A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Motivation: Microarray experiments generate a high data volume. However, often due to financial or experimental considerations, e.g. lack of sample, there is little or no replication of the experiments or hybridizations. These factors combined with the intrinsic variability associated with the measurement of gene expression can result in an unsatisfactory detection rate of differential gene expression (DGE). Our motivation was to provide an easy to use measure of the success rate of DGE detection that could find routine use in the design of microarray experiments or in post-experiment assessment.

Hydrothermal synthesis of a continuous zeolite Beta layer by optimization of time, temperature and heating rate of the precursor mixture

Highly crystalline zeolite Beta coatings in a range of Si/Al ratios of 12-23 were synthesized on a surface-modified molybdenum substrate by hydrothermal synthesis. The average thickness of the coatings was ca. 2 mu m corresponding to a coverage of 2.5 gm(-2). The coatings were obtained from a viscous Na, K, and TEAOH containing aluminosilicate precursor mixture with silica sol as reactive silicon source. A mechanism for the in situ growth of zeolite Beta coatings is proposed. According to this mechanism, the deposition of an amorphous gel layer on the substrate surface in the initial stage of the synthesis is an important step for the crystallization of continuous zeolite Beta coatings. The heating rate of the precursor mixture and the synthesis temperature were optimized to control the level of supersaturation and to stimulate the initial formation of a gel layer. At a Si/Al ratio of 23, fast heating and a temperature of 150 degrees C are required to obtain high coverage, while at a Si/Al ratio of 15, hydrothermal synthesis has to be performed with a slow initial heating rate at 140 degrees C. (c) 2007 Elsevier Inc. All rights reserved.

Investigation of Machining Parameters for Multiple Response Optimization in Microelectrodischarge Milling

This paper investigated the influence of three micro electrodischarge milling process parameters, which were feed rate, capacitance, and voltage. The response variables were average surface roughness (R a ), maximum peak-to-valley roughness height (R y ), tool wear ratio (TWR), and material removal rate (MRR). Statistical models of these output responses were developed using three-level full factorial design of experiment. The developed models were used for multiple-response optimization by desirability function approach to obtain minimum R a , R y , TWR, and maximum MRR. Maximum desirability was found to be 88%. The optimized values of R a , R y , TWR, and MRR were 0.04, 0.34 μm, 0.044, and 0.08 mg min−1, respectively for 4.79 μm s−1 feed rate, 0.1 nF capacitance, and 80 V voltage. Optimized machining parameters were used in verification experiments, where the responses were found very close to the predicted values.

Experimental design and batch experiments for optimization of Cr(VI) removal from aqueous solutions by hydrous cerium oxide nanoparticles

Hydrous cerium oxide (HCO) was synthesized by intercalation of solutions of cerium(III) nitrate and sodium hydroxide and evaluated as an adsorbent for the removal of hexavalent chromium from aqueous solutions. Simple batch experiments and a 2⁵ factorial experimental design were employed to screen the variables affecting Cr(VI) removal efficiency. The effects of the process variables; solution pH, initial Cr(VI) concentration, temperature, adsorbent dose and ionic strength were examined. Using the experimental results, a linear mathematical model representing the influence of the different variables and their interactions was obtained. Analysis of variance (ANOVA) demonstrated that Cr(VI) adsorption significantly increases with decreased solution pH, initial concentration and amount of adsorbent used (dose), but slightly decreased with an increase in temperature and ionic strength. The optimization study indicates 99% as the maximum removal at pH 2, 20 °C, 1.923 mM of metal concentration and a sorbent dose of 4 g/dm³. At these optimal conditions, Langmuir, Freundlich and Redlich–Peterson isotherm models were obtained. The maximum adsorption capacity of Cr(VI) adsorbed by HCO was 0.828 mmol/g, calculated by the Langmuir isotherm model. Desorption of chromium indicated that the HCO adsorbent can be regenerated using NaOH solution 0.1 M (up to 85%). The adsorption interactions between the surface sites of HCO and the Cr(VI) ions were found to be a combined effect of both anion exchange and surface complexation with the formation of an inner-sphere complex.

