Biodegradação de hidrocarbonetos aromáticos policíclicos: prospecção metagenômica e modelagem computacional 3-D de proteínas

Knowledge of the native prokaryotes in hazardous locations favors the application of biotechnology for bioremediation. Independent strategies for cultivation and metagenomics contribute to further microbiological knowledge, enabling studies with non-cultivable about the "native microbiological status and its potential role in bioremediation, for example, of polycyclic aromatic hydrocarbons (HPA's). Considering the biome mangrove interface fragile and critical bordering the ocean, this study characterizes the native microbiota mangrove potential biodegradability of HPA's using a biomarker for molecular detection and assessment of bacterial diversity by PCR in areas under the influence of oil companies in the Basin Petroleum Geology Potiguar (BPP). We chose PcaF, a metabolic enzyme, to be the molecular biomarker in a PCR-DGGE detection of prokaryotes that degrade HPA s. The PCR-DGGE fingerprints obtained from Paracuru-CE, Fortim-CE and Areia Branca-RN samples revealed the occurrence of fluctuations of microbial communities according to the sampling periods and in response to the impact of oil. In the analysis of microbial communities interference of the oil industry, in Areia Branca-RN and Paracuru-CE was observed that oil is a determinant of microbial diversity. Fortim-CE probably has no direct influence with the oil activity. In order to obtain data for better understanding the transport and biodegradation of HPA's, there were conducted in silico studies with modeling and simulation from obtaining 3-D models of proteins involved in the degradation of phenanthrene in the transport of HPA's and also getting the 3-D model of the enzyme PcaF used as molecular marker in this study. Were realized docking studies with substrates and products to a better understanding about the transport mechanism and catalysis of HPA s

3-D Space Vector PWM implementation for Four-Leg Voltage Source Inverter

The Space Vector PWM implementation and operation for a Four-leg Voltage Source Inverter (VSI) is detailed and discussed in this paper. Although less common, four-leg VSIs are a viable solution for situations where neutral connection is necessary, including Active Power Filter applications. This topology presents advantages regarding the VSI DC link and capacitance, which make it useful for high power devices. Theory, implementation and simulations are also discussed in this paper. © 2011 IEEE.

Modelagem direta de dados de eletrorresistividade 3-D

Dentre os métodos geofísicos, o da Eletrorresistividade é um dos mais tradicionais, com o seu desenvolvimento ocorrido há mais de 80 anos. Durante esse tempo o seu uso acompanhou o avanço no poder de processamento numérico e mais recentemente, a modelagem e inversão tridimensional tornou-se uma possibilidade para o geofísico. Apresentamos, neste trabalho, a técnica de elementos finitos aplicada ao método da eletrorresistividade 3-D, através do cálculo do potencial secundário. Para o desenvolvimento da metodologia, simulamos o levantamento do método da eletrorresistividade 3-D com os arranjos Dipolo-Dipolo e Schlumberger, visando medir as variações laterais e verticais da resistividade aparente do solo. Estes arranjos consistem na injeção de corrente elétrica na superfície e de medidas de diferenças de potencial elétrico, resultante da interação da corrente elétrica com o solo. Sendo que, as fontes e receptores são localizados de acordo com os arranjos escolhidos para o levantamento. Neste trabalho, as curvas de sondagem e as pseudo-secções de resistividade aparente, são obtidas através da modelagem de eletrorresistividade 3-D, usando malha de elementos finitos regular. Para efeito de validação, os resultados são comparados com a resposta 3-D obtida a partir dos potenciais totais.

