Ce projet de recherche comporte deux parties principales qui possèdent comme lien unificateur l’amélioration des méthodes et techniques utilisées actuellement pour évaluer aussi bien l’activité que l’expression des cytochromes P450 (CYP450s) et menant par la suite à leur application en clinique. Le premier volet de ce projet de recherche porte sur le développement de méthodes LC-MS/MS pour un cocktail de 7 substrats marqueurs des CYP450s. Notre objectif est de développer et valider une méthode LC-MS/MS spécifique et sensible permettant l’évaluation des activités des CYP1A2, 2B6, 2C9, 2C19, 2D6, 3A4/5 et 2E1 suivant l’administration orale et à faible dose d’un cocktail de substrats marqueurs chez des patients et sujets sains. Les méthodes développées peuvent être utilisées pour évaluer les mécanismes de variabilité interindividuelle comme l’impact de polymorphismes génétiques, de facteurs environnementaux et de maladies dans le processus de métabolisme et d’élimination des médicaments, mais également pour investiguer les interactions médicamenteuses. Ce cocktail a été appliqué avec succès, dans un projet clinique portant sur l’évaluation des effets du diabète sur la capacité métabolique par les CYP450s. Le deuxième volet de ce projet de recherche vise à développer des méthodes analytiques par LC-HRMS afin de caractériser et quantifier les CYP1A1, 1A2, 1B1, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, 2J2, 3A4, 3A5, 3A7 et 4F2 dans l’intestin grêle humain. Notre hypothèse suggère que les CYP450s retrouvés le long de l’intestin grêle peuvent affecter significativement l’effet de premier passage de certains médicaments administrés par voie orale et influencer leurs concentrations plasmatiques et conséquemment, leurs effets pharmacologiques et/ou toxiques. Ma participation à ce projet a permis d’identifier des peptides protéotypiques par digestion in silico et in vitro et de développer des méthodes de quantification absolue par LC-HRMS. Ce projet est une première étape dans la caractérisation des CYP450s majeurs le long de l'intestin grêle. Il permettra de mieux comprendre les mécanismes de variabilité interindividuelle dans la réponse aux médicaments associés au processus d'absorption intestinal et de mieux prédire la variabilité dans la biodisponibilité des médicaments et de développer des modèles pharmacocinétiques plus complexes. / This research project is divided into two sections, both aiming at the development of sensitive and specific LC-MS methods to evaluate activity and expression of CYP450 and finally, looking at their clinical application. The first section of this research project focuses on the development of analytical methods by LC-MS/MS for a seven CYP450 probe-drug cocktail. Although these cocktails have shown value they also suffer from many limitations. Our objective was to develop and validate highly sensitive and selective LC-MS/MS assays allowing the determination of CYP1A2, 2B6, 2C9, 2C19, 2D6, 3A4/5 and 2E1 activities following administration of low oral doses of a modified CYP450 probe-drug cocktail in patients. These methods can be used to phenotype CYP450 activities, evaluate inter-individual variabilities, study the impact of pathological conditions on drug metabolism and elimination, and evaluate drug-drug interactions. Our CYP450 cocktail assays have been successfully applied to phenotype CYP450 activities in type 2 diabetic patients. The second section of this project aims at the development of a LC-HRMS method for the characterization and absolute quantification of CYP1A1, 1A2, 1B1, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, 2J2, 3A4, 3A5, 3A7 and 4F2 in the human small intestine. Our hypothesis suggests that CYP450 isoenzymes found along the small intestine can significantly affect the first-pass effect of certain drugs administered orally and thus influence their pharmacological and/or toxic effects. My participation in this project allowed to identify proteotypic peptides by in silico and in vitro digestion and to develop LC-HRMS methods allowing the absolute quantification of CYP450. This project is a first step in the characterization of the main CYP450 along the small intestine. This project will allow a better understanding of inter-individual variability in drug response associated with intestinal absorption of drugs, a better prediction of variability in drug bioavailability and to develop more complex pharmacokinetic models.

