Showing papers by "University of Melbourne published in 2009"

Multiple imputation for missing data in epidemiological and clinical research: potential and pitfalls.

Abstract: Most studies have some missing data. Jonathan Sterne and colleagues describe the appropriate use and reporting of the multiple imputation approach to dealing with them

Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

Abstract: Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

Natural Language Processing with Python

Abstract: This book offers a highly accessible introduction to natural language processing, the field that supports a variety of language technologies, from predictive text and email filtering to automatic summarization and translation. With it, you'll learn how to write Python programs that work with large collections of unstructured text. You'll access richly annotated datasets using a comprehensive range of linguistic data structures, and you'll understand the main algorithms for analyzing the content and structure of written communication. Packed with examples and exercises, Natural Language Processing with Python will help you: Extract information from unstructured text, either to guess the topic or identify "named entities" Analyze linguistic structure in text, including parsing and semantic analysis Access popular linguistic databases, including WordNet and treebanks Integrate techniques drawn from fields as diverse as linguistics and artificial intelligence This book will help you gain practical skills in natural language processing using the Python programming language and the Natural Language Toolkit (NLTK) open source library. If you're interested in developing web applications, analyzing multilingual news sources, or documenting endangered languages -- or if you're simply curious to have a programmer's perspective on how human language works -- you'll find Natural Language Processing with Python both fascinating and immensely useful.

Synthesis of Light-Emitting Conjugated Polymers for Applications in Electroluminescent Devices

Abstract: A review was presented to demonstrate a historical description of the synthesis of light-emitting conjugated polymers for applications in electroluminescent devices. Electroluminescence (EL) was first reported in poly(para-phenylene vinylene) (PPV) in 1990 and researchers continued to make significant efforts to develop conjugated materials as the active units in light-emitting devices (LED) to be used in display applications. Conjugated oligomers were used as luminescent materials and as models for conjugated polymers in the review. Oligomers were used to demonstrate a structure and property relationship to determine a key polymer property or to demonstrate a technique that was to be applied to polymers. The review focused on demonstrating the way polymer structures were made and the way their properties were controlled by intelligent and rational and synthetic design.

Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data

Abstract: Most methods for modeling species distributions from occurrence records require additional data representing the range of environmental conditions in the modeled region. These data, called background or pseudo-absence data, are usually drawn at random from the entire region, whereas occurrence collection is often spatially biased toward easily accessed areas. Since the spatial bias generally results in environmental bias, the difference between occurrence collection and background sampling may lead to inaccurate models. To correct the estimation, we propose choosing background data with the same bias as occurrence data. We investigate theoretical and practical implications of this approach. Accurate information about spatial bias is usually lacking, so explicit biased sampling of background sites may not be possible. However, it is likely that an entire target group of species observed by similar methods will share similar bias. We therefore explore the use of all occurrences within a target group as biased background data. We compare model performance using target-group background and randomly sampled background on a comprehensive collection of data for 226 species from diverse regions of the world. We find that target-group background improves average performance for all the modeling methods we consider, with the choice of background data having as large an effect on predictive performance as the choice of modeling method. The performance improvement due to target-group background is greatest when there is strong bias in the target-group presence records. Our approach applies to regression-based modeling methods that have been adapted for use with occurrence data, such as generalized linear or additive models and boosted regression trees, and to Maxent, a probability density estimation method. We argue that increased awareness of the implications of spatial bias in surveys, and possible modeling remedies, will substantially improve predictions of species distributions.

Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study.

Abstract: Summary Background Drug treatments for patients with high-risk myelodysplastic syndromes provide no survival advantage. In this trial, we aimed to assess the effect of azacitidine on overall survival compared with the three commonest conventional care regimens. Methods In a phase III, international, multicentre, controlled, parallel-group, open-label trial, patients with higher-risk myelodysplastic syndromes were randomly assigned one-to-one to receive azacitidine (75 mg/m 2 per day for 7 days every 28 days) or conventional care (best supportive care, low-dose cytarabine, or intensive chemotherapy as selected by investigators before randomisation). Patients were stratified by French–American–British and international prognostic scoring system classifications; randomisation was done with a block size of four. The primary endpoint was overall survival. Efficacy analyses were by intention to treat for all patients assigned to receive treatment. This study is registered with ClinicalTrials.gov, number NCT00071799. Findings Between Feb 13, 2004, and Aug 7, 2006, 358 patients were randomly assigned to receive azacitidine (n=179) or conventional care regimens (n=179). Four patients in the azacitidine and 14 in the conventional care groups received no study drugs but were included in the intention-to-treat efficacy analysis. After a median follow-up of 21·1 months (IQR 15·1–26·9), median overall survival was 24·5 months (9·9–not reached) for the azacitidine group versus 15·0 months (5·6–24·1) for the conventional care group (hazard ratio 0·58; 95% CI 0·43–0·77; stratified log-rank p=0·0001). At last follow-up, 82 patients in the azacitidine group had died compared with 113 in the conventional care group. At 2 years, on the basis of Kaplan-Meier estimates, 50·8% (95% CI 42·1–58·8) of patients in the azacitidine group were alive compared with 26·2% (18·7–34·3) in the conventional care group (p Interpretation Treatment with azacitidine increases overall survival in patients with higher-risk myelodysplastic syndromes relative to conventional care. Funding Celgene Corporation.

