Para o aperfeiçoamento das técnicas existentes e para o desenvolvimento de novas técnicas de diagnóstico por ultrassom equipamentos dedicados à pesquisa são necessários. Esses equipamentos devem possibilitar controle total da forma de excitação dos elementos piezoelétricos e acesso aos dados recebidos na sua forma pré-processada. Apesar de existirem equipamentos com essa finalidade, alguns deles ainda são limitados em relação aos controles de emissão e acesso aos dados raw por permitirem acesso apenas após a realização de um beamforming de recepção, como a aplicação de soma e atraso e apodização. Outro fator relevante sobre as máquinas voltadas para a pesquisa é o seu alto custo. Nesse projeto foi proposto um sistema de ultrassom de 8 canais, open source voltado à pesquisa, permitindo assim que seja reduzido o custo relacionado a propriedade intelectual do equipamento, e que permita controle completo dos parâmetros de emissão e recepção das ondas acústicas. Esse sistema de ultrassom foi construído utilizando kits de desenvolvimento comerciais. Os resultados adquiridos mostram que foram alcançadas variações de frequência de emissão de 1,79 MHz a 50 MHz, controles dos atrasos de emissão para controle de focalização dinâmica com resolução de 10 ns, controle de codificação do pulso, amplitude de excitação entre 10 e 140 V e acesso aos mapas RF na forma pré-processada, amostrados à uma frequência de 40 MHz. Os mapas de pressão acústica máxima foram adquiridos para diferentes profundidades de foco utilizando um hidrofone agulha e as imagens obtidas foram similares às simuladas anteriormente no software K-Wave. A etapa de recepção permitiu o acesso aos dados pré-beamforming de recepção, possibilitando o uso em técnicas que utilizam reconstrução por reversão no tempo, por exemplo. O sinal recebido utilizando o código desenvolvido permaneceu com aquisição incorreta de algumas amostras devido à problemas de timings internos do controlador do sistema que precisam ser corrigidos. Ao final do projeto foi demonstrada a utilização da plataforma construída na modalidade de imagem de fotoacústica. / In order to improve existed techniques and to help the development of new diagnostic techniques for ultrasound, research ultrasound equipment is needed. This equipment is focused on providing flexibility for those who involved in improvement of existing and new diagnostic techniques for ultrasound imaging. However, most of the equipment dedicated to research are expensive and sometimes do not provide unrestricted access to the very basic level. For instance, the full control of the form of excitation of piezoelectric elements and accessing to pre-beamformed data are two examples. For this purpose, we developed an 8-channel, open source ultrasound system to overcome beamforming limitations, providing access to raw data before sum-and-delay and apodization. Our purpose was focused on providing an open source ultrasound research system in which we reduced the high-cost related to intellectual property of the commercial available equipment. The system developed allows complete control of emission parameters and reception of acoustic waves, which permitted variations in transmission frequency of 1.79 MHz to 50 MHz, dynamic focusing with 10 ns resolution, pulse coding control, amplitude excitation with range 10 V to 140 V and access to pre-processed signals sampled with 40 MHz frequency. The effects of different configurations were evaluated acquiring sound pressure maps. The maps obtained were in agreement with simulated pressure maps, which were generated using K-Wave software. One example is presented in the project from the evaluation of the system in photoacoustic application. The data acquired were used for reconstruction of photoacoustic imaging, using time-reversal reconstruction. Nevertheless, due to internal system timing, a sampling problem during acquisition needs to be corrected. Although, at the end of the project, a photoacoustic imaging was provided to demonstrate the systems functionality.

