No description available.

This thesis is a flirtation with architectural materials and tailoring techniques that questions industry solutions and standards. Searching with tailoring precision to create architectural seams, edges, darts, and connections. By coincidence, luck, or destiny, this thesis is also the beginning of Washington DC as a fashion capital of the world by being the epicenter to the new movement on fashion in DC. / Master of Architecture

Dans la thèse nous nous occupons de l'estimation de la moyenne d'un petit domaine sous un modèle one-fold et utilisant MINQUE pour estimer les composantes de la variance, sous un modèle two-fold avec variances aléatoires, sous des plans noninformatifs et informatifs.

A escaldadura das folhas, causada pela bactéria Gram-negativa Xanthomonas albilineans, é uma das doenças mais importantes que afetam o cultivo da cana-de-açúcar, causando significativa diminuição da produtividade, necessidade de reforma precoce dos canaviais e queda da qualidade do caldo extraído. O impacto dessa doença somado à ausência de agentes químicos ou biológicos para o controle estimula a pesquisa para a descoberta e desenvolvimento de moléculas bioativas como candidatos a novos defensivos agrícolas. Nesse contexto, a enzima N5, N10-metilenotetrahidrofolato desidrogenase ciclohidrolase (FolD) destaca-se como potencial alvo molecular. O projeto de doutoramento visou a caracterização estrutural e funcional da FolD de X. albilineans (XaFolD), além da triagem de moléculas candidatas a inibidores. Para tanto, foram conduzidos estudos integrados em biologia molecular estrutural e química biológica. A expressão heteróloga e purificação da XaFolD resultaram na produção de proteína funcional e adequada aos ensaios de cristalização. A caracterização das atividades desidrogenase e ciclohidrolase da XaFolD indicou os valores de KM para os substratos de ambas as reações, N5, N10-metileno-tetrahidrofolato (50 ± 10 µM) e N5, N10-metenil-tetrahidrofolato (32 ± 3 µM) e do cofator NADP+ (688 ± 81 µM). A estrutura da XaFolD na forma apo, elucidada a 2,1 Å de resolução, revelou uma proteína constituída por 11 hélices alfa e 9 fitas beta distribuídas em um domínio N-terminal catalítico e um domínio C-terminal de ligação ao dinucleotídeo. A enzima pura foi utilizada para a triagem de 1.124 fragmentos por interferometria de biocamada (BLI) e foram identificados três ligantes, DDD00808259 (KD = 260 μM), DDD01305586 (KD = 3 mM) e DDD00100784 (KD = 210 μM), com valores de afinidade na faixa do submilimolar até baixo milimolar. Paralelamente, uma abordagem computacional foi empregada para a triagem virtual de base de dados de compostos como candidatos a ligantes da XaFolD. Os critérios utilizados resultaram na seleção e aquisição de 31 compostos de diferentes classes químicas para avaliação da atividade inibitória frente a enzima alvo. Por fim, ensaios fenotípicos de triagem de inibidores resultaram na descoberta de compostos capazes de inibir o crescimento in vitro de X. albilineans. Dentre os inibidores identificados o composto THP2 apresentou a maior potência, com valor determinado de EC50 igual a 23 ± 2 μM. Os dados estruturais, cinéticos e biofísicos obtidos nesta tese de doutoramento formam a base experimental e computacional para a descoberta e planejamento de inibidores candidatos a novos agroquímicos para o tratamento da escaldadura das folhas. / The leaf scald disease is a severe condition which affects sugarcane crops. Leaf scald is caused by the Gram-negative bacteria Xanthomonas albilineans and it has a dramatic impact on crop productivity, including the yield reduction and dropping the quality of the juice. The impact of this disease besides the absence of chemical or biological agents to treat it stimulates the research towards the discovery and development of bioactive molecules as lead candidates to new agrochemicals. In this context, the enzyme N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (XaFolD) stands out as a potential molecular target. Facing this scenario, the PhD project comprised the structural and functional characterization of X. albilineans FolD (XaFolD) and the screening of molecules to identify inhibitors. For this purpose, integrated studies in structural molecular biology and biological chemistry have been carried out. Suitable protein for crystallization and kinetic assays was produced by heterologous expression. The XaFolD dehydrogenase and cyclohydrolase activities were