Rule-based approach for identifying assertions in clinical free-text data

A rule-based approach for classifying previously identified medical concepts in the clinical free text into an assertion category is presented. There are six different categories of assertions for the task: Present, Absent, Possible, Conditional, Hypothetical and Not associated with the patient. The assertion classification algorithms were largely based on extending the popular NegEx and Context algorithms. In addition, a health based clinical terminology called SNOMED CT and other publicly available dictionaries were used to classify assertions, which did not fit the NegEx/Context model. The data for this task includes discharge summaries from Partners HealthCare and from Beth Israel Deaconess Medical Centre, as well as discharge summaries and progress notes from University of Pittsburgh Medical Centre. The set consists of 349 discharge reports, each with pairs of ground truth concept and assertion files for system development, and 477 reports for evaluation. The system’s performance on the evaluation data set was 0.83, 0.83 and 0.83 for recall, precision and F1-measure, respectively. Although the rule-based system shows promise, further improvements can be made by incorporating machine learning approaches.

Should we still lecture? Reconsidering pedagogical approaches to promote student engagement, challenging the traditional lecture

The dynamic interplay between existing learning frameworks: people, pedagogy, learning spaces and technology is challenging the traditional lecture. A paradigm is emerging from the correlation of change amongst these elements, offering new possibilities for improving the quality of the learning experience. For many universities, the design of physical learning spaces has been the focal point for blending technology and flexible learning spaces to promote learning and teaching. As the pace of technological change intensifies, affording new opportunities for engaging learners, pedagogical practice in higher education is not comparatively evolving. The resulting disparity is an opportunity for the reconsideration of pedagogical practice for increased student engagement in physical learning spaces as an opportunity for active learning. This interplay between students, staff and technology is challenging the value for students in attending physical learning spaces such as the traditional lecture. Why should students attend for classes devoted to content delivery when streaming and web technologies afford more flexible learning opportunities? Should we still lecture? Reconsideration of pedagogy is driving learning design at Queensland University of Technology, seeking new approaches affording increased student engagement via active learning experiences within large lectures. This paper provides an overview and an evaluation of one of these initiatives, Open Web Lecture (OWL), an experimental web based student response application developed by Queensland University of Technology. OWL seamlessly integrates a virtual learning environment within physical learning spaces, fostering active learning opportunities. This paper will evaluate the pilot of this initiative through consideration of effectiveness in increasing student engagement through the affordance of web enabled active learning opportunities in physical learning spaces.

Should we still lecture? Reconsidering pedagogical approaches to promote student engagement, challenging the traditional lecture

The dynamic interplay between existing learning frameworks: people, pedagogy, learning spaces and technology is challenging the traditional lecture. A paradigm is emerging from the correlation of change amongst these elements, offering new possibilities for improving the quality of the learning experience. For many universities, the design of physical learning spaces has been the focal point for blending technology and flexible learning spaces to promote learning and teaching. As the pace of technological change intensifies, affording new opportunities for engaging learners, pedagogical practice in higher education is not comparatively evolving. The resulting disparity is an opportunity for the reconsideration of pedagogical practice for increased student engagement in physical learning spaces as an opportunity for active learning. This interplay between students, staff and technology is challenging the value for students in attending physical learning spaces such as the traditional lecture. Why should students attend for classes devoted to content delivery when streaming and web technologies afford more flexible learning opportunities? Should we still lecture? Reconsideration of pedagogy is driving learning design at Queensland University of Technology, seeking new approaches affording increased student engagement via active learning experiences within large lectures. This paper provides an overview and an evaluation of one of these initiatives, Open Web Lecture (OWL), an experimental web based student response application developed by Queensland University of Technology. OWL seamlessly integrates a virtual learning environment within physical learning spaces, fostering active learning opportunities. This paper will evaluate the pilot of this initiative through consideration of effectiveness in increasing student engagement through the affordance of web enabled active learning opportunities in physical learning spaces.