Le besoin d'un capteur de gaz sensible,sélectif, stable et compact s'accentue en raison des préoccupations publiques et militaires. La détection photo-acoustique, variante de la spectroscopie par diode laser accordable est une solution prometteuse. Les dispositifs actuels commercialisés et en voie de développement sont encore encombrants et inadaptés pour être transportés par une personne afin de réaliser des mesures embarqués. Cette thèse a pour objectif d'étudier et de développer un micro-résonateur en silicium à transduction capacitive pour la réalisation d'un capteur de gaz par mesure photo-acoustique. Il s'agit d'une approche originale qui n'a jamais été proposée. Elle offre des perspectives nouvelles et une solution pour disposer d'un capteur de gaz à la fois très compact, sensible, sélectif et stable. Une étude théorique des micro-résonateurs capacitifs est tout d'abord menée pour mettre en place des outils de modélisations et déterminer les paramètres clés à optimiser. Les performances sont étroitement liées aux propriétés mécaniques et à l'amortissement visqueux. Un procédé technologique sur substrat SOI divisé en deux grandes étapes est ensuite développé pour permettre de les fabriquer. Nous démontrons ensuite la faisabilité de mesures stables et reproductibles de méthane et d'éthylène à faible concentration. Nous proposons finalement une nouvelle architecture de micro-résonateur adaptée à la spectroscopie photo-acoustique et qui s'affranchira des limites qu'impose la transduction capacitive. / The need of a sensitive, selective, stable and compact gas sensor is increasing due to public and military issues. Photoacoustic detection variant of tunable diode laser spectroscopy is a promosing solution. Current devices available on the market and developing are still cumbersome and unsuitable for being transported by a person. The goal of this thesis is to study and develop silicon capacitive micro-resonator in order to achieve a gas sensor based on photoacoustic spectroscpy. This original approach has never been proposed. It offers new perspectives and a solution to have very compact, sensitive, selective and stable gas sensor. First, theoretical study of capacitive micro resonators is done in order to set up modeling tools and determine the key optimization parameters. The performances are strictly linked to mechanical properties and viscous damping. A SOI process divided into two main steps is then developed in order to produce capacitive micro-resonator. Then, we demonstrate the approach by stable and reproducible methane and ethylene detection. Finally, we propose new micro-resonator adapted to photoacoustic spectroscopy without the constraints of capacitive transduction.

archives@tulane.edu / Photoacoustic imaging functions via two foundations: light delivery and acoustic signal reception. In order for acoustic signal to be received and processed into an image, photons must first penetrate the tissue. However, biological media highly attenuates light, and the maximum imaging depth for photoacoustic images lies between 2-3 centimeters. Thus, models and simulations are integral to approach this problem, and they can be used to easily change imaging parameters and simulate various conditions. This study used a MATLAB Monte Carlo simulation algorithm to model and simulate a homogeneous placental tissue sample. The simulated data was compared to experimental ex vivo placental images taken under identical conditions of the simulation. These two data sets were used to gauge the simulation’s accuracy to predicting fluence trends in tissue, and the results were then applied to a heterogeneous tissue model simulating in vivo placental imaging. It was found that to maximize fluence in the placenta during in vivo imaging, 808 nm and 950 nm both offer different benefits to maximize fluence in the placenta. This simulation toolbox can be used to determine which experimental setup can maximize fluence in photoacoustic images, resulting in high-quality, high-contrast images. / 1 / Adam Kolkin

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Optoacoustic (OA) imaging is an emerging low-cost hybrid imaging investigation/technique currently in clinical feasibility studies for breast cancer diagnosis and staging. The technique applies pulsed light to the tissue of interest where molecules absorb the light photons and generate acoustic pressure waves. The resulting acoustic responses are detected using ultrasound transducers and converted into images. Image contrast within a pixel is dependent on the relative concentration and absorption characteristics (i.e. spectrum) of the chromophores within the illuminated tissue. Thus, tissue responses from illumination using multiple wavelengths, chosen to reflect the differential absorption of oxy-/deoxy- and total haemoglobin, can be measured. In turn, these signals can be regarded as surrogate measures of tissue hypoxia and neoangiogenesis, hallmarks of cancer associated with adverse outcomes. The aim of this PhD was to translate optoacoustic imaging into the breast clinic