The meccano method for automatic 3-d triangulation and volume parametrization of complex solids

[EN]In this paper we review the novel meccano method. We summarize the main stages (subdivision, mapping, optimization) of this automatic tetrahedral mesh generation technique and we concentrate the study to complex genus-zero solids. In this case, our procedure only requires a surface triangulation of the solid. A crucial consequence of our method is the volume parametrization of the solid to a cube. We construct volume T-meshes for isogeometric analysis by using this result. The efficiency of the proposed technique is shown with several examples. A comparison between the meccano method and standard mesh generation techniques is introduced.-1…

Novel functional profiling approach combining reverse phase protein microarrays and human 3-D ex vivo tissue cultures: expression of apoptosis-related proteins in human colon cancer

Cancer is caused by a complex pattern of molecular perturbations. To understand the biology of cancer, it is thus important to look at the activation state of key proteins and signaling networks. The limited amount of available sample material from patients and the complexity of protein expression patterns make the use of traditional protein analysis methods particularly difficult. In addition, the only approach that is currently available for performing functional studies is the use of serial biopsies, which is limited by ethical constraints and patient acceptance. The goal of this work was to establish a 3-D ex vivo culture technique in combination with reverse-phase protein microarrays (RPPM) as a novel experimental tool for use in cancer research. The RPPM platform allows the parallel profiling of large numbers of protein analytes to determine their relative abundance and activation level. Cancer tissue and the respective corresponding normal tissue controls from patients with colorectal cancer were cultured ex vivo. At various time points, the cultured samples were processed into lysates and analyzed on RPPM to assess the expression of carcinoembryonic antigen (CEA) and 24 proteins involved in the regulation of apoptosis. The methodology displayed good robustness and low system noise. As a proof of concept, CEA expression was significantly higher in tumor compared with normal tissue (p<0.0001). The caspase 9 expression signal was lower in tumor tissue than in normal tissue (p<0.001). Cleaved Caspase 8 (p=0.014), Bad (p=0.007), Bim (p=0.007), p73 (p=0.005), PARP (p<0.001), and cleaved PARP (p=0.007) were differentially expressed in normal liver and normal colon tissue. We demonstrate here the feasibility of using RPPM technology with 3-D ex vivo cultured samples. This approach is useful for investigating complex patterns of protein expression and modification over time. It should allow functional proteomics in patient samples with various applications such as pharmacodynamic analyses in drug development.

3-D Audio in Mobile Communication Devices: Methods for Mobile Head-Tracking

Future generations of mobile communication devices will serve more and more as multimedia platforms capable of reproducing high quality audio. In order to achieve a 3-D sound perception the reproduction quality of audio via headphones can be significantly increased by applying binaural technology. To be independent of individual head-related transfer functions (HRTFs) and to guarantee a good performance for all listeners, an adaptation of the synthesized sound field to the listener's head movements is required. In this article several methods of head-tracking for mobile communication devices are presented and compared. A system for testing the identified methods is set up and experiments are performed to evaluate the prosand cons of each method. The implementation of such a device in a 3-D audio system is described and applications making use of such a system are identified and discussed.

A 3-D CT assisted Monte Carlo evaluation of intracavitary brachytherapy implants

Intracavitary brachytherapy (ICB) combined with external beam irradiation for treatment of cervical cancer is highly successful in achieving local control. The M.D. Anderson Cancer Center employs Fletcher Suit Delclos (FSD) applicators. FSD applicators contain shields to limit dose to critical structures. Dosimetric evaluation of ICB implants is limited to assessing dose at reference points. These points serve as surrogates for treatment intensity and critical structure dose. Several studies have mentioned that the ICRU38 reference points inadequately characterize the dose distribution. Also, the ovoid shields are rarely considered in dosimetry. ^ The goal of this dissertation was to ascertain the influence of the ovoid shields on patient dose distributions. Monte Carlo dosimetry (MCD) was applied to patient computed tomography(CT) scans. These data were analyzed to determine the effect of the shields on dose to standard reference points and the bladder and rectum. The hypothesis of this work is that the ICRU38 bladder and rectal points computed conventionally are not clinically acceptable surrogates for the maximum dose points as determined by MCD. ^ MCD was applied to the tandem and ovoids. The FSD ovoids and tandem were modeled in a single input file that allowed dose to be calculated for any patient. Dose difference surface histograms(DDSH) were computed for the bladder and rectum. Reference point doses were compared between shielded and unshielded ovoids, and a commercial treatment planning system. ^ The results of this work showed the tandem tip screw caused a 33% reduction in dose. The ovoid shields reduced the dose by a maximum of 48.9%. DDSHs revealed on average 5% of the bladder surface area was spared 53 cGy and 5% of the rectal surface area was spared 195 cGy. The ovoid shields on average reduced the dose by 18% for the bladder point and 25% for the rectal point. The Student's t-test revealed the ICRU38 bladder and rectal points do not predict the maximum dose for these organs. ^ It is concluded that modeling the tandem and ovoid internal structures is necessary for accurate dose calculations, the bladder shielding segments may not be necessary, and that the ICRU38 bladder point is irrelevant. ^