characterized, revealing KM values of 50 ± 10 µM for N5, N10- methylenetetrahydrofolate, 32 ± 3 µM for N5, N10-methenyltetrahydrofolate, and 688 ± 81 µM for NADP+. The structure of XaFolD in the apo form was elucidated at 2.1 Å resolution and it revealed a protein consisting of 11 alpha helices and 9 beta sheets distributed in the catalytic N-terminal domain and the C-terminal dinucleotide binding domain. Screening of 1,124 fragments by biolayer interferometry (BLI) revealed three ligands, DDD00808259, DDD01305586 and DDD00100784, with determined KD values of 260 µM, 3 mM and 210 M, respectively. Furthermore, a virtual screening was performed to identify XaFolD ligands. As a result, 31 chemically diverse compounds were selected to be evaluated by potency assays. Additionally, phenotypical assays against X. albilineans have been performed and inhibitors were identified. Among them, the compound THP2 presented the highest potency, with a determined value of EC50 equal to 23 ± 2 µM. The structural, kinetic, and biophysical data obtained in this PhD thesis provide the molecular basis for discovering and planning bioactive molecules as agrochemicals to control leaf scald disease.

A escaldadura das folhas, causada pela bactéria Gram-negativa Xanthomonas albilineans, é uma das doenças mais importantes que afetam o cultivo da cana-de-açúcar, causando significativa diminuição da produtividade, necessidade de reforma precoce dos canaviais e queda da qualidade do caldo extraído. O impacto dessa doença somado à ausência de agentes químicos ou biológicos para o controle estimula a pesquisa para a descoberta e desenvolvimento de moléculas bioativas como candidatos a novos defensivos agrícolas. Nesse contexto, a enzima N5, N10-metilenotetrahidrofolato desidrogenase ciclohidrolase (FolD) destaca-se como potencial alvo molecular. O projeto de doutoramento visou a caracterização estrutural e funcional da FolD de X. albilineans (XaFolD), além da triagem de moléculas candidatas a inibidores. Para tanto, foram conduzidos estudos integrados em biologia molecular estrutural e química biológica. A expressão heteróloga e purificação da XaFolD resultaram na produção de proteína funcional e adequada aos ensaios de cristalização. A caracterização das atividades desidrogenase e ciclohidrolase da XaFolD indicou os valores de KM para os substratos de ambas as reações, N5, N10-metileno-tetrahidrofolato (50 ± 10 µM) e N5, N10-metenil-tetrahidrofolato (32 ± 3 µM) e do cofator NADP+ (688 ± 81 µM). A estrutura da XaFolD na forma apo, elucidada a 2,1 Å de resolução, revelou uma proteína constituída por 11 hélices alfa e 9 fitas beta distribuídas em um domínio N-terminal catalítico e um domínio C-terminal de ligação ao dinucleotídeo. A enzima pura foi utilizada para a triagem de 1.124 fragmentos por interferometria de biocamada (BLI) e foram identificados três ligantes, DDD00808259 (KD = 260 μM), DDD01305586 (KD = 3 mM) e DDD00100784 (KD = 210 μM), com valores de afinidade na faixa do submilimolar até baixo milimolar. Paralelamente, uma abordagem computacional foi empregada para a triagem virtual de base de dados de compostos como candidatos a ligantes da XaFolD. Os critérios utilizados resultaram na seleção e aquisição de 31 compostos de diferentes classes químicas para avaliação da atividade inibitória frente a enzima alvo. Por fim, ensaios fenotípicos de triagem de inibidores resultaram na descoberta de compostos capazes de inibir o crescimento in vitro de X. albilineans. Dentre os inibidores identificados o composto THP2 apresentou a maior potência, com valor determinado de EC50 igual a 23 ± 2 μM. Os dados estruturais, cinéticos e biofísicos obtidos nesta tese de doutoramento formam a base experimental e computacional para a descoberta e planejamento de inibidores candidatos a novos agroquímicos para o tratamento da escaldadura das folhas. / The leaf scald disease is a severe condition which affects sugarcane crops. Leaf scald is caused by the Gram-negative bacteria Xanthomonas albilineans and it has a dramatic impact on crop productivity, including the yield reduction and dropping the quality of the juice. The impact of this disease besides the absence of chemical or biological agents to treat it stimulates the research towards the discovery and development of bioactive molecules as lead candidates to new agrochemicals. In this context, the enzyme N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (XaFolD) stands out as a potential molecular target. Facing