published_or_final_version / abstract / Physics / Doctoral / Doctor of Philosophy

A multi-modality imaging system intended for clinical utilization has been developed. It is constructed around an existing fiber-bundle-based fluorescence confocal microendoscope. Additional imaging modalities have been implemented to expand the capabilities of the system and improve the accuracy of disease diagnosis. A multi-spectral mode of operation is one such modality. It acquires fluorescence images of a biological sample across a spectral range of sensitivity and explores the collected image data at any specified wavelength within that spectral range. Cellular structures can be differentiated according to their spectral properties. The relative distribution and concentration of the different cellular structures can potentially provide useful pathologic information about the imaged tissue. A spectral-domain optical coherence tomography (SDOCT) modality is another imaging technique integrated into the system. It provides a cross-sectional imaging perspective that is comparable to microscopic images obtained from histology slides and complementary to the en face view obtained from the confocal imaging modality. The imaging system uses a parallelized architecture (fiber-optic bundle, line of illumination) to increase the data acquisition speed. A one-dimensional scan is needed to capture 2D images in the confocal modality or a 3D data cube (two spatial dimensions and one spectral dimension) in the multi-spectral mode of operation. No scanning is required to capture a 2D OCT image. The fiber-bundle design is particularly critical for the SDOCT modality as it paves the way to novel fast endoscopic OCT imaging that has a high potential for translation into the clinic. The integrated multi-modality imaging system can readily switch between different imaging modalities, which will make it a powerful diagnostic tool in a clinical environment. It can provide valuable information about the morphology, the spectral and biochemical features, and the macroscopic architecture of tissue. It is believed that fast and accurate disease diagnosis can potentially be made based on all these characteristics.

This dissertation merges the optical design and computational aspects of imaging systems to create novel devices that solve engineering problems in optical science and attempts to expand the solution space available to the optical designer. This dissertation is divided into two parts: the first discusses a new active illumination depth sensing modality, while the second part discusses a passive illumination system called plenoptic, or lightfield, imaging. The new depth sensing modality introduced in part one is called depth through controlled aberration. This technique illuminates a target with a known, aberrated projected pattern and takes an image using a traditional, unmodified imaging system. Knowing how the added aberration in the projected pattern changes as a function of depth, we are able to quantitatively determine depth of a series of points from the camera. A major advantage this method permits is the ability for illumination and imaging axes to be coincident. Plenoptic cameras capture both spatial and angular data simultaneously. This dissertation present a new set of parameters that permit the design and comparison of plenoptic devices outside the traditionally published plenoptic 1.0 and plenoptic 2.0 configurations. Additionally, a series of engineering advancements are presented, including full system ray traces of raw plenoptic images, Zernike compression techniques of raw image files, and non-uniform lenslet arrays to compensate for plenoptic system aberrations. Finally, a new snapshot imaging spectrometer is proposed based off the plenoptic configuration.

