The objective of this dissertation is to understand the structural and optoelectronic properties of group III-nitride materials grown by High-Pressure Metal Organic Chemical Vapor Deposition (HP-MOCVD) and Migration Enhanced Plasma Assisted MOCVD by FTIR reflectance spectroscopy, Raman spectroscopy, X-ray diffraction, and Atomic Force Microscopy. The influence of the substrates/templates (Sapphire, AlN, Ga-polar GaN, N-polar GaN, n-GaN, and p-GaN) on the free carrier concentration, carrier mobility, short-range crystalline ordering, and surface morphology of the InN layers grown on HP-MOCVD were investigated using those techniques. The lowest carrier concentration of 7.1×1018 cm-3 with mobility of 660 cm2V-1s-1 was found in the InN film on AlN template, by FTIR reflectance spectra analysis. Furthermore, in addition to the bulk layer, an intermediate InN layers with different optoelectronic properties were identified in these samples. The best local crystalline order was observed in the InN/AlN/Sapphire by the Raman E2 high analysis. The smoothest InN surface was observed on the InN film on p-GaN template. The influence of reactor pressures (2.5–18.5 bar) on the long-range crystalline order, in plane structural quality, local crystalline order, free carrier concentration, and carrier mobility of the InN epilayers deposited on GaN/sapphire by HP-MOCVD has also been studied using those methods. Within the studied process parameter space, the best material properties were achieved at a reactor pressure of 12.5 bar and a group-V/III ratio of 2500 with a free carrier concentration of 1.5x1018 cm-3, a mobility in the bulk InN layer of 270 cm2 V-1s-1 and the Raman (E2 high) FWHM of 10.3 cm-1. The crystalline properties, probed by XRD 2θ–ω scans have shown an improvement with the increasing reactor pressure. The effect of an AlN buffer layer on the free carrier concentration, carrier mobility, local crystalline order, and surface morphology of InN layers grown by Migration-Enhanced Plasma Assisted MOCVD were also investigated. Here, the AlN nucleation layer was varied to assess the physical properties of the InN layers. This study was focused on optimization of the AlN nucleation layer (e.g. temporal precursor exposure, nitrogen plasma exposure, and plasma power) and its effect on the InN layer properties.