This thesis deals with multi-channel methods of speech enhancement. Multichannel methods of speech enhancement use a few microphones for recording signals. From mixtures of signals, for example, individual speakers can be separated, noise should be reduced etc. with using neural networks. The task of separating speakers is known as a cocktail-party effect. The main method of solving this problem is called independent component analysis. At first there are described its theoretical foundation and presented conditions and requirements for its application. Methods of ICA try to separate the mixtures with help of searching the minimal gaussian properties of signals. For the analysis of independent components are used different mathematical properties of signals such as kurtosis and entropy. Signals, which were mixed artificially on a computer, can be relatively well separated using, for example, FastICA algorithm or ICA gradient ascent. However, difficult is situation, if we want to separate the signals created in the real recording enviroment, because the separation of speech people speaking at the same time in the real environment affects other various factors such as acoustic properties of the room, noise, delays, reflections from the walls, the position or the type of microphones, etc. Work presents aproach of independent component analysis in the frequency domain, which can successfully separate also recordings made in the real environment.

Master of Science / Department of Biological and Agricultural Engineering / Philip L. Barnes / The world’s population has passed 7 billion and is expected grow to more alarming numbers by the year 2050. The increase in human life on the planet ushers the need to responsibly and sustainably grow more food. In order to meet the demand necessary, it is crucial that soil remains healthy and crop yields continue to increase in efficiency. Irresponsible or ill-informed practices can lead to depleted resources and degradation of fertile soils that may limit a producers’ ability to sustainably grow food. Cover crops are a tool that can be used to address issues the modern producer may face. Cover crops have been shown to increase cash crop productivity, improve soil health by improving soil physical and chemical properties as well as providing protection from soil erosion runoff or nutrient leaching. A study was conducted in 2014 to examine the short term effects associated with cover cropping systems. The effects of ryegrass, red clover and a cover crop cocktail (mixture of ryegrass, red clover and hairy vetch) compared to bare tilled and bare control plots were studied. The five treatments were replicated three times in a completely randomized study and analyzed. Soil physical health indicators such as bulk density and porosity were calculated. Soil and cover crop nutrient use, as well as, soil moisture content data was collected and analyzed using excel and ANOVA statistical procedures. In the short term, the study found that there was only statistically significant differences between cover cropping regimens, tilled and control plots in regards to biomass production and biomass nutrient concentrations (α=0.05). The cocktail mix provided more biomass, N and P than the ryegrass and clover plots alone. Observable differences in cover crop volumetric soil moisture and water used between plots demonstrated that cover crops utilize soil moisture in the short term, which must be considered in areas experiencing water stress. Although more long-term data is needed to truly quantify how cover crops effect various aspects of soil health, this study demonstrated how cover crops have the potential for providing numerous benefits such as increased erosion control, lower reliance on anthropogenically created nutrients and the reduction of weeds. Overall the benefits associated with cover crops are still being researched and while adoption of cover cropping systems has been slow, a push towards agricultural sustainability while increasing food production will increase the amount of producers utilizing cover crops in the coming years.

Time-Frequency (TF) masking is an audio processing technique useful for isolating an audio source from interfering sources. TF masking has been applied and studied in monaural and binaural applications, but has only recently been applied to distributed microphone arrays. This work focuses on evaluating the TF masking technique's ability to isolate human speech and improve speech intelligibility in an immersive "cocktail party" environment. In particular, an upper-bound on TF masking performance is established and compared to the traditional delay-sum and general sidelobe canceler (GSC) beamformers. Additionally, the novel technique of combining the GSC with TF masking is investigated and its performance evaluated. This work presents a resource-efficient method for studying the performance of these isolation techniques and evaluates their performance using both virtually simulated data and data recorded in a real-life acoustical environment. Further, methods are presented to analyze speech intelligibility post-processing, and automated objective intelligibility measurements are applied alongside informal subjective assessments to evaluate the performance of these processing techniques. Finally, the causes for subjective/objective intelligibility measurement disagreements are discussed, and it was shown that TF masking did enhance intelligibility beyond delay-sum beamforming and that the utilization of adaptive beamforming can be beneficial.