Mechanistic niche modelling: combining physiological and spatial data to predict species' ranges.

Abstract: Species distribution models (SDMs) use spatial environmental data to make inferences on species' range limits and habitat suitability. Conceptually, these models aim to determine and map components of a species' ecological niche through space and time, and they have become important tools in pure and applied ecology and evolutionary biology. Most approaches are correlative in that they statistically link spatial data to species distribution records. An alternative strategy is to explicitly incorporate the mechanistic links between the functional traits of organisms and their environments into SDMs. Here, we review how the principles of biophysical ecology can be used to link spatial data to the physiological responses and constraints of organisms. This provides a mechanistic view of the fundamental niche which can then be mapped to the landscape to infer range constraints. We show how physiologically based SDMs can be developed for different organisms in different environmental contexts. Mechanistic SDMs have different strengths and weaknesses to correlative approaches, and there are many exciting and unexplored prospects for integrating the two approaches. As physiological knowledge becomes better integrated into SDMs, we will make more robust predictions of range shifts in novel or non-equilibrium contexts such as invasions, translocations, climate change and evolutionary shifts.

Globalizing Education Policy

Abstract: Rizvi and Lingard's account of the global politics of education is thoughtful, complex and compelling It is the first really comprehensive discussion and analysis of global trends in education policy, their effects - structural and individual - and resistance to them In the enormous body of writing on globalisation this book stands out and will become a basic text in education policy courses around the world - Stephen J Ball, Karl Mannheim Professor of Sociology of Education, Institute of Education, University of London, UK, In what ways have the processes of globalization reshaped the educational policy terrain?, How might we analyse education policies located within this new terrain, which is at once local, national, regional and global? In Globalizing Education Policy, the authors explore the key global drivers of policy change in education, and suggest that these do not operate in the same way in all nation-states They examine the transformative effects of globalization on the discursive terrain within which educational policies are developed and enacted, arguing that this terrain is increasingly informed by a range of neo-liberal precepts which have fundamentally changed the ways in which we think about educational governance They also suggest that whilst in some countries these precepts are resisted, to some extent, they have nonetheless become hegemonic, and provide an overview of some critical issues in educational policy to which this hegemonic view of globalization has given rise, including: devolution and decentralization new forms of governance the balance between public and private funding of education access and equity and the education of girls curriculum particularly with respect to the teaching of English language and technology pedagogies and high stakes testing and the global trade in education These issues are explored within the context of major shifts in global processes and ideological discourses currently being experienced, and negotiated by all countries The book also provides an approach to education policy analysis in an age of globalization and will be of interest to those studying globalization and education policy across the social sciences

Consensus statement on concussion in sport--the 4th International Conference on Concussion in Sport held in Zurich, November 2012.

Abstract: PreambleThis paper is a revision and update of the recommendations developed following the 1st (Vienna) and 2nd (Prague) International Symposia on Concussion in Sport.1,2 The Zurich Consensus statement is designed to build on the principles outlined in the original Vienna and Prague documents and to

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

Abstract: Basal-like breast cancers arising in women carrying mutations in the BRCA1 gene, encoding the tumor suppressor protein BRCA1, are thought to develop from the mammary stem cell. To explore early cellular changes that occur in BRCA1 mutation carriers, we have prospectively isolated distinct epithelial subpopulations from normal mammary tissue and preneoplastic specimens from individuals heterozygous for a BRCA1 mutation. We describe three epithelial subsets including basal stem/progenitor, luminal progenitor and mature luminal cells. Unexpectedly, we found that breast tissue from BRCA1 mutation carriers harbors an expanded luminal progenitor population that shows factor-independent growth in vitro. Moreover, gene expression profiling revealed that breast tissue heterozygous for a BRCA1 mutation and basal breast tumors were more similar to normal luminal progenitor cells than any other subset, including the stem cell-enriched population. The c-KIT tyrosine kinase receptor (encoded by KIT) emerged as a key marker of luminal progenitor cells and was more highly expressed in BRCA1-associated preneoplastic tissue and tumors. Our findings suggest that an aberrant luminal progenitor population is a target for transformation in BRCA1-associated basal tumors .

