A Constructive Genetic Algorithm for permutation flowshop scheduling

The general flowshop scheduling problem is a production problem where a set of n jobs have to be processed with identical flow pattern on in machines. In permutation flowshops the sequence of jobs is the same on all machines. A significant research effort has been devoted for sequencing jobs in a flowshop minimizing the makespan. This paper describes the application of a Constructive Genetic Algorithm (CGA) to makespan minimization on flowshop scheduling. The CGA was proposed recently as an alternative to traditional GA approaches, particularly, for evaluating schemata directly. The population initially formed only by schemata, evolves controlled by recombination to a population of well-adapted structures (schemata instantiation). The CGA implemented is based on the NEH classic heuristic and a local search heuristic used to define the fitness functions. The parameters of the CGA are calibrated using a Design of Experiments (DOE) approach. The computational results are compared against some other successful algorithms from the literature on Taillard`s well-known standard benchmark. The computational experience shows that this innovative CGA approach provides competitive results for flowshop scheduling; problems. (C) 2007 Elsevier Ltd. All rights reserved.

Jointly multi-user detection and channel estimation with genetic algorithm

This work aims at proposing the use of the evolutionary computation methodology in order to jointly solve the multiuser channel estimation (MuChE) and detection problems at its maximum-likelihood, both related to the direct sequence code division multiple access (DS/CDMA). The effectiveness of the proposed heuristic approach is proven by comparing performance and complexity merit figures with that obtained by traditional methods found in literature. Simulation results considering genetic algorithm (GA) applied to multipath, DS/CDMA and MuChE and multi-user detection (MuD) show that the proposed genetic algorithm multi-user channel estimation (GAMuChE) yields a normalized mean square error estimation (nMSE) inferior to 11%, under slowly varying multipath fading channels, large range of Doppler frequencies and medium system load, it exhibits lower complexity when compared to both maximum likelihood multi-user channel estimation (MLMuChE) and gradient descent method (GrdDsc). A near-optimum multi-user detector (MuD) based on the genetic algorithm (GAMuD), also proposed in this work, provides a significant reduction in the computational complexity when compared to the optimum multi-user detector (OMuD). In addition, the complexity of the GAMuChE and GAMuD algorithms were (jointly) analyzed in terms of number of operations necessary to reach the convergence, and compared to other jointly MuChE and MuD strategies. The joint GAMuChE-GAMuD scheme can be regarded as a promising alternative for implementing third-generation (3G) and fourth-generation (4G) wireless systems in the near future. Copyright (C) 2010 John Wiley & Sons, Ltd.

Genetic diversity in sugar apple (Annona squamosa L.) by using RAPD markers

Genetic diversity in a collection of 64 sugar apple accessions collected from different municipalities in northern Minas Gerais was assessed by RAPD analysis. Using 20 selected RAPD primers 167 fragments were generated, of which 48 were polymorphic (28.7%) producing an average of 2.4 polymorphic fragments per primer. Low percentage of polymorphism (< 29%) was observed by using the set of primers indicating low level of genetic variation among the 64 accessions evaluated. Genetic relationships were estimated using Jaccard's coefficient of similarity. Accessions from different municipalities clustered together indicating no correlation between molecular grouping and geographical origin. The dendrogram revealed five clusters. The first cluster grouped C19 and G29 accessions collected from the municipalities of Verdelândia and Monte Azul, respectively. The second cluster grouped G16 and B11 accessions collected from the municipalities of Monte Azul and Coração de Jesus, respectively. The remaining accessions were grouped in three clusters, with 8, 15 and 37 accessions, respectively. In summary, RAPD showed a low percentage of polymorphism in the germplasm collection.

