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

Melt-textured YBa2Cu3O7-x wires having plate-like grains

YBCO wires which consist of well oriented plate-like fine grains are fabricated using a moving furnace to achieve higher mechanical strength. Melt-texturing experiments have been undertaken on YBCO wires with two different compositions: YBa1.5Cu2.9O7-x, and YBa1.8Cu3.0O7-x. Wires are extruded from a mixture of precursor powders (formed by a coprecipitation process) then textured by firing in a moving furnace. Size of secondary phases such as barium cuprate and copper oxide, and overall composition of the sample affect the orientation of the fine grains. At zero magnetic field, the YBa1.5Cu2.9O7-x wire shows the highest critical current density of 1,450 Acm-2 and 8,770 Acm-2 at 77K and 4.2K, respectively. At 1 T, critical current densities of 30 Acm-2 and 200 Acm-2, respectively, are obtained at 77K and 4.2K. Magnetisation curves are also obtained for one sample to evaluate critical current density using the Bean model. Analysis of the microstructure indicates that the starting composition of the green body significantly affects the achievement of grain alignment via melt-texturing processes.

Calling for help : a responsive evaluation of Child Health Line

The project examined the responsiveness of the telenursing service provided by the Child Health Line (hereinafter referred to as CHL). It aimed to provide an account of population usage of the service, the call request types and the response of the service to the calls. In so doing, the project extends the current body of knowledge pertaining to the provision of parenting support through telenursing. Approximately 900 calls to the CHL were audio-recorded over the December 2005-2006 Christmas-New Year period. A protocol was developed to code characteristics of the call, the interactional features between the caller and nurse call-taker, and the extent to which there was (a) agreement on problem definition and the plan of action and (b) interactional alignment between nurse and caller. A quantitative analysis examined the frequencies of the main topics covered in calls to the CHL and any statistical associations between types of calls, length of calls and nurse-caller alignment. In addition, a detailed qualitative analysis was conducted on a subset of calls dealing with the nurse management of calls seeking medical advice and information. Key findings include: • Overall, 74% of the calls discussed parenting and child development issues, 48% discussed health/medical issues, and 16% were information-seeking calls. • More specifically: o 21% discussed health/medical and parenting and child development issues. o 3% discussed parenting and information-seeking issues. o 5% discussed health/medical, parenting/development and information issues. o 18% exclusively focussed on health and medical issues and therefore were outside the remit of the intended scope of the CHL. These calls caused interactional dilemmas for the nurse call-takers as they simultaneously dealt with parental expectations for help and the CHL guidelines indicating that offering medical advice was outside the remit of the service. • Most frequent reasons for calling were to discuss sleep, feeding, normative infant physical functions and parenting advice. • The average length of calls to the CHL was 7 minutes. • Longer calls were more likely to involve nurse call-takers giving advice on more than one topic, the caller displaying strong emotions, the caller not specifically providing the reason for the call, and the caller discussing parenting and developmental issues. • Shorter calls were characterised by the nurse suggesting that the child receive immediate medical attention, the nurse emphasising the importance or urgency of the plan of action, the caller referring to or requesting confirmation of a diagnosis, and caller and nurse call-taker discussion of health and medical issues. • The majority of calls, 92%, achieved parent-nurse alignment by the conclusion of the call. However, 8% did not. • The 8% of calls that were not aligned require further quantitative and qualitative investigation of the interactional features. The findings are pertinent in the current context where Child Health Line now resides within 13HEALTH. These findings indicate: 1. A high demand for parenting advice. 2. Nurse call-takers have a high level of competency in dealing with calls about parenting and normal child development, which is the remit of the CHL. 3. Nurse call-takers and callers achieve a high degree of alignment when both parties agree on a course of action. 4. There is scope for developing professional practice in calls that present difficulties in terms of call content, interactional behaviour and call closure. Recommendations of the project: 1. There are numerous opportunities for further research on interactional aspects of calls to the CHL, such as further investigations of the interactional features and the association of the features to alignment and nonalignment. The rich and detailed insights into the patterns of nurse-parent interactions were afforded by the audio-recording and analysis of calls to the CHL. 2. The regular recording of calls would serve as a way of increasing understanding of the type and nature of calls received, and provide a valuable training resource. Recording and analysing calls to CHL provides insight into the operation of the service, including evidence about the effectiveness of triaging calls. 3. Training in both recognising and dealing with problem calls may be beneficial. For example, calls where the caller showed strong emotion, appeared stressed, frustrated or troubled were less likely to be rated as aligned calls. In calls where the callers described being ‘at their wits end’, or responded to each proposed suggestion with ‘I’ve tried that’, the callers were fairly resistant to advice-giving. 4. Training could focus on strategies for managing calls relating to parenting support and advice, and parental well-being. The project found that these calls were more likely to be rated as being nonaligned. 5. With the implementation of 13HEALTH, future research could compare nurse-parent interaction following the implementation of triaging. Of the calls, 21% had both medical and parenting topics discussed and 5.3% discussed medical, parenting and information topics. Added to this, in 12% of calls, there was ambiguity between the caller and nurse call-taker as to whether the problem was medical or behavioural.

