Large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

A three-level flying-capacitor rectifier based supercapacitor direct integration scheme for distributed generation systems

Supercapacitors are increasingly used as short term energy storage elements in distributed generation systems. The traditional approach in integrating them to the main system is the use of interfacing dc-dc converters which introduce additional costs and power losses. This paper therefore, presents a novel direct integration scheme for supercapacitors and thereby eliminates associated costs and power losses of interfacing converters. The idea is simply to replace ordinary capacitors of three-level flying-capacitor rectifiers with supercapacitors and operate them under variable voltage conditions. An analysis on the reduction of power losses by the proposed system is presented. Furthermore, supercapacitor sizing and implementation issues such as effects of the variable voltage operation and resistive behavior of supercapacitors at high frequencies are also discussed. Simulation results are presented to verify the efficacy of the proposed system in suppressing short term power fluctuations in wind generation system.

Rectifier systems for variable speed wind generation : a review

The drive towards high efficiency wind energy conversion systems has resulted in almost all the modern wind turbines to operate in the variable speed mode which inevitably requires back-to-back power electronic converters to decouple generator dynamics from the grid. The aim of this paper is to present an analysis on suitable topologies for the generator-side converter (rectifier) of the back-to-back converter arrangement. Performance of the two most popular rectifier systems, namely, the passive diode bridge rectifier and the active six-switch two-level rectifier are taken as two extremes to evaluate other topologies presented in this paper. The other rectifier systems considered in this study include combinations of a diode bridge rectifier and electronic reactance(s), a combination of a rectifier and a dc-dc converter and a half controlled rectifier. Diode-clamped and capacitor-clamped three-level active rectifier topologies and their possible switch reductions are also discussed in relation to the requirements of modern high power wind energy conversion systems (WECSs). Simulation results are presented to support conclusion derived from this analysis.

Cost efficiency of Japanese steam power generation companies : a Bayesian comparison of random and fixed frontier models

This study analyses and compares the cost efficiency of Japanese steam power generation companies using the fixed and random Bayesian frontier models. We show that it is essential to account for heterogeneity in modelling the performance of energy companies. Results from the model estimation also indicate that restricting CO2 emissions can lead to a decrease in total cost. The study finally discusses the efficiency variations between the energy companies under analysis, and elaborates on the managerial and policy implications of the results.

Regulatory reforms and productivity : an empirical analysis of the Japanese electricity industry

The Japanese electricity industry has experienced regulatory reforms since the mid-1990s. This article measures productivity in Japan's steam power-generation sector and examines the effect of reforms on the productivity of this industry over the period 1978-2003. We estimate the Luenberger productivity indicator, which is a generalization of the commonly used Malmquist productivity index, using a data envelopment analysis approach. Factors associated with productivity change are investigated through dynamic generalized method of moments (GMM) estimation of panel data. Our empirical analysis shows that the regulatory reforms have contributed to productivity growth in the steam power-generation sector in Japan.

Three-dimensional off-design numerical analysis of an organic Rankine cycle radial-inflow turbine

Optimisation of organic Rankine cycles(ORCs for binary cycle applications could play a major role in determining the competitiveness of low to moderate renewable sources. An important aspect of the optimisation is to maximise the turbine output power for a given resource. This requires careful attention to the turbine design notably through numerical simulations. Challenges in the numerical modelling of radial-inflow turbines using high-density working fluids still need to be addressed in order to improve the turbine design and better optimise ORCs. Thispaper presents preliminary 3D numerical simulations of a high-density radial-inflow ORC turbine in sensible geothermal conditions. Following extensive investigation of the operating conditions and thermodynamic cycle analysis, therefrigerant R143a is chosen as the high-density working fluid. The 1D design of the candidate radial-inflow turbine is presented in details. Furthermore, commercially-available software Ansys-CFX is used to perform preliminary steady-state 3D CFD simulations of the candidate R143a radial-inflow turbine for a number of operating conditions including off-design conditions. The real-gas properties are obtained using the Peng–Robinson equations of state.The thermodynamic ORC cycle is presented. The preliminary design created using dedicated radial-inflow turbine software Concepts-Rital is discussed and the 3D CFD results are presented and compared against the meanline analysis.