to try and fulfil some of the unmet clinical needs in breast cancer imaging using the imaging biomarker roadmap by O'Connor et al. Translation of this new technology to the clinical environment required extensive preparatory work, including the procurement and installation of a scanner prototype, liaison with UK regulatory bodies to secure ethical and MHRA approval, as well as several technical developments (performed during the course of the PhD) to make the technology suitable for breast cancer imaging. The first chapter of the thesis reviews the unmet needs of breast cancer imaging, being followed by a summary of recent techniques and technologies that may potentially fulfil gaps in knowledge and address some of the specific diagnostic challenges in breast cancer imaging. The capabilities of optoacoustic imaging are then discussed in the context of this evolving landscape of new imaging techniques and technologies with a particular focus on the tumour biology (neoangiogenesis and hypoxia) that can be measured in humans using multimodality and multi parametric imaging. Chapter 2 reviews of the current state of clinical translation of optoacoustic imaging, highlighting the particular areas in which clinical translation has advanced the most (breast cancer, melanoma and inflammatory bowel disease). Chapter 3 discusses the logistical, regulatory and technical challenges and solutions involved in translating optoacoustic imaging to the clinic and setting up a clinical service. Chapter 4 presents a series of validation experiments of oxygen saturation aimed at establishing the relationship between the optoacoustic signal and invasive pO2 measurements with an OxyLite probe in a porcine kidney model. This work was conducted in close collaboration with leading clinicians from the local transplant team. The following chapter describes the results of the first stage of our clinical work in the breast, namely the healthy volunteer study. This part had several aims: to perform qualitative assessment of the optoacoustic features of the normal breast under physiological conditions; to establish a robust scanning technique and identify technical and image interpretation pitfalls; and to perform qualitative evaluation of the hormonal changes that occur during the menstrual cycle and menopause, which, in turn, were used to validate surrogate measures of oxy-, deoxy and total haemoglobin. Chapter 6 then focuses on the qualitative assessment of benign and malignant breast lesions and their appearances on optoacoustic imaging. The patient study was divided into three phases. Phase 1 created a feature set to differentiate benign from malignant lesions, while Phase 2 was a transition between the prototype scanner and the installation of the first-generation clinical scanner. In Phase 3 the feature set created in Phase 1 was validated in a reader study. The sensitivity and specificity of optoacoustic imaging for lesion detection and differentiation of benign from malignant lesions was compared with mammography and ultrasound. Chapter 7 then deals with the quantitative analysis of the Phase 1 and Phase 3 data acquired in Chapter 6, assessing the relationships between the use of single wavelengths, spectral unmixing, vascularity versus receptor status, heterogeneity of signal intensity in relation to tumour stage and grade. This chapter also discusses the potential and limitations of quantifying the optoacoustic signal and leads to the final chapter, a discussion of future directions in optoacoustic imaging in breast cancer. At the end of this thesis, chapter 8 briefly discusses the potential future directions for the use of optoacoustic imaging as a clinical and scientific tool.

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Para o aperfeiçoamento das técnicas existentes e para o desenvolvimento de novas técnicas de diagnóstico por ultrassom equipamentos dedicados à pesquisa são necessários. Esses equipamentos devem possibilitar controle total da forma de excitação dos elementos piezoelétricos e acesso aos dados recebidos na sua forma pré-processada. Apesar de existirem equipamentos com essa finalidade, alguns deles ainda são limitados em relação aos controles de emissão e acesso aos dados raw por permitirem acesso apenas após a realização de um beamforming de recepção, como a aplicação de soma e atraso e apodização. Outro fator relevante sobre as máquinas voltadas para a pesquisa é o seu alto custo. Nesse projeto foi proposto um sistema de ultrassom de 8 canais, open source voltado à pesquisa, permitindo assim que seja reduzido o custo relacionado a propriedade intelectual do equipamento, e que permita controle completo dos parâmetros de emissão e recepção das ondas acústicas. Esse sistema de ultrassom foi construído utilizando kits de desenvolvimento comerciais. Os resultados adquiridos mostram que foram alcançadas variações de frequência de emissão de 1,79 MHz a 50 MHz, controles dos atrasos de emissão para controle de focalização dinâmica com resolução de 10 ns, controle de codificação do pulso, amplitude de excitação entre 