Cluster-based network model for time-course gene expression data

We propose a model-based approach to unify clustering and network modeling using time-course gene expression data. Specifically, our approach uses a mixture model to cluster genes. Genes within the same cluster share a similar expression profile. The network is built over cluster-specific expression profiles using state-space models. We discuss the application of our model to simulated data as well as to time-course gene expression data arising from animal models on prostate cancer progression. The latter application shows that with a combined statistical/bioinformatics analyses, we are able to extract gene-to-gene relationships supported by the literature as well as new plausible relationships.

Case management educational intervention with public health nurses : cluster randomized controlled trial

Aim: This paper is a report of a study conducted to determine the effectiveness of a community case management collaborative education intervention in terms of satisfaction, learning and performance among public health nurses. Background: Previous evaluation studies of case management continuing professional education often failed to demonstrate effectiveness across a range of outcomes and had methodological weaknesses such as small convenience samples and lack of control groups. Method: A cluster randomised controlled trial was conducted between September 2005 and February 2006. Ten health centre clusters (5 control, 5 intervention) recruited 163 public health nurses in Taiwan to the trial. After pre-tests for baseline measurements, public health nurses in intervention centres received an educational intervention of four half-day workshops. Post-tests for both groups were conducted after the intervention. Two-way repeated measures analysis of variance was performed to evaluate the effect of the intervention on target outcomes. Results: A total of 161 participants completed the pre- and post-intervention measurements. This was almost a 99% response rate. Results revealed that 97% of those in the experimental group were satisfied with the programme. There were statistically significant differences between the two groups in knowledge (p = 0.001), confidence in case management skills (p = 0.001), preparedness for case manager role activities (p = 0.001), self-reported frequency in using skills (p = 0.001), and role activities (p = 0.004). Conclusion: Collaboration between academic and clinical nurses is an effective strategy to prepare nurses for rapidly-changing roles.

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.

Estimation of parameters for macroparasite population evolution using approximate Bayesian computation

We estimate the parameters of a stochastic process model for a macroparasite population within a host using approximate Bayesian computation (ABC). The immunity of the host is an unobserved model variable and only mature macroparasites at sacrifice of the host are counted. With very limited data, process rates are inferred reasonably precisely. Modeling involves a three variable Markov process for which the observed data likelihood is computationally intractable. ABC methods are particularly useful when the likelihood is analytically or computationally intractable. The ABC algorithm we present is based on sequential Monte Carlo, is adaptive in nature, and overcomes some drawbacks of previous approaches to ABC. The algorithm is validated on a test example involving simulated data from an autologistic model before being used to infer parameters of the Markov process model for experimental data. The fitted model explains the observed extra-binomial variation in terms of a zero-one immunity variable, which has a short-lived presence in the host.

An evolution of waterfront development in Malaysia

River has long been recognized as one of humanity’s most important natural resources. It is one of the most important of all the natural resources necessary to ensure human health and civilization. A close association between cities and water is inherent since the history of civilization and in fact, many urban cities in Malaysia are located close to river areas. The last two decades shown Malaysia has shifted development strategy from agricultural based to industrialization, and manufacturing industries have become the economy’s main source for the country until now. This transformation in 18th century is clearly shown that rapid urbanization, industrial and intensive agricultural activities, as well as wide-spread land development, have contributed to extensive changing of river functions for economy, national development and environment. In particular, river roles are become less significance for human life and river function limited only for transportation purposes only. So, viewed historically, waterfront development in Malaysia have undergone cycles of change over the decades and the latest in this pattern to more public purposes such as recreational and mixed used development. This paper aims to identify a transition of waterfront development in Malaysia from history time to modernization era and it would give a significance contribution for the research is currently on going.