Resíduos celulósicos por erem ricos em celulose e hemicelulose estão sendo apontados como promissoras fontes para a produção de etanol. Com isso, este trabalho tem como objetivo hidrolisar e fermentar resíduos celulósicos visando a produção de etanol. Para estudo da hidrólise do bagaço de cana-de-açúcar, foram isolados 22 fungos da cidade de Araras-SP e estes testados para produção de endoglucanases (EG). Foram testadas temperatura e pH ótimos, diferentes tampões, estabilidade do coquetel e influência de sais, EDTA e ?-mercaptoetanol para lacase, xilanase, endo-?-1,4-glucanase, celobiohidrolase I, ?-glucosidase e glucoamilase. As condições padronizadas para aplicação do coquetel enzimático foi 55ºC, tampão citrato de sódio 50 mM e pH 5,0. Para elaboração do coquetel enzimático foi realizado um Plackett-Burman seguido de um delineamento composto central rotacional, em que as condições padronizadas para aplicação foram (U/g de bagaço de cana-deaçúcar): 0,122 de lacase; 7 de xilanase; 5 de endoglucanase; 14 de celobiohidrolase e 9 de ?-glucosidase. Foram liberados 4,405 µmol de açúcares redutores por mL, após 48 horas de hidrólise do bagaço a 55ºC, em tampão citrato de sódio 50 mM (7 mL), pH 5,0, agitação de 110 rpm. O hidrolisado obtido foi fermentado pelas leveduras Saccharomyces cerevisiae PE-2 e Meyerozyma guilliermondii 311 (CCT7783), separadamente e em cultivo misto, averiguando a necessidade de suplementação do meio, para a produção de etanol. Os resultados mostraram a necessidade de suplementação para aumento da viabilidade das leveduras. Observou-se que a suplementação manteve a viabilidade acima de 90%. A fermentação com Meyerozyma guilliermondii 311 (CCT7783), sem a necessidade de suplementação, possibilitou a produção de 12,66% de etanol; com a Saccharomyces cerevisiae a produção de etanol foi de 7,03%, quando o meio foi suplementado com 3 g/L de extrato de levedura. A fermentação com cultura mista produziu 0,53% e 1,18% de etanol em 24 e 48 horas de cultivo, respectivamente. Para aplicação enzimática na hidrólise do lodo branco foram utilizadas amilase de Aspergillus carbonarius e celulase comercial. Os produtos de hidrólise enzimática do lodo branco detectados HPLC mostraram a formação de glicose, xilose e traços de maltose. A viabilidade celular da levedura Saccharomyces cerevisiae durante a fermentação se manteve bastante elevada, acima de 95 %. A fermentação do lodo branco, quando o meio foi suplementado com 3g/L de extrato de levedura, foi considerada satisfatória, com 2,37 g/L de etanol. Foram realizadas análise de superfície por ion-tof e microscopia eletrônica de varredura nos resíduos celulósicos. Desta maneira, com este trabalho foi possível estudar a importância da aplicação de enzimas fúngicas para degradação de biomassa lignocelulósica para produção de etanol de segunda geração. / As cellulosic wastes are rich in cellulose and hemicellulose they have been pointed as promising sources for ethanol production. Thereby, this work aimed to hydrolyze and ferment cellulosic residues to produce ethanol. In order to study the hydrolyzes of sugar-cane bagasse and ferment the sugars obtained from this process, twenty-two fungi were isolated in the city of Araras-SP and tested for endoglucanase (EG) production. Aiming to optmize an enzyme cocktail, variables as temperature, optimum pH, different buffers, stability, salt influence, EDTA and ?-mercaptoethanol were tested for laccase, xylanase, endo- ?-1,4-glucanase, cellobiohydrolase I, ?-glucosidase and glucoamylase. The standard conditions for applying the enzyme cocktail were 55°C, sodium citrate buffer 50 mM pH 5.0. For the preparation of the enzyme cocktail a Plackett-Burman was made followed by a central composite design, in which the standard conditions for application were (U/g of sugarcane bagasse): 0.122 of laccase; 7 of xylanase; 5 of endoglucanase; 14 of cellobiohydrolase and 9 of ?