DFIG Machine Design for Maximizing Power Output Based on Surrogate Optimization Algorithm

This paper presents a surrogate-model based optimization of a doubly-fed induction generator (DFIG) machine winding design for maximizing power yield. Based on site-specific wind profile data and the machine’s previous operational performance, the DFIG’s stator and rotor windings are optimized to match the maximum efficiency with operating conditions for rewinding purposes. The particle swarm optimization (PSO)-based surrogate optimization techniques are used in conjunction with the finite element method (FEM) to optimize the machine design utilizing the limited available information for the site-specific wind profile and generator operating conditions. A response surface method in the surrogate model is developed to formulate the design objectives and constraints. Besides, the machine tests and efficiency calculations follow IEEE standard 112-B. Numerical and experimental results validate the effectiveness of the proposed technologies.

Investigation of Utilizing Single Surface Depressions in Optimization of NLF Aerofoil Design

An environment has been created for the optimisation of aerofoil profiles with inclusion of small surface features. For TS wave dominated flows, the paper examines the consequences of the addition of a depression on the aerodynamic optimisation of an NLF aerofoil, and describes the geometry definition fidelity and optimisation algorithm employed in the development process. The variables that define the depression for this optimisation investigation have been fixed, however a preliminary study is presented demonstrating the sensitivity of the flow to the depression characteristics. Solutions to the optimisation problem are then presented using both gradient-based and genetic algorithm techniques, and for accurate representation of the inclusion of small surface perturbations it is concluded that a global optimisation method is required for this type of aerofoil optimisation task due to the nature of the response surface generated. When dealing with surface features, changes in the transition onset are likely to be of a non-linear nature so it is highly critical to have an optimisation algorithm that is robust, suggesting that for this framework, gradient-based methods alone are not suited.

Towards rational catalyst design: a general optimization framework

Rational catalyst design is one of the most fundamental goals in heterogeneous catalysis. Herein, we briefly review our previous design work, and then introduce a general optimization framework, which converts catalyst design into an optimization problem. Furthermore, an example is given using the gradient ascent method to show how this framework can be used for rational catalyst design. This framework may be applied to other design schemes.

A Constrained Optimization Approach to Dynamic State Estimation for Power Systems Including PMU and Missing Measurements.

In this brief, a hybrid filter algorithm is developed to deal with the state estimation (SE) problem for power systems by taking into account the impact from the phasor measurement units (PMUs). Our aim is to include PMU measurements when designing the dynamic state estimators for power systems with traditional measurements. Also, as data dropouts inevitably occur in the transmission channels of traditional measurements from the meters to the control center, the missing measurement phenomenon is also tackled in the state estimator design. In the framework of extended Kalman filter (EKF) algorithm, the PMU measurements are treated as inequality constraints on the states with the aid of the statistical criterion, and then the addressed SE problem becomes a constrained optimization one based on the probability-maximization method. The resulting constrained optimization problem is then solved using the particle swarm optimization algorithm together with the penalty function approach. The proposed algorithm is applied to estimate the states of the power systems with both traditional and PMU measurements in the presence of probabilistic data missing phenomenon. Extensive simulations are carried out on the IEEE 14-bus test system and it is shown that the proposed algorithm gives much improved estimation performances over the traditional EKF method.