Smoking, consumption of alcohol and sedentary life style in population grouping and their relationships with lipemic disorders

The study, part of the project "Atherosclerotic cardiovascular diseases, lipemic disorders, hypertension, obesity and diabetis mellitus in a population of the metropolitan area of the southeastern region of Brazil", had the following objectives: a) the characterization and distribution among typical human socio-economic groupings, of the prevalence of some particular habits which constitute aspects of life-style-the use of tobacco, the use of alcohol and sedentary activity; b) the establishment of the interrelation between the above-mentioned habits and some lipemic disorders. The prevalence of the habits cited behaved in the following manner: the use of tobacco predominated among men, distributed uniformly throughout the social strata; among the women the average percentage of smokers was 18,9%, a significant difference occurring among the highest socio-economic class, where the average was of 40.2%. The sedentary style of life presented high prevalence, among both men and women with exception of the women of the highest socio-economic level and of the skilled working class. The use of alcohol, as one would expect, is a habit basically practised by the men, without any statistically significant differences between classes. For the purpose of establishing associations between these risk fictors and lipemic conditions four situations were chosen, of the following characteristics: 1- total cholesterol > or = 220 mg/dl and triglycerides > or = 150 mg/dl; 2- HDL cholesterol <35 mg/dl for men and <45 mg/dl for women and triglycerides levels > or = 150 mg/dl; 3- HDL cholesterol <35 mg/dl for men and <45 mg/dl for women and triglycerides levels <150 mg/dl; 4- total cholesterol 220 mg/dl with triglycerides levels <150 mg/dl. Six models of multiple (backward) regression were established, with seven independent variables- age, sex, use of tobacco, consumption of alcohol, light physical activity, hypertension and obesity. Significant associations (P<0,05) were revealed with hypercholesterolemia, accompanied by triglyceride levels > or = 150 mg/dl, and the following independent variables: age, use of tobacco and the interactions between obesity and smoking, age and sedentary lifestyle, sex and obesity (R2=22%); the standardized B coefficient showed that the variables with the greatest weight in the forecasting of the variation in the levels of cholesterol were smoking and the interaction between obesity and smoking. The hypercholesterolemia accompanied by triglycerides levels <150 mg/dl showed a positive association between total cholesterol and sex and the interactions obesity/smoking and sex/obesity. As regards HDL cholesterol accompanied by triglyceride/ levels > or = 150 mg/dl was inversely associated with obesity and the interaction smoking/ age and directly with age (R=31%). The standardized B coeffients, indicated that the variables obesity and the interactions smoking/age possessed a weight three times greater than age alone in accounting for the variation in the serum levels of HDL cholesterol. When accompanied by triglycerides <150 mg/dl there was no association between and the independent variables and the set of them presented R equal to 22%. The sum of top, in the population stutied in this project, the component habits of life-style (smoking, alcohol consumption and sedentary activity) which constitute risk factors which determine morbidity from atherosclerotic cardiovascular diseases are be found distributed through all the typical social groupings of this particular form of social organization. On the other hand, the seven independent variables used in the multiple regression models for the explanation of the lipemic conditions considered presented multiple determination coefficients which varied, approximately, between 20% and 30%. Thus it is important that in the genetic epidemiology the study of the morbidities in question be emphasized.

Fitness function evaluation through fractional algorithms

This paper proposes a Genetic Algorithm (GA) for the design of combinational logic circuits. The fitness function evaluation is calculated using Fractional Calculus. This approach extends the classical fitness function by including a fractional-order dynamical evaluation. The experiments reveal superior results when comparing with the classical method.

Project scheduling under multiple resources constraints using a genetic algorithm

The resource constrained project scheduling problem (RCPSP) is a difficult problem in combinatorial optimization for which extensive investigation has been devoted to the development of efficient algorithms. During the last couple of years many heuristic procedures have been developed for this problem, but still these procedures often fail in finding near-optimal solutions. This paper proposes a genetic algorithm for the resource constrained project scheduling problem. The chromosome representation of the problem is based on random keys. The schedule is constructed using a heuristic priority rule in which the priorities and delay times of the activities are defined by the genetic algorithm. 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.