this scenario, the PhD project comprised the structural and functional characterization of X. albilineans FolD (XaFolD) and the screening of molecules to identify inhibitors. For this purpose, integrated studies in structural molecular biology and biological chemistry have been carried out. Suitable protein for crystallization and kinetic assays was produced by heterologous expression. The XaFolD dehydrogenase and cyclohydrolase activities were characterized, revealing KM values of 50 ± 10 µM for N5, N10- methylenetetrahydrofolate, 32 ± 3 µM for N5, N10-methenyltetrahydrofolate, and 688 ± 81 µM for NADP+. The structure of XaFolD in the apo form was elucidated at 2.1 Å resolution and it revealed a protein consisting of 11 alpha helices and 9 beta sheets distributed in the catalytic N-terminal domain and the C-terminal dinucleotide binding domain. Screening of 1,124 fragments by biolayer interferometry (BLI) revealed three ligands, DDD00808259, DDD01305586 and DDD00100784, with determined KD values of 260 µM, 3 mM and 210 M, respectively. Furthermore, a virtual screening was performed to identify XaFolD ligands. As a result, 31 chemically diverse compounds were selected to be evaluated by potency assays. Additionally, phenotypical assays against X. albilineans have been performed and inhibitors were identified. Among them, the compound THP2 presented the highest potency, with a determined value of EC50 equal to 23 ± 2 µM. The structural, kinetic, and biophysical data obtained in this PhD thesis provide the molecular basis for discovering and planning bioactive molecules as agrochemicals to control leaf scald disease.

There are many conditions and diseases that affect voice production. One of these, subglottic stenosis (SGS), is characterized by a narrowing of the trachea near the cricotracheal junction. SGS causes dyspnea (labored breathing) and frequently surgery is necessary to eliminate the airway obstruction. SGS is also believed to adversely affect voice quality. While significant research has been conducted to study the effect of SGS on breathing, relatively few studies concerning its effect on voice production have been performed. The purpose of this research was to provide quantitative results concerning the predicted effects of SGS on vocal fold (VF) vibration and resulting sound production, and to provide tools for more extensive research involving synthetic VF models in the future. This was achieved through an experimental procedure in which a device simulating SGS was coupled with synthetic VF models and acoustic, aerodynamic, and vibratory measurements were acquired. Additionally, a device was developed and tested to study the effects of VF posturing using synthetic VF models. The design of the device is anticipated to serve as a useful tool in future experiments.The device simulating SGS was capable of creating an artificial stenosis of adjustable severity. The device was designed so that synthetic VF models inserted into rigid plates could be placed on top of the device, downstream of the stenosis. An experiment was conducted with the SGS device in conjunction with synthetic four-layer VF models in which flow and pressure were measured, radiated sound data were recorded, and visual data from a high-speed camera were captured as the percent obstruction was changed. The effects of subglottic stenosis were quantified using metrics such as onset pressure, glottal area, smoothed cepstral peak prominence (CPPS), harmonic-to-noise ratio (HNR), acoustic spectra, air flow, and pressure below and above the stenosis. The results show that the glottal area was not noticeably affected by the stenosis until 80% or 90% obstruction, and flow resistance through the stenosis was not significantly affected until 85% obstruction. However, changes in acoustics occurred as low as 65% or 70% obstruction.An MRI-compatible posturing device was developed which was capable of causing abduction/adduction and elongation in synthetic VF models. The device was used to adduct synthetic VF models from an abducted position into a pre-determined final phonatory posture as high-speed video and pressure data were collected. The device adducted to final phonatory posture in 500 ms, and phonation was initiated 680 ms later. In addition, the elongation of the synthetic models was varied as high-speed data were collected. The frequency of vibration of the four-layer models was found to not vary significantly when the models were elongated.

