Deterpenation of Bergamot Essential Oil Using Liquid-Liquid Extraction: Equilibrium Data of Model Systems at 298.2 K

The deterpenation of bergamot essential oil can be performed by liquid liquid extraction using hydrous ethanol as the solvent. A ternary mixture composed of 1-methyl-4-prop-1-en-2-yl-cydohexene (limonene), 3,7-dimethylocta-1,6-dien-3-yl-acetate (linalyl acetate), and 3,7-dimethylocta-1,6-dien-3-ol (linalool), three major compounds commonly found in bergamot oil, was used to simulate this essential oil. Liquid liquid equilibrium data were experimentally determined for systems containing essential oil compounds, ethanol, and water at 298.2 K and are reported in this paper. The experimental data were correlated using the NRTL and UNIQUAC models, and the mean deviations between calculated and experimental data were lower than 0.0062 in all systems, indicating the good descriptive quality of the molecular models. To verify the effect of the water mass fraction in the solvent and the linalool mass fraction in the terpene phase on the distribution coefficients of the essential oil compounds, nonlinear regression analyses were performed, obtaining mathematical models with correlation coefficient values higher than 0.99. The results show that as the water content in the solvent phase increased, the kappa value decreased, regardless of the type of compound studied. Conversely, as the linalool content increased, the distribution coefficients of hydrocarbon terpene and ester also increased. However, the linalool distribution coefficient values were negatively affected when the terpene alcohol content increased in the terpene phase.

Nonlinear spectrum effect on the coherent control of molecular systems

This work demonstrates that the detuning of the fs-laser spectrum from the two-photon absorption band of organic materials can be used to reach further control of the two-photon absorption by pulse spectral phase manipulation. We investigate the coherent control of the two-photon absorption in imidazole-thiophene core compounds presenting distinct two-photon absorption spectra. The coherent control, performed using pulse phase shaping and genetic algorithm, exhibited different growth rates for each sample. Such distinct trends were explained by calculating the two-photon absorption probability considering the intrapulse interference mechanism, taking into account the two-photon absorption spectrum of the samples. Our results indicate that tuning the relative position between the nonlinear absorption and the pulse spectrum can be used as a novel strategy to optimize the two-photon absorption in broadband molecular systems. (C) 2011 Elsevier B.V. All rights reserved.

A WAVELET-BASED SPEAKER VERIFICATION ALGORITHM

This paper presents a study on wavelets and their characteristics for the specific purpose of serving as a feature extraction tool for speaker verification (SV), considering a Radial Basis Function (RBF) classifier, which is a particular type of Artificial Neural Network (ANN). Examining characteristics such as support-size, frequency and phase responses, amongst others, we show how Discrete Wavelet Transforms (DWTs), particularly the ones which derive from Finite Impulse Response (FIR) filters, can be used to extract important features from a speech signal which are useful for SV. Lastly, an SV algorithm based on the concepts presented is described.

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.

Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation

Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by PCR reaction using specific oligonucleotide primers for the 16S rRNA gene. The PCR products were cloned into a pGEM-T-Easy vector (Promega), and Escherichia coli was used as the host cell for recombinant DNAs. The partial clone sequencing was obtained using universal oligonucleotide primers from the vector. The genetic library obtained generated 431 clones. All the sequenced clones presented similarity to phylum Proteobacteria, with Gammaproteobacteria the most present group (49.8 % of the clones), followed by Alphaproteobacteira (44.8 %) and Betaproteobacteria (5.4 %). The Pseudomonas genus was the most abundant in the metagenomic library, followed by the Parvibaculum and the Sphingobium genus, respectively. After partial sequencing of the 16S rRNA, the diversity of the bacterial consortium was estimated using DOTUR software. When comparing these sequences to the database from the National Center for Biotechnology Information (NCBI), a strong correlation was found between the data generated by the software used and the data deposited in NCBI.

