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

Teaching new product development to design led innovation

Recently many international tertiary educational programs have capitalised on the value design and business can have upon their interception (Martin, 2009; Brown, 2008; Bruce and Bessant, 2002; Manzini, 2009). This paper discusses the role that two teaching units – New Product Development and Design Led Innovation – play in forming an understanding of commercialisation needed in today’s Industrial Design education. These units are taught consecutively in the later years of the Bachelor of Industrial Design program at the Queensland University of Technology, Brisbane, Australia. In this paper, each teaching unit is discussed in detail and then as a conglomerate, in order to form a basis of knowledge students need in order to fully capitalise on the value design has in business, and to produce a more capable Industrial Design graduate of the future.

Influencing innovation in SME’s : from designer to transitional engineer

The following paper presents insights found during an ongoing industry engagement with a family-owned manufacturing SME in Australia. The study seeks to unpack cultural, strategic, product opportunities and challenges available to the firm engaging in a design led approach to innovation. Design led innovation finds new market opportunities to innovate through a holistic perspective of both the internal business operations, focusing on the customer experience and external stakeholders. The action research based methodology consisted of 25 semi-structured interviews, a reflective journal and focus group, all of which were analysed thematically. This paper focuses on the resultant themes of the focus group data constituting a discussion around the best strategies to try and integrate design thinking as a fundamental skill across the company. The main thematic results included the participant’s limited views of themselves (in current roles) as being to create ‘buy-in’ to change initiatives, a preference to act as a group to gain traction in the firm, importance of better defining the problem before reaching a design solution and lastly the time required to implement versus the need for change. These findings are valuable in assisting other family owned firms in managing core growth activities with design and innovation initiatives, particularly in the area of new product development.

A methodological approach to modelling design led innovation across secondary education : an Australian case study

Incorporating design thinking as a generic capability at a school level is needed to ensure future generations are empowered for business innovation and active citizenship. This paper describes the methodology of an investigation into modelling design led innovation approaches from the business sector to secondary education, as part of a larger study. It builds on a previously discussed research agenda by outlining the scope, significance and limitations of currently available research in this area, examining an action research methodology utilising an Australian design immersion program case study, and discussing implications and future work. It employs a triangulated approach encompassing thematic analysis of qualitative data collection from student focus groups, semi-structured convergent interviews with teachers and facilitators, and student journals. Eventual outcomes will be reviewed and analysed within the framework of a proposed innovation matrix model for educational growth, synthesising principles responding to 21st century student outcomes. It is anticipated this research will inform a successful design led secondary education innovation model, facilitating new engagement frameworks between tertiary and secondary education sectors, as well as providing new insight into the suitability of action research in prototyping social innovation in Australia.

Cohort normalization based sparse representation for undersampled face recognition

Abstract. In recent years, sparse representation based classification(SRC) has received much attention in face recognition with multipletraining samples of each subject. However, it cannot be easily applied toa recognition task with insufficient training samples under uncontrolledenvironments. On the other hand, cohort normalization, as a way of mea-suring the degradation effect under challenging environments in relationto a pool of cohort samples, has been widely used in the area of biometricauthentication. In this paper, for the first time, we introduce cohort nor-malization to SRC-based face recognition with insufficient training sam-ples. Specifically, a user-specific cohort set is selected to normalize theraw residual, which is obtained from comparing the test sample with itssparse representations corresponding to the gallery subject, using poly-nomial regression. Experimental results on AR and FERET databases show that cohort normalization can bring SRC much robustness against various forms of degradation factors for undersampled face recognition.

Paleomagnetic data support Early Permian age for the Abor Volcanics in the lower Siang Valley, NE India; significance for Gondwana-related break-up models

Confusion exists as to the age of the Abor Volcanics of NE India. Some consider the unit to have been emplaced in the Early Permian, others the Early Eocene, a difference of ∼230 million years. The divergence in opinion is significant because fundamentally different models explaining the geotectonic evolution of India depend on the age designation of the unit. Paleomagnetic data reported here from several exposures in the type locality of the formation in the lower Siang Valley indicate that steep dipping primary magnetizations (mean = 72.7 ± 6.2°, equating to a paleo-latitude of 58.1°) are recorded in the formation. These are only consistent with the unit being of Permian age, possibly Artinskian based on a magnetostratigraphic argument. Plate tectonic models for this time consistently show the NE corner of the sub-continent >50°S; in the Early Eocene it was just north of the equator, which would have resulted in the unit recording shallow directions. The mean declination is counter-clockwise rotated by ∼94°, around half of which can be related to the motion of the Indian block; the remainder is likely due local Himalayan-age thrusting in the Eastern Syntaxis. Several workers have correlated the Abor Volcanics with broadly coeval mafic volcanic suites in Oman, NE Pakistan–NW India and southern Tibet–Nepal, which developed in response to the Cimmerian block peeling-off eastern Gondwana in the Early-Middle Permian, but we believe there are problems with this model. Instead, we suggest that the Abor basalts relate to India–Antarctica/India–Australia extension that was happening at about the same time. Such an explanation best accommodates the relevant stratigraphical and structural data (present-day position within the Himalayan thrust stack), as well as the plate tectonic model for Permian eastern Gondwana.