Project scheduling using a competitive genetic algorithm

- The resource constrained project scheduling problem (RCPSP) is a difficult problem in combinatorial optimization for which extensive investigation has been devoted to the development of efficient algorithms. During the last couple of years many heuristic procedures have been developed for this problem, but still these procedures often fail in finding near-optimal solutions. This paper proposes a genetic algorithm for the resource constrained project scheduling problem. The chromosome representation of the problem is based on random keys. The schedule is constructed using a heuristic priority rule in which the priorities and delay times of the activities are defined by the genetic algorithm. 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

A genetic algorithm for the job shop scheduling with a new local search using Monte Carlo method

This paper presents a methodology for applying scheduling algorithms using Monte Carlo simulation. The methodology is based on a decision support system (DSS). The proposed methodology combines a genetic algorithm with a new local search using Monte Carlo Method. The methodology is applied to the job shop scheduling problem (JSSP). The JSSP is a difficult problem in combinatorial optimization for which extensive investigation has been devoted to the development of efficient algorithms. The methodology is tested on a set of standard instances taken from the literature and compared with others. The computation results validate the effectiveness of the proposed methodology. The DSS developed can be utilized in a common industrial or construction environment.

Analysis of the genetic polymorphism of Paracoccidioides brasiliensis and Paracoccidioides cerebriformis "Moore" by random amplified polymorphic DNA (RAPD) and 28S ribosomal DNA sequencing: Paracoccidioides cerebriformis revisited

Our purpose was to compare the genetic polymorphism of six samples of P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1), with four samples of P. cerebriformis (735, 741, 750, 361) from the Mycological Laboratory of the Instituto de Medicina Tropical de São Paulo, using Random Amplified Polymorphic DNA Analysis (RAPD). RAPD profiles clearly segregated P. brasiliensis and P. cerebriformis isolates. However, the variation on band patterns among P. cerebriformis isolates was high. Sequencing of the 28S rDNA gene showed nucleotide conservancy among P. cerebriformis isolates, providing basis for taxonomical grouping, and disclosing high divergence to P. brasiliensis supporting that they are in fact two distinct species. Moreover, DNA sequence suggests that P. cerebriformis belongs in fact to the Aspergillus genus.

Genetic Characterization of an Insect-Specific Flavivirus Isolated from Culex Theileri Mosquitoes Collected in Southern Portugal

We describe the full genetic characterization of an insect-specific flavivirus (ISF) from Culex theileri (Theobald) mosquitoes collected in Portugal. This represents the first isolation and full characterization of an ISF from Portuguese mosquitoes. The virus, designated CTFV, for Culex theileri flavivirus, was isolated in the C6/36 Stegomyia albopicta (=Aedes albopictus) cell line, and failed to replicate in vertebrate (Vero) cells in common with other ISFs. The CTFV genome encodes a single polyprotein with 3357 residues showing all the features expected for those of flaviviruses. Phylogenetic analyses based on all ISF sequences available to date, place CTFV among Culex-associated flaviviruses, grouping with recently published NS5 partial sequences documented from mosquitoes collected in the Iberian Peninsula, and with Quang Binh virus (isolated in Vietnam) as a close relative. No CTFV sequences were found integrated in their host’s genome using a range of specific PCR primers designed to the prM/E, NS3, and NS5 region.

Preliminary Evaluation of the Genetic Relatedness of Three Species of the Subgenus Dendromyia Theobald and Other Species of the Genus Wyeomyia Theobald (Diptera: Culicidae)

An eletrophoretic analysis of three species of the subgenus Dendromyia (Wyeomyia luteoventralis, Wy. ypsipola and Wy. testei) and three species belonging to different groups in the genus Wyeomyia (Wy. negrensis, Wy. mystes and Wy.confusa) was performed. Eight enzyme loci were analyzed. High values of genetic identity were detected among the species of the subgenus Dendromyia: Wy. luteoventralis, Wy. ypsipola and Wy. testei (mean value 0.63). On the other hand low values of genetic identity were observed among Wy. negrensis, Wy. mystes and Wy. confusa (mean value 0.23), suggesting that they belong, at least, to distinct subgenera within the Genus Wyeomyia. The UPGMA phenogram revealed the grouping of the Dendromyia species, while the others clustered at lower identity levels.