A Randomized Trial of Vertebroplasty for Painful Osteoporotic Vertebral Fractures

Abstract: Background Vertebroplasty has become a common treatment for painful osteoporotic vertebral fractures, but there is limited evidence to support its use. Methods We performed a multicenter, randomized, double-blind, placebo-controlled trial in which participants with one or two painful osteoporotic vertebral fractures that were of less than 12 months' duration and unhealed, as confirmed by magnetic resonance imaging, were randomly assigned to undergo vertebroplasty or a sham procedure. Participants were stratified according to treatment center, sex, and duration of symptoms (<6 weeks or ≥6 weeks). Outcomes were assessed at 1 week and at 1, 3, and 6 months. The primary outcome was overall pain (on a scale of 0 to 10, with 10 being the maximum imaginable pain) at 3 months. Results A total of 78 participants were enrolled, and 71 (35 of 38 in the vertebroplasty group and 36 of 40 in the placebo group) completed the 6-month follow-up (91%). Vertebroplasty did not result in a significant advantage in any measure...

Update of the Stroke Therapy Academic Industry Roundtable Preclinical Recommendations

Abstract: The initial Stroke Therapy Academic Industry Roundtable (STAIR) recommendations published in 1999 were intended to improve the quality of preclinical studies of purported acute stroke therapies Although recognized as reasonable, they have not been closely followed nor rigorously validated Substantial advances have occurred regarding the appropriate quality and breadth of preclinical testing for candidate acute stroke therapies for better clinical translation The updated STAIR preclinical recommendations reinforce the previous suggestions that reproducibly defining dose response and time windows with both histological and functional outcomes in multiple animal species with appropriate physiological monitoring is appropriate The updated STAIR recommendations include: the fundamentals of good scientific inquiry should be followed by eliminating randomization and assessment bias, a priori defining inclusion/exclusion criteria, performing appropriate power and sample size calculations, and disclosing potential conflicts of interest After initial evaluations in young, healthy male animals, further studies should be performed in females, aged animals, and animals with comorbid conditions such as hypertension, diabetes, and hypercholesterolemia Another consideration is the use of clinically relevant biomarkers in animal studies Although the recommendations cannot be validated until effective therapies based on them emerge from clinical trials, it is hoped that adherence to them might enhance the chances for success

Correcting for Cross-Sectional and Time-Series Dependence in Accounting Research

Abstract: We review and evaluate the methods commonly used in the accounting literature to correct for cross-sectional and time-series dependence. While much of the accounting literature studies settings where variables are cross-sectionally and serially correlated, we find that the extant methods are not robust to both forms of dependence. Contrary to claims in the literature, we find that the Z2-statistic and Newey-West corrected Fama-MacBeth do not correct for both cross-sectional and time-series dependence. We show that extant methods produce misspecified test statistics in common accounting research settings, and that correcting for both forms of dependence substantially alters inferences reported in the literature. Specifically, several findings in the cost of equity capital literature, the cost of debt literature, and the conservatism literature appear not to be robust to the use of well-specified test statistics.

The Invention of Tradition: Property Law as a Knowledge Space for the Appropriation of the South

Abstract: The article explores the issues of how law and space intersect in the area known as 'The South'. It examines the intersection between 'Northern' traditions of law and space and indigenous Australians experience of this 'history'. These intersections are germane to the question of how living in the South should now be understood in terms of the shape and pattern of legal relations. Ultimately, the question of indigenous and local traditions that form patterns of the lived experience of local peoples is mediated through law, but is not entirely subsumed by Northern law. Spatial and temporal existence is culturally embedded, and Aboriginal experience of time, for example, does not adhere to Northern parameters. Accordingly, the interleaving of law, tradition and 'existence' is played out in various ways in the colonial and postcolonial history of the South. Thus the interaction between the imposed legal concept and process, and that lived experience of the peoples of the South (whether we designate it as 'tradition' or not) is what is at issue in framing responses to the question of what it means to be positioned in the South.