Connected Communities and Creative Economy; Clash, cluster, complexity, creativity

After a brief personal orientation, this presentation offers an opening section on „clash, cluster, complexity, cities‟ – making the case that innovation (both creative and economic) proceeds not only from incremental improvements within an expert-pipeline process, but also from the clash of different systems, generations, and cultures. The argument is that cultural complexity arises from such clashes, and that clustering is the solution to problems of complexity. The classic, 10,000-year-old, institutional form taken by such clusters is … cities. Hence, a creative city is one where clashing and competitive complexity is clustered… and, latterly, networked.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

An intelligent building model of sustainable architecture in a mechanism of open systems evolution

This paper argues a model of open systems evolution based on evolutionary thermodynamics and complex system science, as a design paradigm for sustainable architecture. The mechanism of open system evolution is specified in mathematical simulations and theoretical discourses. According to the mechanism, the authors propose an intelligent building model of sustainable design by a holistic information system of the end-users, the building and nature. This information system is used to control the consumption of energy and material resources in building system at microscopic scale, to adapt the environmental performance of the building system to the natural environment at macroscopic scale, for an evolutionary emergence of sustainable performance of buildings.

The social media (r)evolution : Obama's political campaign

This paper addresses how social media was used to leverage votes in new media environments. Barack Obama’s social media campaign is analysed and illustrates how the Obama brand benefited from integrating social media into the campaign. Voting behaviour has changed; politicians are continually seeking new ways to communicate with their constituents. Voting on political ‘brands’ is based on an identity or image, rather than central issues. While political parties rely upon an integrated marketing communication (IMC) approach, with a focus on building the (political) brand of the party and brand relationships, communication is no longer fully controlled by the marketers.

Cluster analysis of movement patterns in multiarticular actions: A tutorial

The present paper proposes a technical analysis method for extracting information about movement patterning in studies of motor control, based on a cluster analysis of movement kinematics. In a tutorial fashion, data from three different experiments are presented to exemplify and validate the technical method. When applied to three different basketball-shooting techniques, the method clearly distinguished between the different patterns. When applied to a cyclical wrist supination-pronation task, the cluster analysis provided the same results as an analysis using the conventional discrete relative phase measure. Finally, when analyzing throwing performance constrained by distance to target, the method grouped movement patterns together according to throwing distance. In conclusion, the proposed technical method provides a valuable tool to improve understanding of coordination and control in different movement models, including multiarticular actions.

Shrinking neighborhood evolution : a novel stochastic algorithm for numerical optimization

Focusing on the conditions that an optimization problem may comply with, the so-called convergence conditions have been proposed and sequentially a stochastic optimization algorithm named as DSZ algorithm is presented in order to deal with both unconstrained and constrained optimizations. The principle is discussed in the theoretical model of DSZ algorithm, from which we present the practical model of DSZ algorithm. Practical model efficiency is demonstrated by the comparison with the similar algorithms such as Enhanced simulated annealing (ESA), Monte Carlo simulated annealing (MCS), Sniffer Global Optimization (SGO), Directed Tabu Search (DTS), and Genetic Algorithm (GA), using a set of well-known unconstrained and constrained optimization test cases. Meanwhile, further attention goes to the strategies how to optimize the high-dimensional unconstrained problem using DSZ algorithm.

Empirical analysis of freeway traffic oscillation : its safety impact and evolution

Traffic oscillations are typical features of congested traffic flow that are characterized by recurring decelerations followed by accelerations. However, people have limited knowledge on this complex topic. In this research, 1) the impact of traffic oscillations on freeway crash occurrences has been measured using the matched case-control design. The results consistently reveal that oscillations have a more significant impact on freeway safety than the average traffic states. 2) Wavelet Transform has been adopted to locate oscillations' origins and measure their characteristics along their propagation paths using vehicle trajectory data. 3) Lane changing maneuver's impact on the immediate follower is measured and modeled. The knowledge and the new models generated from this study could provide better understanding on fundamentals of congested traffic; enable improvements to existing traffic control strategies and freeway crash countermeasures; and instigate people to develop new operational strategies with the objective of reducing the negative effects of oscillatory driving.

Power through influence : the evolution of arts management in Australia

The purpose of this paper is to frame effective models of arts management for Australia in the nineties and beyond based on an analysis of historical practices. The evolutionary process of government subvention of the arts through non-profit arts organisations provides a clear statement of the role of power and influence. In particular the ascendancy of arts organisations and their management constitute a background against which to study other non-profit corporations.