Communication by voice is foundational in our society and many rely on their voices for their occupations. Voice disorders affect a significant number of individuals each year, and diagnosis and treatment improvements are therefore sought via advancements in voice research. Contained in this thesis is a description of work intended to contribute to vocal fold research by using synthetic, self-oscillating vocal fold replicas to study the impact of replica vibration on perfusion fluid flow through the replica. Methods for manufacturing vocal fold replicas containing imbedded channels allowing for fluid perfusion are discussed. Experimental procedures developed for delivering perfusion fluid to the imbedded channel at a constant pressure during replica vibration are described. Methods for measuring perfusion parameters of perfusion fluid pressure, imbedded channel diameter, flow rate, and vibration parameters (subglottal pressure, frequency, amplitude, channel length, and glottal width) are detailed. Experiments performed using both stationary and vibrating vocal fold replicas are presented. Correlations between perfusion pressure and channel diameter are discussed. Vibration parameters were correlated to perfusion flow parameters and it is shown that perfusion flow rate through the channels decreased significantly with model vibration. Potential mechanisms for changes in perfusion flow resistance with vibration are discussed and analyzed. Output of a theoretical model, developed to incorporate some of the possible flow resistance mechanisms, was compared to vibrating replica experimental data.

Protein structure prediction has been a fundamental challenge in the biological field. In this post-genomic era, the need for automated protein structure prediction has never been more evident and researchers are now focusing on developing computational techniques to predict three-dimensional structures with high throughput. Consensus-based protein structure prediction methods are state-of-the-art in automatic protein structure prediction. A consensus-based server combines the outputs of several individual servers and tends to generate better predictions than any individual server. Consensus-based methods have proved to be successful in recent CASP (Critical Assessment of Structure Prediction). In this thesis, a Support Vector Machine (SVM) regression-based consensus method is proposed for protein fold recognition, a key component for high throughput protein structure prediction and protein function annotation. The SVM first extracts the features of a structural model by comparing the model to the other models produced by all the individual servers. Then, the SVM predicts the quality of each model. The experimental results from several LiveBench data sets confirm that our proposed consensus method, SVM regression, consistently performs better than any individual server. Based on this method, we developed a meta server, the Alignment by Consensus Estimation (ACE).

