Crossing genetic and swarm intelligence algorithms to generate logic circuits

Genetic Algorithms (GAs) are adaptive heuristic search algorithm based on the evolutionary ideas of natural selection and genetic. The basic concept of GAs is designed to simulate processes in natural system necessary for evolution, specifically those that follow the principles first laid down by Charles Darwin of survival of the fittest. On the other hand, Particle swarm optimization (PSO) is a population based stochastic optimization technique inspired by social behavior of bird flocking or fish schooling. PSO shares many similarities with evolutionary computation techniques such as GAs. The system is initialized with a population of random solutions and searches for optima by updating generations. However, unlike GA, PSO has no evolution operators such as crossover and mutation. In PSO, the potential solutions, called particles, fly through the problem space by following the current optimum particles. PSO is attractive because there are few parameters to adjust. This paper presents hybridization between a GA algorithm and a PSO algorithm (crossing the two algorithms). The resulting algorithm is applied to the synthesis of combinational logic circuits. With this combination is possible to take advantage of the best features of each particular algorithm.

Implementation of fractional-order electromagnetic potential through a genetic algorithm

Several phenomena present in electrical systems motivated the development of comprehensive models based on the theory of fractional calculus (FC). Bearing these ideas in mind, in this work are applied the FC concepts to define, and to evaluate, the electrical potential of fractional order, based in a genetic algorithm optimization scheme. The feasibility and the convergence of the proposed method are evaluated.

Calculation of fractional derivatives of noisy data with genetic algorithms

This paper addresses the calculation of derivatives of fractional order for non-smooth data. The noise is avoided by adopting an optimization formulation using genetic algorithms (GA). Given the flexibility of the evolutionary schemes, a hierarchical GA composed by a series of two GAs, each one with a distinct fitness function, is established.

Development of an interface for ontology‐based transformation between features of different types

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

A random key based genetic algorithm for the resource constrained project scheduling problem

This paper presents a genetic algorithm for the Resource Constrained Project Scheduling Problem (RCPSP). The chromosome representation of the problem is based on random keys. The schedule is constructed using a heuristic priority rule in which the priorities of the activities are defined by the genetic algorithm. The heuristic generates parameterized active schedules. The approach was tested on a set of standard problems taken from the literature and compared with other approaches. The computational results validate the effectiveness of the proposed algorithm.

Trajectory planning of redundant manipulators using genetic algorithms

The trajectory planning of redundant robots is an important area of research and efficient optimization algorithms are needed. This paper presents a new technique that combines the closed-loop pseudoinverse method with genetic algorithms. The results are compared with a genetic algorithm that adopts the direct kinematics. In both cases the trajectory planning is formulated as an optimization problem with constraints.

Dynamical modelling of a genetic algorithm

This work addresses the signal propagation and the fractional-order dynamics during the evolution of a genetic algorithm (GA). In order to investigate the phenomena involved in the GA population evolution, the mutation is exposed to excitation perturbations during some generations and the corresponding fitness variations are evaluated. Three distinct fitness functions are used to study their influence in the GA dynamics. The input and output signals are studied revealing a fractional-order dynamic evolution, characteristic of a long-term system memory.

Optimal fuzzy PID control tuned with genetic algorithms

Fuzzy logic controllers (FLC) are intelligent systems, based on heuristic knowledge, that have been largely applied in numerous areas of everyday life. They can be used to describe a linear or nonlinear system and are suitable when a real system is not known or too difficult to find their model. FLC provide a formal methodology for representing, manipulating and implementing a human heuristic knowledge on how to control a system. These controllers can be seen as artificial decision makers that operate in a closed-loop system, in real time. The main aim of this work was to develop a single optimal fuzzy controller, easily adaptable to a wide range of systems – simple to complex, linear to nonlinear – and able to control all these systems. Due to their efficiency in searching and finding optimal solution for high complexity problems, GAs were used to perform the FLC tuning by finding the best parameters to obtain the best responses. The work was performed using the MATLAB/SIMULINK software. This is a very useful tool that provides an easy way to test and analyse the FLC, the PID and the GAs in the same environment. Therefore, it was proposed a Fuzzy PID controller (FL-PID) type namely, the Fuzzy PD+I. For that, the controller was compared with the classical PID controller tuned with, the heuristic Ziegler-Nichols tuning method, the optimal Zhuang-Atherton tuning method and the GA method itself. The IAE, ISE, ITAE and ITSE criteria, used as the GA fitness functions, were applied to compare the controllers performance used in this work. Overall, and for most systems, the FL-PID results tuned with GAs were very satisfactory. Moreover, in some cases the results were substantially better than for the other PID controllers. The best system responses were obtained with the IAE and ITAE criteria used to tune the FL-PID and PID controllers.

