mCOPA: analysis of heterogeneous features in cancer expression data

Background Cancer outlier profile analysis (COPA) has proven to be an effective approach to analyzing cancer expression data, leading to the discovery of the TMPRSS2 and ETS family gene fusion events in prostate cancer. However, the original COPA algorithm did not identify down-regulated outliers, and the currently available R package implementing the method is similarly restricted to the analysis of over-expressed outliers. Here we present a modified outlier detection method, mCOPA, which contains refinements to the outlier-detection algorithm, identifies both over- and under-expressed outliers, is freely available, and can be applied to any expression dataset. Results We compare our method to other feature-selection approaches, and demonstrate that mCOPA frequently selects more-informative features than do differential expression or variance-based feature selection approaches, and is able to recover observed clinical subtypes more consistently. We demonstrate the application of mCOPA to prostate cancer expression data, and explore the use of outliers in clustering, pathway analysis, and the identification of tumour suppressors. We analyse the under-expressed outliers to identify known and novel prostate cancer tumour suppressor genes, validating these against data in Oncomine and the Cancer Gene Index. We also demonstrate how a combination of outlier analysis and pathway analysis can identify molecular mechanisms disrupted in individual tumours. Conclusions We demonstrate that mCOPA offers advantages, compared to differential expression or variance, in selecting outlier features, and that the features so selected are better able to assign samples to clinically annotated subtypes. Further, we show that the biology explored by outlier analysis differs from that uncovered in differential expression or variance analysis. mCOPA is an important new tool for the exploration of cancer datasets and the discovery of new cancer subtypes, and can be combined with pathway and functional analysis approaches to discover mechanisms underpinning heterogeneity in cancers

Dichotomy in the design studio 2.0 : adapting to new blended learning environments

In a study aimed at better understanding how students adapt to new blended studio learning environments, all undergraduate and masters of architecture students at a large school of architecture in Australia, learned a semester of architectural design in newly renovated, technology embedded, design studio environments. The renovations addressed the lessons learned from a 2011 pilot study of a second year architectural design studio learned in a high technology embedded prototype digital laboratory. The new design studios were purpose designed for the architecture students and adapted Student-Centred Active Learning Environment for Undergraduate Programs design principles. At the end of the semester, the students completed a questionnaire about their experiences of learning in the new design studio environments. Using a dual method qualitative approach, the questionnaire data were coded and extrapolated using both thematic analysis and grounded theory methodology. The results from these two approaches were compared, contrasted and finally merged, to reveal five distinct emerging themes, which were instrumental in offering resistance or influencing adaptation to, the new blended studio learning environments. This paper reports on the study, discusses the major contributors to resistance and adaptation, and proposes points for consideration when renovating or designing new blended studio learning environments. This research extends the 2011 pilot study by the same authors: ‘Dichotomy in the design studio: Adapting to new blended learning environments’.

Pinned fronts in heterogeneous media of jump type

In this paper, we analyse the impact of a (small) heterogeneity of jump type on the most simple localized solutions of a 3-component FitzHugh–Nagumo-type system. We show that the heterogeneity can pin a 1-front solution, which travels with constant (non-zero) speed in the homogeneous setting, to a fixed, explicitly determined, distance from the heterogeneity. Moreover, we establish the stability of this heterogeneous pinned 1-front solution. In addition, we analyse the pinning of 1-pulse, or 2-front, solutions. The paper is concluded with simulations in which we consider the dynamics and interactions of N-front patterns in domains with M heterogeneities of jump type (N = 3, 4, M ≥ 1).