O Brasil é um país expressivo na produção de alimentos, assim para melhorar a eficiência da agricultura se faz necessário seu planejamento. O solo é a base para a agricultura sendo relevante nas questões de segurança alimentar e qualidade ambiental. Dados obtidos por sensoriamento remoto podem auxiliar no levantamento, mapeamento e manejo do solo, que são estratégicos para uma agricultura planejada. As técnicas de espectroscopia de refletância são mais rápidas, menos onerosas e menos poluentes quando comparado aos métodos tradicionais de análise de solos. Um banco de dados com informações de espectros de solo é denominado Biblioteca Espectral (BE). Por meio de uma BE é possível caracterizar classes de solo e estimar atributos. As BEs além de contribuir para o levantamento, mapeamento, manejo de solos e ainda pode auxiliar na agricultura de precisão, modelagem de atributos do solo, monitoramento de solos contaminados, comunicação entre pedólogos e conservação dos solos. Existem Bibliotecas Espectrais de Solos (BES) a nível mundial com amostras de continentes, tais como a Austrália, Europa, Ásia, África e Américas, porém poucas amostras Brasileiras representativas. Sendo assim, o objetivo deste trabalho é elaborar uma primeira versão da BE de solos do Brasil (BESB), caracterizar os espectros das classes de solos e quantificar atributos do solo (argila e areia). O banco recebeu amostras de 17 colaboradores e instituições de diversos estados brasileiros, que incluem: Rio Grande do Sul, Santa Catarina, São Paulo, Minas Gerais, Rio de Janeiro, Mato Grosso do Sul, Mato Grosso, Goiás, Maranhão, Pernambuco, Rio Grande do Norte, Ceará, Paraíba, Pará, Roraima, Amazonas e Distrito Federal. No total 19.537 curvas espectrais de solo provenientes de tradagens e perfis foram caracterizados, essas amostras são de várias classes de solos do Brasil. Perfis de solo e seus horizontes representativos tiveram seus espectros caracterizados em curvas multi-espectrais em profundidade. Foi gerado um modelo de quantificação dos atributos baseado na regressão dos mínimos quadrados parciais (PLSR). Os resultados obtidos para os modelos de quantificação foram utilizados para calibração da fração argila (calibração R2 = 0,82; RMSE = 46,75 g/kg, validaçãp R2 = 0,83 ; RMSE = 46,75 g/kg; RPD = 4,57) e areia (calibração R2 = 0,81; RMSE = 60,9 g/kg, validação R2 = 0,79, RMSE = 60,85 g/kg; RPD = 4,16). Foi possível distinguir diferentes classes de solos através da Análise dos Componentes Principais (ACP), como Organossolos, Latossolos, Argissolos e Nitossolos. A elaboração da BESB permite estabelecer padrões espectrais dos solos e auxilia nos avanços das técnicas de quantificação de atributos. / Brazil is a significant country in food production and to improve efficiency of agriculture is necessary to be planned. Soil is the basis for agriculture, which is relevant for food safety and environmental issues. Mapping and soil management are strategies for planned agriculture and can be assisted by remote sensing. Spectroscopy techniques are faster, less honorable and less polluting when compared to traditional methods. Soils Spectral Library (SSL) composes a diverse and varied database with soil spectra information. Through SSL soil types can be characterize and soil attributes estimated. SSL besides contribute to the soil survey, mapping and soil management it can support precision agriculture, soil attribute modeling, soil contaminated monitoring, communication between the soil scientists and soil conservation. There are SSL worldwide with soil samples from continents, such as Australia, Europe, Asia, Africa and the Americas, but there are few Brazilian samples representative. Thus, the objectives of this study were first to create a Brazilian Soil Spectral Library (BSSB), second to characterize soil spectra of BESB soil classes and finally to quantify soil properties (clay and sand). The BSSL bank received samples from 17 collaborators and institutions from various Brazilian states, including Rio Grande do Sul, Santa Catarina, São Paulo, Minas Gerais, Rio de Janeiro, Mato Grosso do Sul, Mato Grosso, Goiás, Maranhão, Pernambuco, Rio Grande do Norte, Ceará, Paraíba, Pará, Roraima, Amazonas and Distrito Federal. The Spectral Library has 19,537 soil samples from auger and profiles. Spectra of several Brazilian soil classes were characterized. Soil profiles and their horizons had their representative spectra characterized with multi-depth analysis. Quantification model of soil attributes was based on partial least squares regression (PLSR). Prediction models were obtained to quantify clay (calibration R2 = 0,82; RMSE = 46,75 g/kg, validaçãp R2 = 0,83 ; RMSE = 46,75 g/kg; RPD = 4,57) and sand (calibration R2 = 0,81; RMSE = 60,9 g/kg, validação R2 = 0,79, RMSE = 60,85 g/kg; RPD = 4,16). In addition, we distinguish different soil classes by Principal Component Analysis (PCA). Organossolos, Latossolos, Argissolos and Nitossolos were well separated. BESB assembly assisted to establish spectral patterns of land and it could improve advancing attributes techniques measurement.

Catheter ablation therapy attempts to restore sinus rhythm in arrhythmia patients by producing site-specific tissue modification along regions which cause abnormal electrical activity. This treatment, though widely used, often requires repeat procedures to observe long-term therapeutic benefits. This limitation is driven in part by challenges faced by conventional schemes in validating lesion adequacy at the time of the procedure. Optical techniques are well-suited for the interrogation and characterization of biological tissues. In particular, optical coherence tomography (OCT) relies on coherence gating of singly-scattered light to enable high-resolution structural imaging for tissue diagnostics and procedural guidance. Alternatively, optical reflectance spectroscopy (ORS) is a point measurement technique which makes use of incoherent, multiply-scattered light to probe tissue volumes and derive important data from its optical signature. ORS relies on the fact that light-tissue interactions are regulated by absorption and scattering, which directly relate to the intrinsic tissue biochemistry and cellular organization. In this thesis, we explore the integration of these modalities into ablation catheters for obtaining procedural metrics which could be utilized to guide catheter ablation therapy. We first present the development of an accelerated computational light transport model and its application for guiding ORS catheter design. A custom ORS-integrated ablation catheter is then implemented and tested within porcine specimens in vitro. A model is proposed for real-time estimation of lesion size based on changes in spectral morphology acquired during ablation. We then fabricated custom integrated OCT M-mode RF catheters and present a model for detecting contact status based on deep convolutional neural networks trained on endomyocardial images. Additionally, we demonstrate for the first time, tracking of RF-induced lesion formation employing OCT Doppler micro-velocimetry; this response is shown to be commensurate with the degree of treatment. We further demonstrate for the first time spectroscopic tracking of kinetics related to the heme oxidation cascade during thermal treatment, which are linked to tissue denaturation. The pairing of these modalities into a single RF catheter was also validated for guiding lesion delivery in vitro and within live pigs. Finally, we conclude with a proof-of-concept demonstration of ORS as a mapping tool to guide epicardial ablation in human donor hearts. These results showcase the vast potential of ORS and OCT empowered RF catheters for aiding intraprocedural guidance of catheter ablation procedures which could be utilized alongside current practices.

