Seed-based biclustering of gene expression data

Background Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns: (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. Conclusions This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

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

Natural convection of nanofluids in open rectangular cavity

An investigation of the effect of nano particles on natural convection of water based nanofluids contained in an open rectangular cavity is carried out numerically. The flow pattern and heat transfer characteristics are studied for different values of volume fraction in the range 0   0.2 , Rayleigh number in the range 9 1 Ra 10 and the nano particles with different thermo physical properties. It was found that for low Rayleigh numbers, heat transfer exhibits a decreasing trend for increasing values of volume fraction of oxide nanofluids, whereas for higher values of Rayleigh numbers, an increasing trend of heat transfer was observed due to increase in the volume fraction of nanofluids.

Bilingual asynchronous online discussion groups : design and delivery of an e-Learning distance study module for nurse academics in a developing country

The advent of eLearning has seen online discussion forums widely used in both undergraduate and postgraduate nursing education. This paper reports an Australian university experience of design, delivery and redevelopment of a distance education module developed for Vietnamese nurse academics. The teaching experience of Vietnamese nurse academics is mixed and frequently limited. It was decided that the distance module should attempt to utilise the experience of senior Vietnamese nurse academics - asynchronous online discussion groups were used to facilitate this. Online discussion occurred in both Vietnamese and English and was moderated by an Australian academic working alongside a Vietnamese translator. This paper will discuss the design of an online learning environment for foreign correspondents, the resources and translation required to maximise the success of asynchronous online discussion groups, as well as the rationale of delivering complex content in a foreign language. While specifically addressing the first iteration of the first distance module designed, this paper will also address subsequent changes made for the second iteration of the module and comment on their success. While a translator is clearly a key component of success, the elements of simplicity and clarity combined with supportive online moderation must not be overlooked.

Teaching creatively, teaching for creativity : QUT’s Creative Industries Faculty Showcase Panel

In this panel, we showcase approaches to teaching for creativity in disciplines of the Media, Entertainment and Creative Arts School and the School of Design within the Creative Industries Faculty (CIF) at QUT. The Faculty is enormously diverse, with 4,000 students enrolled across a total of 20 disciplines. Creativity is a unifying concept in CIF, both as a graduate attribute, and as a key pedagogic principle. We take as our point of departure the assertion that it is not sufficient to assume that students of tertiary courses in creative disciplines are ‘naturally’ creative. Rather, teachers in higher education must embrace their roles as facilitators of development and learning for the creative workforce, including working to build creative capacity (Howkins, 2009). In so doing, we move away from Renaissance notions of creativity as an individual genius, a disposition or attribute which cannot be learned, towards a 21st century conceptualisation of creativity as highly collaborative, rhizomatic, and able to be developed through educational experiences (see, for instance, Robinson, 2006; Craft; 2001; McWilliam & Dawson, 2008). It has always been important for practitioners of the arts and design to be creative. Under the national innovation agenda (Bradley et al, 2008) and creative industries policy (e.g., Department for Culture, Media and Sport, 2008; Office for the Arts, 2011), creativity has been identified as a key determinant of economic growth, and thus developing students’ creativity has now become core higher education business across all fields. Even within the arts and design, professionals are challenged to be creative in new ways, for new purposes, in different contexts, and using new digital tools and platforms. Teachers in creative disciplines may have much to offer to the rest of the higher education sector, in terms of designing and modelling innovative and best practice pedagogies for the development of student creative capability. Information and Communication Technologies such as mobile learning, game-based learning, collaborative online learning tools and immersive learning environments offer new avenues for creative learning, although analogue approaches may also have much to offer, and should not be discarded out of hand. Each panelist will present a case study of their own approach to teaching for creativity, and will address the following questions with respect to their case: 1. What conceptual view of creativity does the case reflect? 2. What pedagogical approaches are used, and why were these chosen? What are the roles of innovative learning approaches, including ICTs, if any? 3. How is creativity measured or assessed? How do students demonstrate creativity? We seek to identify commonalities and contrasts between and among the pedagogic case studies, and to answer the question: what can we learn about teaching creatively and teaching for creativity from CIF best practice?

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.

OpenRatSLAM : an open source brain-based SLAM system

RatSLAM is a navigation system based on the neural processes underlying navigation in the rodent brain, capable of operating with low resolution monocular image data. Seminal experiments using RatSLAM include mapping an entire suburb with a web camera and a long term robot delivery trial. This paper describes OpenRatSLAM, an open-source version of RatSLAM with bindings to the Robot Operating System framework to leverage advantages such as robot and sensor abstraction, networking, data playback, and visualization. OpenRatSLAM comprises connected ROS nodes to represent RatSLAM’s pose cells, experience map, and local view cells, as well as a fourth node that provides visual odometry estimates. The nodes are described with reference to the RatSLAM model and salient details of the ROS implementation such as topics, messages, parameters, class diagrams, sequence diagrams, and parameter tuning strategies. The performance of the system is demonstrated on three publicly available open-source datasets.