Analysis and characterisation of biomolecules using mass spectrometry has advanced over the past decade due to improvements in instrument design and capability; relevant use of complementary techniques; and available experimental and in silico data for comparison with cutting-edge research. This thesis presents ion mobility data, collected on an in-house modified QToF mass spectrometer (the MoQTOF), for a number of protein systems. Two haemoproteins, cytochrome c and haemoglobin, have been characterised and rotationally-averaged collision cross-sections for a number of multimeric species are presented. Intact multiply-charged multimers of the form [xCyt c + nH]z+ where x = 1 (monomer), x = 2 (dimer) and x = 3 (trimer) for cytochrome c have been elucidated and for species with x ≥ 2, reported for the first time. Fragment ions possibly attributed to a novel fragmentation mechanism, native electron capture dissociation, are reported with a brief discussion into their possible production from the dissociation of the gas-phase dimer species. Haemoglobin monomer globin subunits, dimers and intact tetramer have been successfully transferred to the gas phase, and their cross-sections elucidated. Comparisons with in silico computational data have been made and a discussion of the biologically-active tetramer association/dissociation technique is presented. Three further proteins have been studied and their gas-phase collision cross-sections calculated. Two regions of the large Factor H (fH) complement glycoprotein, fH 10-15 and fH 19-20, have been characterised for the first time by ion mobility-mass spectrometry. Much work using nuclear magnetic resonance spectroscopy has previously been achieved to produce structural information of these protein regions, however further biophysical characterisation using mass spectrometry may aid in greater understanding of the interactions these two specific regions have with other biomolecules. The DNA-binding core domain of the tumour suppressor p53 has been characterised and cross-sections produced in the presence and absence of the zinc metal ion that may control the domain’s biological activity. Within this core domain, p53 inactivation mutations have been shown to occur in up to 50% of human cancers, therefore the potential exists to further cancer-fighting activity through research on this region. Anterior Gradient-2 (AGR2) protein facilitates downregulation of p53 in an as yet unclear mechanism. Recent work using peptide aptamers has demonstrated that this downregulation can be disrupted and levels of p53 restored. Collision cross-sections for six peptide aptamers have been calculated, as well as cross-sections for multimers of AGR2 protein. A complex between one aptamer with the protein has also been elucidated. Use of the commercially available Synapt HDMS ion mobility-mass spectrometer at Waters MS Technologies Centre (Manchester, UK) allowed data to be collected for both Factor H protein regions and for the DNA-binding core domain of p53. Data are compared in the appropriate chapters with data collected using the MoQTOF.

The MIRI-MRS is a future space based Medium Resolution Spectrometer and one of four instruments to be integrated onto The James Webb Space Telescope. The Medium Resolution Spectrometer is designed to be diffraction limited across its entire passband of 5 - 28.3 microns. It achieves this through the spectral filtering of the passband into four channels with each one containing an integral field unit optimised for minimal diffraction losses. The integral field unit enables the simultaneous measurement of the spectral data across the entire field of view. The design of the Medium Resolution Spectrometer is outlined with particular reference to the choice of slice widths used for each channel to minimise the diffraction losses from the slicing mechanism. The slice widths are also used to derive the extent of the field of view and combined with the along slice plate scale at the detector the technique required for complete spatial sampling of the spectrometer is outlined. The operation of the Channel 1 image slicer component was tested cryogenically at 5 microns for diffraction losses due to the slicing of the point spread function. This was so that the actual diffraction losses could be measured and compared with the optical model. From the resulting analysis I concluded that the operation of the image slicers were well understood for diffraction losses. Performance tests were required on the instrument because of its novel design. This was the first implementation of an integral field unit operating between 5 - 28.3 microns and it was necessary to ensure that the operation of the image slicer did not induce unacceptable diffraction losses into the instrument. Tests were required on the assembled instrument to verify the optical design. A Verification Model of MIRI was built to enable test verification of the optical design. This testing was carried out in advance of the MIRI Flight Model assembly so that changes could be made to the Flight Model design if necessary. This testing phase was also designed to define the calibration process necessary to prepare the MIRI Flight Model for scientific operations. For the testing phase it was necessary to create an astronomical source simulator. This MIRI Telescope Simulator was constructed in Madrid where I spent two months ensuring the point source movement across the field of view would be sufficient to investigate the Medium Resolution Spectrometer. My contribution was to help assemble both the Verification and Flight Models. I also participated in the Verification Model testing phase from the test design phase to the test implementation and data analysis. My role in the analysis was to investigate the field of view of the Medium Resolution Spectrometer Verification Model and whether the field of view requirements for the spectrometer were met. During this analysis I also verified that the diffraction effects of the end-to-end instrument were well understood by the optical model. The Medium Resolution Spectrometer Verification Model field of view compromised the field of view requirement for the spectrometer. A similar analysis for the Flight Model showed that there would be a low probability that the field of view requirement would be met. As a result of the analysis I defined a new slit mask design that would align the field of view sampled by Channel 1 to increase the aligned field of view. As a result there is a high probability that the field of view requirement for the Flight Model will be exceeded. The test analysis discovered a magnification effect within the spectrometer which must be properly characterised to enable accurate field of view reconstruction. I designed a test necessary for the calibration phase of the Flight Model to enable full spatial alignment of the Medium Resolution Spectrometer. I also measured an excess flux level in the Channel 1 observations at the detector and there was a ghost detected in the Channel 1 images. Whilst the origin of either the excess flux or the ghost could not be completely determined I investigated the possibility that they will not be present in the Flight Model due to the slight design differences. If present however they will not increase the background level of an observation above the requirement outlined for Channel 1.