Are heat warning systems effective?

Heatwaves are associated with significant health risks particularly among vulnerable groups. To minimize these risks, heat warning systems have been implemented. The question therefore is how effective these systems are in saving lives and reducing heat-related harm. We systematically searched and reviewed 15 studies which examined this. Six studies asserted that fewer people died of excessive heat after the implementation of heat warning systems. Demand for ambulance decreased following the implementation of these systems. One study also estimated the costs of running heat warning systems at US$210,000 compared to the US$468 million benefits of saving 117 lives. The remaining eight studies investigated people?s response to heat warning systems and taking appropriate actions against heat harms. Perceived threat of heat dangers emerged as the main factor related to heeding the warnings and taking proper actions. However, barriers, such as costs of running air-conditioners, were of significant concern, particularly to the poor. The weight of the evidence suggests that heat warning systems are effective in reducing mortality and, potentially, morbidity. However, their effectiveness may be mediated by cognitive, emotive and socio-demographic characteristics. More research is urgently required into the cost-effectiveness of heat warning systems? measures and improving the utilization of the services.

Improving opportunity recognition and business performance in small and medium manufacturing enterprises through design innovation programs

Increasing awareness of the benefits of stimulating entrepreneurial behaviour in small and medium enterprises has fostered strong interest in innovation programs. Recently many western countries have invested in design innovation for better firm performance. This research presents some early findings from a study of companies that participated in a holistic approach to design innovation, where the outcomes include better business performance and better market positioning in global markets. Preliminary findings from in-depth semi-structured interviews indicate the importance of firm openness to new ways of working and to developing new processes of strategic entrepreneurship. Implications for theory and practice are discussed.

Spatial variation of particle number concentration in school microscale environments and its impact on exposure assessment

It has not yet been established whether the spatial variation of particle number concentration (PNC) within a microscale environment can have an effect on exposure estimation results. In general, the degree of spatial variation within microscale environments remains unclear, since previous studies have only focused on spatial variation within macroscale environments. The aims of this study were to determine the spatial variation of PNC within microscale school environments, in order to assess the importance of the number of monitoring sites on exposure estimation. Furthermore, this paper aims to identify which parameters have the largest influence on spatial variation, as well as the relationship between those parameters and spatial variation. Air quality measurements were conducted for two consecutive weeks at each of the 25 schools across Brisbane, Australia. PNC was measured at three sites within the grounds of each school, along with the measurement of meteorological and several other air quality parameters. Traffic density was recorded for the busiest road adjacent to the school. Spatial variation at each school was quantified using coefficient of variation (CV). The portion of CV associated with instrument uncertainty was found to be 0.3 and therefore, CV was corrected so that only non-instrument uncertainty was analysed in the data. The median corrected CV (CVc) ranged from 0 to 0.35 across the schools, with 12 schools found to exhibit spatial variation. The study determined the number of required monitoring sites at schools with spatial variability and tested the deviation in exposure estimation arising from using only a single site. Nine schools required two measurement sites and three schools required three sites. Overall, the deviation in exposure estimation from using only one monitoring site was as much as one order of magnitude. The study also tested the association of spatial variation with wind speed/direction and traffic density, using partial correlation coefficients to identify sources of variation and non-parametric function estimation to quantify the level of variability. Traffic density and road to school wind direction were found to have a positive effect on CVc, and therefore, also on spatial variation. Wind speed was found to have a decreasing effect on spatial variation when it exceeded a threshold of 1.5 (m/s), while it had no effect below this threshold. Traffic density had a positive effect on spatial variation and its effect increased until it reached a density of 70 vehicles per five minutes, at which point its effect plateaued and did not increase further as a result of increasing traffic density.

Designing Innovative Business Models : A Design Catalyst Learning Resource

The term Design Led Innovation is emerging as a fundamental business process, which is rapidly being adopted by large as well as small to medium sized firms. The value that design brings to an organisation is a different way of thinking, of framing situations and possibilities, doing things and tackling problems: essentially a cultural transformation of the way the firm undertakes its business. Being Design Led is increasingly being seen by business as a driver of company growth, allowing firms to provide a strong point of difference to its stakeholders. Achieving this Design Led process, requires strong leadership to enable the organisation to develop a clear vision for top line growth. Specifically, based on deep customer insights and expanded through customer and stakeholder engagements, the outcomes of which are then adopted by all aspects of the business. To achieve this goal, several tools and processes are available, which need to be linked to new organisational capabilities within a business transformation context. The Design Led Innovation Team focuses on embedding tools and processes within an organisation and matching this with design leadership qualities to enable companies to create breakthrough innovation and achieve sustained growth, through ultimately transforming their business model. As all information for these case studies was derived from publicly accessed data, this resource is not intended to be used as reference material, but rather is a learning tool for designers to begin to consider and explore businesses at a strategic level. It is not the results that are key, but rather the process and philosophies that were used to create these case studies and disseminate this way of thinking amongst the design community. It is this process of unpacking a business guided by the framework of Osterwalder’s Business Model Canvas* which provides an important tool for designers to gain a greater perspective of a company’s true innovation potential.