Optimization of multi-stage amplifiers in deep-submicron CMOS using a distributed/parallel genetic algorithm

IEEE International Symposium on Circuits and Systems, pp. 724 – 727, Seattle, EUA

On divisors of pseudovarieties generated by some classes of full transformation semigroups

Algebra Colloquium, 15 (2008), p. 581–588

Multi-agent system for distributed manufacturing scheduling with genetic algorithms and tabu search

Computerized scheduling methods and computerized scheduling systems according to exemplary embodiments. A computerized scheduling method may be stored in a memory and executed on one or more processors. The method may include defining a main multi-machine scheduling problem as a plurality of single machine scheduling problems; independently solving the plurality of single machine scheduling problems thereby calculating a plurality of near optimal single machine scheduling problem solutions; integrating the plurality of near optimal single machine scheduling problem solutions into a main multi-machine scheduling problem solution; and outputting the main multi-machine scheduling problem solution.

Estrogen receptor dependent genetic and epigenetic factors of tamoxifen resistance

Resumo: A decisão da terapêutica hormonal no tratamento do cancro da mama baseiase na determinação do receptor de estrogénio alfa por imunohistoquímica (IHC). Contudo, a presença deste receptor não prediz a resposta em todas as situações, em parte devido a limitações do método IHC. Investigámos se a expressão dos genes ESR1 e ESR2, bem como a metilação dos respectivos promotores, pode estar relacionada com a evolução desfavorável de uma proporção de doentes tratados com tamoxifeno assim como com a perda dos receptores de estrogénio alfa (ERα) e beta (ERß). Amostras de 211 doentes com cancro da mama diagnosticado entre 1988 e 2004, fixadas em formalina e preservadas em parafina, foram utilizadas para a determinação por IHC da presença dos receptores ERα e ERß. O mRNA total do gene ESR1 e os níveis específicos do transcrito derivado do promotor C (ESR1_C), bem como dos transcritos ESR2_ß1, ESR2_ß2/cx, and ESR2_ß5 foram avaliados por Real-time PCR. Os promotores A e C do gene ESR1 e os promotores 0K e 0N do gene ESR2 foram investigados por análise de metilação dos dinucleotidos CpG usando bisulfite-PCR para análise com enzimas de restrição, ou para methylation specific PCR. Atendendo aos resultados promissores relacionados com a metilação do promotor do gene ESR1, complementamos o estudo com um método quantitativo por matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) suportado pelo software Epityper para a medição da metilação nos promotores A e C. Fez-se a avaliação da estabilidade do mRNA nas linhas celulares de cancro da mama MCF-7 e MDA-MB-231 tratadas com actinomicina D. Baixos níveis do transcrito ESR1_C associaram-se a uma melhor sobrevivência global (p = 0.017). Níveis elevados do transcrito ESR1_C associaram-se a uma resposta inferior ao tamoxifeno (HR = 2.48; CI 95% 1.24-4.99), um efeito mais pronunciado em doentes com tumores de fenótipo ERα/PgR duplamente positivo (HR = 3.41; CI 95% 1.45-8.04). A isoforma ESR1_C mostrou ter uma semi-vida prolongada, bem como uma estrutura secundária da região 5’UTR muito mais relaxada em comparação com a isoforma ESR1_A. A análise por Western-blot mostrou que ao nível da 21 proteína, a selectividade de promotores é indistinguivel. Não se detectou qualquer correlação entre os níveis das isoformas do gene ESR2 ou entre a metilação dos promotores do gene ESR2, e a detecção da proteína ERß. A metilação do promotor C do gene ESR1, e não do promotor A, foi responsável pela perda do receptor ERα. Estes resultados sugerem que os níveis do transcrito ESR1_C sejam usados como um novo potencial marcador para o prognóstico e predição de resposta ao tratamento com tamoxifeno em doentes com cancro da mama. Abstract: The decision of endocrine breast cancer treatment relies on ERα IHC-based assessment. However, ER positivity does not predict response in all cases in part due to IHC methodological limitations. We investigated whether ESR1 and ESR2 gene expression and respective promoter methylation may be related to non-favorable outcome of a proportion of tamoxifen treated patients as well as to ERα and ERß loss. Formalin-fixed paraffin-embedded breast cancer samples from 211 patients diagnosed between 1988 and 2004 were submitted to IHC-based ERα and ERß protein determination. ESR1 whole mRNA and promoter C specific transcript levels, as well as ESR2_ß1, ESR2_ß2/cx, and ESR2_ß5 transcripts were assessed by real-time PCR. ESR1 promoters A and C, and ESR2 promoters 0N and 0K were investigated by CpG methylation analysis using bisulfite-PCR for restriction analysis, or methylation specific PCR. Due to the promising results related to ESR1 promoter methylation, we have used a quantification method by matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF MS) together with Epityper software to measure methylation at promoters A and C. mRNA stability was assessed in actinomycin D treated MCF-7 and MDA-MB-231 cells. ERα protein was quantified using transiently transfected breast cancer cells. Low ESR1_C transcript levels were associated with better overall survival (p = 0.017). High levels of ESR1_C transcript were associated with non-favorable response in tamoxifen treated patients (HR = 2.48; CI 95% 1.24-4.99), an effect that was more pronounced in patients with ERα/PgR double-positive tumors (HR = 3.41; CI 95% 1.45-8.04). The ESR1_C isoform had a prolonged mRNA half-life and a more relaxed 5’UTR structure compared to ESR1_A isoform. Western-blot analysis showed that at protein level, the promoter selectivity is undistinguishable. There was no correlation between levels of ESR2 isoforms or ESR2 promoter methylation and ERß protein staining. ESR1 promoter C CpG methylation and not promoter A was responsible for ERα loss. We propose ESR1_C levels as a putative novel marker for breast cancer prognosis and prediction of tamoxifen response.