Mismatch negativity in recent-onset and chronic schizophrenia : a current source density analysis

Mismatch negativity (MMN) is a component of the event-related potential elicited by deviant auditory stimuli. It is presumed to index pre-attentive monitoring of changes in the auditory environment. MMN amplitude is smaller in groups of individuals with schizophrenia compared to healthy controls. We compared duration-deviant MMN in 16 recent-onset and 19 chronic schizophrenia patients versus age- and sex-matched controls. Reduced frontal MMN was found in both patient groups, involved reduced hemispheric asymmetry, and was correlated with Global Assessment of Functioning (GAF) and negative symptom ratings. A cortically-constrained LORETA analysis, incorporating anatomical data from each individual's MRI, was performed to generate a current source density model of the MMN response over time. This model suggested MMN generation within a temporal, parietal and frontal network, which was right hemisphere dominant only in controls. An exploratory analysis revealed reduced CSD in patients in superior and middle temporal cortex, inferior and superior parietal cortex, precuneus, anterior cingulate, and superior and middle frontal cortex. A region of interest (ROI) analysis was performed. For the early phase of the MMN, patients had reduced bilateral temporal and parietal response and no lateralisation in frontal ROIs. For late MMN, patients had reduced bilateral parietal response and no lateralisation in temporal ROIs. In patients, correlations revealed a link between GAF and the MMN response in parietal cortex. In controls, the frontal response onset was 17 ms later than the temporal and parietal response. In patients, onset latency of the MMN response was delayed in secondary, but not primary, auditory cortex. However amplitude reductions were observed in both primary and secondary auditory cortex. These latency delays may indicate relatively intact information processing upstream of the primary auditory cortex, but impaired primary auditory cortex or cortico-cortical or thalamo-cortical communication with higher auditory cortices as a core deficit in schizophrenia.

Approximate Bayesian Computation for astronomical model analysis : a case study in galaxy demographics and morphological transformation at high redshift

Approximate Bayesian Computation’ (ABC) represents a powerful methodology for the analysis of complex stochastic systems for which the likelihood of the observed data under an arbitrary set of input parameters may be entirely intractable – the latter condition rendering useless the standard machinery of tractable likelihood-based, Bayesian statistical inference [e.g. conventional Markov chain Monte Carlo (MCMC) simulation]. In this paper, we demonstrate the potential of ABC for astronomical model analysis by application to a case study in the morphological transformation of high-redshift galaxies. To this end, we develop, first, a stochastic model for the competing processes of merging and secular evolution in the early Universe, and secondly, through an ABC-based comparison against the observed demographics of massive (Mgal > 1011 M⊙) galaxies (at 1.5 < z < 3) in the Cosmic Assembly Near-IR Deep Extragalatic Legacy Survey (CANDELS)/Extended Groth Strip (EGS) data set we derive posterior probability densities for the key parameters of this model. The ‘Sequential Monte Carlo’ implementation of ABC exhibited herein, featuring both a self-generating target sequence and self-refining MCMC kernel, is amongst the most efficient of contemporary approaches to this important statistical algorithm. We highlight as well through our chosen case study the value of careful summary statistic selection, and demonstrate two modern strategies for assessment and optimization in this regard. Ultimately, our ABC analysis of the high-redshift morphological mix returns tight constraints on the evolving merger rate in the early Universe and favours major merging (with disc survival or rapid reformation) over secular evolution as the mechanism most responsible for building up the first generation of bulges in early-type discs.

What is plan B? Using Foucault's archaeology to enhance policy analysis

Many governments in western democracies conduct the work of leading their societies forward through policy generation and implementation. Despite government attempts at extensive negotiation, collaboration and debate, the general populace in these same countries frequently express feelings of disempowerment and undue pressure to be compliant, often leading to disengagement. Here we outline Plan B: a process for examining how policies that emerge from good intentions are frequently interpreted as burdensome or irrelevant by those on whom they have an impact. Using a case study of professional standards for teachers in Australia, we describe how we distilled Foucault’s notions of archaeology into a research approach centring on the creation of ‘polyhedrons of intelligibility’ as an alternative approach by which both policy makers and those affected by their policies may understand how their respective causes are supported and adversely affected.