10 e 140 V e acesso aos mapas RF na forma pré-processada, amostrados à uma frequência de 40 MHz. Os mapas de pressão acústica máxima foram adquiridos para diferentes profundidades de foco utilizando um hidrofone agulha e as imagens obtidas foram similares às simuladas anteriormente no software K-Wave. A etapa de recepção permitiu o acesso aos dados pré-beamforming de recepção, possibilitando o uso em técnicas que utilizam reconstrução por reversão no tempo, por exemplo. O sinal recebido utilizando o código desenvolvido permaneceu com aquisição incorreta de algumas amostras devido à problemas de timings internos do controlador do sistema que precisam ser corrigidos. Ao final do projeto foi demonstrada a utilização da plataforma construída na modalidade de imagem de fotoacústica. / In order to improve existed techniques and to help the development of new diagnostic techniques for ultrasound, research ultrasound equipment is needed. This equipment is focused on providing flexibility for those who involved in improvement of existing and new diagnostic techniques for ultrasound imaging. However, most of the equipment dedicated to research are expensive and sometimes do not provide unrestricted access to the very basic level. For instance, the full control of the form of excitation of piezoelectric elements and accessing to pre-beamformed data are two examples. For this purpose, we developed an 8-channel, open source ultrasound system to overcome beamforming limitations, providing access to raw data before sum-and-delay and apodization. Our purpose was focused on providing an open source ultrasound research system in which we reduced the high-cost related to intellectual property of the commercial available equipment. The system developed allows complete control of emission parameters and reception of acoustic waves, which permitted variations in transmission frequency of 1.79 MHz to 50 MHz, dynamic focusing with 10 ns resolution, pulse coding control, amplitude excitation with range 10 V to 140 V and access to pre-processed signals sampled with 40 MHz frequency. The effects of different configurations were evaluated acquiring sound pressure maps. The maps obtained were in agreement with simulated pressure maps, which were generated using K-Wave software. One example is presented in the project from the evaluation of the system in photoacoustic application. The data acquired were used for reconstruction of photoacoustic imaging, using time-reversal reconstruction. Nevertheless, due to internal system timing, a sampling problem during acquisition needs to be corrected. Although, at the end of the project, a photoacoustic imaging was provided to demonstrate the systems functionality.

Heme proteins carry out a diverse array of functions in vivo while maintaining a well-conserved 3-over-3 α-helical structure. Human hemoglobin (Hb) is well-known for its oxygen transport function. Type 1 non-symbiotic hemoglobins (nsHb1) in plants and bacterial flavohemoglobins (fHb) from a variety of bacterial species have been predicted to carry out a nitric oxide dioxygenase function. In nsHb1 and fHb this function has been linked to protection from nitrosative stress. Herein, I combine photoacoustic calorimetry (PAC), transient absorption spectroscopy (TA), and classical molecular dynamics (cMD) simulations to characterize molecular mechanism of diatomic ligand interactions with a hexa-coordinate globin from plant (rice hemoglobin), bacterial flavohemoglobins and human hemoglobin. In rice type 1 non-symbiotic hemoglobin (rHb1), the dynamics and energetics of structural changes associated with ligand photodissociation is strongly impacted by solvent and temperature, namely CO escape from the protein matrix is slower at pH = 6.0 compare to neutral pH (ns) due to the CD loop reorganization which forms a pathway for ligand escape. In human hemoglobin, exogenous allosteric effectors modulate energetics of conformational changes associated with the CO and O2 escape although the effectors impact on rate constants for ligand association is small. The conformational dynamics associated with ligand photorelease from fHbs from Cupriavidus necator (FHP) and Staphylococcus aureus (HMPSa) are strongly modulated by the presence of azole drugs indicating that drug association modulates structural properties of the heme binding pocket. In addition, we carried out a study of the formation of the DNA intercalated motif (i-motif). The formation of the structure is strongly favored at acidic pH; therefore, PAC was combined with a 2-nitrobenzaldehyde pH-jump to probe formation of the i-motif on fast timescales. i-Motif folding is two-step process with the initial protonation of cytosine residues being endothermic with ΔHfast=8.5 ± 7.0 kcal mol-1 and ΔVfast=10.4 ± 1.6 mL mol-1 and subsequent nucleation/i-motif folding (τ = 140 ns) with ΔHslow=-51.5 ± 4.8 kcal mol-1 and ΔVslow=-6.6 ± 0.9 mL mol-1. The above results indicate that PAC can be employed to study diverse biochemical reactions such as DNA folding, drug binding and ligand photorelease from proteins.