Although the nucleon acid oscillatory spectra have been studied for a long period of time, many of oscillating modes have not been properly explained regarding their geometric sensitivity and weak binding. One of the possibilities how to acquire experimental data for interpretation of theese modes is to confront oscillating spectra of isotopes. The simplest is proton - deutron exchange. When molecules dissolve in heavy water they rapidly exchange the heteroatoms, but this is simultaneous for more stages, which leads to dynamic equilibrium state among various isotope forms. Statistic analysis of temporal progression of Raman spectra give us the possibility to analyze the spectra and to obtain unique experimental data. This technique is very promising for more complex nucleon acid segments to gain more structural information. This diploma thesis represents pilot study of introduced methodics. The objective is to implement adaptation of Raman spectrometr for given types of expiments and undertake first series of measurements. The results should clarify application bounds of proposed method refering to sensitivity, time constant of incident isotope exchange, severity of read-out in comparasion of achieved accuracy of the measurement.

Ce travail porte sur la caractérisation de matériaux en couches minces par spectroscopie terahertz dépendant du temps. Dans ce but, nous avons élaboré un banc d’analyse spectroscopique dont l’émission et la détection terahertz reposent sur l’utilisation de laser femtoseconde, de semi-conducteurs, de photocommutateurs ultrarapides ou de cristaux électro-optiques. La réponse diélectrique quantitative de matériaux ferroélectriques (titanate de baryum/ - Ba1-xSrxTiO3) déposés sous forme de couches minces, a permis de mettre en évidence l’importance des modes mous de phonon par une étude en température. Enfin, le comportement électromagnétique de polymères conducteurs à base de polyaniline a été effectué notamment leur efficacité de blindage en bande millimétrique et submillimétrique. / This work concerns the characterization of thin film materials by terahertz time domain spectroscopy. For this purpose, we elaborated a terahertz setup in which the terahertz emission and terahertz detection are based on the use of femtosecond laser, semiconductors, ultrafast photoswitches or electro-optic crystals. The study of dielectric function of ferroelectrics thin film (barium titanate/-Ba1-xSrxTiO3) with temperature, give the importance of soft phonon mode. Finally, the electromagnetic behavior of conducting polymers based on polyaniline was made, in particular their shelding effectiveness in millimeter and sub-millimeter length.

