Blast atlas: a virtual observatory for genomes

Following the completion of the draft Human Genome in 2001, genomic sequence data is becoming available at an accelerating rate, fueled by advances in sequencing and computational technology. Meanwhile, large collections of astronomical and geospatial data have allowed the creation of virtual observatories, accessible throughout the world and requiring only commodity hardware. Through a combination of advances in data management, data mining and visualization, this infrastructure enables the development of new scientific and educational applications as diverse as galaxy classification and real-time tracking of earthquakes and volcanic plumes. In the present paper, we describe steps taken along a similar path towards a virtual observatory for genomes – an immersive three-dimensional visual navigation and query system for comparative genomic data.

Do ontological deficiencies in modeling grammars matter?

Conceptual modeling grammars are a fundamental means for specifying information systems requirements. However, the actual usage of these grammars is only poorly understood. In particular, little is known about how properties of these grammars inform usage beliefs such as usefulness and ease of use. In this paper we use an ontological theory to describe conceptual modeling grammars in terms of their ontological deficiencies, and formulate two propositions in regard to how these ontological deficiencies influence primary usage beliefs. Using BPMN as an example modeling grammar, we surveyed 528 modeling practitioners to test the theorized relationships. Our results show that users of conceptual modeling grammars perceive ontological deficiencies to exist, and that these deficiency perceptions are negatively associated with usefulness and ease of use of these grammars. With our research we provide empirical evidence in support of the predictions of the ontological theory of modeling grammar expressiveness, and we identify previously unexplored links between conceptual modeling grammars and grammar usage beliefs. This work implies for practice a much closer coupling of the act of (re ) designing modeling grammars with usage-related success metrics.

Engineering an Ecosystem : Taking Cues from Nature’s Paradigm to Build Tissue in the Lab and the Body

This manuscript took a 'top down' approach to understanding survival of inhabitant cells in the ecosystem bone, working from higher to lower length and time scales through the hierarchical ecosystem of bone. Our working hypothesis is that nature “engineered” the skeleton using a 'bottom up' approach,where mechanical properties of cells emerge from their adaptation to their local me-chanical milieu. Cell aggregation and formation of higher order anisotropic struc- ture results in emergent architectures through cell differentiation and extracellular matrix secretion. These emergent properties, including mechanical properties and architecture, result in mechanical adaptation at length scales and longer time scales which are most relevant for the survival of the vertebrate organism [Knothe Tate and von Recum 2009]. We are currently using insights from this approach to har-ness nature’s regeneration potential and to engineer novel mechanoactive materials [Knothe Tate et al. 2007, Knothe Tate et al. 2009]. In addition to potential applications of these exciting insights, these studies may provide important clues to evolution and development of vertebrate animals. For instance, one might ask why mesenchymal stem cells condense at all? There is a putative advantage to self-assembly and cooperation, but this advantage is somewhat outweighed by the need for infrastructural complexity (e.g., circulatory systems comprised of specific differentiated cell types which in turn form conduits and pumps to overcome limitations of mass transport via diffusion, for example; dif-fusion is untenable for multicellular organisms larger than 250 microns in diameter. A better question might be: Why do cells build skeletal tissue? Once cooperatingcells in tissues begin to deplete local sources of food in their aquatic environment, those that have evolved a means to locomote likely have an evolutionary advantage. Once the environment becomes less aquarian and more terrestrial, self-assembled organisms with the ability to move on land might have conferred evolutionary ad-vantages as well. So did the cytoskeleton evolve several length scales, enabling the emergence of skeletal architecture for vertebrate animals? Did the evolutionary advantage of motility over noncompliant terrestrial substrates (walking on land) favor adaptations including emergence of intracellular architecture (changes in the cytoskeleton and upregulation of structural protein manufacture), inter-cellular con- densation, mineralization of tissues, and emergence of higher order architectures?How far does evolutionary Darwinism extend and how can we exploit this knowl- edge to engineer smart materials and architectures on Earth and new, exploratory environments?[Knothe Tate et al. 2008]. We are limited only by our ability to imagine. Ultimately, we aim to understand nature, mimic nature, guide nature and/or exploit nature’s engineering paradigms without engineer-ing ourselves out of existence.

