L'IRM de perfusion et de spectroscopie restent encore peu utilisées en raison de leur mise en oeuvre difficile et de leur manque de quantification. L'objectif de ces travaux a été d'optimiser et de valider des techniques IRM totalement non invasives chez l'Homme en vue d'applications cliniques permettant une exploration sur un large volume cérébral et une quantification absolue des paramètres de perfusion et du métabolisme cérébraux. Concernant la perfusion, 3 séquences de type marquage de spins,PASL PICORE, PASL FAIR et pCASL, ont été comparées en termes de sensibilité et de reproductibilité. pCASL a ensuite été intégrée dans un protocole de recherche sur des patients atteints de sclérose en plaques ou SEP. Quant au métabolisme cérébral, un protocole a été mis en place afin d'accéder à une quantification absolue et pseudo absolue des métabolites par la normalisation du signal de l'eau issue de la CSI par la densité de protons acquise en IRM. Cette technique a été validée en CSI 2D puis transposée en 3D avec la séquence EPSI sur deux orientations différentes : CACP et CACP+15°afin de constituer des valeurs normatives fiables des métabolites principaux sur tout le cerveau. L'élaboration de ces techniques en spectroscopie a abouti à une étude sur des patients souffrant de SEP démontrant la faisabilité de l'utilisation de ces techniques en clinique. Ces travaux démontrent que la quantification absolue en IRM de perfusion et en IRM de spectroscopie peut être obtenue sur un large volume cérébral de manière fiable sur un système IRM disponible en environnement clinique dans un temps d'acquisition acceptable à travers les corrections diverses spécifiques à chaque imagerie. / Conventional MRI's lack of specificity in clinical routine limits our ability to perform correct diagnoses or follow-ups of pathological diseases. Two forms of NMR imaging, perfusion weighed and spectroscopic imaging provide information about two closely related characteristics :cerebral perfusion and metabolism. However, these techniques are not widely used due to the complexity of implementation and a lack of quantification.The general aim was to optimize and validate completely non-invasive NMR techniques for further human clinical applications in the context of exploring large cerebral volumes and determining absolute or pseudo-absolute quantification of cerebral perfusion and metabolism. Concerning perfusion, three arterial spin labeling sequences, PASL PICORE, PASL FAIR and pCASL, were compared in terms of sensitivity and reproducibility. The pCASL sequence was then integrated to a protocol applied to patients suffering from multiple sclerosis. In relation to metabolism, a protocol was applied in order to access absolute and pseudo-absolute metabolite quantification by water SI normalization from MRI proton density. This technique was validated on 2D CSI and then on 3D with EPSI sequence with two orientations, AC-PC and AC-PC+15 in order to generate reliable normative values of metabolites for the whole brain. The use of those spectroscopic techniques on patients suffering from multiple sclerosis allowed demonstrating the feasibility in clinic.This work demonstrates that reliable absolute quantification in perfusion weighted and spectroscopic imaging can be obtained with extensive coverage and with an acquisition time compatible with the reality of clinical exams.