Power of engineering : changing the perceptions of year 9 and 10 female school students towards an engineering career

BACKGROUND The engineering profession in Australia has failed to attract young women for the last decade or so despite all the effort that have gone into promoting engineering as a preferred career choice for girls. It is a missed opportunity for the profession to flourish as a heterogeneous team. Many traditional initiatives and programs have failed to make much impact or at best incremental improvement into attracting and retaining more women in the profession. The reasons why girls and young women in most parts of the world show little interest in engineering haven't changed, despite all the efforts to address them, the issue proposed here in this paper is with the perceptions of engineering in the community and the confidence to pursue it. This gender imbalance is detrimental for the engineering profession, and hence an action-based intervention strategy was devised by the Women in Engineering Qld Chapter of Engineers Australia in 2012 to change the perceptions of school girls by redesigning the engagement strategy and key messages. As a result, the “Power of Engineering Inc” (PoE) was established as a not-for-profit organisation, and is a collaborative effort between government, schools, universities, and industry. This paper examines a case study in changing the perceptions of year 9 and 10 school girls towards an engineering career. PURPOSE To evaluate and determine the effectiveness of an intervention in changing the perceptions of year 9 and 10 school girls about engineering career options, but specifically, “What were their perceptions of engineering before today and have those perceptions changed?” DESIGN/METHOD The inaugural Power of Engineering (PoE) event was held on International Women’s Day, Thursday 8 March 2012 and was attended by 131 high school female students (year 9 and 10) and their teachers. The key message of the day was “engineering gives you the power to change the world”. A questionnaire was conducted with the participating high school female students, collecting both quantitative and qualitative data. The survey instrument has not been validated. RESULTS The key to the success of the event was as a result of collaboration between all participants involved and the connection created between government, schools, universities and industry. Of the returned surveys (109 of 131), 91% of girls would now consider a career in engineering and 57% who had not considered engineering before the day would now consider a career in engineering. Data collected found significant numbers of negative and varying perceptions about engineering careers prior to the intervention. CONCLUSIONS The evidence in this research suggests that the intervention assisted in changing the perceptions of year 9 and 10 female school students towards engineering as a career option. Whether this intervention translates into actual career selection and study enrolment is to be determined. In saying this, the evidence suggests that there is a critical and urgent need for earlier interventions prior to students selecting their subjects for year 11 and 12. This intervention could also play its part in increasing the overall pool of students engaged in STEM education.

Mobility and active ageing in suburban environments : findings from in-depth interviews and person-based GPS tracking

Background. Governments face a significant challenge to ensure that community environments meet the mobility needs of an ageing population. Therefore, it is critical to investigate the effect of suburban environments on the choice of transportation and its relation to participation and active ageing. Objective. This research explores if and how suburban environments impact older people’s mobility and their use of different modes of transport. Methods. Data derived from GPS tracking, travel diaries, brief questionnaires, and semistructured interviews were gathered from thirteen people aged from 56 to 87 years, living in low-density suburban environments in Brisbane, Australia. Results. The suburban environment influenced the choice of transportation and out-of-home mobility. Both walkability and public transportation (access and usability) impact older people’s transportation choices. Impracticality of active and public transportation within suburban environments creates car dependency in older age. Conclusion. Suburban environments often create barriers to mobility, which impedes older people’s engagement in their wider community and ability to actively age in place. Further research is needed to develop approaches towards age-friendly suburban environments which will encourage older people to remain active and engaged in older age.

Hanging out is hard to do : Methodology in non-avatar environments

Ethnography is now a well-established research methodology for virtual environments, and the vast majority of accounts have one aspect in common, whether textual or graphic environments – that of the embodied avatar. In this article, I first discuss the applicability of such a methodology to non-avatar environments such as Eve Online, considering where the methodology works and the issues that arise in its implementation – particularly for the consideration of sub-communities within the virtual environment. Second, I consider what alternative means exist for getting at the information that is obtained through an ethnographic study of the virtual environment. To that end, I consider the practical and ethical implications of utilizing existing accounts, the importance of the meta-game discourse, including those sources outside of the control of the environment developer, and finally the utility in combining personal observations with accounts of other ethnographers, both within and between environments.

