SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

CDKN2A is not the principal target of deletions on the short arm of chromosome 9 in neuroendocrine (Merkel cell) carcinoma of the skin

The majority of small-cell lung cancers (SCLCs) express p16 but not pRb. Given our previous study showing loss of pRb in Merkel cell carcinoma (MCC)/neuroendocrine carcinoma of the skin and the clinicopathological similarities between SCLC and MCC, we wished to determine if this was also the case in MCC. Twenty-nine MCC specimens from 23 patients were examined for deletions at 10 loci on 9p and 1 on 9q. No loss of heterozygosity (LOH) was seen in 9 patients including 2 for which tumour and cell line DNAs were examined. Four patients had LOH for all informative loci on 9p. Ten tumours showed more limited regions of loss on 9p, and from these 2 common regions of deletion were determined. Half of all informative cases had LOH at D9S168, the most telomeric marker examined, and 3 specimens showed loss of only D9S168. A second region (IFNA-D9S126) showed LOH in 10 (44%) cases, and case MCC26 showed LOH for only D9S126, implicating genes centromeric of the CDKN2A locus. No mutations in the coding regions of p16 were seen in 7 cell lines tested, and reactivity to anti-p16 antibody was seen in all 11 tumour specimens examined and in 6 of 7 cell lines from 6 patients. Furthermore, all cell lines examined reacted with anti-p14(ARF) antibody. These results suggest that neither transcript of the CDKN2A locus is the target of deletions on 9p in MCC and imply the existence of tumour-suppressor genes mapping both centromeric and telomeric of this locus.

The Kinaesthetic Fusion Effect : fast-forward 30 years

This study investigated the Kinaesthetic Fusion Effect (KFE) first described by Craske and Kenny in 1981. The current study did not replicate these findings following a change in the reporting method used by participants. Participants did not perceive any reduction in the sagittal separation of a button pressed by the index finger of one arm and a probe touching the other, following repeated exposure to the tactile stimuli present on both unseen arms. This study’s failure to replicate the widely-cited KFE as described by Craske et al. (1984) suggests that it may be contingent on several aspects of visual information, especially the availability of a specific visual reference, the role of instructions regarding gaze direction, and the potential use of a line of sight strategy when referring felt positions to an interposed surface. In addition, a foreshortening effect was found; this may result from a line-of-sight judgment and represent a feature of the reporting method used. Finally, this research will benefit future studies that require participants to report the perceived locations of the unseen limbs.

i-vector based speaker recognition on short utterances

Robust speaker verification on short utterances remains a key consideration when deploying automatic speaker recognition, as many real world applications often have access to only limited duration speech data. This paper explores how the recent technologies focused around total variability modeling behave when training and testing utterance lengths are reduced. Results are presented which provide a comparison of Joint Factor Analysis (JFA) and i-vector based systems including various compensation techniques; Within-Class Covariance Normalization (WCCN), LDA, Scatter Difference Nuisance Attribute Projection (SDNAP) and Gaussian Probabilistic Linear Discriminant Analysis (GPLDA). Speaker verification performance for utterances with as little as 2 sec of data taken from the NIST Speaker Recognition Evaluations are presented to provide a clearer picture of the current performance characteristics of these techniques in short utterance conditions.

Fundus image registration algorithms for a pc-based image processing system

We have developed digital image registration program for a MC 68000 based fundus image processing system (FIPS). FIPS not only is capable of executing typical image processing algorithms in spatial as well as Fourier domain, the execution time for many operations has been made much quicker by using a hybrid of "C", Fortran and MC6000 assembly languages.

Efficient hybrid-game strategies coupled to evolutionary algorithms for robust multidisciplinary design optimization in aerospace engineering

A number of game strategies have been developed in past decades and used in the fields of economics, engineering, computer science, and biology due to their efficiency in solving design optimization problems. In addition, research in multiobjective and multidisciplinary design optimization has focused on developing a robust and efficient optimization method so it can produce a set of high quality solutions with less computational time. In this paper, two optimization techniques are considered; the first optimization method uses multifidelity hierarchical Pareto-optimality. The second optimization method uses the combination of game strategies Nash-equilibrium and Pareto-optimality. This paper shows how game strategies can be coupled to multiobjective evolutionary algorithms and robust design techniques to produce a set of high quality solutions. Numerical results obtained from both optimization methods are compared in terms of computational expense and model quality. The benefits of using Hybrid and non-Hybrid-Game strategies are demonstrated.