Orientador: Ronei Jesus Poppi / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-26T16:15:02Z (GMT). No. of bitstreams: 1 Almeida_MarianaRamosde_D.pdf: 6686279 bytes, checksum: 1e1d5d53538fb99a153ff4425595e0ce (MD5) Previous issue date: 2015 / Resumo: A motivação para o desenvolvimento dessa tese foi a busca por métodos de análise não destrutivos, com nenhum ou mínimo preparo de amostra e que permitam a obtenção do máximo de informação com a realização de uma única análise na área de forense e paleontologia. Em forense, a espectroscopia Raman e o método de classificação supervisionado PLS-DA (Análise Discriminante por Mínimos Quadrados Parciais) foram empregados para construir modelos de classificação. O primeiro modelo foi construído para discriminar cédulas autênticas de cédulas falsas. A análise foi baseada na caracterização das tintas usadas na confecção das cédulas. O segundo modelo de classificação foi construído para diferenciar o óleo essencial extraído de diferentes partes (caule, folhas e galhos) da árvore amazônica Aniba Rosaeodora. A confiabilidade dos modelos foi avaliada pelo cálculo do intervalo de confiança, que foram calculados usando a técnica de reamostragem bootstrap. Os resultados obtidos mostraram que os modelos de classificação podem ser usados como método complementar à inspeção forense clássica e método de triagem. O desempenho dos modelos de classificação foi avaliado pelo cálculo de sensibilidade, especificidade, eficiência e coeficiente de Mathew. A espectroscopia Raman de imagem e o método de análise de componentes independentes (ICA) foram empregados para a identificação de explosivos em superfícies de cédulas. O método ICA foi avaliado como método de resolução de curvas para extrair os perfis espectrais e as imagens Raman dos constituintes presentes nas superfícies analisadas. Os resultados obtidos mostraram que o método ICA é adequado para resolução de curvas, uma vez que alcançou desempenho equivalente ao método clássico MCR-ALS (Resolução Multivariada de Curvas com Mínimos Quadrados Alternados). O limite de detecção da metodologia apresentada foi de 50 µg.cm-2 para o explosivo TNT. Por fim, a espectroscopia Raman de imagem foi empregada no estudo da composição química de fósseis de peixes, com o objetivo de obter informações sobre características biológicas. Os resultados mostraram informações sobre a composição química do fóssil estudado / Abstract: The motivation for the development of this thesis was to search for non-destructive testing methods, with none or minimal sample preparation and allowing them to obtain maximum information with the completion of a single analysis for forensic and paleontology. In the forensics, the Raman spectroscopy and the PLS-DA (discriminant analysis by Partial Least Squares) classification method were explored to build classification models. The first model was built to discriminate authentic and counterfeit banknotes. The analysis was based on the characterization of inks used in the confection of the banknotes. The second classification model was built to differentiate the essential oil extracted from different parts (wood, leaves and branches) of the Brazilian tree Aniba rosaeodora. The reliability of the models was evaluated by calculating the confidence interval, which was calculated using the bootstrap resampling technique. The results show that the classification models can be used as a complementary method to classical forensic inspection and a screening method. The performance of classification models was evaluated by calculating sensitivity, specificity, efficiency and Matthew coefficient. In a third application, Raman hyperspectral imaging and the independent component analysis (ICA) method were used for identification of explosives on the surfaces of banknotes. The ICA method was evaluated as curve resolution method to extract the Raman spectral profiles and the images of the constituents present in the analyzed surfaces. The results showed that the ICA method is appropriate for curves resolution, once achieved equivalent performance to the classical MCR-ALS (Multivariate Curve Resolution with Alternating Least Squares) method. The methodology presented limit of detection of 50 µg.cm-2 for the explosive TNT. Finally, the Raman hyperspectral imaging was applied in paleontology to study the chemical composition of fish fossil with the aim of obtaining information on biological characteristics. The results showed information about the chemical composition of fossil studied / Doutorado / Quimica Analitica / Doutora em Ciências

Indiana University-Purdue University Indianapolis (IUPUI) / Up-to-date and accurate information on soil properties is important for precision farming and environmental management. The spatial information of soil properties allows adjustments of fertilizer applications to be made based on knowledge of local field conditions, thereby maximizing agricultural productivity and minimizing the risk of environmental pollution. While conventional soil sampling procedures are labor-intensive, time-consuming and expensive, remote sensing techniques provide a rapid and efficient tool for mapping soil properties. This study aimed at examining the capacity of hyperspectral reflectance data for mapping soil organic matter (SOM), total nitrogen (N) and total phosphorus (P). Soil samples collected from Eagle Creek Watershed, Cicero Creek Watershed, and Fall Creek Watershed were analyzed for organic matter content, total N and total P; their corresponding spectral reflectance was measured in the laboratory before and after oven drying and in the field using Analytical Spectral Devices spectrometer. Hyperion images for each of the watersheds were acquired, calibrated and corrected and Hyperion image spectra for individual sampled sites were extracted. These hyperspectral reflectance data were related to SOM, total N and total P concentration through partial least squares (PLS) regressions. The samples were split into two datasets: one for calibration, and the other for validation. High PLS performance was observed during the calibration for SOM and total N regardless of the type of the reflectance spectra, and for total P with Hyperion image spectra. The validation of PLS models was carried out with each type of reflectance to assess their predictive power. For laboratory reflectance spectra, PLS models of SOM and total N resulted in higher R2 values and lower RMSEP with oven-dried than those with field-moist soils. The results demonstrate that soil moisture degrades the performance of PLS in estimating soil constituents with spectral reflectance. For in-situ field spectra, PLS estimated SOM with an R2 of 0.74, N with an R2 of 0.79, and P with an R2 of 0.60. For Hyperion image spectra, PLS predictive models yielded an R2 of 0.74 between measured and predicted SOM, an R2 of 0.72 between measured and predicted total N, and an R2 of 0.67 between measured and predicted total P. These results reveal slightly decreased model performance when shifting from laboratory-measured spectra to satellite image spectra. Regardless of the spectral data, the models for estimating SOM and total N consistently outperformed those for estimating total P. These results also indicate that PLS is an effective tool for remotely estimating SOM, total N and P in agricultural soils, but more research is needed to improve the predictive power of the model when applied to satellite hyperspectral imagery.