Conceptualising tax expenditures : commentary

The tax expenditures concept has been part of the Australian tax review system since 1973. In view of the fact that tax expenditures are considered part of the tax-transfer system, and that paragraph 9 of the terms of reference for the Review Panel requires a consideration of all relevant tax expenditures, we can be confident that they will be considered once again in the final report of Australia’s Future Tax System Review Panel. However, an examination of previous Government and Parliamentary reviews suggests that few of the resulting recommendations are adopted. Previous recommendations have resulted in the acknowledgement of and concern over tax expenditures, but have led to only one significant advancement: the publication of an annual tax expenditures statement. It is apparent that Brooks in his paper aims to ensure, and makes a compelling case for, the significance and central role tax expenditures should play in the Review Panel deliberations. In doing so, Brooks explores the concept itself as well as the conceptual implications impacting on the more pragmatic aspects of tax expenditure analysis. At the outset, Brooks explains why tax expenditures cannot be evaluated using traditional criteria of equity, neutrality, and simplicity, but rather can only be understood and evaluated using budgetary criteria.

Post-graduate health promotion students assess their information literacy

Purpose - The purpose of this paper is to examine post-graduate health promotion students’ self-perceptions of information literacy skills prior to, and after completing PILOT, an online information literacy tutorial. Design/methodology/approach – Post graduate students at Queensland University of Technology enrolled in PUP038 New Developments in Health Promotion completed a pre- and post- self-assessment questionnaire. From 2008-2011 students were required to rate their academic writing and research skills before and after completing the PILOT online information literacy tutorial. Quantitative trends and qualitative themes were analysed to establish students’ self-assessment and the effectiveness of the PILOT tutorial. Findings – The results from four years of post-graduate students’ self-assessment questionnaires provide evidence of perceived improvements in information literacy skills after completing PILOT. Some students continued to have trouble with locating quality information and analysis as well as issues surrounding referencing and plagiarism. Feedback was generally positive and students’ responses indicated they found the tutorial highly beneficial in improving their research skills. Originality/value - This paper is original because it describes post-graduate health promotion students’ self-assessment of information literacy skills over a period of four years. The literature is limited in the health promotion domain and self-assessment of post-graduate students’ information literacy skills. Keywords – Self-assessment, Post-graduate, Information literacy, Library instruction, Higher education, Health promotion, Evidence-based practice Paper Type - Research paper

Social network media and political activism: a growing challenge for law enforcement

The use of the internet for political purposes is not new; however, the introduction of social media tools has opened new avenues for political activists. In an era where social media has been credited as playing a critical role in the success of revolutions (Earl & Kimport, 2011; Papic & Noonan, 2011; Wooley, Limperos & 10 Beth, 2010), governments, law enforcement and intelligence agencies need to develop a deeper understanding of the broader capabilities of this emerging social and political environment. This can be achieved by increasing their online presence and through the application of proactive social media strategies to identify and manage potential threats. Analysis of current literature shows a gap 15 in the research regarding the connection between the theoretical understanding and practical implications of social media when exploited by political activists,and the efficacy of existing strategies designed to manage this growing challenge. This paper explores these issues by looking specifically at the use of three popular social media tools: Facebook; Twitter; and YouTube. Through the examination of 20 recent political protests in Iran, the UK and Egypt from 2009�2011, these case studies and research in the use of the three social media tools by political groups, the authors discuss inherent weaknesses in online political movements and discuss strategies for law enforcement and intelligence agencies to monitor these activities.