O Brasil é um país expressivo na produção de alimentos, assim para melhorar a eficiência da agricultura se faz necessário seu planejamento. O solo é a base para a agricultura sendo relevante nas questões de segurança alimentar e qualidade ambiental. Dados obtidos por sensoriamento remoto podem auxiliar no levantamento, mapeamento e manejo do solo, que são estratégicos para uma agricultura planejada. As técnicas de espectroscopia de refletância são mais rápidas, menos onerosas e menos poluentes quando comparado aos métodos tradicionais de análise de solos. Um banco de dados com informações de espectros de solo é denominado Biblioteca Espectral (BE). Por meio de uma BE é possível caracterizar classes de solo e estimar atributos. As BEs além de contribuir para o levantamento, mapeamento, manejo de solos e ainda pode auxiliar na agricultura de precisão, modelagem de atributos do solo, monitoramento de solos contaminados, comunicação entre pedólogos e conservação dos solos. Existem Bibliotecas Espectrais de Solos (BES) a nível mundial com amostras de continentes, tais como a Austrália, Europa, Ásia, África e Américas, porém poucas amostras Brasileiras representativas. Sendo assim, o objetivo deste trabalho é elaborar uma primeira versão da BE de solos do Brasil (BESB), caracterizar os espectros das classes de solos e quantificar atributos do solo (argila e areia). O banco recebeu amostras de 17 colaboradores e instituições de diversos estados brasileiros, que incluem: Rio Grande do Sul, Santa Catarina, São Paulo, Minas Gerais, Rio de Janeiro, Mato Grosso do Sul, Mato Grosso, Goiás, Maranhão, Pernambuco, Rio Grande do Norte, Ceará, Paraíba, Pará, Roraima, Amazonas e Distrito Federal. No total 19.537 curvas espectrais de solo provenientes de tradagens e perfis foram caracterizados, essas amostras são de várias classes de solos do Brasil. Perfis de solo e seus horizontes representativos tiveram seus espectros caracterizados em curvas multi-espectrais em profundidade. Foi gerado um modelo de quantificação dos atributos baseado na regressão dos mínimos quadrados parciais (PLSR). Os resultados obtidos para os modelos de quantificação foram utilizados para calibração da fração argila (calibração R2 = 0,82; RMSE = 46,75 g/kg, validaçãp R2 = 0,83 ; RMSE = 46,75 g/kg; RPD = 4,57) e areia (calibração R2 = 0,81; RMSE = 60,9 g/kg, validação R2 = 0,79, RMSE = 60,85 g/kg; RPD = 4,16). Foi possível distinguir diferentes classes de solos através da Análise dos Componentes Principais (ACP), como Organossolos, Latossolos, Argissolos e Nitossolos. A elaboração da BESB permite estabelecer padrões espectrais dos solos e auxilia nos avanços das técnicas de quantificação de atributos. / Brazil is a significant country in food production and to improve efficiency of agriculture is necessary to be planned. Soil is the basis for agriculture, which is relevant for food safety and environmental issues. Mapping and soil management are strategies for planned agriculture and can be assisted by remote sensing. Spectroscopy techniques are faster, less honorable and less polluting when compared to traditional methods. Soils Spectral Library (SSL) composes a diverse and varied database with soil spectra information. Through SSL soil types can be characterize and soil attributes estimated. SSL besides contribute to the soil survey, mapping and soil management it can support precision agriculture, soil attribute modeling, soil contaminated monitoring, communication between the soil scientists and soil conservation. There are SSL worldwide with soil samples from continents, such as Australia, Europe, Asia, Africa and the Americas, but there are few Brazilian samples representative. Thus, the objectives of this study were first to create a Brazilian Soil Spectral Library (BSSB), second to characterize soil spectra of BESB soil classes and finally to quantify soil properties (clay and sand). The BSSL bank received samples from 17 collaborators and institutions from various Brazilian states, including Rio Grande do Sul, Santa Catarina, São Paulo, Minas Gerais, Rio de Janeiro, Mato Grosso do Sul, Mato Grosso, Goiás, Maranhão, Pernambuco, Rio Grande do Norte, Ceará, Paraíba, Pará, Roraima, Amazonas and Distrito Federal. The Spectral Library has 19,537 soil samples from auger and profiles. Spectra of several Brazilian soil classes were characterized. Soil profiles and their horizons had their representative spectra characterized with multi-depth analysis. Quantification model of soil attributes was based on partial least squares regression (PLSR). Prediction models were obtained to quantify clay (calibration R2 = 0,82; RMSE = 46,75 g/kg, validaçãp R2 = 0,83 ; RMSE = 46,75 g/kg; RPD = 4,57) and sand (calibration R2 = 0,81; RMSE = 60,9 g/kg, validação R2 = 0,79, RMSE = 60,85 g/kg; RPD = 4,16). In addition, we distinguish different soil classes by Principal Component Analysis (PCA). Organossolos, Latossolos, Argissolos and Nitossolos were well separated. BESB assembly assisted to establish spectral patterns of land and it could improve advancing attributes techniques measurement.

