Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2015-02-10T16:07:15Z No. of bitstreams: 1 Bárbara Nascimento R. R. Soares. Soroconversão de galinhas. 2012pdf.pdf: 1498234 bytes, checksum: 68fe5d461b9add9fdefa51341bf5faa6 (MD5) / Approved for entry into archive by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2015-02-10T16:08:01Z (GMT) No. of bitstreams: 1 Bárbara Nascimento R. R. Soares. Soroconversão de galinhas. 2012pdf.pdf: 1498234 bytes, checksum: 68fe5d461b9add9fdefa51341bf5faa6 (MD5) / Approved for entry into archive by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2015-02-10T16:09:25Z (GMT) No. of bitstreams: 1 Bárbara Nascimento R. R. Soares. Soroconversão de galinhas. 2012pdf.pdf: 1498234 bytes, checksum: 68fe5d461b9add9fdefa51341bf5faa6 (MD5) / Made available in DSpace on 2015-02-10T16:09:25Z (GMT). No. of bitstreams: 1 Bárbara Nascimento R. R. Soares. Soroconversão de galinhas. 2012pdf.pdf: 1498234 bytes, checksum: 68fe5d461b9add9fdefa51341bf5faa6 (MD5) Previous issue date: 2012 / Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / A Leishamaniose Visceral (LV) é transmitida pela picada de insetos da espécie vetora Lutzomyialongipalpis através da inoculação dos parasitas juntamente com a saliva na pele do hospedeiro durante a alimentação sanguínea. A saliva deste vetor desempenha um papel importante na obtenção do repasto, sendo também capaz de modular o sistema imune do hospedeiro. Algumas proteínas salivares são imunogênicas e podem induzir a produção de anticorpos específicos. Neste sentido, a presença de anticorpos anti-saliva pode ser utilizada como marcador de exposição ao vetor. Na LV, a presença de galinhas em área endêmica é considerada um fator importante na manutenção da fauna flebotomínica, além de ser citada como um importante fator de risco para a transmissão da doença. Entretanto, o papel da galinha na cadeia epidemiológica da LV ainda não é bem compreendido. Nosso objetivo neste estudo foi detectar nestes animais a presença de anticorpos contra o sonicado de glândula salivar (SGS) a serem utilizados como marcadores de exposição a L. longipalpis e investigar o potencial papel destas aves como sentinela para a presença do vetor em área endêmica. Para isso, quarenta galinhas foram distribuídas em cinco residências em Cavunge, área endêmica para LV na Bahia e naturalmente expostas a picadas de flebotomíneos durante oito meses. Para avaliar a densidade vetorial armadilhas luminosas foram distribuídas e monitoradas mensalmente nas mesmas residências. Amostras de sangue destas aves foram coletadas a cada dois meses e monitorada a soroconversão para SGS. O teste de ELISA foi realizado para avaliar o reconhecimento de SGS onde, após quatro meses do início da exposição 26% das aves se tornaram positivas e com seis meses de exposição detectamos uma soroconversão de 100% das galinhas. Após oito meses, todas apresentavam altos títulos de anticorpos anti-SGS, aumentado 2,7 vezes sobre o valor do cut-off. Além do SGS foram utilizadas as proteínas recombinantes LJM17 e LJM11 da saliva da L. longipalpisque apresentaram desempenho semelhante ao SGS. O teste de correlação aplicado entre a densidade flebotomínica e os níveis de anticorpos específicos após oito meses de exposição não foi positivo, porém pôde-se observar que independente da variação na densidade de vetores, após a soroconversão, galinhas são capazes de manter os níveis de anticorpos IgY anti-SGS constantes. Para avaliar a reatividade cruzada para o reconhecimento a saliva da L. longipalpis, foram utilizados soros de galinhas expostas a picadas de barbeiros e Aedes aegypti, onde identificamos o reconhecimento de duas proteínas da saliva da L. longipalpis com peso de 61 e 79kDa. A proteína recombinante LJM11 não apresentou reatividade cruzada quando testada. Estes resultados demonstram que a exposição natural de galinhas ao vetor L. longipalpis resulta na produção de anticorpos IgY específicos anti-saliva sugerindo o uso destes animais como indicadores da presença do vetor, levantando a possibilidade da utilização de galinhas como um animal sentinela para a detecção da L. longiplapisem áreas endêmicas. / Visceral Leishmaniasis (VL) is transmitted by Lutzomyia longipalpis , when saliva and parasites are injected into the host skin during blood feeding. Saliva has an important role not only in the blood meal process but it is also able to modulate the host’s immune response. Some salivary proteins are immunogenic inducing production of anti-saliva antibodies in the host that can be used as markers of exposure to the vector. In VL, the presence of chicken in the endemic area is indicated as an important source for a blood meal and is often considered as a risk factor for transmission. However the role of the chicken in the VL epidemiology has not been defined. Here we investigate if the detection of antibodies against salivary gland sonicate (SGS) from L. longipalpis could be used as exposure markers to L. longipalpis and the potential role of the chicken as a sentinel animal. Forty chickens were distributed in five houses in Cavunge, a VL endemic area in Bahia, where they were naturally exposed to sand flies during eight months. To evaluate vector density, light traps were distributed and monitored monthly in the same houses. Blood samples were collected every two months to monitor the development of anti-SGS antibodies. ELISA was performed for the recognition of SGS and, after 4 months 26% of the exposed chickens became positive and 6 months later 100% were positive. After 8 months all of them were positive with high antibodies titers against SGS, 2.7x above cut-off value. Beside SGS we also used LJM17 and LJM11 and these recombinants proteins showed similar performance as SGS. There was no correlation between specific anti-saliva antibody levels and sandfly density. Although a cross-reactivity test using sera from chicken exposed to triatomines and Aedes aegypti demonstrated that the proteins of 61 and 79 kDa salivary proteins were only detected in animals exposed to triatomines, LJM11 recombinant protein was shown to be specific to L. longipalpis exposure. Altogether these results show that chicken naturally exposed to the vector develop high titers of anti-saliva antibodies and may be used as important indicators of vector presence, raising the possibility of using chicken as a sentinel animal in endemics areas.

In this thesis, large-eddy simulation (LES) is used to simulate both Newtonian and non-Newtonian physiological pulsatile flows in constricted channels to gain insights into the physical phenomenon of laminar-turbulent flow transition due to the presence of an artificial arterial stenosis. The advanced dynamic nonlinear subgrid-scale stress (SGS) model of Wang and Bergstrom (DNM) was utilized to conduct numerical simulations and its predictive performance was examined in comparison with that of the conventional dynamic model (DM) of Lilly. An in-house LES code has been modified to conduct the unsteady numerical simulations, and the results obtained have been validated against available experimental and direct numerical simulation (DNS) results. The physical characteristics of the flow field have been thoroughly studied in terms of the resolved mean velocity, turbulence kinetic energy, viscous wall shear stress, and turbulence energy spectra along the central streamline of the domain.

In this thesis, large-eddy simulation (LES) is used to simulate both Newtonian and non-Newtonian physiological pulsatile flows in constricted channels to gain insights into the physical phenomenon of laminar-turbulent flow transition due to the presence of an artificial arterial stenosis. The advanced dynamic nonlinear subgrid-scale stress (SGS) model of Wang and Bergstrom (DNM) was utilized to conduct numerical simulations and its predictive performance was examined in comparison with that of the conventional dynamic model (DM) of Lilly. An in-house LES code has been modified to conduct the unsteady numerical simulations, and the results obtained have been validated against available experimental and direct numerical simulation (DNS) results. The physical characteristics of the flow field have been thoroughly studied in terms of the resolved mean velocity, turbulence kinetic energy, viscous wall shear stress, and turbulence energy spectra along the central streamline of the domain.

Subglottic stenosis (SGS) is a narrowing of the airway in the region of the cricoid cartilage below the vocal folds and above the tracheal rings. Individuals with SGS experience difficulty breathing at rest and during exertion both of which become increasingly difficult with the level of stenosis severity. Some individuals also experience negative voice changes. Individuals whose stenoses significantly impact breathing generally require medical procedures or surgery, either balloon dilation or cricotracheal resection (CTR). CTR has been shown to improve patients' ability to breathe, but it can also result in permanent vocal changes. Alternatively, balloon dilation results in similar breathing improvements but for a relatively short period of time. Many studies have been published on the effectiveness of CTR; however, only a few have examined the effects of CTR on vocal production. The purpose of this study is to quantify the acoustic and auditory-perceptual features of subglottic stenosis and examine possible acoustic and auditory-perceptual changes in voice production following a revised CTR aimed to minimize voice impact in a group of women. A retrospective chart review identified women with idiopathic SGS who received revised CTR at The University of Utah Voice Disorders Center between 2008 and 2014. Presurgical and postsurgical groups included patients with both pre and post recordings (n = 11) as well as patients with only pre (n = 6) or post (n = 9) recordings. Acoustic quantification of voice signal periodicity, as well as cepstral, spectral, and fundamental frequency (F0) analyses were performed. Auditory-perceptual ratings of overall quality and monotonicity were performed. Cross-sectional and pre-post surgery analyses were completed. Aggregate analyses revealed that both pre and posttreatment SGS patients demonstrated voice disorders in the mild to moderate severity range. Pre-post comparisons indicated no significant voice change after surgery. Mean fundamental frequency decreased from 215 Hz (SD = 40 Hz) to 201 Hz (SD = 65 Hz). Voice disorder severity based on the cepstral spectral index of dysphoniaTM for sustained vowels decreased (i.e., improved) from 41 (SD = 41) to 25 (SD = 21) points. Semitone standard deviation (2.2 semitones) was equivalent from pretreatment to posttreatment. Auditory-perceptual ratings demonstrated similar results. These preliminary results indicate that the revised CTR procedure is promising in minimizing adverse voice effects. Future research is needed to determine causative factors for pretreatment voice disorders, as well as to optimize treatments in this population.

Buoyant flows are characterized with unsteady large-scale structures and thus time-dependent large eddy simulation (LES) is generally favored. In this dissertation, to further explore LES for buoyant flow, an LES code based on a collocated grid system is first developed. A multigrid solver using a control strategy is developed for the pressure Poisson equations. The control strategy significantly accelerated the convergence rate. A temperature solver using a fourth-order Runge-Kutta approach is also developed. The LES code is extensively tested before it is applied. Although the collocated grid system will introduce conservation errors, in tests of a steady lid-driven cavity flow and transient start-up flow, the effect of the non-conservation of the collocated grid system was not significant. <p>In LES, the effect of SGS scales is represented by SGS models. A novel dynamic nonlinear model (DNM) for SGS stress is tested using isothermal channel flow at Reynolds number 395. The kinetic energy dissipation and geometrical characteristics of the resolved scale and SGS scale with respect to the DNM are investigated. In general, the DNM is reliable and has relatively realistic geometrical properties in comparison with the conventional dynamic model in the present study. In contrast to a pure advecting velocity field, a scalar (temperature) field displays very different characteristics. The modelling of SGS heat flux has not been as extensively studied as that of SGS stress partly due to the complexity of the scalar transport. In this dissertation, LES for a turbulent combined forced and natural convection is studied. The DNM model and a nonlinear dynamic tensor diffusivity model (DTDM-HF) are applied for the SGS stress and heat flux, respectively. The combined effect of the nonlinear models is compared to that of linear models. Notable differences between the nonlinear and linear SGS models are observed at the subgrid-scale level. At the resolved scale, the difference is smaller but relatively more distinguishable in terms of quantities related to the temperature field. <p>Finally, the geometrical properties of the resolved velocity and temperature fields of the thermal flow are investigated based on the LES prediction. Some universal geometrical patterns have been reproduced, e.g. the positively skewed resolved enstrophy generation and the alignment between the vorticity and vortex stretching vectors. The present research demonstrates that LES is an effective tool for the study of the geometrical properties of a turbulent flow at the resolved-scales. The wall imposed anisotropy on the flow structures and orientation of the SGS heat flux vector are also specifically examined. In contrast to the dynamic eddy diffusivity model, the DTDM-HF successfully predicts the near-wall physics and demonstrates a non-alignment pattern between the SGS heat flux and temperature gradient vector.

Buoyant flows are characterized with unsteady large-scale structures and thus time-dependent large eddy simulation (LES) is generally favored. In this dissertation, to further explore LES for buoyant flow, an LES code based on a collocated grid system is first developed. A multigrid solver using a control strategy is developed for the pressure Poisson equations. The control strategy significantly accelerated the convergence rate. A temperature solver using a fourth-order Runge-Kutta approach is also developed. The LES code is extensively tested before it is applied. Although the collocated grid system will introduce conservation errors, in tests of a steady lid-driven cavity flow and transient start-up flow, the effect of the non-conservation of the collocated grid system was not significant. <p>In LES, the effect of SGS scales is represented by SGS models. A novel dynamic nonlinear model (DNM) for SGS stress is tested using isothermal channel flow at Reynolds number 395. The kinetic energy dissipation and geometrical characteristics of the resolved scale and SGS scale with respect to the DNM are investigated. In general, the DNM is reliable and has relatively realistic geometrical properties in comparison with the conventional dynamic model in the present study. In contrast to a pure advecting velocity field, a scalar (temperature) field displays very different characteristics. The modelling of SGS heat flux has not been as extensively studied as that of SGS stress partly due to the complexity of the scalar transport. In this dissertation, LES for a turbulent combined forced and natural convection is studied. The DNM model and a nonlinear dynamic tensor diffusivity model (DTDM-HF) are applied for the SGS stress and heat flux, respectively. The combined effect of the nonlinear models is compared to that of linear models. Notable differences between the nonlinear and linear SGS models are observed at the subgrid-scale level. At the resolved scale, the difference is smaller but relatively more distinguishable in terms of quantities related to the temperature field. <p>Finally, the geometrical properties of the resolved velocity and temperature fields of the thermal flow are investigated based on the LES prediction. Some universal geometrical patterns have been reproduced, e.g. the positively skewed resolved enstrophy generation and the alignment between the vorticity and vortex stretching vectors. The present research demonstrates that LES is an effective tool for the study of the geometrical properties of a turbulent flow at the resolved-scales. The wall imposed anisotropy on the flow structures and orientation of the SGS heat flux vector are also specifically examined. In contrast to the dynamic eddy diffusivity model, the DTDM-HF successfully predicts the near-wall physics and demonstrates a non-alignment pattern between the SGS heat flux and temperature gradient vector.

No description available.

Portfolios of contemporary integrated petroleum companies consist of a few dozen Exploration and Production (E&P) projects that are usually spread all over the world. Therefore, it is important not only to manage individual projects by themselves, but to also take into account different interactions between projects in order to manage whole portfolios. This study is the step-by-step representation of the method of optimizing portfolios of risky petroleum E&P projects, an illustrated method based on Markowitz’s Portfolio Theory. This method uses the covariance matrix between projects’ expected return in order to optimize their portfolio. The developed computer model consists of four major modules. The first module generates petroleum price forecasts. In our implementation we used the price forecasting method based on Sequential Gaussian Simulation. The second module, Monte Carlo, simulates distribution of reserves and a set of expected production profiles. The third module calculates expected after tax net cash flows and estimates performance indicators for each realization, thus yielding distribution of return for each project. The fourth module estimates covariance between return distributions of individual projects and compiles them into portfolios. Using results of the fourth module, analysts can make their portfolio selection decisions. Thus, an advanced computer model for optimization of the portfolio of petroleum assets has been developed. The model is implemented in a MATLAB® computational environment and allows optimization of the portfolio using three different return measures (NPV, GRR, PI). The model has been successfully applied to the set of synthesized projects yielding reasonable solutions in all three return planes. Analysis of obtained solutions has shown that the given computer model is robust and flexible in terms of input data and output results. Its modular architecture allows further inclusion of complementary “blocks” that may solve optimization problems utilizing different measures (than considered) of risk and return as well as different input data formats.

Computational fluid dynamics (CFD) is a significant tool routinely used indesign and optimization in aerospace industry. Often cases with unsteadyflows must be computed, and the long compute times of standard methods hasmotivated the present work on new implicit methods to replace the standardexplicit schemes. The implementation and numerical experiments were donewith the Swedish national flow solver Edge, developed by FOI,universities, and collaboration partners.The work is concentrated on a Lower-Upper Symmetric Gauss-Seidel (LU-SGS)type of time stepping. For the very anisotropic grids needed forReynolds-Averaged Navier-Stokes (RANS) computations of turbulent boundary layers,LU-SGS is combined with a line-implicit technique.  The inviscid flux Jacobians which contribute to the diagonalblocks of the system matrix are based on a flux splitting method with upwind type dissipation giving  control over diagonal dominance and artificial dissipation.The method is  controlled by several parameters, and comprehensivenumerical experiments were carried out to identify their influence andinteraction so that close to optimal values can be suggested. As an example,the optimal number of iterations carried out in a time-step increases with increased resolution of the computational grid.The numbering of the unknowns is important, and the numberings produced by mesh generators of Delaunay- and advancing front-type wereamong the best.The solver has been parallelized with the Message Passing Interface (MPI) for runs on multi-processor hardware,and its performance scales with the number of processors at least asefficiently as the explicit methods. The new method saves typicallybetween 50 and 80 percent of the runtime, depending on the case, andthe largest computations have reached 110M grid nodes. Theclassical multigrid acceleration for 3D RANS simulations was foundineffective in the cases tested in combination with the LU-SGS solverusing optimal parameters. Finally, preliminary time-accurate simulations for unsteady flows have shown promising results. / <p>QC 20141201</p>