Evidence for time dependency of molecular rate estimates

Long-term changes in the genetic composition of a population occur by the fixation of new mutations, a process known as substitution. The rate at which mutations arise in a population and the rate at which they are fixed are expected to be equal under neutral conditions (Kimura, 1968). Between the appearance of a new mutation and its eventual fate of fixation or loss, there will be a period in which it exists as a transient polymorphism in the population (Kimura and Ohta, 1971). If the majority of mutations are deleterious (and nonlethal), the fixation probabilities of these transient polymorphisms are reduced and the mutation rate will exceed the substitution rate (Kimura, 1983). Consequently, different apparent rates may be observed on different time scales of the molecular evolutionary process (Penny, 2005; Penny and Holmes, 2001). The substitution rate of the mitochondrial protein-coding genes of birds and mammals has been traditionally recognized to be about 0.01 substitutions/site/million years (Myr) (Brown et al., 1979; Ho, 2007; Irwin et al., 1991; Shields and Wilson, 1987), with the noncoding D-loop evolving several times more quickly (e.g., Pesole et al., 1992; Quinn, 1992). Over the past decade, there has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al., 2003; Lambert et al., 2002; Mao et al., 2006; Mumm et al., 1997; Parsons et al., 1997; Santos et al., 2005). The immediate reaction to the first of these findings was that the polymorphisms generated by the elevated mutation rate are short-lived, perhaps extending back only a few hundred years (Gibbons, 1998; Macaulay et al., 1997). That is, purifying selection was thought to remove these polymorphisms very rapidly.

Prevalence and prognostic significance of secondary lymphedema following breast cancer

Background The adverse consequences of lymphedema following breast cancer in relation to physical function and quality of life are clear; however, its potential relationship with survival has not been investigated. Our purpose was to determine the prevalence of lymphedema and associated upper-body symptoms at 6 years following breast cancer and to examine the prognostic significance of lymphedema with respect to overall 6-year survival (OS). Methods and Results A population-based sample of Australian women (n=287) diagnosed with invasive, unilateral breast cancer was followed for a median of 6.6 years and prospectively assessed for lymphedema (using bioimpedance spectroscopy [BIS], sum of arm circumferences [SOAC], and self-reported arm swelling), a range of upper-body symptoms, and vital status. OS was measured from date of diagnosis to date of death or last follow-up. Kaplan-Meier methods were used to calculate OS and Cox proportional hazards models quantified the risk associated with lymphedema. Approximately 45% of women had reported at least one moderate to extreme symptom at 6.6 years postdiagnosis, while 34% had shown clinical evidence of lymphedema, and 48% reported arm swelling at least once since baseline assessment. A total of 27 (9.4%) women died during the follow-up period, and lymphedema, diagnosed by BIS or SOAC between 6–18 months postdiagnosis, predicted mortality (BIS: HR=2.5; 95% CI: 0.9, 6.8, p=0.08; SOAC: 3.0; 95% CI: 1.1, 8.7, p=0.04). There was no association (HR=1.2; 95% CI: 0.5, 2.6, p=0.68) between self-reported arm swelling and OS. Conclusions These findings suggest that lymphedema may influence survival following breast cancer treatment and warrant further investigation in other cancer cohorts and explication of a potential underlying biology.

Absence of intersystem crossing in 1,4-didehydrobenzene

The rate of singlet-to-triplet intersystem crossing in 1,4-didehydrobenzene (the biradical produced as a reactive intermediate in the thermal cycloaromatization of enediynes), cannot be increased by the application of an external magnetic field. The rate of product formation and the distribution of stable products of 2,3-di-n-propyl-1,4-didehydrobenzene thermolysis is unchanged at magnetic flux densities in the range 0–2000 G and at 66 000 G. Similarly, the rate of thermolysis of an unsymmetrical enediyne is insensitive to magnetic field flux in the same range. This finding precludes the modulation of enediyne reaction rates in pharmaceutical and synthetic pursuits.

Engaging with the Bailey Review : blogging, academia and authenticity

This article reproduces and discusses a series of blog posts posted by academics in anticipation of the report on commercialisation, sexualisation and childhood, 'Letting Children Be Children' by Reg Bailey for the UK Department of Education in June 2011. The article discusses the difficulty of 'translating' scholarly work for the public in a context where 'impact' is increasingly important and the challenges that academics face in finding new ways of speaking about sex in public.

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae) : robust support for interfamilial relationships and molecular synapomorphies define major clades

Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites + Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus + termites), and a further series of compensatory base changes in this stem loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae + Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae.