisfying both large and small-medium contractors. The perspectives of large and small-medium contractors in respect to the performance of the entire project development were derived from the Co-S models. These were statistically validated and refined before a new Co-S model was developed. Developing such a unique model has the potential to increase project value and benefit all project participants. It is important to improve participant collaboration as it leads to better project performance. This study may encourage key project participants; such as client, consultant, subcontractor and supplier; to increase their attention to contractor needs in the development of a project. Recommendations for future research include investigating other participants‟ perspectives on CoSMo and the impact of the implementation of CoSMo in a project, since this study is focused purely on the contractor perspective.

Sail into one of Europe's greatest cities

A travel article about the university towns of Heidelberg and Tubingen in Germany. "DURING an extended visit to Heidelberg, Germany's oldest university town, Mark Twain was shocked to see students out and about at all hours of the day and night..."--publisher website

One-year delayed effect of fog on malaria transmission : a time-series analysis in the rain forest area of Mengla County, south-west China

Background: Malaria is a major public health burden in the tropics with the potential to significantly increase in response to climate change. Analyses of data from the recent past can elucidate how short-term variations in weather factors affect malaria transmission. This study explored the impact of climate variability on the transmission of malaria in the tropical rain forest area of Mengla County, south-west China. Methods: Ecological time-series analysis was performed on data collected between 1971 and 1999. Auto-regressive integrated moving average (ARIMA) models were used to evaluate the relationship between weather factors and malaria incidence. Results: At the time scale of months, the predictors for malaria incidence included: minimum temperature, maximum temperature, and fog day frequency. The effect of minimum temperature on malaria incidence was greater in the cool months than in the hot months. The fog day frequency in October had a positive effect on malaria incidence in May of the following year. At the time scale of years, the annual fog day frequency was the only weather predictor of the annual incidence of malaria. Conclusion: Fog day frequency was for the first time found to be a predictor of malaria incidence in a rain forest area. The one-year delayed effect of fog on malaria transmission may involve providing water input and maintaining aquatic breeding sites for mosquitoes in vulnerable times when there is little rainfall in the 6-month dry seasons. These findings should be considered in the prediction of future patterns of malaria for similar tropical rain forest areas worldwide.

Identification of long intergenic region sequences involved in maize streak virus replication

The main cis-acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). However, neither the minimum LIR sequence required nor the sequence determinants of replication specificity have been determined experimentally. There are iterated sequences, or iterons, both within the conserved inverted-repeat sequences with the potential to form a stem-loop structure at the origin of virion-strand replication, and upstream of the rep gene TATA box (the rep-proximal iteron or RPI). Based on experimental analyses of similar iterons in viruses from other geminivirus genera and their proximity to known Rep-binding sites in the distantly related mastrevirus wheat dwarf virus, it has been hypothesized that the iterons may be Rep-binding and/or -recognition sequences. Here, a series of LIR deletion mutants was used to define the upper bounds of the LIR sequence required for replication. After identifying MSV strains and distinct mastreviruses with incompatible replication-specificity determinants (RSDs), LIR chimaeras were used to map the primary MSV RSD to a 67 nt sequence containing the RPI. Although the results generally support the prevailing hypothesis that MSV iterons are functional analogues of those found in other geminivirus genera, it is demonstrated that neither the inverted-repeat nor RPI sequences are absolute determinants of replication specificity. Moreover, widely divergent mastreviruses can trans-replicate one another. These results also suggest that sequences in the 67 nt region surrounding the RPI interact in a sequence-specific manner with those of the inverted repeat.

Using the index for inclusion to develop inclusive school communities

This chapter provides an overview of how school communities can work together in processes or review and development to strive towards a more inclusive approach to education. The writers of this chapter have been using a resource called the Index for Inclusion (Booth & Ainscow, 2005, 2011) for a number of years in Australia and in a pilot trail in New Zealand to support education staff in processes of review, with the aim to increase the participation and learning of all students. The resource supports the development of collaborative community processes and defines inclusion as ‘putting values into action’ (Booth & Ainscow, 2011, p.18). The process of review and development for more inclusive and socially just schools supports the development of a school culture, policy and practice where people are valued and treated with respect for their varied knowledge and experiences. In our experience, this resource has been useful to challenge our thinking about education in school communities and in region/districts about inclusive school development. We suggest the Index framework is broad enough to be used in a range of settings and countries. The resource is also useful for pre-service and in-service teacher development to provoke reflection and discussion about inclusion. This chapter provides an overview of the dimensions and framework that inform the Index of Inclusion. We discuss how the Index can be used in school contexts and draw on our own experience to give real examples of how teachers, paraprofessionals, students, principals and parents have experienced the Index when used in their local school communities in Australia and New Zealand. The chapter concludes with some points for discussion to challenge the status quo in schools and to inspire teachers to work towards a more socially just society through making changes at a school level.

Seeking inclusion : views from ‘vulnerable’ communities about reporting by the Australian news media

This conference paper reports on the findings of the 'Vulnerability and the News Media’ project about news reporting on communities that are commonly regarded as ‘vulnerable’ by virtue of their issues or circumstances. The project focuses on news reporting of Indigenous and ethnically diverse communities, as well as people affected by mental health issues, people with disabilities, and survivors of crime and traumatic events. Numerous educational initiatives have tried to improve the quality of media reports about these communities and their issues. Despite this, the project’s research with stakeholders from those communities has found that they continue to raise the same concerns that have been expressed about the news media since the 1970s. In focus group research, stakeholders from these communities expressed concern about their continuing under-representation or omission from the news media. They felt that voices, experiences, perspectives and issues from their communities rarely appeared, or if they did appear, it was in limited contexts – often in circumstances that portrayed them as vulnerable or disruptive. They also pointed to ongoing media misrepresentation, such as stereotyping, inappropriate framing, and over-reliance on ‘usual suspects’ to talk about their communities. A common theme that they voiced was their need for greater inclusiveness in the media. Participants wished that journalists would better represent the diversity of life experiences and perspectives within their communities. Stakeholders also wanted an increased in representation of their political frameworks, such as stories about the difficulties they encountered in dealing with social and bureaucratic systems, and their understandings of causes and potential solutions for issues affecting their communities.

Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

Experience of overseas-trained health professionals in rural and remote areas of destination countries: A literature review

This study aimed to review and synthesise existing literature that investigated the experience of overseastrained health professionals (OTHPs) in rural and remote areas of destination countries. A systematic literature review was conducted using electronic databases and manual search of studies published from January 2004 to February 2011. Data were analysed from the final 17 original report articles that met the inclusion criteria. The reviewed research studies were conducted in Australia, Canada, New Zealand, the UK and the USA. Overseas-trained medical practitioners were the most frequently researched (n = 14); two studies involved nurses and one study included several health professionals. Three main themes emerged from the review and these were: (i) expectations; (ii) cultural diversity; and (iii) orientation and integration to rural and remote health work environment. The OTHPs were expected to possess the appropriate professional and cultural skills while they themselves expected recognition of their previous experiences and adequate organisational orientation and support. A welcoming and accepting community coupled with a relaxed rural lifestyle and the joy of continued patient care resulted in successful integration and contributed to increased staff retention rates. Recognition of expectations and cultural diversity by all parties and comprehensive orientation with sufficient organisational support are important elements in the integration of OTHPs and subsequent delivery of quality health care to people living in rural and remote areas.

Family-based programmes for preventing smoking by children and adolescents

BACKGROUND: There is evidence that children's decisions to smoke are influenced by family and friends. OBJECTIVES: To assess the effectiveness of interventions to help family members to strengthen non-smoking attitudes and promote non-smoking by children and other family members. SEARCH STRATEGY: We searched 14 electronic bibliographic databases, including the Cochrane Tobacco Addiction Group specialized register, MEDLINE, EMBASE, PsycINFO and CINAHL. We also searched unpublished material, and the reference lists of key articles. We performed both free-text Internet searches and targeted searches of appropriate websites, and we hand-searched key journals not available electronically. We also consulted authors and experts in the field. The most recent search was performed in July 2006. SELECTION CRITERIA: Randomized controlled trials (RCTs) of interventions with children (aged 5-12) or adolescents (aged 13-18) and family members to deter the use of tobacco. The primary outcome was the effect of the intervention on the smoking status of children who reported no use of tobacco at baseline. Included trials had to report outcomes measured at least six months from the start of the intervention. DATA COLLECTION AND ANALYSIS: We reviewed all potentially relevant citations and retrieved the full text to determine whether the study was an RCT and matched our inclusion criteria. Two authors independently extracted study data and assessed them for methodological quality. The studies were too limited in number and quality to undertake a formal meta-analysis, and we present a narrative synthesis. MAIN RESULTS: We identified 19 RCTs of family interventions to prevent smoking. We identified five RCTs in Category 1 (minimal risk of bias on all counts); nine in Category 2 (a risk of bias in one or more areas); and five in Category 3 (risks of bias in design and execution such that reliable conclusions cannot be drawn from the study).Considering the fourteen Category 1 and 2 studies together: (1) four of the nine that tested a family intervention against a control group had significant positive effects, but one showed significant negative effects; (2) one of the five RCTs that tested a family intervention against a school intervention had significant positive effects; (3) none of the six that compared the incremental effects of a family plus a school programme to a school programme alone had significant positive effects; (4) the one RCT that tested a family tobacco intervention against a family non-tobacco safety intervention showed no effects; and (5) the one trial that used general risk reduction interventions found the group which received the parent and teen interventions had less smoking than the one that received only the teen intervention (there was no tobacco intervention but tobacco outcomes were measured). For the included trials the amount of implementer training and the fidelity of implementation are related to positive outcomes, but the number of sessions is not. AUTHORS' CONCLUSIONS: Some well-executed RCTs show family interventions may prevent adolescent smoking, but RCTs which were less well executed had mostly neutral or negative results. There is thus a need for well-designed and executed RCTs in this area.

Educational accountability tests, social and legal inclusion approaches to discrimination for students with disability : a national case study from Australia

The UN Convention on the Rights of Persons with Disability (CRPD) promotes equal and full participation by children in education. Equity of educational access for all students, including students with disability, free from discrimination, is the first stated national goal of Australian education (MCEETYA 2008). Australian federal disability discrimination law, the Disability Discrimination Act 1992 (DDA), follows the Convention, with the federal Disability Standards for Education 2005 (DSE) enacting specific requirements for education. This article discusses equity of processes for inclusion of students with disability in Australian educational accountability testing, including international tests in which many countries participate. The conclusion drawn is that equitable inclusion of students with disability in current Australian educational accountability testing in not occurring from a social perspective and is not in principle compliant with law. However, given the reluctance of courts to intervene in education matters and the uncertainty of an outcome in any court consideration, the discussion shows that equitable inclusion in accountability systems is available through policy change rather than expensive, and possibly unsuccessful, legal challenges.

The Chemistry Discipline Network: One Year On

The Chemistry Discipline Network was funded in mid-2011, with the aim of improving communication between chemistry academics in Australia. In our first year of operation, we have grown to over 100 members, established a web presence, and produced substantial mapping reports on chemistry teaching in Australia. We are now working on the definition of standards for a chemistry degree based on the Threshold Learning Outcomes published by the Learning and Teaching Academic Standards Project.

Does the social inclusion discourse add value?

The election of a national Labor Government in 2007 saw ‘social inclusion’ emerge as Australia’s overarching social policy agenda. Being ‘included’ has since been defined as being able to ‘have the resources, opportunities and capabilities needed to learn, work, engage and have a voice’. Various researchers have adopted the social inclusion concept to construct a multi-dimensional framework for measuring disadvantage, beyond poverty alleviation. This research program has enabled various forms of statistical modelling based on some agreement about what it means to be ‘included’ in society. At the same time it is acknowledged that social inclusion remains open and contestable and can be used in the name of both progressive and more punitive programs and policies. This ambiguity raises questions about whether the social inclusion framework, as it is presently defined, has the potential to be a progressive and transformative discourse. In this paper we examine whether the Australian social inclusion agenda has the capacity to address social inequality in a meaningful way, concluding with a discussion about the need to understand social inequality and social disadvantage in relational terms.

Building intercultural competence one “Patch” at a time

This paper describes a program called Patches that was implemented to assist a group of Australian and Malaysian pre-service teachers to enhance their intercultural competence through their involvement in a series of reciprocal learning activities. Each learning experience was considered a “patch” that eventually created a “quilt of intercultural learning.” The purpose of this study was to enhance the intercultural competence of domestic and international students through organized intercultural activities, through a series of reflective writing sessions, and mutual engagement on a common project. The effectiveness of the Patches program was analysed in accordance with Deardorff’s elements of intercultural competence. The qualitative findings indicate that both cohorts of preservice teachers showed elements of intercultural competence through participation in the program, with both groups reporting a deeper appreciation and understanding of how to communicate more effectively in intercultural contexts.