Probabilistic power system contingency analysis considering wind

This thesis was a step forward in developing probabilistic assessment of power system response to faults subject to intermittent generation by renewable energy. It has investigated the wind power fluctuation effect on power system stability, and the developed fast estimation process has demonstrated the feasibility for real-time implementation. A better balance between power network security and efficiency can be achieved based on this research outcome.

Eigenvalue Analysis of a DFIG Based Wind Power System under Different Modes of Operations

This chapter discussed the various modes of operation of the Doubly Fed Induction Generator (DFIG) based wind farm system. The impact of a auxiliary damping controller on the different modes of operation for the DFIG based wind generation system is investigated. The co-ordinated tuning of the damping controller to enhance the damping of the oscillatory modes using Bacteria Foraging (BF) technique is presented. The results from eigenvalue analysis are presented to elucidate the effectiveness of the tuned damping controller in the DFIG system under Super/Sub-synchronous speed of operation. The robustness issue of the damping controller is also investigated.

Experimental and statistical investigation of Australian native plants for second-generation biodiesel production

This work explores the potential of Australian native plants as a source of second-generation biodiesel for internal combustion engines application. Biodiesels were evaluated from a number of non-edible oil seeds which are grow naturally in Queensland, Australia. The quality of the produced biodiesels has been investigated by several experimental and numerical methods. The research methodology and numerical model developed in this study can be used for a broad range of biodiesel feedstocks and for the future development of renewable native biodiesel in Australia.

Improved residential electricity demand management through analysis of the customer perspective

Peak electricity demand requires substantial investment to update transmission, distribution and generation infrastructure. A successful community peak demand reduction project was examined to identify residential consumer motivational and contextual factors involved in their decision to adopt/not adopt interventions. Energy professionals actively worked to achieve community 'peer' membership and by becoming a trusted information source, facilitated voluntary home energy assessment requests from over 80% of the residential community. By combining and tailoring interventions to the specific needs and motivations of individual householders and the community, interventions promoting energy conservation and efficiency can be effective in achieving sustained reduction in peak demand.

Analysis and improvement of a construction permit approval process: A teaching case for developing business process development capabilities, targeting developing nations

With the increasing competitiveness in global markets, many developing nations are striving to constantly improve their services in search for the next competitive edge. As a result, the demand and need for Business Process Management (BPM) in these regions is seeing a rapid rise. Yet there exists a lack of professional expertise and knowledge to cater to that need. Therefore, the development of well-structured BPM training/ education programs has become an urgent requirement for these industries. Furthermore, the lack of textbooks or other self-educating material, that go beyond the basics of BPM, further ratifies the need for case based teaching and related cases that enable the next generation of professionals in these countries. Teaching cases create an authentic learning environment where complexities and challenges of the ‘real world’ can be presented in a narrative, enabling students to evolve crucial skills such as problem analysis, problem solving, creativity within constraints as well as the application of appropriate tools (BPMN) and techniques (including best practices and benchmarking) within richer and real scenarios. The aim of this paper is to provide a comprehensive teaching case demonstrating the means to tackle any developing nation’s legacy government process undermined by inefficiency and ineffectiveness. The paper also includes thorough teaching notes The article is presented in three main parts: (i) Introduction - that provides a brief background setting the context of this paper, (ii) The Teaching Case, and (iii) Teaching notes.

Nigeria's power sector: Analysis of productivity

Nigerian electricity market is characterized by inadequate electricity generation framework, compounded by lack of timely routine maintenances. This results in significant deterioration in plant electricity output. This study analyzes the productivity changes in the Nigerian power sector. Productivity increased on average in the power sector by the adoption of new technologies from best-practice power plants. The assumption of Hicks neutral technological change is found not to be suitable for the Nigerian power sector. This study finds that the plants are not using their capacity meaningfully, instead, there is a tendency to use labor.