<p>Breast conserving surgery (BCS) is a common treatment option for breast cancer patients. The goal of BCS is to remove the entire tumor from the breast while preserving as much normal tissue as possible for a better cosmetic outcome after surgery. Specifically, the excised specimen must have at least 2 mm of normal tissue surrounding the diseased mass. Unfortunately, a staggering 20-70% of patients undergoing BCS require repeated surgeries due to the incomplete removal of the tumor diagnosed post-operatively. Due to these high re-excision rates as well as limited post-operative histopathological sampling of the tumor specimen, there is an unmet clinical need for margin assessment. Quantitative diffuse reflectance spectral imaging has previously been explored as a promising, method for providing real-time visual maps of tissue composition to help surgeons determine breast tumor margins to ensure the complete removal of the disease during breast conserving surgery. We have leveraged the underlying sources of contrast in breast tissue, specifically total hemoglobin content, beta-carotene content, and tissue scattering, and developed various fiber optics based spectral imaging systems for this clinical application. Combined with a fast inverse Monte Carlo model of reflectance, previous studies have shown that this technology may be able to decrease re-excision rates for BCS. However, these systems, which all consist of a broadband source, fiber optics probes, an imaging spectrograph and a CCD, have severe limitations in system footprint, tumor area coverage, and speed for acquisition and analysis. The fiber based spectral imaging systems are not scalable to smaller designs that cover a large surveillance area at a very fast speed, which ultimately makes them impractical for use in the clinical environment. The objective of this dissertation was to design, develop, test, and show clinical feasibility of a novel wide field spectral imaging system that utilizes the same scientific principles of previously developed fiber optics based imaging systems, but improves upon the technical issues, such as size, complexity, and speed,to meet the demands of the intra-operative setting. </p><p>First, our simple re-design of the system completely eliminated the need for an imaging spectrograph and CCD by replacing them with an array of custom annular photodiodes. The geometry of the photodiodes were designed with the goal of minimizing optical crosstalk, maximizing SNR, and achieving the appropriate tissue sensing depth of up to 2 mm for tumor margin assessment. Without the imaging spectrograph and CCD, the system requires discrete wavelengths of light to launch into the tissue sample. A wavelength selection method that combines an inverse Monte Carlo model and a genetic algorithm was developed in order to optimize the wavelength choices specifically for the underlying breast tissue optical contrast. The final system design consisted of a broadband source with an 8-slot filter wheel containing the optimized set of wavelength choices, an optical light guide and quartz light delivery tube to send the 8 wavelengths of light in free space through the back apertures of each annular photodiode in the imaging array, an 8-channel integrating transimpedance amplifier circuit with a switch box and data acquisition card to collect the reflectance signal, and a laptop computer that controls all the components and analyzes the data.</p><p>This newly designed wide field spectral imaging system was tested in tissue-mimicking liquid phantoms and achieved comparable performance to previous clinically-validated fiber optics based systems in its ability to extract optical properties with high accuracy. The system was also tested in various biological samples, including a murine tumor model, porcine tissue, and human breast tissue, for the direct comparison with its fiber optics based counterparts. The photodiode based imaging system achieved comparable or better SNR, comparable extractions of optical properties extractions for all tissue types, and feasible improvements in speed and coverage for future iterations. We show proof of concept in performing fast, wide field spectral imaging with a simple, inexpensive design. With a reduction in size, cost, number of wavelengths used, and overall complexity, the system described by this dissertation allows for a more seamless scaling to higher pixel number and density in future iterations of the technology, which will help make this a clinically translatable tool for breast tumor margin assessment.</p> / Dissertation

