Model and prototype for querying multiple linked scientific datasets

Scientists need to transfer semantically similar queries across multiple heterogeneous linked datasets. These queries may require data from different locations and the results are not simple to combine due to differences between datasets. A query model was developed to make it simple to distribute queries across different datasets using RDF as the result format. The query model, based on the concept of publicly recognised namespaces for parts of each scientific dataset, was implemented with a configuration that includes a large number of current biological and chemical datasets. The configuration is flexible, providing the ability to transparently use both private and public datasets in any query. A prototype implementation of the model was used to resolve queries for the Bio2RDF website, including both Bio2RDF datasets and other datasets that do not follow the Bio2RDF URI conventions.

Super-orbital re-entry in Australia : laboratory measurement, simulation and flight observation

There are large uncertainties in the aerothermodynamic modelling of super-orbital re-entry which impact the design of spacecraft thermal protection systems (TPS). Aspects of the thermal environment of super-orbital re-entry flows can be simulated in the laboratory using arc- and plasma jet facilities and these devices are regularly used for TPS certification work [5]. Another laboratory device which is capable of simulating certain critical features of both the aero and thermal environment of super-orbital re-entry is the expansion tube, and three such facilities have been operating at the University of Queensland in recent years[10]. Despite some success, wind tunnel tests do not achieve full simulation, however, a virtually complete physical simulation of particular re-entry conditions can be obtained from dedicated flight testing, and the Apollo era FIRE II flight experiment [2] is the premier example which still forms an important benchmark for modern simulations. Dedicated super-orbital flight testing is generally considered too expensive today, and there is a reluctance to incorporate substantial instrumentation for aerothermal diagnostics into existing missions since it may compromise primary mission objectives. An alternative approach to on-board flight measurements, with demonstrated success particularly in the ‘Stardust’ sample return mission, is remote observation of spectral emissions from the capsule and shock layer [8]. JAXA’s ‘Hayabusa’ sample return capsule provides a recent super-orbital reentry example through which we illustrate contributions in three areas: (1) physical simulation of super-orbital re-entry conditions in the laboratory; (2) computational simulation of such flows; and (3) remote acquisition of optical emissions from a super-orbital re entry event.

GPFlow: an intuitive environment for web-based scientific workflow

Increasingly scientists are using collections of software tools in their research. These tools are typically used in concert, often necessitating laborious and error-prone manual data reformatting and transfer. We present an intuitive workflow environment to support scientists with their research. The workflow, GPFlow, wraps legacy tools, presenting a high level, interactive web-based front end to scientists. The workflow backend is realized by a commercial grade workflow engine (Windows Workflow Foundation). The workflow model is inspired by spreadsheets and is novel in its support for an intuitive method of interaction enabling experimentation as required by many scientists, e.g. bioinformaticians. We apply GPFlow to two bioinformatics experiments and demonstrate its flexibility and simplicity.

Refining animal models in fracture research: Seeking consensus in optimising both animal welfare and scientific validity for appropriate biomedical use

Background In an attempt to establish some consensus on the proper use and design of experimental animal models in musculoskeletal research, AOVET (the veterinary specialty group of the AO Foundation) in concert with the AO Research Institute (ARI), and the European Academy for the Study of Scientific and Technological Advance, convened a group of musculoskeletal researchers, veterinarians, legal experts, and ethicists to discuss, in a frank and open forum, the use of animals in musculoskeletal research. Methods The group narrowed the field to fracture research. The consensus opinion resulting from this workshop can be summarized as follows: Results & Conclusion Anaesthesia and pain management protocols for research animals should follow standard protocols applied in clinical work for the species involved. This will improve morbidity and mortality outcomes. A database should be established to facilitate selection of anaesthesia and pain management protocols for specific experimental surgical procedures and adopted as an International Standard (IS) according to animal species selected. A list of 10 golden rules and requirements for conduction of animal experiments in musculoskeletal research was drawn up comprising 1) Intelligent study designs to receive appropriate answers; 2) Minimal complication rates (5 to max. 10%); 3) Defined end-points for both welfare and scientific outputs analogous to quality assessment (QA) audit of protocols in GLP studies; 4) Sufficient details for materials and methods applied; 5) Potentially confounding variables (genetic background, seasonal, hormonal, size, histological, and biomechanical differences); 6) Post-operative management with emphasis on analgesia and follow-up examinations; 7) Study protocols to satisfy criteria established for a "justified animal study"; 8) Surgical expertise to conduct surgery on animals; 9) Pilot studies as a critical part of model validation and powering of the definitive study design; 10) Criteria for funding agencies to include requirements related to animal experiments as part of the overall scientific proposal review protocols. Such agencies are also encouraged to seriously consider and adopt the recommendations described here when awarding funds for specific projects. Specific new requirements and mandates related both to improving the welfare and scientific rigour of animal-based research models are urgently needed as part of international harmonization of standards.