Design and optimization next generation passive all-optical networks

Este trabalho investiga novas metodologias para as redes óticas de acesso de próxima geração (NG-OAN). O trabalho está dividido em quatro tópicos de investigação: projeto da rede, modelos numéricos para efeitos não lineares da fibra ótica, impacto dos efeitos não lineares da fibra ótica e otimização da rede. A rede ótica de acesso investigada nesse trabalho está projetado para suprir os requisitos de densidade de utilizadores e cobertura, isto é, suportar muitos utilizadores ( 1000) com altas velocidades de conexão dedicada ( 1 Gb/s) ocupando uma faixa estreita do espectro ( 25 nm) e comprimentos de fibra ótica até 100 km. Os cenários são baseados em redes óticas passivas com multiplexagem por divisão no comprimento de onda de alta densidade (UDWDM-PON) utilizando transmissores/receptores coerentes nos terminais da rede. A rede é avaliada para vários ritmos de transmissão usando formatos de modulação avançados, requisitos de largura de banda por utilizador e partilha de banda com tecnologias tradicionais de redes óticas passivas (PON). Modelos numéricos baseados em funções de transferência das séries de Volterra (VSTF) são demonstrados tanto para a análise dos efeitos não lineares da fibra ótica quanto para avaliação do desempenho total da rede. São apresentadas as faixas de potência e distância de transmissão nas quais as séries de Volterra apresentam resultados semelhantes ao modelo referência Split-Step Fourier (SSF) (validado experimentalmente) para o desempenho total da rede. Além disso, um algoritmo, que evita componentes espectrais com intensidade nulo, é proposto para realizar cálculos rápidos das séries. O modelo VSTF é estendido para identificar unicamente os efeitos não lineares da fibra ótica mais relevantes no cenário investigado: Self-Phase Modulation (SPM), Cross-Phase Modulation (XPM) e Four-Wave Mixing (FWM). Simulações numéricas são apresentadas para identificar o impacto isolado de cada efeito não linear da fibra ótica, SPM, XPM e FWM, no desempenho da rede com detecção coerente UDWDM-PON, transportando canais com modulação digital em fase (M-ária PSK) ou modulação digital em amplitude (M-ária QAM). A análise numérica é estendida para diferentes comprimentos de fibra ótica mono modo (SSMF), potência por canal e ritmo de transmissão por canal. Por conseguinte, expressões analíticas são extrapoladas para determinar a evolução do SPM, XPM e FWM em função da potência e distância de transmissão em cenários NG-OAN. O desempenho da rede é otimizada através da minimização parcial da interferência FWM (via espaçamento desigual dos canais), que nesse caso, é o efeito não linear da fibra ótica mais relevante. Direções para melhorias adicionas no desempenho da rede são apresentados para cenários em que o XPM é relevante, isto é, redes transportando formatos de modulação QAM. A solução, nesse caso, é baseada na utilização de técnicas de processamento digital do sinal.

Analysis, modeling, design and optimization of future communications systems: from theory to practice

Esta tese descreve uma framework de trabalho assente no paradigma multi-camada para analisar, modelar, projectar e optimizar sistemas de comunicação. Nela se explora uma nova perspectiva acerca da camada física que nasce das relações entre a teoria de informação, estimação, métodos probabilísticos, teoria da comunicação e codificação. Esta framework conduz a métodos de projecto para a próxima geração de sistemas de comunicação de alto débito. Além disso, a tese explora várias técnicas de camada de acesso com base na relação entre atraso e débito para o projeto de redes sem fio tolerantes a atrasos. Alguns resultados fundamentais sobre a interação entre a teoria da informação e teoria da estimação conduzem a propostas de um paradigma alternativo para a análise, projecto e optimização de sistemas de comunicação. Com base em estudos sobre a relação entre a informação recíproca e MMSE, a abordagem descrita na tese permite ultrapassar, de forma inovadora, as dificuldades inerentes à optimização das taxas de transmissão de informação confiáveis em sistemas de comunicação, e permite a exploração da atribuição óptima de potência e estruturas óptimas de pre-codificação para diferentes modelos de canal: com fios, sem fios e ópticos. A tese aborda também o problema do atraso, numa tentativa de responder a questões levantadas pela enorme procura de débitos elevados em sistemas de comunicação. Isso é feito através da proposta de novos modelos para sistemas com codificação de rede (network coding) em camadas acima da sua camada física. Em particular, aborda-se a utilização de sistemas de codificação em rede para canais que variam no tempo e são sensíveis a atrasos. Isso foi demonstrado através da proposta de um novo modelo e esquema adaptativo, cujos algoritmos foram aplicados a sistemas sem fios com desvanecimento (fading) complexo, de que são exemplos os sistemas de comunicação via satélite. A tese aborda ainda o uso de sistemas de codificação de rede em cenários de transferência (handover) exigentes. Isso é feito através da proposta de novos modelos de transmissão WiFi IEEE 801.11 MAC, que são comparados com codificação de rede, e que se demonstram possibilitar transferência sem descontinuidades. Pode assim dizer-se que esta tese, através de trabalho de análise e de propostas suportadas por simulações, defende que na concepção de sistemas de comunicação se devem considerar estratégias de transmissão e codificação que sejam não só próximas da capacidade dos canais, mas também tolerantes a atrasos, e que tais estratégias têm de ser concebidas tendo em vista características do canal e a camada física.