Dichotomy in the design studio : adapting to new blended learning environments

Since the architectural design studio learning environment was first established in the early 19th century at the École des Beaux-Arts in Paris, there has been a complete transformation in how the discipline of architecture is practiced and how students of architecture acquire information. Digital technologies allow students to access information instantly and learning is no longer confined to the rigid boundaries of a physical campus environment. In many schools of architecture in Australia, the physical design studio learning environments however, remain largely unchanged. Many learning environments could be mistaken for those last refurbished 30 years ago, being devoid of any significant technological intervention. While some teaching staff are eagerly embracing new digital technologies and attempting to modify their pedagogical approaches, the physical design studio learning environment is resistant to such efforts. In a study aimed at better understanding how staff and students adapt to new blended learning environments, a group of 165 second year architecture students at a large school of architecture in Australia were separated into two different design studio learning environments. 70% of students were allocated to a traditional design studio setting and 30% to a new, high technology embedded, prototype digital learning laboratory. The digital learning laboratory was purpose designed for the case-study users, adapted Student-Centred Active Learning Environment for Undergraduate Programs [SCALE-UP] principles, and built as part of a larger university research project. The architecture students attended the same lectures, followed the same studio curriculum and completed the same pieces of assessment; the only major differences were the teaching staff and physical environment within which the studios were conducted. At the end of the semester, all staff and students were asked to complete a questionnaire about their experiences and preferences within the two respective learning environments. The questionnaire response rate represented the opinions of 100% of the 10 teaching staff and over 70% of the students. Using a qualitative grounded theory approach, data were coded, extrapolated and compared, to reveal emerging key themes. The key themes formed the basis for in-depth interviews and focus groups of teaching staff and students, allowing the researchers to understand the data in more detail. The results of the data verified what had become increasingly evident during the course of the semester: an underlying negative resistance to the new digital studio learning environment, by both staff and students. Many participants openly exhibited a yearning for a return to the traditional design studio learning environments, particularly when the new technology caused frustration, by being unreliable or failing altogether. This paper reports on the study, discusses the negative resistance and explores the major contributors to resistance. The researchers are not aware of any similar previous studies across these particular settings and believe that it offers a necessary and important contribution to emergent research about adaptation to new digital learning environments.

The smart skies project : enabling technologies for future airspace environments

This paper summarises the achievements of the Smart Skies Project, a three-year, multi-award winning international project that researched, developed and extensively flight tested four enabling aviation technologies: an electrooptical mid-air collision avoidance system, a static obstacle avoidance system, a mobile ground-based air traffic surveillance system, and a global automated airspace separation management system. The project included the development of manned and unmanned flight test aircraft, which were used to characterise the performance of the prototype systems for a range of realistic scenarios under a variety of environmental conditions. In addition to the collection of invaluable flight data, the project achieved world-firsts in the demonstration of future automated collision avoidance and separation management concepts. This paper summarises these outcomes, the overall objectives of the project, the research and the development of the prototype systems, the engineering of the flight test systems, and the results obtained from flight-testing.

Cryo-electron tomography of Marburg Virus particles and their morphogenesis within infected cells

Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma membrane of the infected cell to release enveloped virions. The virions are often heterogeneous in shape, which makes it difficult to study their structure and assembly mechanisms. We have applied cryo-electron tomography and sub-tomogram averaging methods to derive structures of Marburg virus, a highly pathogenic filovirus, both after release and during assembly within infected cells. The data demonstrate the potential of cryo-electron tomography methods to derive detailed structural information for intermediate steps in biological pathways within intact cells. We describe the location and arrangement of the viral proteins within the virion. We show that the N-terminal domain of the nucleoprotein contains the minimal assembly determinants for a helical nucleocapsid with variable number of proteins per turn. Lobes protruding from alternate interfaces between each nucleoprotein are formed by the C-terminal domain of the nucleoprotein, together with viral proteins VP24 and VP35. Each nucleoprotein packages six RNA bases. The nucleocapsid interacts in an unusual, flexible "Velcro-like" manner with the viral matrix protein VP40. Determination of the structures of assembly intermediates showed that the nucleocapsid has a defined orientation during transport and budding. Together the data show striking architectural homology between the nucleocapsid helix of rhabdoviruses and filoviruses, but unexpected, fundamental differences in the mechanisms by which the nucleocapsids are then assembled together with matrix proteins and initiate membrane envelopment to release infectious virions, suggesting that the viruses have evolved different solutions to these conserved assembly steps.