-glucosidase per gram of sugarcane bagasse. After 48 hours of hydrolyzes in the following conditions, 55ºC, sodium citrate buffer 50 mM (7 mL), pH 7.0, 110 rpm, 4.405 µmol of reducing sugar per mL were released. The hydrolyzate obtained was separately fermented by the yeasts Saccharomyces cerevisiae PE-2, Meyerozyma guilliermondii 311 (CCT7783) and with both yeasts in a mixed cultivation, in order to investigate the need of medium supplementation for ethanol production. The results showed the need of supplementation to increase the viability of the yeasts. It was observed that this procedure kept the viability over 90%. The fermentation with Meyerozyma guilliermondii 311 (CCT7783), without supplementation, allowed the production of 12.66% of ethanol and with Saccharomyces cerevisiae the production was 7.03% with a supplementation of 3 g/L of yeast extract. The fermentation with mixed cultivation produced 0.53% and 1.18% in 24 and 48 hours of cultivation, respectively. Another objective of this work was the hydrolysis of paper sludge which was obtained by using amylases from Aspergillus carbonarius and commercial cellulases. The products of enzymatic hydrolysis of the white sludge detected in HPLC showed the formation of glucose, xylose and maltose traits. Cell viability counting of the yeast, analyzes of pH, reducing sugar and alcohol content were carried out. Cellular viability of Saccharomyces cerevisiae along the fermentation was kept over 95%. Paper sludge fermentation using Saccharomyces cerevisiae, in medium supplemented with yeast extract 3 g/L, was considered satisfactory, showing 2.37 g/L of ethanol. Surface analysis was performed by Ion-tof and scanning electron microscopy in the cellulosic waste. Thus, this work made possible to study the importance of fungal enzymes application in lignocellulosic biomass degradation for the production of second generation ethanol.

Systems designed to enhance intelligibility of speech in noise are difficult to evaluate quantitatively because intelligibility is subjective and often requires feedback from large populations for consistent evaluations. Attempts to quantify the evaluation have included related measures such as the Speech Intelligibility Index. These require separating speech and noise signals, which precludes its use on experimental recordings. This thesis develops a procedure using an Intelligibility Ruler (IR) for efficiently quantifying intelligibility. A calibrated Mean Opinion Score (MOS) method is also implemented in order to compare repeatability over a population of 24 subjective listeners. Results showed that subjects using the IR consistently estimated SII values of the test samples with an average standard deviation of 0.0867 between subjects on a scale from zero to one and R2=0.9421. After a calibration procedure from a subset of subjects, the MOS method yielded similar results with an average standard deviation of 0.07620 and R2=0.9181.While results suggest good repeatability of the IR method over a broad range of subjects, the calibrated MOS method is capable of producing results more closely related to actual SII values and is a simpler procedure for human subjects.

Philosophiae Doctor - PhD / The aim of this study was to design and build an electrohydraulic discharge reactor in such a way that the synthetic immobilized TiO2 nanophotocatalytic components could be integrated, for the production of active species such as OH radicals, ozone and hydrogen peroxide, as a cocktail to clean drinking water without the addition of chemicals. The research objectives include: • To design and construct the different AOP prototypes based on various electrode configurations and compare their operation. • To optimize the discharge parameters and conditions of the best AOP system. • To determine the effectiveness of the best prototype for the degradation of methylene blue as model pollutant. • To compare the designed AOP system with the Sodis method for the disinfection of contaminated river water. • To prepare supported TiO2 nanoparticles via electro spinning, followed by combustion and study the effect on the morphology of TiO2 nanoparticles. • To determine the stability and robustness of composite nano-crystalline TiO2 photocatalysts by sonication • To determine the enhanced effect of combining the composite TiO2 in the AOP system on degradation of methylene blue under the same conditions. • To detect the active species promoting disinfection.

