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.

Educating the Other: Standpoint and Theory on the 'Internationalisation' of Higher Education

How adequate are current theoretical standpoints, tools and categories for explaining the flows of international students to Anglo/American/European universities? This essay takes a different analytic tact and historical standpoint to the study of them and us, insiders and outsiders (cf. Foley, Levinson & Hurtig, 2001), in the internationalisation of education.

Varieties of Asian capitalism : toward an institutional theory of Asian enterprise

In this paper we respond to calls for an institution-based perspective on strategy. With its emphasis upon mimetic, coercive, and normative isomorphism, institutional theory has earned a deterministic reputation and seems an unlikely foundation on which to construct a theory of strategy. However, a second movement in institutional theory is emerging that gives greater emphasis to creativity and agency. We develop this approach by highlighting co-evolutionary processes that are shaping the varieties of capitalism (VoC) in Asia. To do so, we examine the extent to which the VoC model can be fruitfully applied in the Asian context. In the spirit of the second movement of institutional theory, we describe three processes in which firm strategy collectively and intentionally feeds back to shape institutions: (1) filling institutional voids, (2) retarding institutional innovation, and (3) deploying institutional escape. We outline the key contributions contained in the articles of this Special Issue and discuss a research agenda generated by the VoC perspective.

Organic and acquisitive employment growth : re-examining,testing and extending Penrose's Growth Theory.

Edith Penrose’s theory of firm growth postulates that a firm’s current growth rate will be influenced by the adjustment costs of, and changes to a firm’s productive opportunity set arising from, previous growth. Although she explicitly considered the impact of previous organic growth on current organic growth, she was largely silent about the impact of previous acquisitive growth. In this paper we extend Penrose’s work to examine that the relative impact of organic and acquisitive growth on the adjustment costs and productive opportunity set of the firm. Employing a panel of commercially active enterprises in Sweden over a 10 year period our results suggest the following. First, previous organic growth acts as a constraint on current organic growth. Second, previous acquisitive growth has a positive effect on current organic growth. We conclude that organic growth and acquisitive growth constitute two distinct strategic options facing the firm, which have a differential impact on the future organic growth of the firm.

Adaptive unsupervised learning of human actions

Automatic detection of suspicious activities in CCTV camera feeds is crucial to the success of video surveillance systems. Such a capability can help transform the dumb CCTV cameras into smart surveillance tools for fighting crime and terror. Learning and classification of basic human actions is a precursor to detecting suspicious activities. Most of the current approaches rely on a non-realistic assumption that a complete dataset of normal human actions is available. This paper presents a different approach to deal with the problem of understanding human actions in video when no prior information is available. This is achieved by working with an incomplete dataset of basic actions which are continuously updated. Initially, all video segments are represented by Bags-Of-Words (BOW) method using only Term Frequency-Inverse Document Frequency (TF-IDF) features. Then, a data-stream clustering algorithm is applied for updating the system's knowledge from the incoming video feeds. Finally, all the actions are classified into different sets. Experiments and comparisons are conducted on the well known Weizmann and KTH datasets to show the efficacy of the proposed approach.

Tests of the elaborated intrusion theory of craving and desire : features of alcohol craving during treatment for an alcohol disorder

Objectives. We tested predictions from the elaborated intrusion (EI) theory of desire, which distinguishes intrusive thoughts and elaborations, and emphasizes the importance of imagery. Secondarily, we undertook preliminary evaluations of the Alcohol Craving Experience (ACE) questionnaire, a new measure based on EI Theory. Methods. Participants (N ¼ 232) were in correspondence-based treatment trials for alcohol abuse or dependence. The study used retrospective reports obtained early in treatment using the ACE, and daily self-monitoring of urges, craving, mood and alcohol consumption. Results. The ACE displayed high internal consistency and test – retest reliability and sound relationships with self-monitored craving, and was related to Baseline alcohol dependence, but not to consumption. Imagery during craving was experienced by 81%,with 2.3 senses involved on average. More frequent imagery was associated with longer episode durations and stronger craving. Transient intrusive thoughts were reported by 87% of respondents, and were more common if they frequently attempted to stop alcohol cognitions. Associations between average daily craving and weekly consumption were seen. Depression and negative mood were associated with more frequent, stronger and longer lasting desires for alcohol. Conclusions. Results supported the distinction of automatic and controlled processes in craving, together with the importance of craving imagery. They were also consistent with prediction of consumption from cross-situational averages of craving, and with positive associations between craving and negative mood. However, this study’s retrospective reporting and correlational design require that its results be interpreted cautiously. Research using ecological momentary measures and laboratory manipulations is needed before confident inferences about causality can be made.

Theory and its role in mathematics education

The increased recognition of the theory in mathematics education is evident in numerous handbooks, journal articles, and other publications. For example, Silver and Herbst (2007) examined ―Theory in Mathematics Education Scholarship‖ in the Second Handbook of Research on Mathematics Teaching and Learning (Lester, 2007) while Cobb (2007) addressed ―Putting Philosophy to Work: Coping with Multiple Theoretical Perspectives‖ in the same handbook. And a central component of both the first and second editions of the Handbook of International Research in Mathematics Education (English, 2002; 2008) was ―advances in theory development.‖ Needless to say, the comprehensive second edition of the Handbook of Educational Psychology (Alexander & Winne, 2006) abounds with analyses of theoretical developments across a variety of disciplines and contexts. Numerous definitions of ―theory‖ appear in the literature (e.g., see Silver & Herbst, in Lester, 2007). It is not our intention to provide a ―one-size-fits-all‖ definition of theory per se as applied to our discipline; rather we consider multiple perspectives on theory and its many roles in improving the teaching and learning of mathematics in varied contexts.