Modeling and Simulation of Scalable Cloud Computing Environments and the CloudSim Toolkit: Challenges and Opportunities

Abstract: Cloud computing aims to power the next generation data centers and enables application service providers to lease data center capabilities for deploying applications depending on user QoS (Quality of Service) requirements. Cloud applications have different composition, configuration, and deployment requirements. Quantifying the performance of resource allocation policies and application scheduling algorithms at finer details in Cloud computing environments for different application and service models under varying load, energy performance (power consumption, heat dissipation), and system size is a challenging problem to tackle. To simplify this process, in this paper we propose CloudSim: an extensible simulation toolkit that enables modelling and simulation of Cloud computing environments. The CloudSim toolkit supports modelling and creation of one or more virtual machines (VMs) on a simulated node of a Data Center, jobs, and their mapping to suitable VMs. It also allows simulation of multiple Data Centers to enable a study on federation and associated policies for migration of VMs for reliability and automatic scaling of applications.

Memory T cells in nonlymphoid tissue that provide enhanced local immunity during infection with herpes simplex virus

Abstract: Effective immunity is dependent on long-surviving memory T cells. Various memory subsets make distinct contributions to immune protection, especially in peripheral infection. It has been suggested that T cells in nonlymphoid tissues are important during local infection, although their relationship with populations in the circulation remains poorly defined. Here we describe a unique memory T cell subset present after acute infection with herpes simplex virus that remained resident in the skin and in latently infected sensory ganglia. These T cells were in disequilibrium with the circulating lymphocyte pool and controlled new infection with this virus. Thus, these cells represent an example of tissue-resident memory T cells that can provide protective immunity at points of pathogen entry.

Genomic selection: prediction of accuracy and maximisation of long term response

Abstract: Genomic selection refers to the use of dense markers covering the whole genome to estimate the breeding value of selection candidates for a quantitative trait. This paper considers prediction of breeding value based on a linear combination of the markers. In this case the best estimate of each marker’s effect is the expectation of the effect conditional on the data. To calculate this requires a prior distribution of marker effects. If the marker effects are normally distributed with constant variance, BLUP can be used to calculate the estimated effects of the markers and hence the estimated breeding value (EBV). In this case the model is equivalent to a conventional animal model in which the relationship matrix among the animals is estimated from the markers instead of the pedigree. The accuracy of the EBV can approach 1.0 but a very large amount of data is required. An alternative model was investigated in which only some markers have non-zero effects and these effects follow a reflected exponential distribution. In this case the expected effect of a marker is a non-linear function of the data such that apparently small effects are regressed back almost to zero and consequently these markers can be deleted from the model. The accuracy in this case is considerably higher than when marker effects are normally distributed. If genomic selection is practiced for several generations the response declines in a manner that can be predicted from the marker allele frequencies. Genomic selection is likely to lead to a more rapid decline in the selection response than phenotypic selection unless new markers are continually added to the prediction of breeding value. A method to find the optimum index to maximise long term selection response is derived. This index varies the weight given to a marker according to its frequency such that markers where the favourable allele has low frequency receive more weight in the index.

Evidence-based guidelines for treating bipolar disorder: Revised third edition recommendations from the British Association for Psychopharmacology

Abstract: The British Association for Psychopharmacology guidelines specify the scope and targets of treatment for bipolar disorder. The third version is based explicitly on the available evidence and presented, like previous Clinical Practice Guidelines, as recommendations to aid clinical decision making for practitioners: it may also serve as a source of information for patients and carers, and assist audit. The recommendations are presented together with a more detailed review of the corresponding evidence. A consensus meeting, involving experts in bipolar disorder and its treatment, reviewed key areas and considered the strength of evidence and clinical implications. The guidelines were drawn up after extensive feedback from these participants. The best evidence from randomized controlled trials and, where available, observational studies employing quasi-experimental designs was used to evaluate treatment options. The strength of recommendations has been described using the GRADE approach. The guidelines cover the diagnosis of bipolar disorder, clinical management, and strategies for the use of medicines in short-term treatment of episodes, relapse prevention and stopping treatment. The use of medication is integrated with a coherent approach to psychoeducation and behaviour change.

Psychiatric Comorbidities and Schizophrenia

Abstract: Psychiatric comorbidities are common among patients with schizophrenia. Substance abuse comorbidity predominates. Anxiety and depressive symptoms are also very common throughout the course of illness, with an estimated prevalence of 15% for panic disorder, 29% for posttraumatic stress disorder, and 23% for obsessive-compulsive disorder. It is estimated that comorbid depression occurs in 50% of patients, and perhaps (conservatively) 47% of patients also have a lifetime diagnosis of comorbid substance abuse. This article chronicles these associations, examining whether these comorbidities are "more than chance" and might represent (distinct) phenotypes of schizophrenia. Among the anxiety disorders, the evidence at present is most abundant for an association with obsessive-compulsive disorder. Additional studies in newly diagnosed antipsychotic-naive patients and their first-degree relatives and searches for genetic and environmental risk factors are needed to replicate preliminary findings and further investigate these associations.

Gold nanoparticles: past, present, and future.