Time-domain optimization of amplifiers based on distributed genetic algorithms

Thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Electrical and Computer Engineering

Schistosoma mansoni: the effect of dexamethasone on the cercaria-schistosomulum transformation, in vivo

Treatment with dexamethasone (DMS) in the early phases of the experimental Schistosoma mansoni infection causes an indirect effect on the cercaria-schistosomulum transformation process. This is observed when naive albino mice are treated with that drug (50 mg/Kg, subcutaneously) and infected intraperitonealy 01 hour later with about 500 S. mansoni cercariae (LE strain). An inhibition in the host cell adhesion to the larvae, with a simultaneous delay in the cercaria-schistosomulum transformation, is observed. This effect is probably due to a blockade of the neutrophil migration to the peritoneal cavity of mice, by an impairment of the release of chemotactic substances. Such delay probably favors the killing of S. mansoni larvae, still in the transformation process, by the vertebrate host defenses, as the complement system.

Genetic structure of Neisseria meningitidis serogroup C epidemic strains in South Brazil

In the present study we report the results of an analysis, based on serotyping, multilocus enzyme electrophoresis (MEE), and ribotyping of N. meningitidis serogroup C strains isolated from patients with meningococcal disease (MD) in Rio Grande do Sul (RS) and Santa Catarina (SC) States, Brazil, as the Center of Epidemiology Control of Ministry of Health detected an increasing of MD cases due to this serogroup in the last two years (1992-1993). We have demonstrated that the MD due to N.meningitidis serogroup C strains in RS and SC States occurring in the last 4 years were caused mainly by one clone of strains (ET 40), with isolates indistinguishable by serogroup, serotype, subtype and even by ribotyping. One small number of cases that were not due to an ET 40 strains, represent closely related clones that probably are new lineages generated from the ET 40 clone referred as ET 11A complex. We have also analyzed N.meningitidis serogroup C strains isolated in the greater São Paulo in 1976 as representative of the first post epidemic year in that region. The ribotyping method, as well as MEE, could provide useful information about the clonal characteristics of those isolates and also of strains isolated in south Brazil. The strains from 1976 have more similarity with the actual endemic than epidemic strains, by the ribotyping, sulfonamide sensitivity, and MEE results. In conclusion, serotyping with monoclonal antibodies (C:2b:P1.3), MEE (ET 11 and ET 11A complex), and ribotyping by using ClaI restriction enzyme (Rb2), were useful to characterize these epidemic strains of N.meningitidis related to the increased incidence of MD in different States of south Brazil. It is mostly probable that these N.meningitidis serogroup C strains have poor or no genetic corelation with 1971-1975 epidemic serogroup C strains. The genetic similarity of members of the ET 11 and ET 11A complex were confirmed by the ribotyping method by using three restriction endonucleases.