Surface sulfur measurements on stratospheric particles

The surface chemistries of three particulate samples collected from the lower stratosphere have been determined using a Scanning Auger Microprobe (SAM). These samples are typical of the most abundant natural and anthropogenic particles observed within the stratosphere in the >2µm diameter size fraction. Successive sputtering and analysis below the first few adsorbed monolayers of all particles shows the presence of a thin <150A) sulphur layer. These sulphur regions probably formed by surface reaction of sulphur-rich aerosols with each particle within the stratosphere. Settling rate calculations show that a typical sphere (10µm diameter) may reside within the aerosol layer for ~20 days and thus, provide a qualitative guide to surface sulphur reaction rates.

Developing a method for assessing product inclusivity

In order to develop more inclusive products and services, designers need a means of assessing the inclusivity of existing products and new concepts. Following previous research on the development of scales for inclusive design at University of Cambridge, Engineering Design Centre (EDC) [1], this paper presents the latest version of the exclusion audit method. For a specific product interaction, this estimates the proportion of the Great British population who would be excluded from using a product or service, due to the demands the product places on key user capabilities. A critical part of the method involves rating of the level of demand placed by a task on a range of key user capabilities, so the procedure to perform this assessment was operationalised and then its reliability was tested with 31 participants. There was no evidence that participants rated the same demands consistently. The qualitative results from the experiment suggest that the consistency of participants’ demand level ratings could be significantly improved if the audit materials and their instructions better guided the participant through the judgement process.

Integrated genomic characterization of endometrial carcinoma

We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.

Decision and reasons for calling an ambulance : patients’ perspective

Background: Demand for pre-hospital emergency care is increasing in Australia as in many other countries. Using posthoc criteria such as triage, diagnosis and admission status, some authors view a considerable number of these as "inappropriate". Yet, calling an ambulance at the time of emergency is rarely studied from the patients’ or their carers’ perspective. This study interviewed patients about the decision, circumstances surrounding and reasons for calling an ambulance in Queensland, Australia. Methods: A cross-sectional survey of patients attending a sample of eight public hospital emergency departments in Queensland was undertaken between March and May 2011. In total, 911 questionnaires were collected (response rate: 67%), of whom 226 (24.8%) had arrived by ambulance. Results: In 35.6% of ambulance arrivals, the decision to request an ambulance was made by the patient; 25% by a doctor; 20% by a family member, friend or carer. Other callers included nurse, people at work or school, and passers-by. Reasons to request an ambulance included urgency (87%) and severity (84%) of the condition. Other reasons included requiring special care (76%), getting higher priority at the emergency department (34%), not having a car (34%), and financial concerns (17%). Decision to request an ambulance varied significantly according to the time of illness onset (e.g. on the day, week before), and location (e.g. home, outside). Conclusion: The decision to call an ambulance is made mostly by non-medical professionals in a perceived emergency situation. They call the ambulance for different reasons but mainly take into account the patient’s welfare and safety. Better understanding of these reasons will affect the direction and effectiveness of demand management strategies.

The growing demand for emergency healthcare

Emergency health is a critical component of health systems; one increasingly congested from growing demand and blocked access to care. The Emergency Health Services Queensland (EHSQ) study aimed to identify the factors driving increased demand for emergency healthcare. This study examined data on patients treated by the ambulance service and Emergency Departments across Queensland. Data was derived from the Queensland Ambulance Service’s (QAS) Ambulance Information Management System and electronic Ambulance Report Form and from the Emergency Department Information System (EDIS). Data was obtained for the period 2001-02 through to 2009-10. A snapshot of users for the 2009-10 year was used to describe the characteristics of users and comparisons made with the year 2003-04 to identify trends. Per capita demand for EDs has increased by 2% per annum over the decade and for ambulance by 3.7% per annum. The growth in ED demand is most significant in more urgent triage categories with decline in less urgent patients. The growth is most prominent amongst patients suffering injuries and poisoning, amongst both men and women and across all age groups. Patients from lower socioeconomic areas appear to have higher utilisation rates and the utilisation rate for indigenous people exceeds those of other backgrounds. The utilisation rates for immigrant people is less than Australian born however it has not been possible to eliminate the confounding impact of age and socioeconomic profiles. These findings contribute to an understanding of the growth in demand for emergency health. It is evident that the growth is amongst patients in genuine need of emergency healthcare and public rhetoric that congested emergency health services is due to inappropriate attendees is unsustainable. The growth in demand over the last decade reflects not only on changing demographics of the Australian population but also changes in health status, standards of acute health care and other social factors.