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.

Identification and feature selection of non-technical losses for industrial consumers using the software WEKA

This work has as objectives the implementation of a intelligent computational tool to identify the non-technical losses and to select its most relevant features, considering information from the database with industrial consumers profiles of a power company. The solution to this problem is not trivial and not of regional character, the minimization of non-technical loss represents the guarantee of investments in product quality and maintenance of power systems, introduced by a competitive environment after the period of privatization in the national scene. This work presents using the WEKA software to the proposed objective, comparing various classification techniques and optimization through intelligent algorithms, this way, can be possible to automate applications on Smart Grids. © 2012 IEEE.

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.

Structural and Phylogenetic Studies with MjTX-I Reveal a Multi-Oligomeric Toxin - a Novel Feature in Lys49-PLA2s Protein Class

The mortality caused by snakebites is more damaging than many tropical diseases, such as dengue haemorrhagic fever, cholera, leishmaniasis, schistosomiasis and Chagas disease. For this reason, snakebite envenoming adversely affects health services of tropical and subtropical countries and is recognized as a neglected disease by the World Health Organization. One of the main components of snake venoms is the Lys49-phospholipases A2, which is catalytically inactive but possesses other toxic and pharmacological activities. Preliminary studies with MjTX-I from Bothrops moojeni snake venom revealed intriguing new structural and functional characteristics compared to other bothropic Lys49-PLA2s. We present in this article a comprehensive study with MjTX-I using several techniques, including crystallography, small angle X-ray scattering, analytical size-exclusion chromatography, dynamic light scattering, myographic studies, bioinformatics and molecular phylogenetic analyses.Based in all these experiments we demonstrated that MjTX-I is probably a unique Lys49-PLA2, which may adopt different oligomeric forms depending on the physical-chemical environment. Furthermore, we showed that its myotoxic activity is dramatically low compared to other Lys49-PLA2s, probably due to the novel oligomeric conformations and important mutations in the C-terminal region of the protein. The phylogenetic analysis also showed that this toxin is clearly distinct from other bothropic Lys49-PLA2s, in conformity with the peculiar oligomeric characteristics of MjTX-I and possible emergence of new functionalities inresponse to environmental changes and adaptation to new preys. © 2013 Salvador et al.

Exterior orientation of CBERS-2B imagery using multi-feature control and orbital data

The major contribution of this paper relates to the practical advantages of combining Ground Control Points (GCPs), Ground Control Lines (GCLs) and orbital data to estimate the exterior orientation parameters of images collected by CBERS-2B (China-Brazil Earth Resources Satellite) HRC (High-resolution Camera) and CCD (High-resolution CCD Camera) sensors. Although the CBERS-2B is no longer operational, its images are still being used in Brazil, and the next generations of the CBERS satellite will have sensors with similar technical features, which motivates the study presented in this paper. The mathematical models that relate the object and image spaces are based on collinearity (for points) and coplanarity (for lines) conditions. These models were created in an in-house developed software package called TMS (Triangulation with Multiple Sensors) with multi-feature control (GCPs and GCLs). Experiments on a block of four CBERS-2B HRC images and on one CBERS-2B CCD image were performed using both models. It was observed that the combination of GCPs and GCLs provided better bundle block adjustment results than conventional bundle adjustment using only GCPs. The results also demonstrate the advantages of using primarily orbital data when the number of control entities is reduced. © 2013 International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS).

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.

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.

Optimizing feature selection through binary charged system search

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 inviable for a exhaustive search. In this paper we propose a new nature-inspired feature selection technique based on the Charged System Search (CSS), which has never been applied to this context so far. The wrapper approach combines the power of exploration of CSS 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 four public datasets have demonstrated the validity of the proposed approach can outperform some well-known swarm-based techniques. © 2013 Springer-Verlag.

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3′UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.Genes and Immunity advance online publication, 3 October 2013; doi:10.1038/gene.2013.47.

A wrapper approach for feature selection based on Bat Algorithm and Optimum-Path Forest

Besides optimizing classifier predictive performance and addressing the curse of the dimensionality problem, feature selection techniques support a classification model as simple as possible. In this paper, we present a wrapper feature selection approach based on Bat Algorithm (BA) and Optimum-Path Forest (OPF), in which we model the problem of feature selection as an binary-based optimization technique, guided by BA using the OPF accuracy over a validating set as the fitness function to be maximized. Moreover, we present a methodology to better estimate the quality of the reduced feature set. Experiments conducted over six public datasets demonstrated that the proposed approach provides statistically significant more compact sets and, in some cases, it can indeed improve the classification effectiveness. © 2013 Elsevier Ltd. All rights reserved.

A contribuition to the study of channel coding in wireless communication systems

Pós-graduação em Engenharia Elétrica - FEIS

Sequence characterization of coding regions of the myostatin gene (GDF8) from Brazilian Murrah buffaloes (Bubalus bubalis) and comparison with the Bos taurus sequence

Within about 30 years the Brazilian buffalo (Bubalus bubalis) herd will reach approximately 50 million head as a result of the great adaptive capacity of these animals to tropical climates, together with the good productive and reproductive potential which make these animals an important animal protein source for poor and developing countries. The myostatin gene (GDF8) is important in the physiology of stock animals because its product produces a direct effect on muscle development and consequently also on meat production. The myostatin sequence is known in several mammalian species and shows a high degree of amino acid sequence conservation, although the presence of non-silent and silent changes in the coding sequences and several alterations in the introns and untranslated regions have been identified. The objective of our work was to characterize the myostatin coding regions of B. bubalis (Murrah breed) and to compare them with the Bos taurus regions looking for variations in nucleotide and protein sequences. In this way, we were able to identify 12 variations at DNA level and five alterations on the presumed myostatin protein sequence as compared to non double-muscled bovine sequences.

Worldwide HLA-E nucleotide and haplotype variability reveals a conserved gene for coding and 3 ' untranslated regions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)