miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface, which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of known and novel miRNAs are predicted using the TargetScan algorithm, and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation and graphical display are purely Java coded. This application tool can be executed using a normal personal computer with 1.5 GB of memory. Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star

Data transformations in custom digital workflows : property graphs as a data model for user-defined mappings

This paper describes the use of property graphs for mapping data between AEC software tools, which are not linked by common data formats and/or other interoperability measures. The intention of introducing this in practice, education and research is to facilitate the use of diverse, non-integrated design and analysis applications by a variety of users who need to create customised digital workflows, including those who are not expert programmers. Data model types are examined by way of supporting the choice of directed, attributed, multi-relational graphs for such data transformation tasks. A brief exemplar design scenario is also presented to illustrate the concepts and methods proposed, and conclusions are drawn regarding the feasibility of this approach and directions for further research.

Phenomenography : opening a new territory for library and information science research

Phenomenography is a research approach devised to allow the investigation of varying ways in which people experience aspects of their world. Whilst growing attention is being paid to interpretative research in LIS, it is not always clear how the outcomes of such research can be used in practice. This article explores the potential contribution of phenomenography in advancing the application of phenomenological and hermeneutic frameworks to LIS theory, research and practice. In phenomenography we find a research toll which in revealing variation, uncovers everyday understandings of phenomena and provides outcomes which are readily applicable to professional practice. THe outcomes may be used in human computer interface design, enhancement, implementation and training, in the design and evaluation of services, and in education and training for both end users and information professionals. A proposed research territory for phenomenography in LIS includes investigating qualitative variation in the experienced meaning of: 1) information and its role in society 2) LIS concepts and principles 3) LIS processes and; 4) LIS elements.

Analysis of multilateral service conversations in global business networks

The rapid growth of services available on the Internet and exploited through ever globalizing business networks poses new challenges for service interoperability. New services, from consumer “apps”, enterprise suites, platform and infrastructure resources, are vying for demand with quickly evolving and overlapping capabilities, and shorter cycles of extending service access from user interfaces to software interfaces. Services, drawn from a wider global setting, are subject to greater change and heterogeneity, demanding new requirements for structural and behavioral interface adaptation. In this paper, we analyze service interoperability scenarios in global business networks, and propose new patterns for service interactions, above those proposed over the last 10 years through the development of Web service standards and process choreography languages. By contrast, we reduce assumptions of design-time knowledge required to adapt services, giving way to run-time mismatch resolutions, extend the focus from bilateral to multilateral messaging interactions, and propose declarative ways in which services and interactions take part in long-running conversations via the explicit use of state.

Skype : a communications framework for robotics

This paper describes an architecture for robotic telepresence and teleoperation based on the well known tools ROS and Skype. We discuss how Skype can be used as a framework for robotic communication and can be integrated into a ROS/Linux framework to allow a remote user to not only interact with people near the robot, but to view maps, sensory data, robot pose and to issue commands to the robot’s navigation stack. This allows the remote user to exploit the robot’s autonomy, providing a much more convenient navigation interface than simple remote joysticking.

A lightweight biometric signature scheme for user authentication over networks

We introduce a lightweight biometric solution for user authentication over networks using online handwritten signatures. The algorithm proposed is based on a modified Hausdorff distance and has favorable characteristics such as low computational cost and minimal training requirements. Furthermore, we investigate an information theoretic model for capacity and performance analysis for biometric authentication which brings additional theoretical insights to the problem. A fully functional proof-of-concept prototype that relies on commonly available off-the-shelf hardware is developed as a client-server system that supports Web services. Initial experimental results show that the algorithm performs well despite its low computational requirements and is resilient against over-the-shoulder attacks.

Approaches to designing for older adults' intuitive interaction with complex devices

Many older people have difficulties using modern consumer products due to increased product complexity both in terms of functionality and interface design. Previous research has shown that older people have more difficulty in using complex devices intuitively when compared to the younger. Furthermore, increased life expectancy and a falling birth rate have been catalysts for changes in world demographics over the past two decades. This trend also suggests a proportional increase of older people in the work-force. This realisation has led to research on the effective use of technology by older populations in an effort to engage them more productively and to assist them in leading independent lives. Ironically, not enough attention has been paid to the development of interaction design strategies that would actually enable older users to better exploit new technologies. Previous research suggests that if products are designed to reflect people's prior knowledge, they will appear intuitive to use. Since intuitive interfaces utilise domain-specific prior knowledge of users, they require minimal learning for effective interaction. However, older people are very diverse in their capabilities and domain-specific prior knowledge. In addition, ageing also slows down the process of acquiring new knowledge. Keeping these suggestions and limitations in view, the aim of this study was set to investigate possible approaches to developing interfaces that facilitate their intuitive use by older people. In this quest to develop intuitive interfaces for older people, two experiments were conducted that systematically investigated redundancy (the use of both text and icons) in interface design, complexity of interface structure (nested versus flat), and personal user factors such as cognitive abilities, perceived self-efficacy and technology anxiety. All of these factors could interfere with intuitive use. The results from the first experiment suggest that, contrary to what was hypothesised, older people (65+ years) completed the tasks on the text only based interface design faster than on the redundant interface design. The outcome of the second experiment showed that, as expected, older people took more time on a nested interface. However, they did not make significantly more errors compared with younger age groups. Contrary to what was expected, older age groups also did better under anxious conditions. The findings of this study also suggest that older age groups are more heterogeneous in their capabilities and their intuitive use of contemporary technological devices is mediated more by domain-specific technology prior knowledge and by their cognitive abilities, than chronological age. This makes it extremely difficult to develop product interfaces that are entirely intuitive to use. However, by keeping in view the cognitive limitations of older people when interfaces are developed, and using simple text-based interfaces with flat interface structure, would help them intuitively learn and use complex technological products successfully during early encounter with a product. These findings indicate that it might be more pragmatic if interfaces are designed for intuitive learning rather than for intuitive use. Based on this research and the existing literature, a model for adaptable interface design as a strategy for developing intuitively learnable product interfaces was proposed. An adaptable interface can initially use a simple text only interface to help older users to learn and successfully use the new system. Over time, this can be progressively changed to a symbols-based nested interface for more efficient and intuitive use.

