Pattern-based phylogenetic distance estimation and tree reconstruction

We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.

Applying a disciplined approach to the development of a context-aware communication application

Pervasive computing applications must be engineered to provide unprecedented levels of flexibility in order to reconfigure and adapt in response to changes in computing resources and user requirements. To meet these challenges, appropriate software engineering abstractions and infrastructure are required as a platform on which to build adaptive applications. In this paper, we demonstrate the use of a disciplined, model-based approach to engineer a context-aware Session Initiation Protocol (SIP) based communication application. This disciplined approach builds on our previously developed conceptual models and infrastructural components, which enable the description, acquisition, management and exploitation of arbitrary types of context and user preference information to enable adaptation to context changes

Chaos Theory as an Approach to Understanding MICE in Time of Crisis

MICE (meetings, incentives, conventions, and exhibitions), has generated high foreign exchange revenue for the economy worldwide. In Thailand, MICE tourists are recognized as ‘quality’ visitors, mainly because of their high-spending potential. Having said that, Thailand’s MICE sector has been influenced by a number of crises following September 11, 2001. Consequently, professionals in the MICE sector must be prepared to deal with such complex phenomena of crisis that might happen in the future. While a number of researches have examined the complexity of crises in the tourism context, there has been little focus on such issues in the MICE sector. As chaos theory provides a particularly good model for crisis situations, it is the aim of this paper to propose a chaos theory-based approach to the understanding of complex and chaotic system of the MICE sector in time of crisis.

Monitoring the condition of savanna riparian zones in Northern Australia using high spatial resolution imagery and a field based rapid assessment method

Government agencies responsible for riparian environments are assessing the combined utility of field survey and remote sensing for mapping and monitoring indicators of riparian zone condition. The objective of this work was to compare the Tropical Rapid Appraisal of Riparian Condition (TRARC) method to a satellite image based approach. TRARC was developed for rapid assessment of the environmental condition of savanna riparian zones. The comparison assessed mapping accuracy, representativeness of TRARC assessment, cost-effectiveness, and suitability for multi-temporal analysis. Two multi-spectral QuickBird images captured in 2004 and 2005 and coincident field data covering sections of the Daly River in the Northern Territory, Australia were used in this work. Both field and image data were processed to map riparian health indicators (RHIs) including percentage canopy cover, organic litter, canopy continuity, stream bank stability, and extent of tree clearing. Spectral vegetation indices, image segmentation and supervised classification were used to produce RHI maps. QuickBird image data were used to examine if the spatial distribution of TRARC transects provided a representative sample of ground based RHI measurements. Results showed that TRARC transects were required to cover at least 3% of the study area to obtain a representative sample. The mapping accuracy and costs of the image based approach were compared to those of the ground based TRARC approach. Results proved that TRARC was more cost-effective at smaller scales (1-100km), while image based assessment becomes more feasible at regional scales (100-1000km). Finally, the ability to use both the image and field based approaches for multi-temporal analysis of RHIs was assessed. Change detection analysis demonstrated that image data can provide detailed information on gradual change, while the TRARC method was only able to identify more gross scale changes. In conclusion, results from both methods were considered to complement each other if used at appropriate spatial scales.

A strategy-as-practice approach to strategy research and education

This conclusion to the Dialog proposes a strategy-as-practice based approach to bringing strategy research and education closer to practice. Strategy-as-practice rejects the choice, proposed in the previous articles, between theory and practice. The authors argue for strategy research based rigorously on sociological theories of practice. Such research complements the parsimony and generalizability of economics-driven theory, extending strategy research to incorporate the messy realities of doing strategy in practice, with a view to developing theory that is high in accuracy. The authors suggest that practice-based research can also inform strategy teaching by providing students with rich case studies of strategy work as actually practiced, analyzed through such sociological lenses as ethnomethodology, dramaturgy, and institutional theory. Strategy-as-practice research does not aim to give students parsimonious models for analysis or expose them to cases of best practice but rather to help them develop practical wisdom through a better understanding of strategy in practice.

Perception of concurrent sentences with harmonic or frequency-shifted voiced excitation:performance of human listeners and of computational models based on autocorrelation