The threat to scientific integrity in environmental and occupational medicine

Over the last century, environmental and occupational medicine has played a significant role in the protection and improvement of public health. However, scientific integrity in this field has been increasingly threatened by pressure from some industries and governments. For example, it has been reported that the tobacco industry manipulated eminent scientists to legitimise their industrial positions, irresponsibly distorted risk and deliberately subverted scientific processes, and influenced many organisations in receipt of tobacco funding. Many environmental whistleblowers were sued and encountered numerous personal attacks. In some countries, scientific findings have been suppressed and distorted, and scientific advisory committees manipulated for political purposes by government agencies. How to respond to these threats is an important challenge for environmental and occupational medicine professionals and their societies. The authors recommend that professional organisations adopt a code of ethics that requires openness from public health professionals; that they not undertake research or use data where they do not have freedom to publish their results if these data have public health implications; that they disclose all possible conflicts; that the veracity of their research results should not be compromised; and that their research independence be protected through professional and legal support. The authors furthermore recommend that research funding for public health not be directly from the industry to the researcher. An independent, intermediate funding scheme should be established to ensure that there is no pressure to analyse data and publish results in bad faith. Such a funding system should also provide equal competition for funds and selection of the best proposals according to standard scientific criteria.

The design and development of an undergraduate signal processing laboratory

The School of Electrical and Electronic Systems Engineering of Queensland University of Technology (like many other universities around the world) has recognised the importance of complementing the teaching of signal processing with computer based experiments. A laboratory has been developed to provide a "hands-on" approach to the teaching of signal processing techniques. The motivation for the development of this laboratory was the cliche "What I hear I remember but what I do I understand." The laboratory has been named as the "Signal Computing and Real-time DSP Laboratory" and provides practical training to approximately 150 final year undergraduate students each year. The paper describes the novel features of the laboratory, techniques used in the laboratory based teaching, interesting aspects of the experiments that have been developed and student evaluation of the teaching techniques

Expert science teacher's notion of scientific literacy

This paper will report on the way expert science teachers’ conceive of scientific literacy in their classrooms, the values related to scientific literacy they hold and how this conception and the underpinning values affect their teaching practice. Three perceived expert science teachers who teach both at senior and middle school levels and across the range of sub-disciplines (one senior biology, one senior chemistry and one senior physics) were interviewed about their understanding of scientific literacy and how this influenced their teaching practice. The three teachers were video recorded teaching a junior science class and a senior science class. The data were analysed to identify values that underpin their conceptions of science and science education. The analysis focussed on the matching of the verbalised conceptions and values with their practice of teaching science. This paper will report on these data.

Funding grant proposals for scientific research : retrospective analysis of scores by members of grant review panel

Objectives: To quantify randomness and cost when choosing health and medical research projects for funding. Design: Analysis of retrospective data from grant review panels. Setting: The National Health & Medical Research Council of Australia. Participants/Data: All panel members’ scores for grant proposals submitted in 2009. Main outcome measure: The proportion of grant proposals that were always, sometimes and never funded after accounting for random variability arising from variation in panel members’ scores; the cost-effectiveness of different size assessment panels. Results: 59% of 620 funded grants were sometimes not funded when random variability was accounted for. Only 9% of grant proposals were always funded, 61% were never funded and 29% were sometimes funded. The extra cost per grant effectively funded from the most effective system was $18,541. Conclusions: Allocating funding for scientific research in health and medicine is costly and somewhat random. There are many useful research questions to be addressed that could improve current processes.

