Analysis of HCV quasispecies dynamic under selective pressure of combined therapy

Background: The quasispecies composition of Hepatitis C virus (HCV) could have important implications with regard to viral persistence and response to interferon-based therapy. The complete NS5A was analyzed to evaluate whether the composition of NS5A quasispecies of HCV 1a/1b is related to responsiveness to combined interferon pegylated (PEG-IFN) and ribavirin therapy.Methods: Viral RNA was isolated from serum samples collected before, during and after treatment from virological sustained responder (SVR), non-responder (NR) and the end-of-treatment responder patients (ETR). NS5A region was amplified, cloned and sequenced. Six hundred and ninety full-length NS5A sequences were analyzed.Results: This study provides evidence that lower nucleotide diversity of the NS5A region pre-therapy is associated with viral clearance. Analysis of samples of NRs and the ETRs time points showed that genetic diversity of populations tend to decrease over time. Post-therapy population of ETRs presented higher genetic distance from baseline probably due to the bottleneck phenomenon observed for those patients in the end of treatment. The viral effective population of those patients also showed a strong decrease after therapy. Otherwise, NRs demonstrated a continuous variation or stability of effective populations and genetic diversity over time that did not seem to be related to therapy. Phylogenetic relationships concerning complete NS5A sequences obtained from patients did not demonstrate clustering associated with specific response patterns. However, distinctive clustering of pre/post-therapy sequences was observed. In addition, the evolution of quasispecies over time was subjected to purifying or relaxed purifying selection. Codons 157 (P03), 182 and 440 (P42), 62 and 404 (P44) were found to be under positive selective pressure but it failed to be related to the therapy.Conclusion: These results confirm the hypothesis that a relationship exists between NS5A heterogeneity and response to therapy in patients infected with chronic hepatitis C. © 2013 Jardim et al.; licensee BioMed Central Ltd.

Energetic, ecologic and fluid-dynamic analysis of a fluidized bed gasifier operating with sugar cane bagasse

This work aims to study the thermodynamic, ecological and fluid-dynamic aspects of a circulating fluidized bed gasifier using sugar cane bagasse as biomass, in order to estimate a model of its normal operation. In the initial stage was analysed the composition of biomass selected (sugar cane bagasse) and its lower heating value (LHV) was calculated. The energy balance of the gasifier was done, being the volumetric flow of air, synthesis gas and biomass estimated. Also the power produced by this gasifier was theoretically estimated. Then the circulating fluidized bed gasifier was designed for operation with approximately 100 kg/h of processed biomass. Cross-sectional area of the reactor, feeder size, diameter of the exit zone of the gases and minimum height of the expanded bed were selected. Some bed gasifier hydrodynamic factors were also studied. The minimum fluidization velocity, fluidization terminal velocity, and average fluidizing velocity were calculated, in order to understand the fluid-dynamic behaviour of gasification of this fuel. It was obtained a theoretical model that can support a possible prototype of circulating fluidized bed gasifier biomass. Finally, there were studied the ecological aspects of the gasifier, through an overall methodology. Ecological efficiencies were estimated for two scenarios: first considering the carbon cycle and thereafter disregarding the carbon cycle. In both cases, it can be proved the ecological viability of the project. © 2013 Elsevier Ltd. All rights reserved.

The dynamic behavior of a cantilever beam coupled to a non-ideal unbalanced motor through numerical and experimental analysis

An excitation force that is not influenced by the system state is said to be an ideal energy source. In real situations, a direct and feedback coupling between the excitation source and the system must always exist at a certain level. This manifestation of the law of conservation of energy is known as the Sommerfeld effect. In the case of obtaining a mathematical model for such a system, additional equations are usually necessary to describe the vibration sources with limited power and its coupling with the mechanical system. In this work, a cantilever beam and a non-ideal DC motor fixed to its free end are analyzed. The motor has an unbalanced mass that provides excitation to the system which is proportional to the current applied to the motor. During the coast up operation of the motor, if the drive power is increased slowly, making the excitation frequency pass through the first natural frequency of the beam, the DC motor speed will remain the same until it suddenly jumps to a much higher value (simultaneously its amplitude jumps to a much lower value) upon exceeding a critical input power. It was found that the Sommerfeld effect depends on some system parameters and the motor operational procedures. These parameters are explored to avoid the resonance capture in the Sommerfeld effect. Numerical simulations and experimental tests are used to help gather insight of this dynamic behavior. (C) 2014 Elsevier Ltd. All rights reserved.