Keyword identification in one of two simultaneous sentences is improved when the sentences differ in F0, particularly when they are almost continuously voiced. Sentences of this kind were recorded, monotonised using PSOLA, and re-synthesised to give a range of harmonic ?F0s (0, 1, 3, and 10 semitones). They were additionally re-synthesised by LPC with the LPC residual frequency shifted by 25% of F0, to give excitation with inharmonic but regularly spaced components. Perceptual identification of frequency-shifted sentences showed a similar large improvement with nominal ?F0 as seen for harmonic sentences, although overall performance was about 10% poorer. We compared performance with that of two autocorrelation-based computational models comprising four stages: (i) peripheral frequency selectivity and half-wave rectification; (ii) within-channel periodicity extraction; (iii) identification of the two major peaks in the summary autocorrelation function (SACF); (iv) a template-based approach to speech recognition using dynamic time warping. One model sampled the correlogram at the target-F0 period and performed spectral matching; the other deselected channels dominated by the interferer and performed matching on the short-lag portion of the residual SACF. Both models reproduced the monotonic increase observed in human performance with increasing ?F0 for the harmonic stimuli, but not for the frequency-shifted stimuli. A revised version of the spectral-matching model, which groups patterns of periodicity that lie on a curve in the frequency-delay plane, showed a closer match to the perceptual data for frequency-shifted sentences. The results extend the range of phenomena originally attributed to harmonic processing to grouping by common spectral pattern.

Agent Based Models of Competition and Collaboration

Swarm intelligence is a popular paradigm for algorithm design. Frequently drawing inspiration from natural systems, it assigns simple rules to a set of agents with the aim that, through local interactions, they collectively solve some global problem. Current variants of a popular swarm based optimization algorithm, particle swarm optimization (PSO), are investigated with a focus on premature convergence. A novel variant, dispersive PSO, is proposed to address this problem and is shown to lead to increased robustness and performance compared to current PSO algorithms. A nature inspired decentralised multi-agent algorithm is proposed to solve a constrained problem of distributed task allocation. Agents must collect and process the mail batches, without global knowledge of their environment or communication between agents. New rules for specialisation are proposed and are shown to exhibit improved eciency and exibility compared to existing ones. These new rules are compared with a market based approach to agent control. The eciency (average number of tasks performed), the exibility (ability to react to changes in the environment), and the sensitivity to load (ability to cope with differing demands) are investigated in both static and dynamic environments. A hybrid algorithm combining both approaches, is shown to exhibit improved eciency and robustness. Evolutionary algorithms are employed, both to optimize parameters and to allow the various rules to evolve and compete. We also observe extinction and speciation. In order to interpret algorithm performance we analyse the causes of eciency loss, derive theoretical upper bounds for the eciency, as well as a complete theoretical description of a non-trivial case, and compare these with the experimental results. Motivated by this work we introduce agent "memory" (the possibility for agents to develop preferences for certain cities) and show that not only does it lead to emergent cooperation between agents, but also to a signicant increase in efficiency.

QoS guarantee with adaptive transmit power and message rate control for DSRC vehicle network based road safety applications

Quality of services (QoS) support is critical for dedicated short range communications (DSRC) vehicle networks based collaborative road safety applications. In this paper we propose an adaptive power and message rate control method for DSRC vehicle networks at road intersections. The design objective is to provide high availability and low latency channels for high priority emergency safety applications while maximizing channel utilization for low priority routine safety applications. In this method an offline simulation based approach is used to find out the best possible configurations of transmit power and message rate for given numbers of vehicles in the network. The identified best configurations are then used online by roadside access points (AP) according to estimated number of vehicles. Simulation results show that this adaptive method significantly outperforms a fixed control method. © 2011 Springer-Verlag.

Enhanced renewable energy adoption for sustainable development in India:interpretive structural modeling approach

Poverty alleviation and social upliftment of rural India is closely linked with the availability and use of energy for development. At the same time, sustainable supply of clean and affordable renewable energy sources is required if development is to be sustainable, so that it does not cause any environmental problems. The purpose of this paper is to determine the key variables of renewable energy implementation for sustainable development, on which the top management should focus. In this paper, an interpretive structural modeling (ISM) - based approach has been employed to model the implementation variables of renewable energy for sustainable development. These variables have been categorized under ‘enablers’ that help to increase the implementation of renewable energy for sustainable development. A major finding of this research is that public awareness regarding renewable energy for sustainable development is a very significant enabler. In this paper, an interpretation of variables of renewable energy for sustainable development in terms of their driving and dependence powers has been examined. For better results, top management should focus on improving the high-driving power enablers such as leadership, strategic planning, public awareness, top management support, availability of finance, government support, and support from interest groups.