Fourier Lucas-Kanade Algorithm

In this paper we propose a framework for both gradient descent image and object alignment in the Fourier domain. Our method centers upon the classical Lucas & Kanade (LK) algorithm where we represent the source and template/model in the complex 2D Fourier domain rather than in the spatial 2D domain. We refer to our approach as the Fourier LK (FLK) algorithm. The FLK formulation is advantageous when one pre-processes the source image and template/model with a bank of filters (e.g. oriented edges, Gabor, etc.) as: (i) it can handle substantial illumination variations, (ii) the inefficient pre-processing filter bank step can be subsumed within the FLK algorithm as a sparse diagonal weighting matrix, (iii) unlike traditional LK the computational cost is invariant to the number of filters and as a result far more efficient, and (iv) this approach can be extended to the inverse compositional form of the LK algorithm where nearly all steps (including Fourier transform and filter bank pre-processing) can be pre-computed leading to an extremely efficient and robust approach to gradient descent image matching. Further, these computational savings translate to non-rigid object alignment tasks that are considered extensions of the LK algorithm such as those found in Active Appearance Models (AAMs).

Dimensions of short break destination attractiveness : a comparison of cognitive, affective and conative perceptions

Although there has been exponential growth in the number of studies of destination image appearing in the tourism literature, few have addressed the role of affective perceptions. This paper analyses the market positions held by a competitive set of destinations, through a comparison of cognitive, affective and conative perceptions. Cognitive perceptions were measured by trialling a factor analytic adaptation of importance-performance analysis. Affective perceptions were measured using an affective response grid. The alignment of the results from these techniques identified leadership positions held by two quite different destinations on two quite different dimensions of short break destination attractiveness.

Tackling the health burden from household air pollution (HAP) : development and implementation of new WHO Guidelines

Household air pollution (HAP), arising mainly from the combustion of solid and other polluting fuels, is responsible for a very substantial public health burden, most recently estimated as causing 3.5 million premature deaths in 2010. These patterns of household fuel use have also important negative impacts on safety, prospects for poverty reduction and the environment, including climate change. Building on previous air quality guidelines, the WHO is developing new guidelines focused on household fuel combustion, covering cooking, heating and lighting, and although global, the key focus is low and middle income countries reflecting the distribution of disease burden. As discussed in this paper, currently in development, the guidelines will include reviews of a wide range of evidence including fuel use in homes, emissions from stoves and lighting, household air pollution and exposure levels experienced by populations, health risks, impacts of interventions on HAP and exposure, and also key factors influencing sustainable and equitable adoption of improved stoves and cleaner fuels. GRADE, the standard method used for guidelines evidence review may not be well suited to the variety and nature of evidence required for this project, and a modified approach is being developed and tested. Work on the guidelines is being carried out in close collaboration with the UN Foundation Global Alliance on Clean cookstoves, allowing alignment with specific tools including recently developed international voluntary standards for stoves, and the development of country action plans. Following publication, WHO plans to work closely with a number of countries to learn from implementation efforts, in order to further strengthen support and guidance. A case study on the situation and policy actions to date in Bhutan provide an illustration of the challenges and opportunities involved, and the timely importance of the new guidelines and associated research, evaluation and policy development agendas.

A self-assessment tool for knowledge management implementation in the construction industry

Knowledge management (KM) provides a structured process to establish the link between knowledgebased assets within an organisation and its desired business objectives. Although KM issues are becoming increasingly important to the construction industry, there is currently no measurement tool for assessing the implementation of KM programmes. This paper reports on the development of such a tool which can be used as both a means of self-assessment and also for benchmarking purposes. Important practices needed for successful KM implementation were identified from the literature and via a self-administered survey targeting large and medium construction organisations in Hong Kong. Survey findings demonstrate the potential of the proposed self-assessment tool to measure the individual’s perception of the relative importance of KM antecedents and practices, also providing early insight of KM implementation by highlighting the negative gaps between what “is” and “should be” happening, thus identifying areas that need re alignment of KM strategies and tactics. The paper also suggests this tool could be further developed to help organisations to formulate and modify their KM programmes according to their own specific internal business environment, and the nature of their projects.

