BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Multiple indicators of ambient and personal ultraviolet radiation exposure and risk of non-Hodgkin lymphoma (United States)

Recent epidemiologic studies have suggested that ultraviolet radiation (UV) may protect against non-Hodgkin lymphoma (NHL), but few, if any, have assessed multiple indicators of ambient and personal UV exposure. Using the US Radiologic Technologists study, we examined the association between NHL and self-reported time outdoors in summer, as well as average year-round and seasonal ambient exposures based on satellite estimates for different age periods, and sun susceptibility in participants who had responded to two questionnaires (1994–1998, 2003–2005) and who were cancer-free as of the earlier questionnaire. Using unconditional logistic regression, we estimated the odds ratio (OR) and 95% confidence intervals for 64,103 participants with 137 NHL cases. Self-reported time outdoors in summer was unrelated to risk. Lower risk was somewhat related to higher average year-round and winter ambient exposure for the period closest in time, and prior to, diagnosis (ages 20–39). Relative to 1.0 for the lowest quartile of average year-round ambient UV, the estimated OR for successively higher quartiles was 0.68 (0.42–1.10); 0.82 (0.52–1.29); and 0.64 (0.40–1.03), p-trend = 0.06), for this age period. The lower NHL risk associated with higher year-round average and winter ambient UV provides modest additional support for a protective relationship between UV and NHL.

Applying SVMs and weight-based factor analysis to unsupervised adaptation for speaker verification

This paper presents an extended study on the implementation of support vector machine(SVM) based speaker verification in systems that employ continuous progressive model adaptation using the weight-based factor analysis model. The weight-based factor analysis model compensates for session variations in unsupervised scenarios by incorporating trial confidence measures in the general statistics used in the inter-session variability modelling process. Employing weight-based factor analysis in Gaussian mixture models (GMM) was recently found to provide significant performance gains to unsupervised classification. Further improvements in performance were found through the integration of SVM-based classification in the system by means of GMM supervectors. This study focuses particularly on the way in which a client is represented in the SVM kernel space using single and multiple target supervectors. Experimental results indicate that training client SVMs using a single target supervector maximises performance while exhibiting a certain robustness to the inclusion of impostor training data in the model. Furthermore, the inclusion of low-scoring target trials in the adaptation process is investigated where they were found to significantly aid performance.

Performance optimization for parallel processing on a multiple-CPU server

Symmetric multi-processor (SMP) systems, or multiple-CPU servers, are suitable for implementing parallel algorithms because they employ dedicated communication devices to enhance the inter-processor communication bandwidth, so that a better performance can be obtained. However, the cost for a multiple-CPU server is high and therefore, the server is usually shared among many users. The work-load due to other users will certainly affect the performance of the parallel programs so it is desirable to derive a method to optimize parallel programs under different loading conditions. In this paper, we present a simple method, which can be applied in SPMD type parallel programs, to improve the speedup by controlling the number of threads within the programs.

Automatic generation of assertions to detect potential security vulnerabilities in C programs that use union and pointer types

Type unions, pointer variables and function pointers are a long standing source of subtle security bugs in C program code. Their use can lead to hard-to-diagnose crashes or exploitable vulnerabilities that allow an attacker to attain privileged access over classified data. This paper describes an automatable framework for detecting such weaknesses in C programs statically, where possible, and for generating assertions that will detect them dynamically, in other cases. Exclusively based on analysis of the source code, it identifies required assertions using a type inference system supported by a custom made symbol table. In our preliminary findings, our type system was able to infer the correct type of unions in different scopes, without manual code annotations or rewriting. Whenever an evaluation is not possible or is difficult to resolve, appropriate runtime assertions are formed and inserted into the source code. The approach is demonstrated via a prototype C analysis tool.

Post-occupancy analysis of a Zero Energy Hojme (ZEH)

Zero energy buildings (ZEB) and zero energy homes (ZEH) are a current hot topic globally for policy makers (what are the benefits and costs), designers (how do we design them), the construction industry (can we build them), marketing (will consumers buy them) and researchers (do they work and what are the implications). This paper presents initial findings from actual measured data from a 9 star (as built), off-ground detached family home constructed in south-east Queensland in 2008. The integrated systems approach to the design of the house is analysed in each of its three main goals: maximising the thermal performance of the building envelope, minimising energy demand whilst maintaining energy service levels, and implementing a multi-pronged low carbon approach to energy supply. The performance outcomes of each of these stages are evaluated against definitions of Net Zero Carbon / Net Zero Emissions (Site and Source) and Net Zero Energy (onsite generation v primary energy imports). The paper will conclude with a summary of the multiple benefits of combining very high efficiency building envelopes with diverse energy management strategies: a robustness, resilience, affordability and autonomy not generally seen in housing.

Multiple Health Behavior Changes and Co-variation in a Telephone Counseling Trial

Background Delivering effective multiple health behavior interventions to large numbers of adults with chronic conditions via primary care settings is a public health priority. Purpose Within a 12-month, telephone-delivered diet and physical activity intervention with multiple behavioral outcomes, we examined the extent and co-variation of multiple health behavior change. Methods A cluster-randomized trial with 434 patients with type 2 diabetes or hypertension were recruited from 10 general practices, which were randomized to receive telephone counseling or usual care. Results Those receiving telephone counseling were significantly more likely than those in usual care to make greater reductions in multiple behaviors after adjusting for baseline risk behaviors (OR 2.42; 95%CI 1.43, 4.11). Controlling for baseline risk and group allocation, making changes to either physical activity, fat, vegetable, or fiber intake was associated with making significantly more improvements in other behaviors. Conclusions For patients with chronic conditions, telephone counseling can significantly improve multiple health behaviors, with behavioral changes tending to co-vary.