The effect of boundary conditions in the numerical solution of 3-D thermoelastic problems

After the extensive research on the capabilities of the Boundary Integral Equation Method produced during the past years the versatility of its applications has been well founded. Maybe the years to come will see the in-depth analysis of several conflictive points, for example, adaptive integration, solution of the system of equations, etc. This line is clear in academic research. In this paper we comment on the incidence of the manner of imposing the boundary conditions in 3-D coupled problems. Here the effects are particularly magnified: in the first place by the simple model used (constant elements) and secondly by the process of solution, i.e. first a potential problem is solved and then the results are used as data for an elasticity problem. The errors add to both processes and small disturbances, unimportant in separated problems, can produce serious errors in the final results. The specific problem we have chosen is especially interesting. Although more general cases (i.e. transient)can be treated, here the domain integrals can be converted into boundary ones and the influence of the manner in which boundary conditions are applied will reflect the whole importance of the problem.

A Compact Formula for the Derivative of a 3-D Rotation in Exponential Coordinates

We present a compact formula for the derivative of a 3-D rotation matrix with respect to its exponential coordinates. A geometric interpretation of the resulting expression is provided, as well as its agreement with other less-compact but better-known formulas. To the best of our knowledge, this simpler formula does not appear anywhere in the literature. We hope by providing this more compact expression to alleviate the common pressure to reluctantly resort to alternative representations in various computational applications simply as a means to avoid the complexity of differential analysis in exponential coordinates.

Simultaneous strain and temperature measurement of advanced 3-D braided composite materials using an improved EFPI/FBG system

Simultaneous strain and temperature measurement for advanced 3-D braided composite materials using fibre-optic sensor technology is demonstrated, for the first time. These advanced 3-D braided composites can virtually eliminate the most serious problem of delamination for conventional composites. A tandem in-fibre Bragg-grating (FBG)/extrinsic Fabry-Perot interferometric sensor (EFPI) system with improved accuracy has been used to facilitate simultaneous temperature and strain measurement in this work. The non-symmetric distortion of the optical spectrum of the FBG, due to the combination of the FBG and the EFPI, is observed for the first time. Experimental and theoretical studies indicate that this type of distortion can affect the measurement accuracy seriously and it is mainly caused by the modulation of the periodic output of the EFPI. A simple method has been demonstrated to improve the accuracy for detection of the wavelength-shift of the FBG induced by temperature change. A strain accuracy of ∼ ±20 με and a temperature accuracy of ∼ ±1 °C have been achieved, which can meet the requirements for practical applications of 3-D braided composites. © 2002 Elsevier Science Ltd. All rights reserved.

Parallelisation of a 3-D electromagnetic scattering code

A high-frequency time domain finite element scattering code using a combination of edge and piecewise constant elements on unstructured tetrahedral meshes is described. A comparison of computation with theory is given for scattering from a sphere. A parallel implementation making use of the bulk synchronous parallel (BSP) programming model is described in detail; a BSP performance model of the parallelized field calculation is derived and compared to timing measurements on up to 128 processors on a Cray T3D.