Dynamic capabilities and performance : strategy, structure and environment

Dynamic capabilities are widely considered to incorporate those processes that enable organizations to sustain superior performance over time. In this paper, we argue theoretically and demonstrate empirically that these effects are contingent on organizational structure and the competitive intensity in the market. Results from partial least square structural equation modeling (PLS-SEM) analyses indicate that organic organizational structures facilitate the impact of dynamic capabilities on organizational performance. Furthermore, we find that the performance effects of dynamic capabilities are contingent on the competitive intensity faced by firms. Our findings demonstrate the performance effects of internal alignment between organizational structure and dynamic capabilities, as well as the external fit of dynamic capabilities with competitive intensity. We outline the advantages of PLS-SEM for modeling latent constructs, such as dynamic capabilities, and conclude with managerial implications.

Reconceptualising policy integration in road safety management

Unless sustained, coordinated action is generated in road safety, road traffic deaths are poised to rise from approximately 1.3 to 1.9 million a year by 2020 (Krug, 2012). To generate this harmonised response, road safety management agencies are being urged to adopt multisectoral collaboration (WHO, 2009b), which is achievable through the principle of policy integration. Yet policy integration, in its current hierarchical format, is marred by a lack of universality of its interpretation, a failure to anticipate the complexities of coordinated effort, dearth of information about its design and the absence of a normative perspective to share responsibility. This paper addresses this ill-conception of policy integration by reconceptualising it through a qualitative examination of 16 road safety stakeholders’ written submissions, lodged with the Australian Transport Council in 2011. The resulting, new principle of policy integration, Participatory Deliberative Integration, provides a conceptual framework for the alignment of effort across stakeholders in transport, health, traffic law enforcement, relevant trades and the community. With the adoption of Participatory Deliberative Integration, road safety management agencies should secure the commitment of key stakeholders in the development and implementation of, amongst other policy measures, National Road Safety Strategies and Mix Mode Integrated Timetabling.

A comparative analysis of the integration of SOA elements in widely-used enterprise architecture frameworks

In recent years, enterprise architecture (EA) has captured increasing interest as a means to systematically consolidate and manage various enterprise artefacts in order to provide holistic decision support for business/IT alignment and business/IT landscapes management. To provide a holistic perspective on the enterprise over time, EA frameworks need to co-evolve with the changes in the enterprise and its IT over time. In this paper we focus on the emergence of Service-Oriented Architecture (SOA). There is a need to integrate SOA with EA to keep EA relevant and to use EA products to help drive successful SOA. This paper investigates and compares the integration of SOA elements in five widely used EA frameworks: Archimate, The Open Group Architecture Framework (TOGAF), Federal Enterprise Architecture Framework (FEAF), Department of Defence Architecture Framework (DoDAF) and the Ministry of Defence Architecture Framework (MODAF). It identifies what SOA elements are considered and their relative position in the overall structure. The results show that services and related elements are far from being well-integrated constructs in current EA frameworks and that the different EA frameworks integrated SOA elements in substantially different ways. Our results can support the academic EA and SOA communities with a closer and more consistent integration of EA and SOA and support practitioners in identifying an EA framework that provides the SOA support that matches their requirements.

Catalysing design principles through the dreaming of sustainable subtropical cityscapes : the collaborative construction of new place identities

This paper addresses the question of how to open up pathways and build capacity to facilitate the movement towards sustainable sub-tropical cities. The focus is on outlining a collaborative planning and co-design process that can help catalyse the emergence of sustainable place-habitats and so re-weave and colour anew the tapestry of our sub-tropical cities. Cities are portrayed as self-organising complex adaptive system phenomena, being constantly re-shaped by local and global social-political, environmental, cultural and economic forces as well as planning regimes. While constructing a sustainable city is at essence a design process incorporating new sustainable practices and legislation to reinforce their use, these steps are necessary but not sufficient. Sustainable sub-tropical city-making could be re-thought as a dreaming-re-storying process. This paper explores a new co-design process, which can channel collaborative efforts around re-inventing sustainable place-habitats across the cityscape. A further outcome of this co-design process is the alignment of the emergent design principles and planning actions that can trigger the re-storying of a new sustainable sub-tropical city. Besides a new co-design process, we also advocate the building of sub-tropical city learning networks to facilitate the cross-fertilization for Dreaming sustainable sub-tropical cities.

Footprint-based estimates of arch structure are confounded by body composition in adults

Previous research employing indirect measures of arch structure, such as those derived from footprints, have indicated that obesity results in a “flatter” foot type. In the absence of radiographic measures, however, definitive conclusions regarding the osseous alignment of the foot cannot be made. We determined the effect of body mass index (BMI) on radiographic and footprint‐based measures of arch structure. The research was a cross‐sectional study in which radiographic and footprint‐based measures of foot structure were made in 30 subjects (10 males, 20 female) in addition to standard anthropometric measures of height, weight, and BMI. Multiple (univariate) regression analysis demonstrated that both BMI ( β  = 0.39, t 26  = 2.12, p  = 0.04) and radiographic arch alignment ( β  = 0.51, t 26  = 3.32, p  < 0.01) were significant predictors of footprint‐based measures of arch height after controlling for all variables in the model ( R 2  = 0.59, F 3,26  = 12.3, p  < 0.01). In contrast, radiographic arch alignment was not significantly associated with BMI ( β  = −0.03, t 26  = −0.13, p  = 0.89) when Arch Index and age were held constant ( R 2  = 0.52, F 3,26  = 9.3, p  < 0.01). Adult obesity does not influence osseous alignment of the medial longitudinal arch, but selectively distorts footprint‐based measures of arch structure. Footprint‐based measures of arch structure should be interpreted with caution when comparing groups of varying body composition.

The acute transverse strain response of the patellar tendon to quadriceps exercise

Introduction: The human patellar tendon is highly adaptive to changes in habitual loading but little is known about its acute mechanical response to exercise. This research evaluated the immediate transverse strain response of the patellar tendon to a bout of resistive quadriceps exercise. Methods: Twelve healthy adult males (mean age 34.0+/-12.1 years, height 1.75+/-0.09 m and weight 76.7+/-12.3 kg) free of knee pain participated in the research. A 10-5 MHz linear-array transducer was used to acquire standardised sagittal sonograms of the right patellar tendon immediately prior to and following 90 repetitions of a double-leg parallel-squat exercise performed against a resistance of 175% bodyweight. Tendon thickness was determined 20-mm distal to the pole of the patellar and transverse Hencky strain was calculated as the natural log of the ratio of post- to pre-exercise tendon thickness and expressed as a percentage. Measures of tendon echotexture (echogenicity and entropy) were also calculated from subsequent gray-scale profiles. Results: Quadriceps exercise resulted in an immediate decrease in patellar tendon thickness (P<.05), equating to a transverse strain of -22.5+/-3.4%, and was accompanied by increased tendon echogenicity (P<.05) and decreased entropy (P<.05). The transverse strain response of the patellar tendon was significantly correlated with both tendon echogenicity (r = -0.58, P<.05) and entropy following exercise (r=0.73, P<.05), while older age was associated with greater entropy of the patellar tendon prior to exercise (r=0.79, P<.05) and a reduced transverse strain response (r=0.61, P<.05) following exercise. Conclusions: This study is the first to show that quadriceps exercise invokes structural alignment and fluid movement within the matrix that are manifest by changes in echotexture and transverse strain in the patellar tendon., (C)2012The American College of Sports Medicine

Technological innovation and operational effectiveness : their role in achieving performance improvements

The purpose of this article is to examine the role of the alignment between technological innovation effectiveness and operational effectiveness after the implementation of enterprise information systems, and the impact of this alignment on the improvement in operational performance. Confirmatory factor analysis was used to examine structural relationships between the set of observed variables and the set of continuous latent variables. The findings from this research suggest that the dimensions stemming from technological innovation effectiveness such as system quality, information quality, service quality, user satisfaction and the performance objectives stemming from operational effectiveness such as cost, quality, reliability, flexibility and speed are important and significantly well-correlated factors. These factors promote the alignment between technological innovation effectiveness and operational effectiveness and should be the focus for managers in achieving effective implementation of technological innovations. In addition, there is a significant and direct influence of this alignment on the improvement of operational performance. The principal limitation of this study is that the findings are based on investigation of small sample size.

Barriers to the adoption of health information technology

Information Technology (IT) is successfully applied in a diverse range of fields. Though, the field of Medical Informatics is more than three decades old, it shows a very slow progress compared to many other fields in which the application of IT is growing rapidly. The spending on IT in health care is shooting up but the road to successful use of IT in health care has not been easy. This paper discusses about the barriers to the successful adoption of information technology in clinical environments and outlines the different approaches used by various countries and organisations to tackle the issues successfully. Investing financial and other resources to overcome the barriers for successful adoption of HIT is highly important to realise the dream of a future healthcare system with each customer having secure, private Electronic Health Record (EHR) that is available whenever and wherever needed, enabling the highest degree of coordinated medical care based on the latest medical knowledge and evidence. Arguably, the paper reviews barriers to HIT from organisations’ alignment in respect to the leadership; with their stated values when accepting or willingness to consider the HIT as a determinant factor on their decision-making processes. However, the review concludes that there are many aspects of the organisational accountability and readiness to agree to the technology implementation.