Multi-version documents : A digitisation solution for textual cultural artefacts

Textual cultural heritage artefacts present two serious problems for the encoder: how to record different or revised versions of the same work, and how to encode conflicting perspectives of the text using markup. Both are forms of textual variation, and can be accurately recorded using a multi-version document, based on a minimally redundant directed graph that cleanly separates variation from content.

Patient preference for falls prevention in hospitals revealed through willingness-to-pay, contingent valuation survey

Rationale, aims and objectives: Patient preference for interventions aimed at preventing in-hospital falls has not previously been investigated. This study aims to contrast the amount patients are willing to pay to prevent falls through six intervention approaches. ----- ----- Methods: This was a cross-sectional willingness-to-pay (WTP), contingent valuation survey conducted among hospital inpatients (n = 125) during their first week on a geriatric rehabilitation unit in Queensland, Australia. Contingent valuation scenarios were constructed for six falls prevention interventions: a falls consultation, an exercise programme, a face-to-face education programme, a booklet and video education programme, hip protectors and a targeted, multifactorial intervention programme. The benefit to participants in terms of reduction in risk of falls was held constant (30% risk reduction) within each scenario. ----- ----- Results: Participants valued the targeted, multifactorial intervention programme the highest [mean WTP (95% CI): $(AUD)268 ($240, $296)], followed by the falls consultation [$215 ($196, $234)], exercise [$174 ($156, $191)], face-to-face education [$164 ($146, $182)], hip protector [$74 ($62, $87)] and booklet and video education interventions [$68 ($57, $80)]. A ‘cost of provision’ bias was identified, which adversely affected the valuation of the booklet and video education intervention. ----- ----- Conclusion: There may be considerable indirect and intangible costs associated with interventions to prevent falls in hospitals that can substantially affect patient preferences. These costs could substantially influence the ability of these interventions to generate a net benefit in a cost–benefit analysis.

Model-order selection in Zernike polynomial expansion of corneal surfaces using the efficient detection criterion

Corneal-height data are typically measured with videokeratoscopes and modeled using a set of orthogonal Zernike polynomials. We address the estimation of the number of Zernike polynomials, which is formalized as a model-order selection problem in linear regression. Classical information-theoretic criteria tend to overestimate the corneal surface due to the weakness of their penalty functions, while bootstrap-based techniques tend to underestimate the surface or require extensive processing. In this paper, we propose to use the efficient detection criterion (EDC), which has the same general form of information-theoretic-based criteria, as an alternative to estimating the optimal number of Zernike polynomials. We first show, via simulations, that the EDC outperforms a large number of information-theoretic criteria and resampling-based techniques. We then illustrate that using the EDC for real corneas results in models that are in closer agreement with clinical expectations and provides means for distinguishing normal corneal surfaces from astigmatic and keratoconic surfaces.

Intake of isoflavone and lignan phytoestrogens and associated demographic and lifestyle factors in older Australian women

The purpose was to determine intake of phytoestrogens in a sample of older Australian women, and to investigate associated lifestyle factors. Subjects were an age-stratified sample of 511 women aged 40-80 y, randomly selected from the electoral roll and participating in the Longitudinal Assessment of Ageing in Women at the Royal Brisbane and Women’s Hospital. A cross-sectional study was conducted to assess isoflavone and lignan intake over the past month from food and supplements using a 112-item phytoestrogen frequency questionnaire. Data were also collected on nutrient intakes, physical activity, smoking, alcohol, non-prescription supplements, hormone therapy, education and occupation. Logistic regression was used to evaluate associations between demographic and lifestyle variables and soy/linseed consumption while controlling for age. Isoflavone intakes were significantly higher in the younger compared to older age groups (p<0.001); there were no age-related differences in lignan intake. Forty-five percent of women consumed at least one serve of a soy and/or linseed item and were defined as a soy/linseed consumer. Median (range) intakes by consumers for isoflavones and lignans (3.9 (0-172) mg/d and 2.4 (0.1-33) mg/d) were higher than intakes by non-consumers (0.004 (0-2.6) mg/d and 1.57 (0.44-4.7) mg/d), respectively (p<0.001). Consumers had higher intakes of dietary fibre (p=0.003), energy (p=0.04) and polyunsaturated fat (p=0.004), and higher levels of physical activity (p=0.006), socio-economic position (p<0.001), education (p<0.001) and supplement use (p<0.001). Women who consumed soy or linseed foods differed in lifestyle and demographic characteristics suggesting these factors should be considered when investigating associations with chronic disease outcomes.