Systematic analysis of protein-detergent complexes applying dynamic light scattering to optimize solutions for crystallization trials

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Dynamic analysis for different finite element models of beams with viscoelastic damping layer

Many new viscoelastic materials have been developed recently to help improve noise and vibration levels in mechanical structures for applications in automobile and aeronautical industry. The viscoelastic layer treatment applied to solid metal structures modifies two main properties which are related to the mass distribution and the damping mechanism. The other property controlling the dynamics of a mechanical system is the stiffness that does not change much with the viscoelastic material. The model of such system is usually complex, because the viscoelastic material can exhibit nonlinear behavior, in contrast with the many available tools for linear dynamics. In this work, the dynamic behavior of sandwich beam is modeled by finite element method using different element types which are then compared with experimental results developed in the laboratory for various beams with different viscoelastic layer materials. The finite element model is them updated to help understand the effects in the damping for various natural frequencies and the trade-off between attenuation and the mass add to the structure.

Detecting an abnormality in a recovery boiler using dynamic multivariate data analysis with parallel coordinate plots

Data visualization techniques are powerful in the handling and analysis of multivariate systems. One such technique known as parallel coordinates was used to support the diagnosis of an event, detected by a neural network-based monitoring system, in a boiler at a Brazilian Kraft pulp mill. Its attractiveness is the possibility of the visualization of several variables simultaneously. The diagnostic procedure was carried out step-by-step going through exploratory, explanatory, confirmatory, and communicative goals. This tool allowed the visualization of the boiler dynamics in an easier way, compared to commonly used univariate trend plots. In addition it facilitated analysis of other aspects, namely relationships among process variables, distinct modes of operation and discrepant data. The whole analysis revealed firstly that the period involving the detected event was associated with a transition between two distinct normal modes of operation, and secondly the presence of unusual changes in process variables at this time.

A quantitative analysis of current security concerns and solutions for cloud computing

The development of cloud computing services is speeding up the rate in which the organizations outsource their computational services or sell their idle computational resources. Even though migrating to the cloud remains a tempting trend from a financial perspective, there are several other aspects that must be taken into account by companies before they decide to do so. One of the most important aspect refers to security: while some cloud computing security issues are inherited from the solutions adopted to create such services, many new security questions that are particular to these solutions also arise, including those related to how the services are organized and which kind of service/data can be placed in the cloud. Aiming to give a better understanding of this complex scenario, in this article we identify and classify the main security concerns and solutions in cloud computing, and propose a taxonomy of security in cloud computing, giving an overview of the current status of security in this emerging technology.

Numerical Model for the Dynamic Analysis of Pile Foundations

Programa de doctorado: Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería Instituto Universitario (SIANI)

Dynamic analysis of piled foundations in stratified soils by a BEM-FEM model

[EN] 3D BEM-FEM coupling model is used to study the dynamic behavior of piled foundations in elastic layered soils in presenceof a rigid bedrock. Piles are modelled by FEM as beams according to the Bernoulli hpothesis, and every layer of the soil is modelled by BEM as a cointinuum, semi-infinite, isotropic, homogeneous, linear, viscoelastic medium.

Be analysis of bottom sediments in dynamic fluid-structure interaction problems

[EN] Sediment materials play an important role on the dynamic response of large structures where fluid-soil-structure interaction is relevant and materials of that kind are present. Dam-reservoir systems and harbor structures are examples of civil engineering constructions where those effects are significant.

BEM-FEM coupling model for the dynamic analysis of piles and pile groups

[EN] This paper shows a BEM-FEM coupling model for the time harmonic dynamic analysis of piles and pile groups embeddes in an elastic half-space. Piles are modelled using Finite Elements (FEM) as a beam according to the Bernoulli hypothesis, while the soil modelled using  Boundary Elements (BEM) as a continuum, semi-infinite, isotropic, homogeneous or zoned homogeneous, linear, viscoelastic medium.

Simple superposition approach for dynamic analysis of piled embedded footings.

[EN]The effectiveness and accuracy of the superposition method in assessing the dynamic stiffness and damping functions of embedded footings supported by vertical piles in homogeneous viscoelastic soil is addressed. To the end, the impedances of piled embedded footings are compared to those obtained by suporposing the impedance functions of the corresponding pile groups and embedded footing treated separately.

3-D Boundary element-finite element method for the dynamic analysis of piled buildings.

[EN]A boundary element-finite element model is presented for the three-dimensional dynamic analysis of piled buildings in the frequency domain. Piles are modelled as compressible Euler-Bernoulli beams founded on a linear, isotropic, viscoelastic, zoned-homogeneous, unbounded layered soil, while multi-storey buildings are assumed to be comprised of vertical compressible piers and rigid slabs.

A BEM-FEM model for the dynamic analysis of building structures founded on elastic or poroelastic soils.

[EN]This work presents a time-harmonic boundary elementfinite element three-dimensional model for the dynamic analysis of building structures founded on elastic or porelastic soils. The building foundation and soil domains are modelled as homogeneous, isotropic, elastic or poroelastic media using boundary elements.