Intensive Case Management: A Critical Re-Appraisal of the Scientific Evidence for Effectiveness

Intensive Case Management (ICM) is widely claimed to be an evidence-based and cost effective program for people with high levels of disability as a result of mental illness. However, the findings of recent randomized controlled trials comparing ICM with ‘usual services’ suggest that both clinical and cost effectiveness of ICM may be weakening. Possible reasons for this, including fidelity of implementation, researcher allegiance effects and changes in the wider service environment within which ICM is provided, are considered. The implications for service delivery and research are discussed.

But does it work? Effectiveness of scientific visualisations in high school chemistry and physics instruction.

Scientific visualisations such as computer-based animations and simulations are increasingly a feature of high school science instruction. Visualisations are adopted enthusiastically by teachers and embraced by students, and there is good evidence that they are popular and well received. There is limited evidence, however, of how effective they are in enabling students to learn key scientific concepts. This paper reports the results of a quantitative study conducted in Australian physics and chemistry classrooms. In general there was no statistically significant difference between teaching with and without visualisations, however there were intriguing differences around student sex and academic ability.

Measuring the effectiveness of computer-based scientific visualisations for conceptual development in Australian chemistry classrooms

Visual modes of representation have always been very important in science and science education. Interactive computer-based animations and simulations offer new visual resources for chemistry education. Many studies have shown that students enjoy learning with visualisations but few have explored how learning outcomes compare when teaching with or without visualisations. This study employs a quasi-experimental crossover research design and quantitative methods to measure the educational effectiveness - defined as level of conceptual development on the part of students - of using computer-based scientific visualisations versus teaching without visualisations in teaching chemistry. In addition to finding that teaching with visualisations offered outcomes that were not significantly different from teaching without visualisations, the study also explored differences in outcomes for male and female students, students with different learning styles (visual, aural, kinesthetic) and students of differing levels of academic ability.

One approach to finding evidence for the effectiveness of scientific visualisations in high school physics and chemistry education

Enormous amounts of money and energy are being devoted to the development, use and organisation of computer-based scientific visualisations (e.g. animations and simulations) in science education. It seems plausible that visualisations that enable students to gain visual access to scientific phenomena that are too large, too small or occur too quickly or too slowly to be seen by the naked eye, or to scientific concepts and models, would yield enhanced conceptual learning. When the literature is searched, however, it quickly becomes apparent that there is a dearth of quantitative evidence for the effectiveness of scientific visualisations in enhancing students’ learning of science concepts. This paper outlines an Australian project that is using innovative research methodology to gather evidence on this question in physics and chemistry classrooms.

Room ventilation and the risk of airborne infection transmission in three health care settings within a large teaching hospital

Background: Room ventilation is a key determinant of airborne disease transmission. Despite this, ventilation guidelines in hospitals are not founded on robust scientific evidence related to prevention of airborne transmission. Methods: We sought to assess the effect of ventilation rates on influenza, tuberculosis (TB) and rhinovirus infection risk within three distinct rooms in a major urban hospital; a Lung Function Laboratory, Emergency Department (ED) Negative-pressure Isolation Room and an Outpatient Consultation Room were investigated. Air exchange rate measurements were performed in each room using CO2 as a tracer. Gammaitoni and Nucci’s model was employed to estimate infection risk. Results: Current outdoor air exchange rates in the Lung Function Laboratory and ED Isolation Room limited infection risks to between 0.1 and 3.6%. Influenza risk for individuals entering an Outpatient Consultation Room after an infectious individual departed ranged from 3.6 to 20.7%, depending on the duration for which each person occupied the room. Conclusions: Given the absence of definitive ventilation guidelines for hospitals, air exchange measurements combined with modelling afford a useful means of assessing, on a case-by-case basis, the suitability of room ventilation at preventing airborne disease transmission.