Survey of novice motorcycle riders and their riding experience before licensing

Graduated licensing schemes have been found to reduce the crash risk of young novice drivers, but there is less evidence of their success with novice motorcycle riders. This study examined the riding experience of a sample of Australian learner-riders to establish the extent and variety of their riding practice during the learner stage. Riders completed an anonymous questionnaire at a compulsory rider-training course for the licensing test. The majority of participants were male (81%) with an average age of 33 years. They worked full time (81%), held an unrestricted driver's license (81%), and owned the motorcycle that they rode (79%). These riders had held their learner's license for an average of 6 months. On average, they rode 6.4 h/week. By the time they attempted the rider-licensing test, they had ridden a total of 101 h. Their total hours of on-road practice were comparable to those of learner-drivers at the same stage of licensing, but they had less experience in adverse or challenging road conditions. A substantial proportion had little or no experience of riding in the rain (57%), at night (36%), in heavy traffic (22%), on winding rural roads (52%), or on high-speed roads (51%). These findings highlight the differences in the learning processes between unsupervised novice motorcycle riders and supervised novice drivers. Further research is necessary to clarify whether specifying the conditions under which riders should practice during the graduated licensing process would likely reduce or increase their crash risk.

Use of IEEE 1588-2008 for a sampled value process bus in transmission substations

IEC Technical Committee 57 (TC57) published a series of standards and technical reports for “Communication networks and systems for power utility automation” as the IEC 61850 series. Sampled value (SV) process buses allow for the removal of potentially lethal voltages and damaging currents inside substation control rooms and marshalling kiosks, reduce the amount of cabling required in substations, and facilitate the adoption of non-conventional instrument transformers. IEC 61850-9-2 provides an inter-operable solution to support multi-vendor process bus solutions. A time synchronisation system is required for a SV process bus, however the details are not defined in IEC 61850-9-2. IEEE Std 1588-2008, Precision Time Protocol version 2 (PTPv2), provides the greatest accuracy of network based time transfer systems, with timing errors of less than 100 ns achievable. PTPv2 is proposed by the IEC Smart Grid Strategy Group to synchronise IEC 61850 based substation automation systems. IEC 61850-9-2, PTPv2 and Ethernet are three complementary protocols that together define the future of sampled value digital process connections in substations. The suitability of PTPv2 for use with SV is evaluated, with preliminary results indicating that steady state performance is acceptable (jitter < 300 ns), and that extremely stable grandmaster oscillators are required to ensure SV timing requirements are met when recovering from loss of external synchronisation (such as GPS).

Critical literacies in place : teachers who work for just and sustainable communities

This chapter draws upon theories of social justice, critical literacy and place-based pedagogies and two research projects to discuss how teachers are working ethically and creatively towards a sustainable and just society in their place(s).

Digital dawn : a revolution in movie distribution?

How will the digital technology revolution impact the movie business? Hollywood developed a highly successful industrial system that has functioned well for almost a century in the sense that it enabled the Major film studios to largely control and dominate the industry. However, the new digital technology may now be propelling Hollywood toward the biggest technological transition since the creation of the studio system almost a century ago. For example, Major Hollywood studios are already beginning to provide video-on-demand (VOD) digital distribution of movies over the Internet. This article examines what is happening, and why. It sets out the background and the incipient changes already occurring. It makes an argument regarding the fundamental strategic dynamics, that acetate film was the key to the control of the Hollywood system, and speculates about how a shift away from acetate film to digital video may transform that system. The focus is on the impact on how the Major studios release and market their movies, and how new market and marketing opportunities for the low-budget independent filmmaking sector may arise.

