Automated design of microwave discrete tuning differential capacitance circuits in Si-integrated technologies

A genetic algorithm used to design radio-frequency binary-weighted differential switched capacitor arrays (RFDSCAs) is presented in this article. The algorithm provides a set of circuits all having the same maximum performance. This article also describes the design, implementation, and measurements results of a 0.25 lm BiCMOS 3-bit RFDSCA. The experimental results show that the circuit presents the expected performance up to 40 GHz. The similarity between the evolutionary solutions, circuit simulations, and measured results indicates that the genetic synthesis method is a very useful tool for designing optimum performance RFDSCAs.

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.

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

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.

Double power laws, fractals and self-similarity

Power law (PL) distributions have been largely reported in the modeling of distinct real phenomena and have been associated with fractal structures and self-similar systems. In this paper, we analyze real data that follows a PL and a double PL behavior and verify the relation between the PL coefficient and the capacity dimension of known fractals. It is to be proved a method that translates PLs coefficients into capacity dimension of fractals of any real data.

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

Genetic relationships of Corynebacterium diphtheriae strains isolated from a diphtheria case and carriers by restriction fragment length polymorphism of rRNA genes

In the present study we report the results of an analysis, based on ribotyping of Corynebacterium diphtheriae intermedius strains isolated from a 9 years old child with clinical diphtheria and his 5 contacts. Quantitative analysis of RFLPs of rRNA was used to determine relatedness of these 7 C.diphtheriae strains providing support data in the diphtheria epidemiology. We have also tested those strains for toxigenicity in vitro by using the Elek's gel diffusion method and in vivo by using cell culture method on cultured monkey kidney cell (VERO cells). The hybridization results revealed that the 5 C.diphtheriae strains isolated from contacts and one isolated from the clinical case (nose case strain) had identical RFLP patterns with all 4 restriction endonucleases used, ribotype B. The genetic distance from this ribotype and ribotype A (throat case strain), that we initially assumed to be responsible for the illness of the patient, was of 0.450 showing poor genetic correlation among these two ribotypes. We found no significant differences concerned to the toxin production by using the cell culture method. In conclusion, the use of RFLPs of rRNA gene was successful in detecting minor differences in closely related toxigenic C.diphtheriae intermedius strains and providing information about genetic relationships among them.

New Strategies on Molecular Biology Applied to Microbial Systematics

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint