Forests have been proposed as a means of reducing atmospheric carbon dioxide levels due to their ability to store carbon as biomass. To quantify the amount of atmospheric carbon sequestered by forests, biomass and density estimates are often needed. This study develops, implements, and tests an individual tree-based algorithm for obtaining forest density and biomass using orthophotographs and small footprint LiDAR imagery. It was designed to work with a range of forests and image types without modification, which is accomplished by using generic properties of trees found in many types of images. Multiple parameters are employed to determine how these generic properties are used. To set these parameters, training data is used in conjunction with an optimization algorithm (a modified Nelder-Mead simplex algorithm or a genetic algorithm). The training data consist of small images in which density and biomass are known. A first test of this technique was performed using 25 circular plots (radius = 15 m) placed in young pine plantations in central Virginia, together with false color othophotograph (spatial resolution = 0.5 m) or small footprint LiDAR (interpolated to 0.5 m) imagery. The highest density prediction accuracies (r2 up to 0.88, RMSE as low as 83 trees / ha) were found for runs where photointerpreted densities were used for training and testing. For tests run using density measurements made on the ground, accuracies were consistency higher for orthophotograph-based results than for LiDAR-based results, and were higher for trees with DBH ≥10cm than for trees with DBH ≥7 cm. Biomass estimates obtained by the algorithm using LiDAR imagery had a lower RMSE (as low as 15.6 t / ha) than most comparable studies. The correlations between the actual and predicted values (r2 up to 0.64) were lower than comparable studies, but were generally highly significant (p ≤ 0.05 or 0.01). In all runs there was no obvious relationship between accuracy and the amount of training data used, but the algorithm was sensitive to which training and testing data were selected. Methods were evaluated for combining predictions made using different parameter sets obtained after training using identical data. It was found that averaging the predictions produced improved results. After training using density estimates from the human photointerpreter, 89% of the trees located by the algorithm corresponded to trees found by the human photointerpreter. A comparison of the two optimization techniques found them to be comparable in speed and effectiveness. / Ph. D.

La résistance du virus de l’herpès simplex (VHS) aux antiviraux est un problème courant chez les individus immunosupprimés. Des mutations au sein du gène de la thymidine kinase (TK) virale sont principalement à l’origine de la résistance au traitement de première ligne, i.e. les analogues des nucléosides. La cible ultime de tous les antiviraux anti-herpétique demeure cependant l’ADN polymérase (pol) virale. Ces deux gènes viraux (TK et ADN pol) démontrent un certain degré de polymorphisme génétique et il peut devenir difficile d’identifier avec certitude les mutations responsables de la résistance aux antiviraux. Les travaux présentés dans cette thèse de Doctorat démontrent le développement de nouvelles méthodes afin d’établir un lien entre l’apparition de mutations au niveau de gênes viraux et un phénotype de résistance particulier. Un système d’expression du gène de la TK virale chez le parasite Leishmania et un ensemble de cosmides et de plasmides recombinants permettant de générer des virus ADN pol mutants ont été mis au point. Ces nouvelles stratégies nous ont permis de caractériser les mutations virales impliquées dans la résistance aux antiviraux. / Drug resistant HSV isolates are responsible form substantial morbidity among immunocompromised subjects. The genetic basis for resistance to nucleoside analogs such as acyclovir (ACV) have been mapped to point mutations in the viral thymidine kinase (TK) gene while mutations within the viral DNA pol gene, the main target for all anti-herpetic drug actually available, could lead to a multidrug resistance phenotype. However, the distinction between viral mutations (TK and DNA pol) involved in antiviral resistance or part of viral polymorphism can be difficult to evaluate with current methodologies. OBJECTIVE: The aim of this research project is thus to evaluate the role of particular mutations within the HSV TK and DNA pol gene with regard to drug-resistance patterns and viral fitness, by designing new gene expression systems. METHODS: The protozoan parasite Leishmania stably transfected with a TK expression vector (pSP72αNEOα) was used as an heterologous system to evaluate the role of several different point mutations within the coding region of the TK gene in conferring resistance to nucleoside analogs. Susceptibility of TK-expressing parasites to nucleoside analogs can thus be tested very easily by a simple measurement of the optic density of cultures grown in the presence or in the absence of the drug. Finally, a set of overlapping viral cosmids and plasmids for the rapid generation of recombinant HSV-1 DNA pol mutants have been developed. RESULTS: Expression of the TK gene from ACV-susceptible clinical isolates resulted in Leishmania susceptibility to the antiviral, whereas expression of a TK gene with frameshift mutations or nucleotide substitutions from ACV-resistant isolates gave rise to parasites with high levels of antiviral resistance. Twenty HSV-1 recombinants with single or dual mutations within the DNA pol gene were successfully generated with the cosmid/plasmid based approach. Mutations within the central part of the enzyme’s catalytic domain (regions II and VI) were associated with resistance to ACV, FOS, and ADV, whereas mutations inserted within extremities (δ-region C, I, V, and VII) were mostly related to the replicative activity of the enzyme. CONCLUSION: Such new strategies provide an easy, reliable, and sensitive means of evaluating the functional role of viral mutations which should translate in improved management of drug-resistant HSV infections.

À l'échelle mondiale, le norovirus humain (HuNoV) et le virus de l'hépatite A (VHA) sont associés aux maladies d'origine alimentaire, ce qui constitue une préoccupation majeure pour le secteur de la santé et de l'alimentation. Afin de garantir la salubrité des aliments et des produits transformés en industrie agroalimentaire, plusieurs méthodes d'inactivation virale physiques et chimiques sont employées. Cependant, elles ne sont pas nécessairement applicables sur toutes les matrices alimentaires et certaines peuvent même générer des substances nocives. De ce fait, la présente étude porte sur la détermination du potentiel virucide des substances naturelles. Dans cette étude, le potentiel antiviral de deux huiles essentielles et de quatre extraits naturels a été évalué sur deux virus non enveloppés, soit le norovirus murin 1 (MNV-1), le VHA et un virus enveloppé, le virus de l'herpès simplex 1 (VHS-1). Des concentrations de chaque substance allant de 50 à 200 000 ppm ont été appliquées pendant 90 min de contact. L'extrait de pépins de raisin a été le plus efficace quant à la réduction de l'infectivité du VHA et du MNV-1 soit de 1,94 ± 0,17 log₁₀, 2,85 ± 0,44 log₁₀ respectivement. Pour le VHS-1, une inactivation totale a été observée à 1000 ppm. En revanche, les extraits de canneberge et de thé vert n'ont pas réussi à réduire l'infectivité des trois types de virus de plus de 1 log₁₀. Ces résultats enrichissent les connaissances actuelles sur les propriétés virucides des substances naturelles en démontrant leur potentiel antiviral contre ces trois types de virus. Cette étude ouvre de nouvelles perspectives quant à l'utilisation des composés naturelles, offrant ainsi des applications prometteuses dans divers secteurs / Enteric viruses such as hepatitis A (HAV) and human norovirus (HuNoV) are the main cause of foodborne diseases worldwide. They are recognized as a major concern for public health and food sector. To minimise the risk of infection, many physical and chemical viral inactivation methods have been used. However, these approaches are not applicable to all food matrices and may generate harmful substances. Therefore, the aim of this project is to study the antiviral potential of natural compounds. For this purpose, the antiviral potential of two essential oils and four natural extracts was evaluated with two non-enveloped viruses: murine norovirus 1 (MNV-1), HAV and one enveloped virus, herpes simplex virus 1 (HSV-1) at concentrations ranging from 50 to 200,000 ppm for 90 min contact in viral pre-incubation. Grape seed extract was the most effective in reducing HAV and MNV-1 infectivity by 1.94±0.17 log10, 2.85±0.44 log₁₀ respectively. For HSV-1, a total inactivation was observed at 1000 ppm. Cranberry extract and green tea extract failed to reduce the infectivity of all three virus types by more than 1 log₁₀. This study has contributed to a better understanding of the antiviral potential of natural substances against the three types of viruses tested. Eventually, this project ultimately aims to reveal new perspectives on the use of natural compounds, thus offering promising applications in various sectors.

Pro optimalizaci letových trajektorií ve velmi malé nadmorské výšce, terenní vlastnosti musí být zahrnuty velice přesne. Proto rychlá a efektivní evaluace terenních dat je velice důležitá vzhledem nato, že čas potrebný pro optimalizaci musí být co nejkratší. Navyše, na optimalizaci letové trajektorie se využívájí metody založené na výpočtu gradientu. Proto musí být aproximační funkce terenních dat spojitá do určitého stupne derivace. Velice nádejná metoda na aproximaci terenních dat je aplikace víceroměrných simplex polynomů. Cílem této práce je implementovat funkci, která vyhodnotí dané terenní data na určitých bodech spolu s gradientem pomocí vícerozměrných splajnů. Program by měl vyčíslit více bodů najednou a měl by pracovat v $n$-dimensionálním prostoru.

Background: Herpes Simplex Virus Type 2 (HSV 2) is one of the most common sexually transmitted infections (STIs) worldwide. HSV 2 infection is a risk factor for the acquisition and transmission of other STIs. Aim: The aim of this study is to determine prevalence and predictors of HSV 2 infection in Durban, South Africa by using available data that has not been previously analysed for the purpose of adding scientific evidence to the existing body of knowledge relating to HSV 2. Method: The study involves secondary analyses of data collected as a prospective study which enrolled women who participated in a clinical trial. A total of 3472 sexually active women were screened in the primary study from two clinics in Durban. All consenting participants were tested for HIV, HSV 2, Trichomonas vaginalis (TV), Neisseria gonorrhoea (NG) and Chlamydia trachomatis (CT) infection. Results: There were 2532 women who had HSV 2 giving a prevalence of 73%. Of these, 53% also tested positive for HIV infection. In univariate analysis, co-infection with HIV was strongly associated with HSV2 (Odds Ratio (OR): 7.4, 95% Confidence Interval (CI): 6.0, 9.1, p<0.001). There was also an association between other STIs, such as CT, NG and syphilis and HSV 2, although only NG was significantly associated with prevalent of HSV 2 (OR: 2.3, 95% CI: 1.3, 4.1, p=0.005). Women older than 25 years of age more likely to have HSV 2 (OR: 2.4, 95% CI: 2.0,2.8, p<0.001). A risk of being infected with HSV 2 increased with the number of reported lifetime sexual partners Those with two and three or more were 2,5 and 4.6 times more likely to have HSV2 respectively (OR: 2.5, 95% CI: 2.1,3.1, p<0.001 and OR: 4.6, 95% CI: 3.8, 5.6, p<0.001 respectively). Women who had less than high school education were also found to have higher risk for HSV 2. Conclusion: The secondary analysis showed a high prevalence of HSV 2 infection and a strong association of HSV 2 and HIV. A significant association of HSV 2 was noted in women having more than two sex partners and lower high school education. Therefore, it is recommended that screening for HSV 2 among high risk populations be incorporated into the STI screening and treatment packages. / Prevalence and risk factors associated with HSV 2 / Herpes Simplex Virus Type 2 / HSV 2 / Department of Health Studies / M. (Public health)

Background: Herpes Simplex Virus Type 2 (HSV 2) is one of the most common sexually transmitted infections (STIs) worldwide. HSV 2 infection is a risk factor for the acquisition and transmission of other STIs. Aim: The aim of this study is to determine prevalence and predictors of HSV 2 infection in Durban, South Africa by using available data that has not been previously analysed for the purpose of adding scientific evidence to the existing body of knowledge relating to HSV 2. Method: The study involves secondary analyses of data collected as a prospective study which enrolled women who participated in a clinical trial. A total of 3472 sexually active women were screened in the primary study from two clinics in Durban. All consenting participants were tested for HIV, HSV 2, Trichomonas vaginalis (TV), Neisseria gonorrhoea (NG) and Chlamydia trachomatis (CT) infection. Results: There were 2532 women who had HSV 2 giving a prevalence of 73%. Of these, 53% also tested positive for HIV infection. In univariate analysis, co-infection with HIV was strongly associated with HSV2 (Odds Ratio (OR): 7.4, 95% Confidence Interval (CI): 6.0, 9.1, p<0.001). There was also an association between other STIs, such as CT, NG and syphilis and HSV 2, although only NG was significantly associated with prevalent of HSV 2 (OR: 2.3, 95% CI: 1.3, 4.1, p=0.005). Women older than 25 years of age more likely to have HSV 2 (OR: 2.4, 95% CI: 2.0,2.8, p<0.001). A risk of being infected with HSV 2 increased with the number of reported lifetime sexual partners Those with two and three or more were 2,5 and 4.6 times more likely to have HSV2 respectively (OR: 2.5, 95% CI: 2.1,3.1, p<0.001 and OR: 4.6, 95% CI: 3.8, 5.6, p<0.001 respectively). Women who had less than high school education were also found to have higher risk for HSV 2. Conclusion: The secondary analysis showed a high prevalence of HSV 2 infection and a strong association of HSV 2 and HIV. A significant association of HSV 2 was noted in women having more than two sex partners and lower high school education. Therefore, it is recommended that screening for HSV 2 among high risk populations be incorporated into the STI screening and treatment packages. / Prevalence and risk factors associated with HSV 2 / Herpes Simplex Virus Type 2 / HSV 2 / Department of Health Studies / M. (Public health)

Herpesviruses can enter host cells by pH-dependent endocytic pathways in a cell-specific manner. The role of pH in herpesvirus endocytosis is unclear. Herpes simplex virus (HSV) is a paradigm for virus membrane fusion via a complex of glycoproteins. HSV glycoproteins B, D and the heterodimer H-L are necessary and sufficient for membrane fusion. This work analyzes the structure and function of HSV glycoproteins B, D, and H-L at neutral pH, and at the physiological low-pH encountered during endocytic entry. It is demonstrated that mildly acidic low pH triggers specific conformational changes in HSV gB at a pH of 5.7 to 6.0. The antigenic structure of gB functional region I that is critical for fusion is specifically altered by mildly acidic pH both in vitro and during entry into host cells. Point mutations within gB functional region 1 that block membrane fusion still allow conformational changes in region 1. This suggests that specific hydrophobic residues are essential for fusion domain insertion into the host cell membrane but not conformational change. The detected conformational changes were reversible, similar to other class III fusion glycoproteins. Exposure to mildly acidic pH directly triggered the fusion function of HSV glycoproteins and caused gB, but not other glycoproteins, to become more hydrophobic. The oligomeric conformation of gB is altered at a similar pH range. In addition, several approaches were used to monitor gB throughout glycoprotein synthesis and maturation. It is shown that gB may cotranslationally fold and oligomerize as it is synthesized on the ribosome. As gB matures it then alters conformation and/or binding partner to form antigenically distinct populations of gB within the cell and virion. I conclude that intracellular low pH induces changes in gB conformation that, together with additional triggers such as receptor-binding, are essential for virion-cell fusion during herpesviral entry by endocytosis.

Modeling of compositional data is emerging as an active area in statistics. It is assumed that compositional data represent the convex linear mixing of definite numbers of independent sources usually referred to as end members. A generic problem in practice is to appropriately separate the end members and quantify their fractions from compositional data subject to nonnegative and unit-sum constraints. A number of methods essentially related to polytope expansion have been proposed. However, these deterministic methods have some potential problems. In this study, a hierarchical Bayesian model was formulated, and the algorithms were coded in MATLABÒ. A test run using both a synthetic and real-word dataset yields scientifically sound and mathematically optimal outputs broadly consistent with other non-Bayesian methods. Also, the sensitivity of this model to the choice of different priors and structure of the covariance matrix of error were discussed.

O presente trabalho desenvolve uma extensão do problema de corte de estoque unidimensional no caso em que a demanda pelos vários tipos de itens não é exatamente conhecida. Para considerar a aleatoriedade, foi proposto um modelo de programação estocástica de dois estágios com recurso. As varáveis de primeiro estágio são os números de barras cortadas por padrão de corte, e as variáveis de segundo estágio, os números de itens produzidos em escassez e em escassez. O objetivo do modelo é minimizar o custo total esperado. Para resolver a relaxação linear do modelo, foram propostos um método exato baseado no método Simplex com geração de colunas e uma estratégia heurística, que considera o valor esperado da demanda na resolução do problema de corte de estoque. As duas estratégias foram comparadas, assim como a possibilidade de resolver o problema de corte ignorando as incertezas. Finalmente, observou-se que é mais interessante determinar o valor ótimo do modelo recurso quando o problema sofre mais influência da aleatoriedade / This paper presents an integer linear optimization model of large scale for the one-dimensional cutting stock problem in the case which a demand is considered a random variable. To take this randomness into account, the problem was formulated as a two-stage stochastic linear program with recourse. The first stage decision variables are given by the number of bars that has to be cut according to each pattern, and the second stage decision variables by the number of holding items or backordering items production. The model objective is minimizes the total expected cost. We propose two methods to solve the model linear relaxation, one of them it is a Simplex-based method with column generation. The second method is a heuristic strategy that adopted the expected value of demand. We compare both strategies and the possibly of ignoring uncertainties on model. Finally, we observe that is much more interesting to determine the optimal recourse model solution when we have problems that are more afected by randomness

This thesis investigates an alternative solution to deal with the civil structure vibration. Non-contact electromagnetic or Eddy current damping is selected as a score of vibration suppression. Electromagnetic damping relies on the interaction between a permanent magnet and conductor. An electromagnetic damper (EMD) is applied both to a laboratory footbridge structure and 6-storey model-scale aluminium moment resisting frame (AMRF). In this first study the EMD is connected in series with an electronic shunt circuit to construct an electromagnetic shunt damper (EMSD). A robust optimisation method is applied to develop the corresponding optimal design formula of the EMSD. The principle of an EMSD is to convert mechanical energy to electrical energy. Hence, the induced electromotive force (emf) is generated by electromagnetic induction. This emf induces an amount of shunt damping, which is fedback to the structure to achieve vibration suppression. It was found that when the impedance was applied, the shunt damping feature was of a similar nature to viscous dampers. In contrast, when an RLC (resistance-inductance-capacitance) circuit is connected, the shunt damping is analogous to a tuned mass damper. A second form of EMD is Eddy current damper (ECD), which relies on a geometrical arrangement of permanent magnets and conductors to produce damping forces. The vertical and horizontal orientation of the magnet, unidirectional and alternative pole projection and moving different direction of the conductor are investigated. A theoretical study involving the infinite boundary and finite boundary (the method of images current) is carried out to obtain an analytical calculation of the damping force. On the basis of this analysis, one type of ECD prototype was physically built. A performance test was carried out to determine the damping characteristics of the ECD, which agreed with the results of the numerical analysis. In addition, the ECD was applied to control the dynamics of the 6-storey AMRF. It was found that, the ECD can effectively increase system damping and have a satisfactory control effect.