Resíduos celulósicos por erem ricos em celulose e hemicelulose estão sendo apontados como promissoras fontes para a produção de etanol. Com isso, este trabalho tem como objetivo hidrolisar e fermentar resíduos celulósicos visando a produção de etanol. Para estudo da hidrólise do bagaço de cana-de-açúcar, foram isolados 22 fungos da cidade de Araras-SP e estes testados para produção de endoglucanases (EG). Foram testadas temperatura e pH ótimos, diferentes tampões, estabilidade do coquetel e influência de sais, EDTA e ?-mercaptoetanol para lacase, xilanase, endo-?-1,4-glucanase, celobiohidrolase I, ?-glucosidase e glucoamilase. As condições padronizadas para aplicação do coquetel enzimático foi 55ºC, tampão citrato de sódio 50 mM e pH 5,0. Para elaboração do coquetel enzimático foi realizado um Plackett-Burman seguido de um delineamento composto central rotacional, em que as condições padronizadas para aplicação foram (U/g de bagaço de cana-deaçúcar): 0,122 de lacase; 7 de xilanase; 5 de endoglucanase; 14 de celobiohidrolase e 9 de ?-glucosidase. Foram liberados 4,405 µmol de açúcares redutores por mL, após 48 horas de hidrólise do bagaço a 55ºC, em tampão citrato de sódio 50 mM (7 mL), pH 5,0, agitação de 110 rpm. O hidrolisado obtido foi fermentado pelas leveduras Saccharomyces cerevisiae PE-2 e Meyerozyma guilliermondii 311 (CCT7783), separadamente e em cultivo misto, averiguando a necessidade de suplementação do meio, para a produção de etanol. Os resultados mostraram a necessidade de suplementação para aumento da viabilidade das leveduras. Observou-se que a suplementação manteve a viabilidade acima de 90%. A fermentação com Meyerozyma guilliermondii 311 (CCT7783), sem a necessidade de suplementação, possibilitou a produção de 12,66% de etanol; com a Saccharomyces cerevisiae a produção de etanol foi de 7,03%, quando o meio foi suplementado com 3 g/L de extrato de levedura. A fermentação com cultura mista produziu 0,53% e 1,18% de etanol em 24 e 48 horas de cultivo, respectivamente. Para aplicação enzimática na hidrólise do lodo branco foram utilizadas amilase de Aspergillus carbonarius e celulase comercial. Os produtos de hidrólise enzimática do lodo branco detectados HPLC mostraram a formação de glicose, xilose e traços de maltose. A viabilidade celular da levedura Saccharomyces cerevisiae durante a fermentação se manteve bastante elevada, acima de 95 %. A fermentação do lodo branco, quando o meio foi suplementado com 3g/L de extrato de levedura, foi considerada satisfatória, com 2,37 g/L de etanol. Foram realizadas análise de superfície por ion-tof e microscopia eletrônica de varredura nos resíduos celulósicos. Desta maneira, com este trabalho foi possível estudar a importância da aplicação de enzimas fúngicas para degradação de biomassa lignocelulósica para produção de etanol de segunda geração. / As cellulosic wastes are rich in cellulose and hemicellulose they have been pointed as promising sources for ethanol production. Thereby, this work aimed to hydrolyze and ferment cellulosic residues to produce ethanol. In order to study the hydrolyzes of sugar-cane bagasse and ferment the sugars obtained from this process, twenty-two fungi were isolated in the city of Araras-SP and tested for endoglucanase (EG) production. Aiming to optmize an enzyme cocktail, variables as temperature, optimum pH, different buffers, stability, salt influence, EDTA and ?-mercaptoethanol were tested for laccase, xylanase, endo- ?-1,4-glucanase, cellobiohydrolase I, ?-glucosidase and glucoamylase. The standard conditions for applying the enzyme cocktail were 55°C, sodium citrate buffer 50 mM pH 5.0. For the preparation of the enzyme cocktail a Plackett-Burman was made followed by a central composite design, in which the standard conditions for application were (U/g of sugarcane bagasse): 0.122 of laccase; 7 of xylanase; 5 of endoglucanase; 14 of cellobiohydrolase and 9 of ?