The role of disulfide bridges in the 3-D structures of the antimicrobial peptides gomesin and protegrin-1: a molecular dynamics study

Some antimicrobial peptides have a broad spectrum of action against many different kinds of microorganisms. Gomesin and protegrin-1 are examples of such antimicrobial peptides, and they were studied by molecular dynamics in this research. Both have a beta-hairpin conformation stabilized by two disulfide bridges and are active against Gram-positive and Gram-negative bacteria, as well as fungi. In this study, the role of the disulfide bridge in the maintenance of the tertiary peptide structure of protegrin-1 and gomesin is analyzed by the structural characteristics of these peptides and two of their respective variants, gomy4 and proty4, in which the four cysteines are replaced by four tyrosine residues. The absence of disulfide bridges in gomy4 and proty4 is compensated by overall reinforcement of the original hydrogen bonds and extra attractive interactions between the aromatic rings of the tyrosine residues. The net effects on the variants with respect to the corresponding natural peptides are: i) maintenance of the original beta-hairpin conformation, with great structural similarities between the mutant and the corresponding natural peptide; ii) combination of positive F and. Ramachandran angles within the hairpin head region with a qualitative change to a combination of positive (F) and negative (.) angles, and iii) significant increase in structural flexibility. Experimental facts about the antimicrobial activity of the gomesin and protegrin-1 variants have also been established here, in the hope that the detailed data provided in the present study may be useful for understanding the mechanism of action of these peptides.

Chrysotile effects on human lung cell carcinoma in culture: 3-D reconstruction and DNA quantification by image analysis

Background: Chrysotile is considered less harmful to human health than other types of asbestos fibers. Its clearance from the lung is faster and, in comparison to amphibole forms of asbestos, chrysotile asbestos fail to accumulate in the lung tissue due to a mechanism involving fibers fragmentation in short pieces. Short exposure to chrysotile has not been associated with any histopathological alteration of lung tissue. Methods: The present work focuses on the association of small chrysotile fibers with interphasic and mitotic human lung cancer cells in culture, using for analyses confocal laser scanning microscopy and 3D reconstructions. The main goal was to perform the analysis of abnormalities in mitosis of fibers-containing cells as well as to quantify nuclear DNA content of treated cells during their recovery in fiber-free culture medium. Results: HK2 cells treated with chrysotile for 48 h and recovered in additional periods of 24, 48 and 72 h in normal medium showed increased frequency of multinucleated and apoptotic cells. DNA ploidy of the cells submitted to the same chrysotile treatment schedules showed enhanced aneuploidy values. The results were consistent with the high frequency of multipolar spindles observed and with the presence of fibers in the intercellular bridge during cytokinesis. Conclusion: The present data show that 48 h chrysotile exposure can cause centrosome amplification, apoptosis and aneuploid cell formation even when long periods of recovery were provided. Internalized fibers seem to interact with the chromatin during mitosis, and they could also interfere in cytokinesis, leading to cytokinesis failure which forms aneuploid or multinucleated cells with centrosome amplification.

A geometrical approach of 3-D FEA for educational purposes applied to electrostatic fields

A geometrical approach of the finite-element analysis applied to electrostatic fields is presented. This approach is particularly well adapted to teaching Finite Elements in Electrical Engineering courses at undergraduate level. The procedure leads to the same system of algebraic equations as that derived by classical approaches, such as variational principle or weighted residuals for nodal elements with plane symmetry. It is shown that the extension of the original procedure to three dimensions is straightforward, provided the domain be meshed in first-order tetrahedral elements. The element matrices are derived by applying Maxwell`s equations in integral form to suitably chosen surfaces in the finite-element mesh.

Multiphase flow in the vascular system of wood: From microscopic exploration to 3-D Lattice Boltzmann experiments

This paper provides insights into liquid free water dynamics in wood vessels based on Lattice Boltzmann experiments. The anatomy of real wood samples was reconstructed from systematic 3-D analyses of the vessel contours derived from successive microscopic images. This virtual vascular system was then used to supply fluid-solid boundary conditions to a two-phase Lattice Boltzmann scheme and investigate capillary invasion of this hydrophilic porous medium. Behavior of the liquid phase was strongly dependent on anatomical features, especially vessel bifurcations and reconnections. Various parameters were examined in numerical experiments with ideal vessel bifurcations, to clarify our interpretation of these features. (c) 2010 Elsevier Ltd. All rights reserved.