QoS-aware web service composition using genetic algorithms

Web service technology is increasingly being used to build various e-Applications, in domains such as e-Business and e-Science. Characteristic benefits of web service technology are its inter-operability, decoupling and just-in-time integration. Using web service technology, an e-Application can be implemented by web service composition — by composing existing individual web services in accordance with the business process of the application. This means the application is provided to customers in the form of a value-added composite web service. An important and challenging issue of web service composition, is how to meet Quality-of-Service (QoS) requirements. This includes customer focused elements such as response time, price, throughput and reliability as well as how to best provide QoS results for the composites. This in turn best fulfils customers’ expectations and achieves their satisfaction. Fulfilling these QoS requirements or addressing the QoS-aware web service composition problem is the focus of this project. From a computational point of view, QoS-aware web service composition can be transformed into diverse optimisation problems. These problems are characterised as complex, large-scale, highly constrained and multi-objective problems. We therefore use genetic algorithms (GAs) to address QoS-based service composition problems. More precisely, this study addresses three important subproblems of QoS-aware web service composition; QoS-based web service selection for a composite web service accommodating constraints on inter-service dependence and conflict, QoS-based resource allocation and scheduling for multiple composite services on hybrid clouds, and performance-driven composite service partitioning for decentralised execution. Based on operations research theory, we model the three problems as a constrained optimisation problem, a resource allocation and scheduling problem, and a graph partitioning problem, respectively. Then, we present novel GAs to address these problems. We also conduct experiments to evaluate the performance of the new GAs. Finally, verification experiments are performed to show the correctness of the GAs. The major outcomes from the first problem are three novel GAs: a penaltybased GA, a min-conflict hill-climbing repairing GA, and a hybrid GA. These GAs adopt different constraint handling strategies to handle constraints on interservice dependence and conflict. This is an important factor that has been largely ignored by existing algorithms that might lead to the generation of infeasible composite services. Experimental results demonstrate the effectiveness of our GAs for handling the QoS-based web service selection problem with constraints on inter-service dependence and conflict, as well as their better scalability than the existing integer programming-based method for large scale web service selection problems. The major outcomes from the second problem has resulted in two GAs; a random-key GA and a cooperative coevolutionary GA (CCGA). Experiments demonstrate the good scalability of the two algorithms. In particular, the CCGA scales well as the number of composite services involved in a problem increases, while no other algorithms demonstrate this ability. The findings from the third problem result in a novel GA for composite service partitioning for decentralised execution. Compared with existing heuristic algorithms, the new GA is more suitable for a large-scale composite web service program partitioning problems. In addition, the GA outperforms existing heuristic algorithms, generating a better deployment topology for a composite web service for decentralised execution. These effective and scalable GAs can be integrated into QoS-based management tools to facilitate the delivery of feasible, reliable and high quality composite web services.

A multidisciplinary examination of fast bowling talent development in cricket

Research on expertise, talent identification and development has tended to be mono-disciplinary, typically adopting geno-centric or environmentalist positions, with an overriding focus on operational issues. In this thesis, the validity of dualist positions on sport expertise is evaluated. It is argued that, to advance understanding of expertise and talent development, a shift towards a multidisciplinary and integrative science focus is necessary, along with the development of a comprehensive multidisciplinary theoretical rationale. Dynamical systems theory is utilised as a multidisciplinary theoretical rationale for the succession of studies, capturing how multiple interacting constraints can shape the development of expert performers. Phase I of the research examines experiential knowledge of coaches and players on the development of fast bowling talent utilising qualitative research methodology. It provides insights into the developmental histories of expert fast bowlers, as well as coaching philosophies on the constraints of fast bowling expertise. Results suggest talent development programmes should eschew the notion of common optimal performance models and emphasize the individual nature of pathways to expertise. Coaching and talent development programmes should identify the range of interacting constraints that impinge on the performance potential of individual athletes, rather than evaluating current performance on physical tests referenced to group norms. Phase II of this research comprises three further studies that investigate several of the key components identified as important for fast bowling expertise, talent identification and development extrapolated from Phase I of this research. This multidisciplinary programme of work involves a comprehensive analysis of fast bowling performance in a cross-section of the Cricket Australia high performance pathways, from the junior, emerging and national elite fast bowling squads. Briefly, differences were found in trunk kinematics associated with the generation of ball speed across the three groups. These differences in release mechanics indicated the functional adaptations in movement patterns as bowlers’ physical and anatomical characteristics changed during maturation. Second to the generation of ball speed, the ability to produce a range of delivery types was highlighted as a key component of expertise in the qualitative phase. The ability of athletes to produce consistent results on different surfaces and in different environments has drawn attention to the challenge of measuring consistency and flexibility in skill assessments. Examination of fast bowlers in Phase II demonstrated that national bowlers can make adjustments to the accuracy of subsequent deliveries during performance of a cricket bowling skills test, and perform a range of delivery types with increased accuracy and consistency. Finally, variability in selected delivery stride ground reaction force components in fast bowling revealed the degenerate nature of this complex multi-articular skill where the same performance outcome can be achieved with unique movement strategies. Utilising qualitative and quantitative methodologies to examine fast bowling expertise, the importance of degeneracy and adaptability in fast bowling has been highlighted alongside learning design that promotes dynamic learning environments.