A presença de nove ésteres (acetato de etila, butanoato de etila, hexanoato de etila, lactato de etila, octanoato de etila, nonanoato de etila, decanoato de etila, octanoato de isoamila e dodecanoato de etila) foi investigada por cromatografia gasosa hifenada à espectrometria de massas via injeção direta de amostras (ID-CG-EM). Cento e trinta e seis amostras de aguardente de cana foram coletadas durante sua destilação em diferentes produtores em diferentes cidades localizadas no interior do estado de São Paulo. Também foram analisadas 21 amostras de cachaça comercial, 10 amostras de rum e 10 amostras de uísque importados e obtidos em lojas \"duty free shop\". A metodologia analítica desenvolvida para análise de ésteres demonstrou-se apropriada para a determinação destes compostos em bebidas destiladas, sendo simples (injeção direta), seletiva e relativamente rápida. Apresentou baixos limites de detecção e quantificação e boa repetibilidade. O acetato de etila é o principal éster presente nas bebidas destiladas seguido pelo lactato de etila. Em todas as amostras de bebidas destiladas analisadas neste trabalho foi detectada a presença do éster lactato etila. A presença deste éster está relacionada com a contaminação do mosto por bactérias (Lactobacillus spp) responsáveis pela fermentação láctica. A concentração de lactato de etila nas amostras de cachaça e rum é muito superior à encontrada nas amostras de uísque. A análise multivariada dos resultados analíticos aplicada ao banco de dados dos ésteres juntamente com as concentrações de carbamato de etila e benzaldeído levaram à formação de dois grupos bem distintos: amostras destiladas em alambiques de cobre e amostras destiladas em colunas de aço inox. Os modelos estatísticos gerados pelas análises exploratórias de PCA, PLS e LDA utilizando o carbamato de etila, benzaldeído, decanoato de etila e o dodecanoato de etila como discriminantes revelaram ser possíveis a diferenciação entre estes dois grupos de destilados com uma porcentagem de acerto de 81% para PCA, 78,4 % para a PLS e 97,6% para LDA. Os métodos cromatográficos sugeridos pelo Ministério da Agricultura, Pecuária e Abastecimento (MAPA) para a determinação de ésteres não englobam o monitoramento do lactato de etila, subestimando o resultado final. / The presence of nine esters (ethyl acetate, ethyl butanoate, ethyl hexanoate, ethyl lactate, ethyl octanoate, ethyl nonanoate, ethyl decanoate, isoamyl octanoate, and ethyl dodecanoate) was investigated by gas chromatography hyphenated to a mass spectrometry through sample direct inject (DI-GC-MS). One hundred and thirty six sugar cane spirits collected immediately after its distillation from different producers and different cities located in the countryside of São Paulo state. Also, it was analyzed 21 commercial samples of cachaça, 10 samples of rum and 10 samples of whiskey imported and purchased from the duty free shop. The analytical method applied to esters analysis was appropriated for the determination of these compounds in distilled spirits, since it is simple (direct inject), selective and reasonably fast. It presented low detection and quantification limits and good reproducibility. Ethyl acetate is the main ester present in the distilled spirits followed by ethyl lactate. Ethyl lactate was detected in all the distilled beverage samples analyzed herein. The occurrence of this ester is related to bacterial contamination of must (Lactobacillus spp) responsible for the lactic fermentation. The ethyl lactate content in cachaça and rum samples are superior that presented by whiskey samples. The multivariate analysis of the analytical results applied to the esters data set jointly with the content of ethyl carbamate and benzaldehyde lead to the clustering of two quite distinct groups: sugar cane spirits distilled in copper alembic and sugar cane spirits distilled in stainless steel column. The resulting statistical model generated by PCA, PLS and LDA exploratory analysis employing ethyl carbamate, benzaldehyde, ethyl decanoate, and ethyl dodecanoate as discriminators was able to distinguish between these two groups with a accuracy of 81 % for PCA, 78,4 % for PLS and 97,6 % for LDA. The chromatographic method recommended by the Ministério da Agricultura, Pecuária e Abastecimento (MAPA) for the esters determination does not include the monitoring of ethyl lactate leading to a underestimating of the final result.

O objetivo do presente trabalho é determinar a concentração de atividade de isótopos de ocorrência natural de urânio e tório e o polônio em perfis de sedimento marinho da Baixada Santista. A Baixada Santista é uma região populosa e abrange os municípios de Bertioga, Guarujá, Santos, São Vicente, Cubatão, Praia Grande, Mongaguá, Itanhaém e Peruíbe. Esta é uma das mais importantes regiões industriais do Brasil, dado ao grande número de indústrias, como as de fertilizantes, petroquímicas e do aço. A grande atividade industrial, juntamente com a grande população da região, exerce forte pressão sobre a biota marinha. O presente trabalho analisou 10 perfis de sedimentos marinhos extraídos da região. Foram coletados perfis com tamanhos variando de 41 a 98 cm, na região de Santos, Cubatão, São Vicente e Bertioga. Os perfis foram fatiados a cada 2 cm e passaram por um pré-tratamento físico e químico. Para a dissolução total e digestão foram utilizados ataques com ácidos fortes. As técnicas radioquímicas utilizadas para a separação dos radionuclídeos e preparação das fontes radioativas, para a contagem alfa, foram separação por cromatografia de troca iônica e eletrodeposição para urânio e tório e deposição espontânea para o polônio. Os resultados obtidos para as concentrações de atividade dos radionuclídeos são semelhantes aos de sedimentos marinhos em regiões não contaminadas, exceto em alguns pontos amostrados, nos quais foi possível identificar influência antrópica. / The objective of the present work is to determine the activity concentration of uranium and thorium isotopes and polonium in estuarine sediments from BaixadaSantista. The area comprehends nine cities in the Brazilian coast (Bertioga, Guarujá, Santos, São Vicente, Cubatão, Praia Grande, Mongaguá, Itanhaém and Peruíbe). It is one of the most important industrial areas in Brazil due to the large number of industries operating in Cubatão, such as steel, petrochemical and fertilizer industries. That, together with a large population, causes a negative impact on the marine biota. In the present work 10 profiles of sediment cores, with depth varying from 41 to 98 cm, were analyzed. The cores were obtained from Santos, Cubatão, São Vicente and Bertioga. The cores were sliced every 2 cm and were treated with both physical and chemical processes, including drying, grinding and sieving. The samples were dissolved by acid digestion, till total dissolution and destruction of organic matter. After the acid digestion, the samples were filtered and evaporated till dryness. The radiochemical techniques used to separate the radionuclides and to prepare the final source for alpha counting were ion exchange chromatography and spontaneous deposition for polonium and electrodeposition for U and Th. The final sources were counted in a surface barrier alpha spectrometer. Values obtained for the radionuclides analyzed were similar to the activity concentrations of sediments in non polluted areas, with the exception of a few samples that showed anthropic influence.