Interpersonal pattern dynamics and adaptive behavior in multiagent neurobiological systems : conceptual model and data

Ecological dynamics characterizes adaptive behavior as an emergent, self-organizing property of interpersonal interactions in complex social systems. The authors conceptualize and investigate constraints on dynamics of decisions and actions in the multiagent system of team sports. They studied coadaptive interpersonal dynamics in rugby union to model potential control parameter and collective variable relations in attacker–defender dyads. A videogrammetry analysis revealed how some agents generated fluctuations by adapting displacement velocity to create phase transitions and destabilize dyadic subsystems near the try line. Agent interpersonal dynamics exhibited characteristics of chaotic attractors and informational constraints of rugby union boxed dyadic systems into a low dimensional attractor. Data suggests that decisions and actions of agents in sports teams may be characterized as emergent, self-organizing properties, governed by laws of dynamical systems at the ecological scale. Further research needs to generalize this conceptual model of adaptive behavior in performance to other multiagent populations.

Power law distributions in pattern dynamics of attacker-defender dyads in the team sport of Rugby Union : phenomena in a region of self-organized criticality?

In the region of self-organized criticality (SOC) interdependency between multi-agent system components exists and slight changes in near-neighbor interactions can break the balance of equally poised options leading to transitions in system order. In this region, frequency of events of differing magnitudes exhibits a power law distribution. The aim of this paper was to investigate whether a power law distribution characterized attacker-defender interactions in team sports. For this purpose we observed attacker and defender in a dyadic sub-phase of rugby union near the try line. Videogrammetry was used to capture players’ motion over time as player locations were digitized. Power laws were calculated for the rate of change of players’ relative position. Data revealed that three emergent patterns from dyadic system interactions (i.e., try; unsuccessful tackle; effective tackle) displayed a power law distribution. Results suggested that pattern forming dynamics dyads in rugby union exhibited SOC. It was concluded that rugby union dyads evolve in SOC regions suggesting that players’ decisions and actions are governed by local interactions rules.

Imaginary relish and exquisite torture : the elaborated intrusion theory of desire

The authors argue that human desire involves conscious cognition that has strong affective connotation and is potentially involved in the determination of appetitive behavior rather than being epiphenomenal to it. Intrusive thoughts about appetitive targets are triggered automatically by external or physiological cues and by cognitive associates. When intrusions elicit significant pleasure or relief, cognitive elaboration usually ensues. Elaboration competes with concurrent cognitive tasks through retrieval of target related information and its retention in working memory. Sensory images are especially important products of intrusion and elaboration because they simulate the sensory and emotional qualities of target acquisition. Desire images are momentarily rewarding but amplify awareness of somatic and emotional deficits. Effects of desires on behavior are moderated by competing incentives, target availability, and skills. The theory provides a coherent account of existing data and suggests new directions for research and treatment.

Modernity and the 'failure' of crime control

Rather than understanding the recurrent failure of various attempts at crime control as unfortunate and undesirable aberrations, all too familiar glitches an otherwise uninterrupted teleological march to a better society, such failures are instead positioned as part of the fabric of late modernity itself. That is, society changes not according to a predetermined logic along neatly defined and clearly reasoned tracks, rather it hurtles from crisis to crisis, from failure to failure, and it is the regulation of that failure which produces new initiatives and new forms of governance. Utilising the example of the modern prison, this chapter contends that too great an emphasis upon this institution’s ‘failure’ results not only in a neglect of the many other functions that it serves in the regulation of difference, but also, and more generally, it results in an underestimation of the importance of failure in providing new impetus for social transformation.

Critical Systems Theory: A Political Economy of Language, Thought, and Technology

An emergent form of political economy, facilitated by information and communication technologies (ICTs), is widely propagated as the apotheosis of unmitigated social, economic, and technological progress. Meanwhile, throughout the world, social degradation and economic inequality are increasing logarithmically. Valued categories of thought are, axiomatically, the basic commodities of the “knowledge economy”. Language is its means of exchange. This paper proposes a sociolinguistic method with which to critically engage the hyperbole of the “Information Age”. The method is grounded in a systemic social theory that synthesises aspects of autopoiesis and Marxist political economy. A trade policy statement is analysed to exemplify the sociolinguistically created aberrations that are today most often construed as social and political determinants.

Youth cultures, style and education

If our only sources of information were the newspapers and the television, the available evidence would suggest that youth is a terrible problem. Not only would we be convinced that most crime is committed by the social category of youth, but that young people are running out of control, that the streets are no longer safe, that all manner of standards are dropping, that the schools are in chaos, and that, as a consequence of these facts, society faces ruin. Fortunately, there is a considerable body of academic literature which rebuts these assertions, and via a more rigorous and objective analysis of society, it has sought to explain the practices, cultures and circumstances through and by which contemporary youth is formed.