The effectiveness of a short-term group music therapy intervention for young parents and their children

The quality of early life experiences are known to influence a child’s capacities for emotional, social, cognitive and physical competence throughout their life (Peterson, 1996; Zubrick et al., 2008). These early life experiences are directly affected by parenting and family environments. A lack of positive parenting has significant implications both for children, and the broader communities in which they live (Davies & Cummings, 1994; Dryfoos, 1990; Sanders, 1995). Young parents are known to be at risk of experiencing adverse circumstances that affect their ability to provide positive parenting to their children (Milan et al., 2004; Trad, 1995). There is a need to provide parenting support programs to young parents that offer opportunities for them to come together, support each other and learn ways to provide for their children’s developmental needs in a friendly, engaging and non-judgemental environment. This research project examines the effectiveness of a 10 week group music therapy program Sing & Grow as an early parenting intervention for 535 young parents. Sing & Grow is a national early parenting intervention program funded by the Australian Government and delivered by Playgroup Queensland. It is designed and delivered by Registered Music Therapists for families at risk of marginalisation with children aged from birth to three years. The aim of the program is to improve parenting skills and parent-child interactions, and increase social support networks through participation in a group that is strengths-based and structured in a way that lends itself to modelling, peer learning and facilitated learning. During the 10 weeks parents have opportunities to learn practical, hands-on ways to interact and play with their children that are conducive to positive parent-child relationships and ongoing child development. A range of interactive, nurturing, stimulating and developmental music activities provide the framework for parents to interact and play with their children. This research uses data collected through the Sing & Grow National Evaluation Study to examine outcomes for all participants aged 25 years and younger, who attended programs during the Sing & Grow pilot study and main study from mid-2005 to the end of 2007. The research examines the change from pre to post in self-reported parent behaviours, parent mental health and parent social support, and therapist observed parent-child interactions. A range of statistical analyses are used to address each Research Objective for the young parent population, and for subgroups within this population. Research Objective 1 explored the patterns of attendance in the Sing & Grow program for young parents, and for subgroups within this population. Results showed that levels of attendance were lower than expected and influenced by Indigenous status and source of family income. Patterns of attendance showed a decline over time and incomplete data rates were high which may indicate high dropout rates. Research Objective 2 explored perceived satisfaction, benefits and social support links made. Satisfaction levels with the program and staff were very high. Indigenous status was associated with lower levels of reported satisfaction with both the program and staff. Perceived benefits from participation in the program were very high. Employment status was associated with perceived benefits: parents who were not employed were more likely than employed parents to report that their understanding of child development had increased as a result of participation in the program. Social support connections were reported for participants with other professionals, services and parents. In particular, families were more likely to link up with playgroup staff and services. Those parents who attended six or more sessions were significantly more likely to attend a playgroup than those who attended five sessions or less. Social support connections were related to source of family income, level of education, Indigenous status and language background. Research Objective 3 investigated pre to post change on self-report parenting skills and parent mental health. Results indicated that participation in the Sing & Grow program was associated with improvements in parent mental health. No improvements were found for self-reported parenting skills. Research Objective 4 investigated pre to post change in therapist observation measures of parent-child interactions. Results indicated that participation in the Sing & Grow program was associated with large and significant improvements in parent sensitivity to, engagement with and acceptance of the child. There were significant interactions across time (pre to post) for the parent characteristics of Indigenous status, family income and level of education. Research Objective 5 explored the relationship between the number of sessions attended and extent of change on self-report outcomes and therapist observed outcomes, respectively. For each, an overall change score was devised to ascertain those parents who had made any positive changes over time. Results showed that there was no significant relationship between high attendance and positive change in either the self-report or therapist observed behavioural measures. A risk index was also constructed to test for a relationship between the risk status of the parent. Parents with the highest risk status were significantly more likely to attend six or more sessions than other parents, but risk status was not associated with any differences in parent reported outcomes or therapist observations. The results of this research study indicate that Sing & Grow is effective in improving outcomes for young parents’ mental health, parent-child interactions and social support connections. High attendance by families in the highest category for risk factors may indicate that the program is effective at engaging and retaining parents who are most at-risk and therefore traditionally hard to reach. Very high levels of satisfaction and perceived benefits support this. Further research is required to help confirm the promising evidence from the current study that a short term group music therapy program can support young parents and improve their parenting outcomes. In particular, this needs to address the more disappointing outcomes of the current research study to improve attendance and engagement of all young parents in the program and especially the needs of young Indigenous parents.

Fast and effective focused retrieval

Building an efficient and an effective search engine is a very challenging task. In this paper, we present the efficiency and effectiveness of our search engine at the INEX 2009 Efficiency and Ad Hoc Tracks. We have developed a simple and effective pruning method for fast query evaluation, and used a two-step process for Ad Hoc retrieval. The overall results from both tracks show that our search engine performs very competitively in terms of both efficiency and effectiveness.