Generation evolution in GA application on railway traffic control

This paper presents a Genetic Algorithms (GA) approach to resolve traffic conflicts at a railway junction. The formulation of the problem for the suitable application of GA will be discussed and three neighborhoods have been proposed for generation evolution. The performance of the GA is evaluated by computer simulation. This study paves the way for more applications of artificial intelligence techniques on a rather conservative industry.

Theoretical analysis of the motion and evaporation of exhaled respiratory droplets of mixed composition

The dynamics of droplets exhaled from the respiratory system during coughing or talking is addressed. A mathematical model is presented accounting for the motion of a droplet in conjunction with its evaporation. Droplet evaporation and motion are accounted for under two scenarios: 1) A well mixed droplet and 2) A droplet with inner composition variation. A multiple shells model was implemented to account for internal mass and heat transfer and for concentration and temperature gradients inside the droplet. The trajectories of the droplets are computed for a range of conditions and the spatial distribution and residence times of such droplets are evaluated.

Incorporating authentic assessment into different university learning scenarios

There is a current requirement for universities to prepare graduates who are skilled in practical as well as theoretical knowledge of the workplace. It is argued in this paper that assessment, as integral to the teaching/learning process, should also relate to the real world context of the workplace, in that students are able to transform, use and apply the knowledge that they learn into these contexts. While assessment authentic for students in a university setting is often a difficult task for lecturers. This paper discusses three different learning contexts that involved different assessment experiences linked in some way to real world learning and application of the theory. The results of the trial indicated that as contexts became close to a real world experience, the sustainability of the assessment became more problematic. While acknowledging the difficulty of these practices, it is suggested that there is a need for a continuous cycle of evaluation amid some creative and innovative approaches to assessment practice.

Directional earth fault relay operation in mutually coupled multiple circuit distribution lines

Many of the power utilities around the world experienced spurious tripping of directional earth fault relays in their mesh distribution networks due to induced circulating currents. This circulating current is zero sequence and induced in the healthy circuit due to the zero sequence current flow resulting from a ground fault of a parallel circuit. This paper quantitatively discusses the effects of mutual coupling on earth fault protection of distribution systems. An actual spurious tripping event is analyzed to support the theory and to present options for improved resilience to spurious tripping.

Measuring export readiness using a multiple-item index

Since the 1970s the internationalisation process of firms has attracted wide research interest. One of the dominant explanations of firm internationalisation resulting from this research activity is the Uppsala stages model. In this paper, a pre-internationalisation phase is incorporated into the traditional Uppsala model to address the question: What are the antecedents of this model? Four concepts are proposed as the key components that define the experiential learning process underlying a firm’s pre-export phase: export stimuli, attitudinal/psychological commitment, resources and lateral rigidity. Through a survey of 290 Australian exporting and non-exporting small-medium sized firms, data relating to the four pre-internationalisation concepts is collected and an Export Readiness Index (ERI) is constructed through factor analysis. Using logistic regression, the ERI is tested as a tool for analysing export readiness among Australian SMEs.

Queensland Aborigines, multiple realities and the social sources of suffering. Part 2: Suicide, spirits and symbolism

This is the second part of a paper that explores a range of magico-religious experiences such as immaterial voices and visions, in terms of local cultural, moral and socio-political circumstances in an Aboriginal town in rural Queensland. This part of the paper explores the political and cultural symbolism and meaning of suicide. It charts the saliency of suicide amongst two groups of kin and cohorts and the social meaningfulness and problematic of the voices and visions in relation to suicide, to identity and family forms and to funerals and a heavily drinking lifestyle. I argue that voices and visions are used to reinterpret social experience and to establish meaning and that tragically suicide evokes connectivity rather than anomie and here cannot be understood merely as an individualistic act or evidence of individual pathology. Rather it is about transformation and crossing a threshold to join an enduring domain of Aboriginality. In this life world, where family is the highest social value and where a relational view of persons holds sway, the individualistic practice of psychiatric and other helping professions, is a considerable problem.

Prospective bus rapid transit scenarios for pilot corridor in Dhaka

Dhaka doesn’t have a mature transport system. Lacking in institutional arrangements, policy and planning, and law enforcement, the transport system operates has developed ad hoc and is situationally problematic. Absence of proper coordination between modes, poor public transport system, inadequate pedestrian facilities, and environmental degradation justify full consideration of Bus Rapid Transit (BRT) in Dhaka. BRT centres on sustainable transport principles. BRT is a system, which is capable to mitigate Dhaka’s transport problem if properly planned. In Strategic transport plan of Dhaka three BRT transport corridor has been proposed and BRT pre-feasibility study came up with one pilot corridor for early implementation of BRT. This paper first reviews international best practices then explores various BRT system packages and evaluates the suitability of these BRT packages by analyzing current bus service condition and physical and geometric configuration along the BRT pilot corridor. It concludes by proposing some BRT scenarios, which can be considered for further evaluation with respect to speed, delay, travel time and environmental pollution.