BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

Producing new Asian masculinities

An exploration of issues of Asian masculinity in white cultures, integrating film and literary analysis, autobiography and postcolonial theory.

Case study of collaborative learning in two contexts : what do English language learners gain?

This chapter describes the use of collaborative learning as an approach to enhance English language learning by students from non-English speaking backgrounds. Communicative Language Teaching (CLT) principles were applied to two case studies, one comprising of undergraduate English as Foreign Language Learners in Turkey and the other involved English as Second Language learners in Australia. Social constructivism inspired communicative language teaching using collaborative learning activities such as team work, interactive peer-based learning, and iterative stages of learning matrix were incorporated to enhance students' learning outcomes. Data collected after the CLT intervention was made up of field notes, reflective logs and focus group interviews which revealed complementarities, as well as subtle differences between the two cases. The findings were summarized as learning dispositions; speaking fluency and confidence; learning diagnostics and completion deficiencies; task engagement, flow theory and higher order thinking skills; in addition to self efficacy and development of student identity. CLT has the potential to provide a more inclusive and dynamic education for diverse learners through vital outcomes and benefits which resonate with the real world.

Extending the advanced forensic format to accommodate multiple data sources, logical evidence, arbitrary information and forensic workflow

Forensic analysis requires the acquisition and management of many different types of evidence, including individual disk drives, RAID sets, network packets, memory images, and extracted files. Often the same evidence is reviewed by several different tools or examiners in different locations. We propose a backwards-compatible redesign of the Advanced Forensic Formatdan open, extensible file format for storing and sharing of evidence, arbitrary case related information and analysis results among different tools. The new specification, termed AFF4, is designed to be simple to implement, built upon the well supported ZIP file format specification. Furthermore, the AFF4 implementation has downward comparability with existing AFF files.

The YAWL Architecture

The YAWL system is structured as a service-oriented architecture. It is composed of an extensible set of YAWL Services [1], each of which is deployed at a certain endpoint and offers one or multiple interfaces. Some of these services are userfacing, meaning that they offer interfaces to end users, while others offer interfaces to applications or other services.

Maltreated children in the early years : international perspectives on the teacher’s role

Child abuse and neglect is a significant health and social problem with serious consequences for children, families and communities. This chapter provides students, early childhood teachers, and administrators with an evidence base for understanding their role in relation to child abuse and neglect. The chapter draws from international and interdisciplinary research to address four key areas of responsibility: i) recognising signs of child abuse and neglect; ii) reporting child abuse and neglect; iii) supporting children in the classroom; and iv) teaching children to protect themselves (Watts, 1997).

FIA : an open foresic integration architecture for composing digital evidence

The analysis and value of digital evidence in an investigation has been the domain of discourse in the digital forensic community for several years. While many works have considered different approaches to model digital evidence, a comprehensive understanding of the process of merging different evidence items recovered during a forensic analysis is still a distant dream. With the advent of modern technologies, pro-active measures are integral to keeping abreast of all forms of cyber crimes and attacks. This paper motivates the need to formalize the process of analyzing digital evidence from multiple sources simultaneously. In this paper, we present the forensic integration architecture (FIA) which provides a framework for abstracting the evidence source and storage format information from digital evidence and explores the concept of integrating evidence information from multiple sources. The FIA architecture identifies evidence information from multiple sources that enables an investigator to build theories to reconstruct the past. FIA is hierarchically composed of multiple layers and adopts a technology independent approach. FIA is also open and extensible making it simple to adapt to technological changes. We present a case study using a hypothetical car theft case to demonstrate the concepts and illustrate the value it brings into the field.

The role of periosteum : a neglected aspect of osteoporosis

Most current studies on the pathogenesis of osteoporosis emphasize the bone metabolic activities occurring on endosteal surfaces, whereas the periosteal aspect is somewhat neglected. In terms of bone physiology, periosteum plays a determining role in de novo cortical bone formation and cortical bone expansion through periosteum is the most efficient way of increasing bone strength against fractures. Despite the important role of periosteum in the pathogenesis and treatment of osteoporosis, little is known about the structural and cellular features of periosteum in osteoporosis. This chapter will focus on the major changes occurring in the periosteum of osteoporosis and possible implications of these changes in the pathogenesis of osteoporosis. The changes identified in the periosteum of osteoporosis are mainly located in the metaphyseal compartment, which include: (a) much thicker and more cellular cambial layer; (b) increased number of TRAP (tartrate resistant acid phosphatase), VEGF (vascular endothelial growth factor) cells and the degree of vascularization; and (c) enhanced expression of sympathetic nerve fibers. The structural and cellular changes of osteoporotic periosteum indicate that periosteum plays an important role in the cortical bone resorption in metaphyseal areas and this pathological process may be regulated by the sympathetic nervous system.