STALKERBOT : learning to navigate dynamic human environments by following people

Service robots that operate in human environments will accomplish tasks most efficiently and least disruptively if they have the capability to mimic and understand the motion patterns of the people in their workspace. This work demonstrates how a robot can create a humancentric navigational map online, and that this map re ects changes in the environment that trigger altered motion patterns of people. An RGBD sensor mounted on the robot is used to detect and track people moving through the environment. The trajectories are clustered online and organised into a tree-like probabilistic data structure which can be used to detect anomalous trajectories. A costmap is reverse engineered from the clustered trajectories that can then inform the robot's onboard planning process. Results show that the resultant paths taken by the robot mimic expected human behaviour and can allow the robot to respond to altered human motion behaviours in the environment.

CAT-GRAPH+ : towards odometry-driven place consolidation in changing environments

Changing environments present a number of challenges to mobile robots, one of the most significant being mapping and localisation. This problem is particularly significant in vision-based systems where illumination and weather changes can cause feature-based techniques to fail. In many applications only sections of an environment undergo extreme perceptual change. Some range-based sensor mapping approaches exploit this property by combining occasional place recognition with the assumption that odometry is accurate over short periods of time. In this paper, we develop this idea in the visual domain, by using occasional vision-driven loop closures to infer loop closures in nearby locations where visual recognition is difficult due to extreme change. We demonstrate successful map creation in an environment in which change is significant but constrained to one area, where both the vanilla CAT-Graph and a Sum of Absolute Differences matcher fails, use the described techniques to link dissimilar images from matching locations, and test the robustness of the system against false inferences.

Multi-device key management using visual side channels in pervasive computing environments

In the modern connected world, pervasive computing has become reality. Thanks to the ubiquity of mobile computing devices and emerging cloud-based services, the users permanently stay connected to their data. This introduces a slew of new security challenges, including the problem of multi-device key management and single-sign-on architectures. One solution to this problem is the utilization of secure side-channels for authentication, including the visual channel as vicinity proof. However, existing approaches often assume confidentiality of the visual channel, or provide only insufficient means of mitigating a man-in-the-middle attack. In this work, we introduce QR-Auth, a two-step, 2D barcode based authentication scheme for mobile devices which aims specifically at key management and key sharing across devices in a pervasive environment. It requires minimal user interaction and therefore provides better usability than most existing schemes, without compromising its security. We show how our approach fits in existing authorization delegation and one-time-password generation schemes, and that it is resilient to man-in-the-middle attacks.

Continuous and non-intrusive identity verification in real-time environments based on free-text keystroke dynamics

Internet services are important part of daily activities for most of us. These services come with sophisticated authentication requirements which may not be handled by average Internet users. The management of secure passwords for example creates an extra overhead which is often neglected due to usability reasons. Furthermore, password-based approaches are applicable only for initial logins and do not protect against unlocked workstation attacks. In this paper, we provide a non-intrusive identity verification scheme based on behavior biometrics where keystroke dynamics based-on free-text is used continuously for verifying the identity of a user in real-time. We improved existing keystroke dynamics based verification schemes in four aspects. First, we improve the scalability where we use a constant number of users instead of whole user space to verify the identity of target user. Second, we provide an adaptive user model which enables our solution to take the change of user behavior into consideration in verification decision. Next, we identify a new distance measure which enables us to verify identity of a user with shorter text. Fourth, we decrease the number of false results. Our solution is evaluated on a data set which we have collected from users while they were interacting with their mail-boxes during their daily activities.

Visioning technology-based simulated learning environments in the social work curriculum

This report, prepared by QUT Social Work and Human Services, in collaboration with key sector stakeholders, identifies the current and potentially expanded uses of Simulated Learning Environments (SLE) as part of the Health Workforce Australia (HWA) National Project. An expert Reference Group guided the project, facilitated the data collection, and provided feedback and support on the findings and broad recommendations.