Isolation of genetic mutation leading to abnormal phenotype in human through ultra-high-throughput sequencing (UHTS)

The introduction of Next Generation Sequencing (NGS) facilitated the task of localizing DNA variation and identifying the genetic cause of yet unsolved Mendelian disorders. Using Whole Exome Capture method and NGS, we identified the causative genetic aberration responsible for a number of monogenic disorders previously undetermined. Due to the novelty of the NGS method we benchmarked different algorithms to assess their merits and defects. This allowed us to establish a pipeline that we successfully used to pinpoint genes responsible for a form of West's syndrome, a Complex Intellectual Disability syndrome associated with patellar dislocation and celiac disease, and correcting some erroneous molecular diagnosis of Alport's syndrome in a Saudi Arabian family.

Additive effects of LPL, APOA5 and APOE variant combinations on triglyceride levels and hypertriglyceridemia: results of the ICARIA genetic sub-study.

BACKGROUND Hypertriglyceridemia (HTG) is a well-established independent risk factor for cardiovascular disease and the influence of several genetic variants in genes related with triglyceride (TG) metabolism has been described, including LPL, APOA5 and APOE. The combined analysis of these polymorphisms could produce clinically meaningful complementary information. METHODS A subgroup of the ICARIA study comprising 1825 Spanish subjects (80% men, mean age 36 years) was genotyped for the LPL-HindIII (rs320), S447X (rs328), D9N (rs1801177) and N291S (rs268) polymorphisms, the APOA5-S19W (rs3135506) and -1131T/C (rs662799) variants, and the APOE polymorphism (rs429358; rs7412) using PCR and restriction analysis and TaqMan assays. We used regression analyses to examine their combined effects on TG levels (with the log-transformed variable) and the association of variant combinations with TG levels and hypertriglyceridemia (TG > or = 1.69 mmol/L), including the covariates: gender, age, waist circumference, blood glucose, blood pressure, smoking and alcohol consumption. RESULTS We found a significant lowering effect of the LPL-HindIII and S447X polymorphisms (p < 0.0001). In addition, the D9N, N291S, S19W and -1131T/C variants and the APOE-epsilon4 allele were significantly associated with an independent additive TG-raising effect (p < 0.05, p < 0.01, p < 0.001, p < 0.0001 and p < 0.001, respectively). Grouping individuals according to the presence of TG-lowering or TG-raising polymorphisms showed significant differences in TG levels (p < 0.0001), with the lowest levels exhibited by carriers of two lowering variants (10.2% reduction in TG geometric mean with respect to individuals who were homozygous for the frequent alleles of all the variants), and the highest levels in carriers of raising combinations (25.1% mean TG increase). Thus, carrying two lowering variants was protective against HTG (OR = 0.62; 95% CI, 0.39-0.98; p = 0.042) and having one single raising polymorphism (OR = 1.20; 95% CI, 1.39-2.87; p < 0.001) or more (2 or 3 raising variants; OR = 2.90; 95% CI, 1.56-5.41; p < 0.001) were associated with HTG. CONCLUSION Our results showed a significant independent additive effect on TG levels of the LPL polymorphisms HindIII, S447X, D9N and N291S; the S19W and -1131T/C variants of APOA5, and the epsilon4 allele of APOE in our study population. Moreover, some of the variant combinations studied were significantly associated with the absence or the presence of hypertriglyceridemia.

A genetic algorithm to ensemble feature selection

We are going to implement the "GA-SEFS" by Tsymbal and analyse experimentally its performance depending on the classifier algorithms used in the fitness function (NB, MNge, SMO). We are also going to study the effect of adding to the fitness function a measure to control complexity of the base classifiers.