Modeling circulation of train-set with multiple routing

Planning on utilization of train-set is one of the key tasks of transport organization for passenger dedicated railway in China. It also has strong relationships with timetable scheduling and operation plans at a station. To execute such a task in a railway hub pooling multiple railway lines, the characteristics of multiple routing for train-set is discussed in term of semicircle of train-sets' turnover. In programming the described problem, the minimum dwell time is selected as the objectives with special derive constraints of the train-set's dispatch, the connecting conditions, the principle of uniqueness for train-sets, and the first plus for connection in the same direction based on time tolerance σ. A compact connection algorithm based on time tolerance is then designed. The feasibility of the model and the algorithm is proved by the case study. The result indicates that the circulation model and algorithm about multiple routing can deal with the connections between the train-sets of multiple directions, and reduce the train's pulling in or leaving impact on the station's throat.

Barrow Island's biosecurity : catching the unknown invader

When industry meets a conservation area, animals or plants from outside may hitch a lift and potentially wreak havoc. How can you be sure of catching the intruders – or at least 80% sure? A government directive instructed Frith Jarrad, Peter Whittle, Susan Barrett and Kerrie Mengersen to come up with a statistically measurable scheme.

Mechanical Behavior of Articular Cartilage After Osteochondral Autograft Transfer in an Ovine Model

BACKGROUND: Grafting of autologous hyaline cartilage and bone for articular cartilage repair is a well-accepted technique. Although encouraging midterm clinical results have been reported, no information on the mechanical competence of the transplanted joint surface is available. HYPOTHESIS: The mechanical competence of osteochondral autografts is maintained after transplantation. STUDY DESIGN: Controlled laboratory study. METHODS: Osteochondral defects were filled with autografts (7.45 mm in diameter) in one femoral condyle in 12 mature sheep. The ipsilateral femoral condyle served as the donor site, and the resulting defect (8.3 mm in diameter) was left empty. The repair response was examined after 3 and 6 months with mechanical and histologic assessment and histomorphometric techniques. RESULTS: Good surface congruity and plug placement was achieved. The Young modulus of the grafted cartilage significantly dropped to 57.5% of healthy tissue after 3 months (P < .05) but then recovered to 82.2% after 6 months. The aggregate and dynamic moduli behaved similarly. The graft edges showed fibrillation and, in some cases (4 of 6), hypercellularity and chondrocyte clustering. Subchondral bone sclerosis was observed in 8 of 12 cases, and the amount of mineralized bone in the graft area increased from 40% to 61%. CONCLUSIONS: The mechanical quality of transplanted cartilage varies considerably over a short period of time, potentially reflecting both degenerative and regenerative processes, while histologically signs of both cartilage and bone degeneration occur. CLINICAL RELEVANCE: Both the mechanically degenerative and restorative processes illustrate the complex progression of regeneration after osteochondral transplantation. The histologic evidence raises doubts as to the long-term durability of the osteochondral repair.

Adaptive GPS duty cycling and radio ranging for energy-efficient localization

This paper addresses the tradeoff between energy consumption and localization performance in a mobile sensor network application. The focus is on augmenting GPS location with more energy-efficient location sensors to bound position estimate uncertainty in order to prolong node lifetime. We use empirical GPS and radio contact data from a largescale animal tracking deployment to model node mobility, GPS and radio performance. These models are used to explore duty cycling strategies for maintaining position uncertainty within specified bounds. We then explore the benefits of using short-range radio contact logging alongside GPS as an energy-inexpensive means of lowering uncertainty while the GPS is off, and we propose a versatile contact logging strategy that relies on RSSI ranging and GPS lock back-offs for reducing the node energy consumption relative to GPS duty cycling. Results show that our strategy can cut the node energy consumption by half while meeting application specific positioning criteria.