As condições de pressão e temperatura existentes no evento tectônico que atuou na zona de fold-and-thrust da margem oeste do Cráton do São Francisco foram estimadas com base em estudos estruturais, microestruturais, petrográficos e de inclusões fluidas de veios sintectônicos. A presença de veios de diferentes gerações na zona de fold-and-thrust é evidenciada por fluidos atuando em diferentes cenários de paleoestresse ao longo da história deformacional da área. A área é composta por rochas do Grupo Bambuí fracamente deformadas que registram condições de metamorfismo que variam de diagênese a fácies subxisto verde. Dois eventos tectônicos foram identificados através da disposição geométrica dos veios e da superfície dobrada: (i) uma compressão principal NE-SW (D1) com \'sigma\'1 subhorizontal de orientação SW e \'sigma\'3 sub-vertical, relacionado à formação de veios sintectônicos sub-horizontais de orientação NW formados em condições que atingiram pelo menos 140- 160°C e pressões em torno de 200-363 MPa; (ii) uma compressão posterior NW-SE (D2) com \'sigma\'1 sub-horizontal de orientação NW e \'sigma\'3 também sub-horizontal de orientação NE. Estão relacionados à D2 a formação de veios sintectônicos sub-verticais paralelos à clivagem, formados nas mesmas condições mínimas de temperatura de 140-160°C e pressões entre 181- 295 MPa. A indicação de flutuações na pressão durante esses eventos desempenhou um papel crucial, pois os fluidos influenciam significativamente os processos mecânicos, os mecanismos de deformação e as reações químicas que operam em cinturões de fold-andthrust. Os fluidos apresentam composição formada por H2O-NaCl-CaCl2, onde o processo de mistura de diferentes fontes de fluidos (metamórficas e meteóricas) é evidenciado pela tendência evolutiva de temperaturas de homogeneização e salinidades, resultando em alguma variação na salinidade (12 contra 4% em peso equivalente de NaCl para os veios subhorizontais e para os paralelos à clivagem, respectivamente). Este trabalho confirma que a combinação entre a reconstrução do paleoestresse e o estudo de inclusões fluidas podem fornecer informações fundamentais sobre a relação entre o fluxo de fluidos e a tectônica de terrenos orogênicos, contribuindo para o conhecimento científico sobre a evolução deformacional/metamórfica do Grupo Bambuí e, consequentemente, da zona de fold-andthrust da margem ocidental do Cráton do São Francisco. / P-T conditions existing at the tectonic event that acted at the fold-and-thrust zone of the western margin of the São Francisco Craton were estimated on the basis of structural, microstructural, petrographic and fluid inclusion study of syntectonic veins. The presence of veins of different generations in the fold-and-thrust zone is evidenced by fluids operating at different scenarios of paleostress throughout the deformation history. The area are composed of weakly deformed rocks of the Bambuí Group recording a metamorphism with conditions ranging from diagenetic to sub-greenschist facies. Two tectonic events were identified by vein geometric arrangement and folded surface, a major early NE-SW compression (D1 - \'sigma\'1 subhorizontal SW-trending and \'sigma\'3 subvertical), related with subhorizontal NW-trending syntectonic veins formed at conditions that have reached at least 140°C and pressures around 200-363 MPa; and later NW-SE compression (D2 - \'sigma\'1 subhorizontal NW-trending and \'sigma\'3 subhorizontal NE-trending), related with subvertical syntectonic cleavage-parallel veins formed at the same range of temperature and pressures between 181-295 MPa. Indication of fluctuations in pressure during these events played a crucial role as fluids significantly influence the mechanical processes, deformation mechanisms and chemical reactions that operate in fold-thrust belts. Fluids show H2O-NaCl-CaCl2 composition where mixing process of different fluids sources (metamorphic and meteoric) are evidenced by evolutive trending of homogenization temperatures and salinities resulting in some variation in salinity (12 against 4 wt.% NaCl eq. for subhorizontal and cleavage-parallel veins respectively). This research confirms that combine the reconstruction of the paleostress states and fluid inclusion studies can provide fundamental information of relationship between fluid flow and tectonic of orogenic terrains contributing to the scientific knowledge about the deformational/metamorphic evolution of the Bambuí Group and the fold-and-thrust zone of the western margin of the São Francisco Craton.