Successful outcomes in vocational education and training courses : how pedagogy and expectations influence achievement

This paper reports on a four year Australian Research Council funded Linkage Project titled Skilling Indigenous Queensland, conducted in regional areas of Queensland, Australia from 2009 to 2013. The project sought to investigate vocational education, training (VET) and teaching, Indigenous learners’ needs, employer cultural and expectations and community culture and expectations to identify best practice in numeracy teaching for Indigenous VET learners. Specifically it focused on ways to enhance the teaching and learning of courses and the associated mathematics in such courses to benefit learners and increase their future opportunities of employment. To date thirty-nine teachers/trainers/teacher aides and two hundred and thirty-one students consented to participate in the project. Nine VET courses were nominated to be the focus on the study. This paper focuses on questionnaire and interview responses from four trainers, two teacher aides and six students. In recent years a considerable amount of funding has been allocated to increasing Indigenous Peoples’ participation in education and employment. This increased funding is predicated on the assumption that it will make a difference and contribute to closing the education gap between Indigenous and non-Indigenous Australians (Council of Australia Governments, 2009). The central tenet is that access to education for Indigenous People will create substantial social and economic benefits for regional and remote Indigenous People. The project’s aim is to address some of the issues associated with the gap. To achieve the aims, the project adopted a mixed methods design aimed at benefitting research participants and included: participatory collaborative action research (Kemmis & McTaggart, 1988) and, community research (Smith, 1999). Participatory collaborative action research refers to a is a “collective, self-reflective enquiry undertaken by participants in social situations in order to improve the rationality and justice of their own social and educational practices” (Kemmis et al., 1988, p. 5). Community research is described as an approach that “conveys a much more intimate, human and self-defined space” (p. 127). Community research relies on and validates the community’s own definitions. As the project is informed by the social at a community level, it is described as “community action research or emancipatory research” (Smith, 1999, p. 127). It seeks to demonstrate benefit to the community, making positive differences in the lives of Indigenous People and communities. The data collection techniques included survey questionnaires, video recording of teaching and learning processes, teacher reflective video analysis of teaching, observations, semi-structured interviews and student numeracy testing. As a result of these processes, the findings indicate that VET course teachers work hard to adopt contextualising strategies to their teaching, however this process is not always straight forward because of the perceptions of how mathematics has been taught and learned historically. Further teachers, trainers and students have high expectations of one another with the view to successful outcomes from the courses.

Design of open source framework for traffic and travel simulation

For the evaluation, design, and planning of traffic facilities and measures, traffic simulation packages are the de facto tools for consultants, policy makers, and researchers. However, the available commercial simulation packages do not always offer the desired work flow and flexibility for academic research. In many cases, researchers resort to designing and building their own dedicated models, without an intrinsic incentive (or the practical means) to make the results available in the public domain. To make matters worse, a substantial part of these efforts pertains to rebuilding basic functionality and, in many respects, reinventing the wheel. This problem not only affects the research community but adversely affects the entire traffic simulation community and frustrates the development of traffic simulation in general. For this problem to be addressed, this paper describes an open source approach, OpenTraffic, which is being developed as a collaborative effort between the Queensland University of Technology, Australia; the National Institute of Informatics, Tokyo; and the Technical University of Delft, the Netherlands. The OpenTraffic simulation framework enables academies from geographic areas and disciplines within the traffic domain to work together and contribute to a specific topic of interest, ranging from travel choice behavior to car following, and from response to intelligent transportation systems to activity planning. The modular approach enables users of the software to focus on their area of interest, whereas other functional modules can be regarded as black boxes. Specific attention is paid to a standardization of data inputs and outputs for traffic simulations. Such standardization will allow the sharing of data with many existing commercial simulation packages.

Internet and e-commerce law, business and policy

Over the last two decades, the internet and e-commerce have reshaped the way we communicate, interact and transact. In the converged environment enabled by high speed broadband, web 2.0, social media, virtual worlds, user-generated content, cloud computing, VoIP, open source software and open content have rapidly become established features of our online experience. Business and government alike are increasingly using the internet as the preferred platform for delivery of their goods and services and for effective engagement with their clients. New ways of doing things online and challenges to existing business, government and social activities have tested current laws and often demand new policies and laws, adapted to the new realities. The focus of this book is the regulation of social, cultural and commercial activity on the World Wide Web. It considers developments in the law that have been, and continue to be, brought about by the emergence of the internet and e-commerce. It analyses how the law is applied to define rights and obligations in relation to online infrastructure, content and practices.

The influence of online reviews on consumers’ attributions of service quality and control for service standards in hotels

Online travel reviews are emerging as a powerful source of information affecting tourists' pre-purchase evaluation of a hotel organization. This trend has highlighted the need for a greater understanding of the impact of online reviews on consumer attitudes and behaviors. In view of this need, we investigate the influence of online hotel reviews on consumers' attributions of service quality and firms' ability to control service delivery. An experimental design was used to examine the effects of four independent variables: framing; valence; ratings; and target. The results suggest that in reviews evaluating a hotel, remarks related to core services are more likely to induce positive service quality attributions. Recent reviews affect customers' attributions of controllability for service delivery, with negative reviews exerting an unfavorable influence on consumers' perceptions. The findings highlight the importance of managing the core service and the need for managers to act promptly in addressing customer service problems.

Analyzing the effectiveness of graph metrics for anomaly detection in online social networks

Online social networks can be modelled as graphs; in this paper, we analyze the use of graph metrics for identifying users with anomalous relationships to other users. A framework is proposed for analyzing the effectiveness of various graph theoretic properties such as the number of neighbouring nodes and edges, betweenness centrality, and community cohesiveness in detecting anomalous users. Experimental results on real-world data collected from online social networks show that the majority of users typically have friends who are friends themselves, whereas anomalous users’ graphs typically do not follow this common rule. Empirical analysis also shows that the relationship between average betweenness centrality and edges identifies anomalies more accurately than other approaches.

Open Access Books

Although digital technology has, in theory, made it possible for many more people to access content at no extra cost, fewer people than ever before are able to read the books written by university-based researchers. This article looks, very briefly, at the role that open access licenses might play in reviving the scholarly monograph: a specialised area of academic publishing that has seen sales decline by more than 90% over the past three decades. It also introduces a new approach to funding open-access scholarly books being pioneered by the not-for-profit social enterprise Knowledge Unlatched.