Use of Property Rights Registers for sustainability : a Queensland Case Study

Sustainable natural resource management has been a concern of governments and legislators for the last 20 years. A key aspect of an effective management framework is easy access to information about rights and obligations in land and the natural resources in, on or below the land. Information about legal interests in land is managed through a Torrens register in each Australian State. These registers are primarily focused on the registration of a narrow group of legal interests in the land, and rights or obligations that fall outside of these recognised interests are not capable of registration. Practices have developed however for the recording of property rights in natural resources either on separate registers, with no link to the Torrens register or on a separate register managed by the Registrar of Titles but having no legal effect on the title to the land. This paper will discuss and analyse the various ways in which registers have been used in Queensland to provide access to information about rights in natural resources, and provide examples as to how this approach has impacted on the desire for sustainable management. It will also provide a critique of the Queensland model, and call for reform of the present system.

The organisation of action in complex neurobiological systems

This chapter elucidates key ideas behind neurocomputational and ecological dynamics and perspectives of understanding the organisation of action in complex neurobiological systems. The need to study the close link between neurobiological systems and their environments (particularly their sensory and movement subsystems and the surrounding energy sources) is advocated. It is proposed how degeneracy in complex neurobiological systems provides the basis for functional variability in organisation of action. In such systems processes of cognition and action facilitate the specific interactions of each performer with particular task and environmental constraints.

Interpersonal coordination tendencies, decision-making and information governing dynamics in rugby union

In this chapter, ideas from ecological psychology and nonlinear dynamics are integrated to characterise decision-making as an emergent property of self-organisation processes in the interpersonal interactions that occur in sports teams. A conceptual model is proposed to capture constraints on dynamics of decisions and actions in dyadic systems, which has been empirically evaluated in simulations of interpersonal interactions in team sports. For this purpose, co-adaptive interpersonal dynamics in team sports such as rubgy union have been studied to reveal control parameter and collective variable relations in attacker-defender dyads. Although interpersonal dynamics of attackers and defenders in 1 vs 1 situations showed characteristics of chaotic attractors, the informational constraints of rugby union typically bounded dyadic systems into low dimensional attractors. Our work suggests that the dynamics of attacker-defender dyads can be characterised as an evolving sequence since players' positioning and movements are connected in diverse ways over time.

The development of decision making skill in sport : An ecological dynamics perspective

In this chapter we introduce a theoretical framework for studying decision making in sport: the ecological dynamics approach, which we integrate with key ideas from the literature on learning complex motor skills. Our analysis will include insights from Berstein (1967) on the coordination of degrees of freedom and Newell's (1985) model of motor learning. We particularly focus on the role of perceptual degrees of freedom advocated in an ecological approach to learning. In introducing this framework to readers we contrast this perspective with more traditional models of decision-making. Finally, we propose some implications to the training of decision-making skill in sport.

How does knowledge constrain sport performance? An ecological perspective

From an ecological perspective knowledge signifies the degree of fitness of a performer and his/her environment. From this viewpoint, the role of training is to enhance this degree of fit between a specific athlete and the performance environment, instead of the enrichment of memory in the performer. In this regard, ecological psychology distinguishes between perceptual knowledge or "knowledge of" the environment and symbolic knowledge or "knowledge about" the environment. This distinction elucidates how knowing how to act (knowing of) as well as knowing how to verbalise memorial representations (e.g., a verbal description of performance) (knowing about) are both rooted in perception. In this chapter we demonstrate these types of knowledge in decision-making behaviour and exemplify how they can be presented in 1 v 1 practice task contraints in basketball.

Increasing stochastic perturbations enhances acquisition and learning of complex sport movements

Traditionally, the aquisition of skills and sport movement has been characterised by numerous repetitions of presumed model movement pattern to be acquired by learners. This approach has been questioned by research identifying the presence of individualised movement patterns and the low probability of occurrence of two identical movements within and between individuals. In contrast, the differential learning approach claims advantage for incurring variability in the learning process by adding stochastic perturbations during practice. These ideas are exemplified by data from a high jump experiment which compared the effectiveness of classical and a differential training approach with pre-post test design. Results showed clear advantages for the group with additional stochastic perturbation during the aquisition phase in comparison to classically trained athletes. Analogies to similar phenomenological effects in the neurobiological literature are discussed.