Genetic Algorithms (Binary and Real Codes) for the Optimisation of a Fermentation Process for Butanol Production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bayesian outlier analysis in binary regression

We propose alternative approaches to analyze residuals in binary regression models based on random effect components. Our preferred model does not depend upon any tuning parameter, being completely automatic. Although the focus is mainly on accommodation of outliers, the proposed methodology is also able to detect them. Our approach consists of evaluating the posterior distribution of random effects included in the linear predictor. The evaluation of the posterior distributions of interest involves cumbersome integration, which is easily dealt with through stochastic simulation methods. We also discuss different specifications of prior distributions for the random effects. The potential of these strategies is compared in a real data set. The main finding is that the inclusion of extra variability accommodates the outliers, improving the adjustment of the model substantially, besides correctly indicating the possible outliers.

Spectrophotometric study of binary and ternary systems involving metal ions and benzylidenepyruvates: Equilibria in aqueous solutions

The protonation of 4-dimethylaminobenzylidenepyruvate (DMBP) and 2-chloro-4-dimethylaminobenzylidenepyruvate (2-CI-DMBP) and their complex formation with Mn(II), Co(II), Ni(II), Cu(II), Zn(II), Pb(II), Cd(II) and Al(III) have been studied by potentiometric and spectrophotometric methods at 25 °C and ionic strength 0.500 M, held with sodium perchlorate. The stability order found for 1 :1 complexes of both ligands is Al(III) > Cu(II) > Pb(II) > Ni(II) > Zn(II) > Co(II) > Cd(II) > Mn(II). The stability changes move in the same direction as the pKa of the ligands. The results are compared with literature values reported for metal ion pyruvate systems. Thermodynamic stabilities of ternary complexes formed in Cu(II)-B-L- systems, where B = 2,2′-bipyridyl (bipy), ethylenediamine or glycinate and L = DMBP or 2-CI-DMBP, were also determined. The Cu(bipy)L+ species are more stable than would be expected on purely statistical grounds. The importance of the :t system associated with bipy on the enhanced stability of its mixed ligand complexes is stressed. Analytical applications of the investigated ligands are outlined.

Phonons in binary BCC lithium-sodium alloys

The dispersion relations along the principal symmetry directions in BCC lithium-sodium alloys are calculated using second-order perturbation theory. The local modified Hoshino-Youngmodel potential was used for the lithium and the local Harrison model potential for sodium. The phonon density of states, the root mean square displacements and (Θ-T) curves are also calculated. In the absence of experimental data, just the theoretical predictions are presented here.

EXAFS and Raman spectroscopy study of binary indium fluoride glasses

Extended X-ray absorption fine spectroscopy (EXAFS) and Raman scattering studies of InF3-BaF2 and InF3-SrF2 binary glasses are reported. For all compositions, the local structure of the glasses is built with InF6 units. For all glasses studied, the indium neighbour's number and the In-F mean bond length are equal to the values of the InF3 crystalline phase (6 and 0.205 nm, respectively). © 1996 Chapman & Hall.

Variational studies and replica symmetry breaking in the generalization problem of the binary perceptron

We analyze the average performance of a general class of learning algorithms for the nondeterministic polynomial time complete problem of rule extraction by a binary perceptron. The examples are generated by a rule implemented by a teacher network of similar architecture. A variational approach is used in trying to identify the potential energy that leads to the largest generalization in the thermodynamic limit. We restrict our search to algorithms that always satisfy the binary constraints. A replica symmetric ansatz leads to a learning algorithm which presents a phase transition in violation of an information theoretical bound. Stability analysis shows that this is due to a failure of the replica symmetric ansatz and the first step of replica symmetry breaking (RSB) is studied. The variational method does not determine a unique potential but it allows construction of a class with a unique minimum within each first order valley. Members of this class improve on the performance of Gibbs algorithm but fail to reach the Bayesian limit in the low generalization phase. They even fail to reach the performance of the best binary, an optimal clipping of the barycenter of version space. We find a trade-off between a good low performance and early onset of perfect generalization. Although the RSB may be locally stable we discuss the possibility that it fails to be the correct saddle point globally. ©2000 The American Physical Society.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage. ©FUNPEC-RP.

Human interferon B1 ser17: Coding DNA synthesis, expression, purification and characterization of bioactive recombinant protein

A protocol to produce large amounts of bioactive homogeneous human interferon β1 expressed in Escherichia coli was developed. Human interferon β1 ser17 gene was constructed, cloned and subcloned, and the recombinant protein expressed in E. coli cells. Solubilization of recombinant human interferon β1 ser17 (rhIFN-β1 ser17) was accomplished by employing a brief shift to high alkaline pH in the presence of non-ionic detergent. The recombinant protein was purifi ed by three chromatographic steps. N-terminal amino acid sequencing and mass spectrometry analysis provided experimental evidence for the identity of the recombinant protein. Reverse phase liquid chromatography demonstrated that the content of deamidates and sulphoxides was similar to a commercial standard. Size exclusion chromatography demonstrated the absence of high molecular mass aggregates and dimers. The protocol represents an effi cient and high-yield method to obtain bioactive homogeneous monomeric rhIFN-β1 ser17 protein. It may thus represent an important step towards scaling up for rhIFN-β1 ser17 large-scale production. © 2010 Villela AD, et al.

Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs

Sugarcane is the most important crop for sugar industry and raw material for bioethanol. Here we present a quantitative analysis of the gene content from publicly available sugarcane ESTs. The current sugarcane EST collection sampled orthologs for ~58 % of the closely-related sorghum proteome, suggesting that more than 10,000 sugarcane coding-genes remain undiscovered. Moreover the existence of more than 2,000 ncRNAs conserved between sugarcane and sorghum was revealed, among which over 500 are also detected in rice, supporting the existence of hundreds of conserved ncRNAs in grasses. New efforts towards sugarcane transcriptome sequencing were needed to sample the missing coding-genes as well as to expand the catalog of ncRNAs. © 2012 Springer Science+Business Media, LLC.

BBA: A binary bat algorithm for feature selection

Feature selection aims to find the most important information from a given set of features. As this task can be seen as an optimization problem, the combinatorial growth of the possible solutions may be in-viable for a exhaustive search. In this paper we propose a new nature-inspired feature selection technique based on the bats behaviour, which has never been applied to this context so far. The wrapper approach combines the power of exploration of the bats together with the speed of the Optimum-Path Forest classifier to find the set of features that maximizes the accuracy in a validating set. Experiments conducted in five public datasets have demonstrated that the proposed approach can outperform some well-known swarm-based techniques. © 2012 IEEE.

Rheological behavior of binary aqueous solutions of poly(ethylene glycol) of 1500 g·mol-1 as affected by temperature and polymer concentration

The rheological behavior of poly(ethylene glycol) of 1500 g·mol -1(PEG1500) aqueous solutions with various polymer concentrations (w = 0.05, 0.10, 0.15, 0.20 and 0.25) was studied at different temperatures (T = 283.15, 288.15, 293.15, 298.15 and 303.15) K. The analyses were carried out considering shear rates ranging from (20 to 350) s-1, using a cone-and-plate rheometer under controlled stress and temperature. Classical rheological models (Newton, Bingham, Power Law, Casson, and Herschel-Bulkley) were tested. The Power Law model was shown suitable to mathematically represent the rheological behavior of these solutions. Well-adjusted empirical models were derived for consistency index variations in function of temperature (Arrhenius-type model; R2 > 0.96), polymer concentration (exponential model; R2 > 0.99) or the combination of both (R 2 > 0.99). Additionally, linear models were used to represent the variations of behavior index in the functions of temperature (R2 > 0.83) and concentration (R2 > 0.87). © 2013 American Chemical Society.

Irregular satellites of Jupiter: Three-dimensional study of binary-asteroid captures

Among the hidden pieces of the giant puzzle, which is our Solar system, the origins of irregularsatellites of the giant planets stand to be explained, while the origins of regular satellites arewell explained by the in situ formation model through matter accretion. Once they are notlocally formed, the most acceptable theory predicts that they had been formed elsewhere andbecame captured later, most likely during the last stage of planet formation. However, underthe restricted three-body problem theory, captures are temporary and there is still no assistedcapture mechanism which is well established. In a previous work, we showed that the capturemechanism of a binary asteroid under the co-planar four-body scenario yielded permanentcaptured objects with an orbital shape which is very similar to those of the actual progradeirregular Jovian satellites. By extending our previous study to a 3D case, here we demonstratethat the capture mechanism of a binary asteroid can produce permanent captures of objects byitself which have very similar orbits to irregular Jovian satellites. Some of the captured objectswithout aid of gas drag or other mechanisms present a triplet: semi-major axis, eccentricityand inclination, which is comparable to the already known irregular Jovian objects. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Binary Bat Algorithm for Feature Selection

Feature selection aims to find the most important information to save computational efforts and data storage. We formulated this task as a combinatorial optimization problem since the exponential growth of possible solutions makes an exhaustive search infeasible. In this work, we propose a new nature-inspired feature selection technique based on bats behavior, namely, binary bat algorithm The wrapper approach combines the power of exploration of the bats together with the speed of the optimum-path forest classifier to find a better data representation. Experiments in public datasets have shown that the proposed technique can indeed improve the effectiveness of the optimum-path forest and outperform some well-known swarm-based techniques. © 2013 Copyright © 2013 Elsevier Inc. All rights reserved.

A decoding method of an n length binary BCH code through (n + 1)n length binary cyclic code

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

BCS: A Binary Cuckoo Search algorithm for feature selection

Feature selection has been actively pursued in the last years, since to find the most discriminative set of features can enhance the recognition rates and also to make feature extraction faster. In this paper, the propose a new feature selection called Binary Cuckoo Search, which is based on the behavior of cuckoo birds. The experiments were carried out in the context of theft detection in power distribution systems in two datasets obtained from a Brazilian electrical power company, and have demonstrated the robustness of the proposed technique against with several others nature-inspired optimization techniques. © 2013 IEEE.