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<p>The Auroral Large Imaging System (ALIS) was proposed in 1989 by Åke Steen as a joint Scandinavian ground-based nework of automated auroral imaging stations. The primary scientic objective was in the field of auroral physics, but it was soon realised that ALIS could be used in other fields, for example, studies of Polar Stratospheric Clouds (PSC), meteors, as well as other atmospheric phenomena.</p><p>This report describes the design, operation and scientic results from a Swedish prototype of ALIS consisting of six unmanned remote-controlled stations located in a grid of about 50 km in northern Sweden. Each station is equipped with a sensitive high-resolution (1024 x 1024 pixels) unintensified monochromatic CCDimager. A six-position filter-wheel for narrow-band interference filters facilitates absolute spectroscopic measurements of, for example, auroral and airglow emissions. Overlapping fields-of-view resulting from the station baseline of about 50 km combined with the station field-of-view of 50° to 60°, enable triangulation as well as tomographic methods to be employed for obtaining altitude information of the observed phenomena.</p><p>ALIS was probably one of the first instruments to take advantage of unintensi- fied (i.e. no image-intensifier) scientific-grade CCDs as detectors for spectroscopic imaging studies with multiple stations of faint phenomena such as aurora, airglow, etc. This makes absolute calibration a task that is as important as it is dificult.</p><p>Although ALIS was primarily designed for auroral studies, the majority of the scientific results so far have, quite unexpectedly, been obtained from observations of HF pump-enhanced airglow (recently renamed Radio-Induced Aurora). ALIS made the first unambiguous observation of this phenomena at high-latitudes and the first tomography-like inversion of height profiles of the airglow regions. The scientific results so far include tomographic estimates of the auroral electron spectra, coordinated observations with satellite and radar, as well as studies of polar stratospheric clouds. An ALIS imager also participated in a joint project that produced the first ground-based daytime auroral images. Recently ALIS made spectroscopic observations of a Leonid meteor-trail and preliminary analysis indicates the possible detection of water in the Leonid.</p>

The Auroral Large Imaging System (ALIS) was proposed in 1989 by Åke Steen as a joint Scandinavian ground-based nework of automated auroral imaging stations. The primary scientic objective was in the field of auroral physics, but it was soon realised that ALIS could be used in other fields, for example, studies of Polar Stratospheric Clouds (PSC), meteors, as well as other atmospheric phenomena. This report describes the design, operation and scientic results from a Swedish prototype of ALIS consisting of six unmanned remote-controlled stations located in a grid of about 50 km in northern Sweden. Each station is equipped with a sensitive high-resolution (1024 x 1024 pixels) unintensified monochromatic CCDimager. A six-position filter-wheel for narrow-band interference filters facilitates absolute spectroscopic measurements of, for example, auroral and airglow emissions. Overlapping fields-of-view resulting from the station baseline of about 50 km combined with the station field-of-view of 50° to 60°, enable triangulation as well as tomographic methods to be employed for obtaining altitude information of the observed phenomena. ALIS was probably one of the first instruments to take advantage of unintensi- fied (i.e. no image-intensifier) scientific-grade CCDs as detectors for spectroscopic imaging studies with multiple stations of faint phenomena such as aurora, airglow, etc. This makes absolute calibration a task that is as important as it is dificult. Although ALIS was primarily designed for auroral studies, the majority of the scientific results so far have, quite unexpectedly, been obtained from observations of HF pump-enhanced airglow (recently renamed Radio-Induced Aurora). ALIS made the first unambiguous observation of this phenomena at high-latitudes and the first tomography-like inversion of height profiles of the airglow regions. The scientific results so far include tomographic estimates of the auroral electron spectra, coordinated observations with satellite and radar, as well as studies of polar stratospheric clouds. An ALIS imager also participated in a joint project that produced the first ground-based daytime auroral images. Recently ALIS made spectroscopic observations of a Leonid meteor-trail and preliminary analysis indicates the possible detection of water in the Leonid.