As condições de pressão e temperatura existentes no evento tectônico que atuou na zona de fold-and-thrust da margem oeste do Cráton do São Francisco foram estimadas com base em estudos estruturais, microestruturais, petrográficos e de inclusões fluidas de veios sintectônicos. A presença de veios de diferentes gerações na zona de fold-and-thrust é evidenciada por fluidos atuando em diferentes cenários de paleoestresse ao longo da história deformacional da área. A área é composta por rochas do Grupo Bambuí fracamente deformadas que registram condições de metamorfismo que variam de diagênese a fácies subxisto verde. Dois eventos tectônicos foram identificados através da disposição geométrica dos veios e da superfície dobrada: (i) uma compressão principal NE-SW (D1) com \'sigma\'1 subhorizontal de orientação SW e \'sigma\'3 sub-vertical, relacionado à formação de veios sintectônicos sub-horizontais de orientação NW formados em condições que atingiram pelo menos 140- 160°C e pressões em torno de 200-363 MPa; (ii) uma compressão posterior NW-SE (D2) com \'sigma\'1 sub-horizontal de orientação NW e \'sigma\'3 também sub-horizontal de orientação NE. Estão relacionados à D2 a formação de veios sintectônicos sub-verticais paralelos à clivagem, formados nas mesmas condições mínimas de temperatura de 140-160°C e pressões entre 181- 295 MPa. A indicação de flutuações na pressão durante esses eventos desempenhou um papel crucial, pois os fluidos influenciam significativamente os processos mecânicos, os mecanismos de deformação e as reações químicas que operam em cinturões de fold-andthrust. Os fluidos apresentam composição formada por H2O-NaCl-CaCl2, onde o processo de mistura de diferentes fontes de fluidos (metamórficas e meteóricas) é evidenciado pela tendência evolutiva de temperaturas de homogeneização e salinidades, resultando em alguma variação na salinidade (12 contra 4% em peso equivalente de NaCl para os veios subhorizontais e para os paralelos à clivagem, respectivamente). Este trabalho confirma que a combinação entre a reconstrução do paleoestresse e o estudo de inclusões fluidas podem fornecer informações fundamentais sobre a relação entre o fluxo de fluidos e a tectônica de terrenos orogênicos, contribuindo para o conhecimento científico sobre a evolução deformacional/metamórfica do Grupo Bambuí e, consequentemente, da zona de fold-andthrust da margem ocidental do Cráton do São Francisco. / P-T conditions existing at the tectonic event that acted at the fold-and-thrust zone of the western margin of the São Francisco Craton were estimated on the basis of structural, microstructural, petrographic and fluid inclusion study of syntectonic veins. The presence of veins of different generations in the fold-and-thrust zone is evidenced by fluids operating at different scenarios of paleostress throughout the deformation history. The area are composed of weakly deformed rocks of the Bambuí Group recording a metamorphism with conditions ranging from diagenetic to sub-greenschist facies. Two tectonic events were identified by vein geometric arrangement and folded surface, a major early NE-SW compression (D1 - \'sigma\'1 subhorizontal SW-trending and \'sigma\'3 subvertical), related with subhorizontal NW-trending syntectonic veins formed at conditions that have reached at least 140°C and pressures around 200-363 MPa; and later NW-SE compression (D2 - \'sigma\'1 subhorizontal NW-trending and \'sigma\'3 subhorizontal NE-trending), related with subvertical syntectonic cleavage-parallel veins formed at the same range of temperature and pressures between 181-295 MPa. Indication of fluctuations in pressure during these events played a crucial role as fluids significantly influence the mechanical processes, deformation mechanisms and chemical reactions that operate in fold-thrust belts. Fluids show H2O-NaCl-CaCl2 composition where mixing process of different fluids sources (metamorphic and meteoric) are evidenced by evolutive trending of homogenization temperatures and salinities resulting in some variation in salinity (12 against 4 wt.% NaCl eq. for subhorizontal and cleavage-parallel veins respectively). This research confirms that combine the reconstruction of the paleostress states and fluid inclusion studies can provide fundamental information of relationship between fluid flow and tectonic of orogenic terrains contributing to the scientific knowledge about the deformational/metamorphic evolution of the Bambuí Group and the fold-and-thrust zone of the western margin of the São Francisco Craton.