Characterization of the genetic variability among Caesalpinia pulcherrima (L.) Sw. (Fabaceae) plants using RAPD molecular markers

O flamboyanzinho (Caesalpinia pulcherrima, Fabaceae) é muito utilizado como cerca-viva e na arborização de ruas, parques e jardins. de florescimento exuberante, suas flores podem apresentar coloração rosa, laranja ou amarela, conforme a variedade. Como características florais são essenciais para a definição do valor comercial de espécies ornamentais, o objetivo principal do trabalho foi verificar a existência de polimorfismo entre plantas de C. pulcherrima, que produzem flores de diferentes colorações, por marcadores moleculares RAPD. Foram escolhidas aleatoriamente 30 plantas adultas, cultivadas no município de Jaboticabal, Estado de São Paulo, para a retirada de amostras foliares para a extração de DNA. Dentre essas matrizes, 20 possuem flores alaranjadas, oito, flores amarelas, e apenas duas produzem flores de coloração rosa. Dos 140 primers de RAPD avaliados, 94 foram capazes de ampliar fragmentos definidos, gerando 246 bandas, das quais se observou 100% de bandas monomórficas, indicando que nenhum dos primers utilizados detectou polimorfismo entre os tratamentos. Concluiu-se que a técnica para detecção de polimorfismo por marcadores RAPD não foi eficiente, e que existe a necessidade de se testarem marcadores moleculares mais específicos. Além disso, a característica morfológica cor de flor é, possivelmente, controlada por vários genes ou pela combinação deles.

DNA extraction from hair shafts of wild Brazilian felids and canids

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

Extraction of Building Roof Contours From LiDAR Data Using a Markov-Random-Field-Based Approach

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

Object-Space Road Extraction in Rural Areas Using Stereoscopic Aerial Images

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

Three-Dimensional Semiautomatic Road Extraction From a High-Resolution Aerial Image by Dynamic-Programming Optimization in the Object Space

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

Extração automática de contornos de telhados usando dados de varredura a laser e campos randômicos de Markov

This paper proposes a methodology for automatic extraction of building roof contours from a Digital Elevation Model (DEM), which is generated through the regularization of an available laser point cloud. The methodology is based on two steps. First, in order to detect high objects (buildings, trees etc.), the DEM is segmented through a recursive splitting technique and a Bayesian merging technique. The recursive splitting technique uses the quadtree structure for subdividing the DEM into homogeneous regions. In order to minimize the fragmentation, which is commonly observed in the results of the recursive splitting segmentation, a region merging technique based on the Bayesian framework is applied to the previously segmented data. The high object polygons are extracted by using vectorization and polygonization techniques. Second, the building roof contours are identified among all high objects extracted previously. Taking into account some roof properties and some feature measurements (e. g., area, rectangularity, and angles between principal axes of the roofs), an energy function was developed based on the Markov Random Field (MRF) model. The solution of this function is a polygon set corresponding to building roof contours and is found by using a minimization technique, like the Simulated Annealing (SA) algorithm. Experiments carried out with laser scanning DEM's showed that the methodology works properly, as it delivered roof contours with approximately 90% shape accuracy and no false positive was verified.

Assessment of the quality of dna extracted by two techniques from Mycobacterium tuberculosis for fast molecular identification and genotyping

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

Classic and molecular study of Giardia duodenalis in children from a daycare center in the region of Presidente Prudente, São Paulo, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Identificação e comparação entre controle preditivo com modelo não linear e PI sintonizados com PSO em sistema de separação gravitacional de águia-óleo

The separation methods are reduced applications as a result of the operational costs, the low output and the long time to separate the uids. But, these treatment methods are important because of the need for extraction of unwanted contaminants in the oil production. The water and the concentration of oil in water should be minimal (around 40 to 20 ppm) in order to take it to the sea. Because of the need of primary treatment, the objective of this project is to study and implement algorithms for identification of polynomial NARX (Nonlinear Auto-Regressive with Exogenous Input) models in closed loop, implement a structural identification, and compare strategies using PI control and updated on-line NARX predictive models on a combination of three-phase separator in series with three hydro cyclones batteries. The main goal of this project is to: obtain an optimized process of phase separation that will regulate the system, even in the presence of oil gushes; Show that it is possible to get optimized tunings for controllers analyzing the mesh as a whole, and evaluate and compare the strategies of PI and predictive control applied to the process. To accomplish these goals a simulator was used to represent the three phase separator and hydro cyclones. Algorithms were developed for system identification (NARX) using RLS(Recursive Least Square), along with methods for structure models detection. Predictive Control Algorithms were also implemented with NARX model updated on-line, and optimization algorithms using PSO (Particle Swarm Optimization). This project ends with a comparison of results obtained from the use of PI and predictive controllers (both with optimal state through the algorithm of cloud particles) in the simulated system. Thus, concluding that the performed optimizations make the system less sensitive to external perturbations and when optimized, the two controllers show similar results with the assessment of predictive control somewhat less sensitive to disturbances