Porcine reproductive and respiratory syndrome virus (PRRSV) is arguably the most economically devastating pathogen affecting the global swine industry. Since the emergence of the virus in the late 1980s, vaccination strategies aimed to control the virus have not been very effective. Current commercial vaccines are generally protective against homologous or closely-related strains but ineffective at conferring heterologous protection against genetically-diverse strains of the virus. Consequently, emergence of variant and sometime more pathogenic strains of PRRSV continues in global swine herds. As such, there is a need for better understanding of the molecular mechanisms involved in the replication of the virus. In order to better understand the molecular mechanisms of host responses to PRRSV replication, we first sought to evaluate the ability of the virus to induce stress granules (SGs) during PRRSV infection. SGs are intracellular, cytoplasmic aggregates of RNA-binding proteins (RBPs) and mRNA. Formation of SGs is observed upon cellular stress and ultimately function to arrest cellular translation to promote cellular survival until the stress has been remedied. Indeed, several viruses have been shown to modulate the SG pathways to facilitate viral replication and even suppress the host's immune response. However, it is currently unknown whether PRRSV modulates the SG response. First, we used confocal microscopy and fluorescent in situ hybridization (FISH) to determine the distribution of known SG marker proteins and cellular mRNAs. Our findings revealed that PRRSV induces a potent SG response at late time points post-infection, and that SGs were closely associated with viral replication complexes (VRCs). Subsequently, we demonstrated that SGs are dispensable for viral replication, as short hairpin RNA (shRNA)-mediated knockdown of critical SG components (G3BP1 and G3BP2) did not affect viral replication. Interestingly, we found that the PRRSV-induced SGs are formed in a PERK-dependent manner. PERK is an important sensor of ER stress and activator of the unfolded protein response (UPR). Further investigation into the PERK signaling pathway revealed that PRRSV induces a significant amount of ER stress upon the cell during viral infection, and that exogenous stress significantly impaired the ability of the virus to replicate in MARC145 cells. We also showed that PRRSV potently induces all three signaling branches of the UPR, including PERK. While PERK knockdown had no effect on cell viability or viral replication, it significantly upregulated the mRNA expression of interferon-β and interferon stimulated genes (ISGs). The results from our studies suggest a critical role for PERK in regulating the host innate immune response to PRRSV infection. Only with a better understanding of the underlying molecular mechanisms of PRRSV replication will we be able to rationally design more effective vaccines against the virus. / Doctor of Philosophy / Porcine reproductive and respiratory syndrome virus (PRRSV) causes an economically-devastating disease in the global swine industry. Annually, PRRSV is estimated to cause more than $600 million in economic losses to the swine industry in the United States alone. Current commercial vaccines against the virus are not effective against the diverse field strains largely due to the extreme heterogeneity of the virus. PRRSV is also able to potently suppress several aspects of the host's immune response and therefore establish a persistent infection. The underlying mechanisms of PRRSV-mediated immune suppression are not well understood. Therefore, in this dissertation we decided to investigate the molecular mechanisms of host responses to PRRSV infection. We first investigated the ability of the virus to induce stress granules (SGs). SGs are important intracellular regulatory components that modulate many aspects of the host's cellular processes, and have even been shown to play roles in regulating viral replication and controlling immune responses to viral infection. We demonstrate that PRRSV not only induces SGs, but that the PRRSV-induced SGs are closely associated with viral replication complexes (VRCs) within infected cells. The PRRSV-induced SGs were dispensable for viral replication. PRRSV-induced SGs were previously shown to form in a PERK dependent manner. Therefore, in the second part of this dissertation research, we decided to investigate the PERK signaling pathway during PRRSV infection. PERK is an important sensor of ER stress and activator of the unfolded protein response (UPR). Our results showed that PRRSV potently induces ER stress and all three signaling branches of the UPR, including PERK. Furthermore, we revealed that PERK may play an important role in regulating the type I interferon response to PRRSV infection. The results from our studies will aid in understanding the underlying molecular mechanism of PRRSV replication which will help rationally design the next generation of more effective vaccines against this devastating swine pathogen.