Mid-infrared (MIR) spectroscopy has been recognized as an important analytical technique, and is widely applied for qualitative and quantitative analysis of materials with an increasing interest in addressing complex organic or biologic constituents. In the presented thesis, (a) the fundamental principles for IR spectroscopic applications via in vivo catheters in combination with multivariate data analysis technique were developed, and (b) the combination with a second analytical technique ¨C scanning electrochemical microscopy (SECM) - for enhancing the information obtained at complex or frequently changing matrices was demonstrated. The first part of this thesis focused on the combination of different MIR measurment techniques with specific focus on evanescent field absorption spectroscopy along with multivariate data analysis methods, for the discrimination of atherosclerotic and normal rabbit aorta tissues. Atherosclerotic and normal rabbit aorta tissues are characterized by marked differences in chemical composition governed by their water, lipid, and protein content. Strongly overlapping infrared absorption features of the different constituents and the complexity of the tissue matrix render the direct evaluation of molecular spectroscopic characteristics obtained from IR measurements challenging for classification. We have successfully applied multivariate data analysis and classification techniques based on principal component analysis (PCA), partial least squares regression (PLS), and linear discriminant analysis (LDA) to IR spectroscopic data obtained by infrared attenuated total reflectance (IR-ATR) measurements, reflection IR microscopy, and a recently developed IR-ATR catheter prototype for future in vivo diagnostic applications. Training and test data were collected ex vivo at atherosclerotic and normal rabbit aorta samples. The successful classification results at atherosclerotic and normal aorta samples utilizing the developed data evaluation routines reveals the potential of IR spectroscopy combined with multivariate classification strategies for in vitro, and ¨C in future - in vivo applications. The second part of this thesis aimed at the development of a novel multifunctional analytical platform by combining SECM with single-bounce IR-ATR spectroscopy for in situ studies of electrochemically active or electrochemically induced processes at the IR waveguide surface via simultaneous evanescent field absorption spectroscopy. The utility of the developed SECM-IR-ATR platform was demonstrated by spectroscopically monitoring microstructured polymer depositions induced via feedback mode SECM experiments using a 25μm Pt disk ultramicroelectrode (UME). The surface of a ZnSe ATR crystal was coated with a thin layer of 2,5-di-(2-thienyl)-pyrrole (SNS), which was then polymerized in a Ru(bpy) ₃ ² ⁺-mediated feedback mode SECM experiment. The polymerization reaction was simultaneously spectroscopically monitored by recording the absorption intensity changes of specific IR bands characteristic for SNS, thereby providing information on the polymerization progress, mechanism, and level of surface modification. Furthermore, a novel current-independent approach mechanism for positioning the UME in aqueous electrolyte solution was demonstrated by monitoring IR absorption changes of borosilicate glass (BSG) shielding the UME, and of water within the penetration depth of the evanescent field.

No description available.

Brassica napus is grown as an edible oil (canola) and an industrial oil (HEAR). Its fatty acid profile and chlorophyll concentration affect the quality. It is important to develop accurate and efficient methods to evaluate these traits. The first objective of this study was to improve the single nucleotide polymorphism (SNP) and sequence characterized amplified region (SCAR) molecular markers for erucic acid genotypes in the Bn-FAE1.1 and Bn-FAE1.2 genes in the A and C genomes in Brassica napus originally developed by Rahman et al. (2008). When put into practice, the error rate was unacceptably high. With the modifications that were made to the protocols, the overall accuracy remained relatively consistent indicating that further improvements are still required. The second objective was to develop a near infrared reflectance (NIR) based calibration equation for chlorophyll concentration in whole Brassica napus seeds. In this case, an equation was successfully created.

Brassica napus is grown as an edible oil (canola) and an industrial oil (HEAR). Its fatty acid profile and chlorophyll concentration affect the quality. It is important to develop accurate and efficient methods to evaluate these traits. The first objective of this study was to improve the single nucleotide polymorphism (SNP) and sequence characterized amplified region (SCAR) molecular markers for erucic acid genotypes in the Bn-FAE1.1 and Bn-FAE1.2 genes in the A and C genomes in Brassica napus originally developed by Rahman et al. (2008). When put into practice, the error rate was unacceptably high. With the modifications that were made to the protocols, the overall accuracy remained relatively consistent indicating that further improvements are still required. The second objective was to develop a near infrared reflectance (NIR) based calibration equation for chlorophyll concentration in whole Brassica napus seeds. In this case, an equation was successfully created.

Thesis (Ph.D.)--McMaster University (Canada), 1995. / Source: Dissertation Abstracts International, Volume: 57-03, Section: B, page: 1867. Adviser: T. Timusk.