-glucosidase per gram of sugarcane bagasse. After 48 hours of hydrolyzes in the following conditions, 55ºC, sodium citrate buffer 50 mM (7 mL), pH 7.0, 110 rpm, 4.405 µmol of reducing sugar per mL were released. The hydrolyzate obtained was separately fermented by the yeasts Saccharomyces cerevisiae PE-2, Meyerozyma guilliermondii 311 (CCT7783) and with both yeasts in a mixed cultivation, in order to investigate the need of medium supplementation for ethanol production. The results showed the need of supplementation to increase the viability of the yeasts. It was observed that this procedure kept the viability over 90%. The fermentation with Meyerozyma guilliermondii 311 (CCT7783), without supplementation, allowed the production of 12.66% of ethanol and with Saccharomyces cerevisiae the production was 7.03% with a supplementation of 3 g/L of yeast extract. The fermentation with mixed cultivation produced 0.53% and 1.18% in 24 and 48 hours of cultivation, respectively. Another objective of this work was the hydrolysis of paper sludge which was obtained by using amylases from Aspergillus carbonarius and commercial cellulases. The products of enzymatic hydrolysis of the white sludge detected in HPLC showed the formation of glucose, xylose and maltose traits. Cell viability counting of the yeast, analyzes of pH, reducing sugar and alcohol content were carried out. Cellular viability of Saccharomyces cerevisiae along the fermentation was kept over 95%. Paper sludge fermentation using Saccharomyces cerevisiae, in medium supplemented with yeast extract 3 g/L, was considered satisfactory, showing 2.37 g/L of ethanol. Surface analysis was performed by Ion-tof and scanning electron microscopy in the cellulosic waste. Thus, this work made possible to study the importance of fungal enzymes application in lignocellulosic biomass degradation for the production of second generation ethanol.

Objectives: Development of accurate auditory attention decoding (AAD) algorithms, capable of identifying the attended sound source from the speech evoked electroencephalography (EEG) responses, could lead to new solutions for hearing impaired listeners: neuro-steered hearing aids. Many of the existing AAD algorithms are either inaccurate or very slow. Therefore, there is a need to develop new EEG-based AAD methods. The first objective of this project was to investigate deep neural network (DNN) models for AAD and compare them to the state-of-the-art linear models. The second objective was to investigate whether generative adversarial networks (GANs) could be used for speech-evoked EEGdata augmentation to improve the AAD performance. Design: The proposed methods were tested in a dataset of 34 participants who performed an auditory attention task. They were instructed to attend to one of the two talkers in the front and ignore the talker on the other side and back-ground noise behind them, while high density EEG was recorded. Main Results: The linear models had an average attended vs ignored speech classification accuracy of 95.87% and 50% for ∼30 second and 8 seconds long time windows, respectively. A DNN model designed for AAD resulted in an average classification accuracy of 82.32% and 58.03% for ∼30 second and 8 seconds long time windows, respectively, when trained only on the real EEG data. The results show that GANs generated relatively realistic speech-evoked EEG signals. A DNN trained with GAN-generated data resulted in an average accuracy 90.25% for 8 seconds long time windows. On shorter trials the GAN-generated EEG data have shown to significantly improve classification performances, when compared to models only trained on real EEG data. Conclusion: The results suggest that DNN models can outperform linear models in AAD tasks, and that GAN-based EEG data augmentation can be used to further improve DNN performance. These results extend prior work and brings us closer to the use of EEG for decoding auditory attention in next-generation neuro-steered hearing aids.

Excerpt: The title and conclusions of the study recently published by Jones et al. (1) concluded that monkeys were protected from dying from a form of simian-human immunodeficiency virus (SHIV) by an psoralen- and ultraviolet-inactivated vaccinia virus in a multi-envelope DNA-VV-protein (DVP). However, the findings in the study are more equivocal than indicated by the title because the effectiveness of the modified vaccinia virus was not decisively demonstrated.