O foco central desse trabalho é a utilização e aprimoramento de um framework Peripheral Component Interconnect Express (PCI Express®) para a comunicação de dados em um Espectrômetro Digital de Ressonância Magnética (Digital Magnetic Resonance Spectrometer – DMRS) utilizando o conceito de Field-Programmable Gate Array (FPGA). Esse trabalho foi desenvolvido para servir como base de comunicação para o Espectrômetro Digital de Ressonância Magnética do Centro de Imagens e Espectroscopia in vivo por Ressonância Magnética (CIERMag) devido ao requerimento de altas taxas de transferência dos dados adquiridos. A integração dessa nova comunicação, entre o software e o hardware do espectrômetro, mantém compatibilidade com as interfaces já existentes possibilitando a execução de todas as sequências desenvolvidas sem nenhuma alteração. A incorporação da comunicação PCI Express provê uma solução com um número menor de etapas por transferência em comparação com a comunicação Ethernet. Com isso é possível aumentar o desempenho do sistema e obter taxas de transferência mais elevadas. Para isso, foram feitas mudanças no hardware de forma a torná-lo mais eficiente, reduzindo o número de ciclos de clock por operação e também a quantidade de lógica sintetizada. Além disso, a latência do software durante as transferências também foi reduzida através da utilização de interrupções Message Signaled Interrupt (MSI) e do método Scatter and Gather usado para reduzir a quantidade de cópias de dados na memória principal do computador. Dessa forma, obteve-se, como resultados reais, uma taxa de transferência efetiva (throughput) de 97% do valor máximo da banda possível do barramento PCI Express. / The central focus of this work is the implementation and use of a Peripheral Component Interconnect Express (PCI Express®) framework for data communication on a Digital Magnetic Resonance Spectrometer (DMRS) using the concept of Field-Programmable Gate Array (FPGA). This work is being developed to serve as a communication basis for the magnetic resonance Digital Spectrometer of the Centro de Imagens e Espectroscopia in vivo por Ressonância Magnética (CIERMag) due to demand of high transfer rates of acquired data. The integration of this new communication, between spectrometer software and hardware, keeps compatibility with existing interfaces, making it possible to execute all developed magnetic resonance sequences without any change. The incorporation of PCI Express communication provides solution with a lower number of steps per transfer when compared to Ethernet communication. By this means it\'s possible to increase system performance and, as result, have higher transfer rates. To accomplish that, the number of clock cycles per operation was reduced, so was the synthesized logic. Furthermore, software latency for data transfer was also reduced consequence of MSI interruption implementation and the use of Scatter and Gather method to remove data movement across the computer main memory. Therefore, it was obtained, as measured real result, a throughput value of 97% the theoretical maximum value for the hardware.