From simulation to emulation : an integrated approach for network security evaluation

We present a virtual test bed for network security evaluation in mid-scale telecommunication networks. Migration from simulation scenarios towards the test bed is supported and enables researchers to evaluate experiments in a more realistic environment. We provide a comprehensive interface to manage, run and evaluate experiments. On basis of a concrete example we show how the proposed test bed can be utilized.

User facilitated congestion and attack mitigation

The IEEE Wireless LAN standard has been a true success story by enabling convenient, efficient and low-cost access to broadband networks for both private and professional use. However, the increasing density and uncoordinated operation of wireless access points, combined with constantly growing traffic demands have started hurting the users' quality of experience. On the other hand, the emerging ubiquity of wireless access has placed it at the center of attention for network attacks, which not only raises users' concerns on security but also indirectly affects connection quality due to proactive measures against security attacks. In this work, we introduce an integrated solution to congestion avoidance and attack mitigation problems through cooperation among wireless access points. The proposed solution implements a Partially Observable Markov Decision Process (POMDP) as an intelligent distributed control system. By successfully differentiating resource hampering attacks from overload cases, the control system takes an appropriate action in each detected anomaly case without disturbing the quality of service for end users. The proposed solution is fully implemented on a small-scale testbed, on which we present our observations and demonstrate the effectiveness of the system to detect and alleviate both attack and congestion situations.

Non-intrusive continuous user behaviour analysis using computerized systems

There are different ways to authenticate humans, which is an essential prerequisite for access control. The authentication process can be subdivided into three categories that rely on something someone i) knows (e.g. password), and/or ii) has (e.g. smart card), and/or iii) is (biometric features). Besides classical attacks on password solutions and the risk that identity-related objects can be stolen, traditional biometric solutions have their own disadvantages such as the requirement of expensive devices, risk of stolen bio-templates etc. Moreover, existing approaches provide the authentication process usually performed only once initially. Non-intrusive and continuous monitoring of user activities emerges as promising solution in hardening authentication process: iii-2) how so. behaves. In recent years various keystroke dynamic behavior-based approaches were published that are able to authenticate humans based on their typing behavior. The majority focuses on so-called static text approaches, where users are requested to type a previously defined text. Relatively few techniques are based on free text approaches that allow a transparent monitoring of user activities and provide continuous verification. Unfortunately only few solutions are deployable in application environments under realistic conditions. Unsolved problems are for instance scalability problems, high response times and error rates. The aim of this work is the development of behavioral-based verification solutions. Our main requirement is to deploy these solutions under realistic conditions within existing environments in order to enable a transparent and free text based continuous verification of active users with low error rates and response times.

A web application to perform linkage disequilibrium and linkage analyses on a computational grid

Motivation: Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. Methods: Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. Results: We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. © The Author 2009. Published by Oxford University Press. All rights reserved.

Hybrid graphene/titania nanocomposite : interface charge transfer, hole doping, and sensitization for visible light response

We demonstrated for the first time by large-scale ab initio calculations that a graphene/titania interface in the ground electronic state forms a charge-transfer complex due to the large difference of work functions between graphene and titania, leading to substantial hole doping in graphene. Interestingly, electrons in the upper valence band can be directly excited from graphene to the conduction band, that is, the 3d orbitals of titania, under visible light irradiation. This should yield well-separated electron−hole pairs, with potentially high photocatalytic or photovoltaic performance in hybrid graphene and titania nanocomposites. Experimental wavelength-dependent photocurrent generation of the graphene/titania photoanode demonstrated noticeable visible light response and evidently verified our ab initio prediction.

The interface of the national Australian curriculum and the pre-Year 1 class in school : exploring tensions

The Australian state -based educational system of a national school curriculum that includes a pre-Year 1 Foundation Year has raised questions about the purpose of this year of early education. A document analysis was undertaken across three Australian states, examining three constructions of the pre-Year 1 class and tensions arising from varied perspectives. Tensions have emerged over state-based adaptations of the national curriculum, scripted pedagogies for change management, differing ideological perspectives and positioning of stakeholders. The results indicate that since 2012 there has been a shift in constructions of the pre-Year 1 class towards school-based ideologies, especially in Queensland. Accordingly, positioning of children, parents and teachers has also changed. These results resonate with previous international indications of ‘schooling’ early education. The experiences of Australian early adopters of the curriculum offer insights for other jurisdictions in Australia and internationally, and raise questions about future development in early years education.

The Australian Business Assessment of Computer User Security (ABACUS): A national survey.

The Australian Business Assessment of Computer User Security (ABACUS) survey is a nationwide assessment of the prevalence and nature of computer security incidents experienced by Australian businesses. This report presents the findings of the survey which may be used by businesses in Australia to assess the effectiveness of their information technology security measures.