An activity theory approach to strategy as practice

This chapter introduces activity theory as an approach for studying strategy as practice. Activity theory conceptualizes the ongoing construction of activity as a product of activity systems, comprising the actor, the community with which that actor interacts and those symbolic and material tools that mediate between actors, their community and their pursuit of activity. The focus on the mediating role of tools and cultural artefacts in human activity seems especially promising for advancing the strategy-as-practice agenda, for example as a theoretical resource for the growing interest in sociomateriality and the role of tools and artefacts in (strategy) practice (for example, Balogun et al. 2014; Lanzara 2009; Nicolini 2009; Spee and Jarzabkowski 2009; Stetsenko 2005). Despite its potential, in a recent review Vaara and Whittington (2012) identified only three strategy-as-practice articles explicitly applying an activity theory lens. In the wider area of practice-based studies in organizations, activity theory has been slightly more popular (for example, Blackler 1993; 1995; Blackler, Crump and McDonald 2000; Engeström, Kerosuo and Kajamaa 2007; Groleau 2006; Holt 2008; Miettinen and Virkkunen 2005). It still lags behind its potential, however, primarily because of its origins as a social psychology theory developed in Russia with little initial recognition outside the Russian context, particularly in the area of strategy and organization theory, until recently (Miettinen, Samra-Fredericks and Yanow 2009). This chapter explores activity theory as a resource for studying strategy as practice as it is socially accomplished by individuals in interaction with their wider social group and the artefacts of interaction. In particular, activity theory’s focus on actors as social individuals provides a conceptual basis for studying the core question in strategy-as-practice research: what strategy practitioners do. The chapter is structured in three parts. First, an overview of activity theory is provided. Second, activity theory as a practice-based approach to studying organizational action is introduced and an activity system conceptual framework is developed. Third, the elements of the activity system are explained in more detail and explicitly linked to each of the core SAP concepts: practitioners, practices and praxis. In doing so, links are made to existing strategy-as-practice research, with brief empirical examples of topics that might be addressed using activity theory. Throughout the chapter, we introduce key authors in the development of activity theory and its use in management and adjacent disciplinary fields, as further resources for those wishing to make greater use of activity theory.

Agent-based Anomalies Monitoring in Distributed Systems

In this paper an agent-based approach for anomalies monitoring in distributed systems such as computer networks, or Grid systems is proposed. This approach envisages on-line and off-line monitoring in order to analyze users’ activity. On-line monitoring is carried in real time, and is used to predict user actions. Off-line monitoring is done after the user has ended his work, and is based on the analysis of statistical information obtained during user’s work. In both cases neural networks are used in order to predict user actions and to distinguish normal and anomalous user behavior.

Improving T cell-induced response to subunit vaccines:opportunities for a proteomic systems approach

Prophylactic vaccines are an effective strategy to prevent development of many infectious diseases. With new and re-emerging infections posing increasing risks to food stocks and the health of the population in general, there is a need to improve the rationale of vaccine development. One key challenge lies in development of an effective T cell-induced response to subunit vaccines at specific sites and in different populations. Objectives: In this review, we consider how a proteomic systems-based approach can be used to identify putative novel vaccine targets, may be adopted to characterise subunit vaccines and adjuvants fully. Key findings: Despite the extensive potential for proteomics to aid our understanding of subunit vaccine nature, little work has been reported on identifying MHC 1-binding peptides for subunit vaccines generating T cell responses in the literature to date. Summary: In combination with predictive and structural biology approaches to mapping antigen presentation, proteomics offers a powerful and as yet un-tapped addition to the armoury of vaccine discovery to predict T-cell subset responses and improve vaccine design strategies.

Dialog Based on Graphical Static Scenes Managed by an Ontology

A new method to implementation of dialog based on graphical static scenes using an ontology-based approach to user interface development is proposed. The main idea of the approach is to form necessary to the user interface development and implementation information using ontologies and then based on this high-level specification to generate the user interface.

An Approach to Collaborative Filtering by ARTMAP Neural Networks

Recommender systems are now widely used in e-commerce applications to assist customers to find relevant products from the many that are frequently available. Collaborative filtering (CF) is a key component of many of these systems, in which recommendations are made to users based on the opinions of similar users in a system. This paper presents a model-based approach to CF by using supervised ARTMAP neural networks (NN). This approach deploys formation of reference vectors, which makes a CF recommendation system able to classify user profile patterns into classes of similar profiles. Empirical results reported show that the proposed approach performs better than similar CF systems based on unsupervised ART2 NN or neighbourhood-based algorithm.

Founders' human capital and the performance of UK new technology based firms

This paper investigates the role of entrepreneurs' general and specific human capital on the performance of UK new technology based firms using a resource based approach to the entrepreneurship theory. The effect of entrepreneurial human capital on the performance of NTBFs is investigated using data derived from a survey of 412 firms operating in both high-tech manufacturing and the services sectors. According to the resource based theory it is found that specific human capital is more important for the performance of NTBFs in relation to general. More specifically individual entrepreneurs or entrepreneurial teams with high levels of formal business education, commercial, managerial or same sector experience are found to have created better performing NTBFs. Finally it is found that the performance of a NTBF can improve through the combination of heterogeneous but complementary skills, including, for example, technical education and commercial experience or managerial technical and managerial commercial experience. © 2010 Springer Science+Business Media, LLC.