Abstract: This perspective reviews recent developments in the synthesis, electrochemistry, and optical properties of gold nanoparticles, with emphasis on papers initiating the developments and with an eye to their consequences. Key aspects of Au nanoparticle synthesis have included the two-phase synthesis of thiolated nanoparticles, the sequestration and reduction of Au salts within dendrimers, the controlled growth of larger particles of well-defined shapes via the seeded approach, and the assembling of a variety of nanoparticle networks and nanostructures. The electrochemistry of thiolated Au nanoparticles is systemized as regions of bulk-continuum voltammetry, voltammetry reflective of quantized double-layer charging, and molecule-like voltammetry reflective of molecular energy gaps. These features are principally determined by the nanoparticle core. Interesting multielectron Au nanoparticle voltammetry is observed when the thiolate ligand shell has been decorated with redox groupings. Another development is that Au nanoparticles were discovered to exhibit unanticipated properties as heterogeneous catalysts, starting with the low-temperature oxidation of CO. Substantial progress has also been made in understanding the surface plasmon spectroscopy of Au nanoparticles and nanorods. The need to investigate the optical properties of metal particles of a single, well-defined shape and size has motivated the development of a number of new techniques, leading to the study of electron transfer and redox catalysis on single nanoparticles.

Mapping genes for complex traits in domestic animals and their use in breeding programmes

Abstract: Genome-wide panels of SNPs have recently been used in domestic animal species to map and identify genes for many traits and to select genetically desirable livestock. This has led to the discovery of the causal genes and mutations for several single-gene traits but not for complex traits. However, the genetic merit of animals can still be estimated by genomic selection, which uses genome-wide SNP panels as markers and statistical methods that capture the effects of large numbers of SNPs simultaneously. This approach is expected to double the rate of genetic improvement per year in many livestock systems.

The potential for behavioral thermoregulation to buffer “cold-blooded” animals against climate warming

Abstract: Increasing concern about the impacts of global warming on biodiversity has stimulated extensive discussion, but methods to translate broad-scale shifts in climate into direct impacts on living animals remain simplistic. A key missing element from models of climatic change impacts on animals is the buffering influence of behavioral thermoregulation. Here, we show how behavioral and mass/energy balance models can be combined with spatial data on climate, topography, and vegetation to predict impacts of increased air temperature on thermoregulating ectotherms such as reptiles and insects (a large portion of global biodiversity). We show that for most "cold-blooded" terrestrial animals, the primary thermal challenge is not to attain high body temperatures (although this is important in temperate environments) but to stay cool (particularly in tropical and desert areas, where ectotherm biodiversity is greatest). The impact of climate warming on thermoregulating ectotherms will depend critically on how changes in vegetation cover alter the availability of shade as well as the animals' capacities to alter their seasonal timing of activity and reproduction. Warmer environments also may increase maintenance energy costs while simultaneously constraining activity time, putting pressure on mass and energy budgets. Energy- and mass-balance models provide a general method to integrate the complexity of these direct interactions between organisms and climate into spatial predictions of the impact of climate change on biodiversity. This methodology allows quantitative organism- and habitat-specific assessments of climate change impacts.

Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework

Abstract: Aim Invasion ecology includes many hypotheses Empirical evidence suggests that most of these can explain the success of some invaders to some degree in some circumstances If they all are correct, what does this tell us about invasion? We illustrate the major themes in invasion ecology, and provide an overarching framework that helps organize research and foster links among subfields of invasion ecology and ecology more generally Location Global Methods We review and synthesize 29 leading hypotheses in plant invasion ecology Structured around propagule pressure (P), abiotic characteristics (A) and biotic characteristics (B), with the additional influence of humans (H) on P, A and B (hereon PAB), we show how these hypotheses fit into one paradigm P is based on the size and frequency of introductions, A incorporates ecosystem invasibility based on physical conditions, and B includes the characteristics of invading species (invasiveness), the recipient community and their interactions Having justified the PAB framework, we propose a way in which invasion research could progress Results By highlighting the common ground among hypotheses, we show that invasion ecology is encumbered by theoretical redundancy that can be removed through integration Using both holistic and incremental approaches, we show how the PAB framework can guide research and quantify the relative importance of different invasion mechanisms Main conclusions If the prime aim is to identify the main cause of invasion success, we contend that a top-down approach that focuses on PAB maximizes research efficiency This approach identifies the most influential factors first, and subsequently narrows the number of potential causal mechanisms By viewing invasion as a multifaceted process that can be partitioned into major drivers and broken down into a series of sequential steps, invasion theory can be rigorously tested, understanding improved and effective weed management techniques identified