Prostate cancer is the most common malignancy afflicting Canadian men in 2011. Physicians use digital rectal exams (DRE), blood tests for prostate specific antigen (PSA) and transrectal ultrasound (TRUS)-guided biopsies for the initial diagnosis of prostate cancer. None of these tests detail the spatial extent of prostate cancer - information critical for using new therapies that can target cancerous prostate. With an MRI technique called proton magnetic resonance spectroscopic imaging (1H-MRSI), biochemical analysis of the entire prostate can be done without the need for biopsy, providing detailed information beyond the non-specific changes in hardness felt by an experienced urologist in a DRE, the presence of PSA in blood, or the “blind-guidance” of TRUS-guided biopsy. A hindrance to acquiring high quality 1H-MRSI data comes from signal originating from fatty tissue surrounding prostate that tends to mask or distort signal from within the prostate, thus reducing the overall clinical usefulness of 1H-MRSI data. This thesis has three major areas of focus: 1) The development of an optimized 1H-MRSI technique, called conformal voxel magnetic resonance spectroscopy (CV-MRS), to deal the with removal of unwanted lipid contaminating artifacts at short and long echo times. 2) An in vivo human study to test the CV-MRS technique, including healthy volunteers and cancer patients scheduled for radical prostatectomy or radiation therapy. 3) A study to determine the efficacy of using the 1H-MRSI data for optimized radiation treatment planning using modern delivery techniques like intensity modulated radiation treatment. Data collected from the study using the optimized CV-MRS method show significantly reduced lipid contamination resulting in high quality spectra throughout the prostate. Combining the CV-MRS technique with spectral-spatial excitation further reduced lipid contamination and opened up the possibility of detecting metabolites with short T2 relaxation times. Results from the in vivo study were verified with post-histopathological data. Lastly, 1H-MRSI data was incorporated into the radiation treatment planning software and used to asses tumour control by escalating the radiation to prostate lesions that were identified by 1H-MRSI. In summary, this thesis demonstrates the clinical feasibility of using advanced spectroscopic imaging techniques for improved diagnosis and treatment of prostate cancer.

Prostate cancer is the most common malignancy afflicting Canadian men in 2011. Physicians use digital rectal exams (DRE), blood tests for prostate specific antigen (PSA) and transrectal ultrasound (TRUS)-guided biopsies for the initial diagnosis of prostate cancer. None of these tests detail the spatial extent of prostate cancer - information critical for using new therapies that can target cancerous prostate. With an MRI technique called proton magnetic resonance spectroscopic imaging (1H-MRSI), biochemical analysis of the entire prostate can be done without the need for biopsy, providing detailed information beyond the non-specific changes in hardness felt by an experienced urologist in a DRE, the presence of PSA in blood, or the “blind-guidance” of TRUS-guided biopsy. A hindrance to acquiring high quality 1H-MRSI data comes from signal originating from fatty tissue surrounding prostate that tends to mask or distort signal from within the prostate, thus reducing the overall clinical usefulness of 1H-MRSI data. This thesis has three major areas of focus: 1) The development of an optimized 1H-MRSI technique, called conformal voxel magnetic resonance spectroscopy (CV-MRS), to deal the with removal of unwanted lipid contaminating artifacts at short and long echo times. 2) An in vivo human study to test the CV-MRS technique, including healthy volunteers and cancer patients scheduled for radical prostatectomy or radiation therapy. 3) A study to determine the efficacy of using the 1H-MRSI data for optimized radiation treatment planning using modern delivery techniques like intensity modulated radiation treatment. Data collected from the study using the optimized CV-MRS method show significantly reduced lipid contamination resulting in high quality spectra throughout the prostate. Combining the CV-MRS technique with spectral-spatial excitation further reduced lipid contamination and opened up the possibility of detecting metabolites with short T2 relaxation times. Results from the in vivo study were verified with post-histopathological data. Lastly, 1H-MRSI data was incorporated into the radiation treatment planning software and used to asses tumour control by escalating the radiation to prostate lesions that were identified by 1H-MRSI. In summary, this thesis demonstrates the clinical feasibility of using advanced spectroscopic imaging techniques for improved diagnosis and treatment of prostate cancer.

La technique laser-induced breakdown spectroscopy (LIBS), qui consiste à exploiter le spectre du plasma induit par laser sur la surface de l'échantillon pour déterminer sa composition élémentaire, a été inventée il y a plus de 50 ans. Récemment, elle connaît un développement rapide, poussée par des besoins d'application dans différents domaines, citons par exemple, exploration océanique, détection de pollution environnementale, ou contrôle de procédés industriels. Cette technique utilise le plasma généré par ablation laser comme la source spectroscopique. La particularité de LIBS est que le plasma induit par laser présente un comportement transitoire et une distribution spatiale qui ne soit pas uniforme en général. Bien que la détection résolue en temps puisse améliorer considérablement la performance de LIBS, surtout pour le procédé de LIBS autocalibration avec une meilleure détermination de température, l'évolution temporelle du plasma est souvent corrélée avec sa morphologie et son inhomogénéité spatiale. L'étude de la morphologie ainsi que la structure interne du plasma avec l'évolution pendant l'expansion de celui-ci dans un gaz ambiant, représente donc un point crucial pour l'optimisation du plasma entant qu'une source spectroscopique. Suite à la thèse de Qianli Ma réalisée dans notre équipe et soutenue en décembre 2012, qui a été notamment consacrée à l'étude de l'effet de la longueur d'onde du laser d'ablation sur les propriétés et l'évolution du plasma dans un gaz ambiant d'argon, la présente thèse s'intéresse aux effets des autres paramètres, la fluence du laser d'ablation, la durée de l'impulsion, et les différents gaz ambiants (argon ou air), sur la morphologie et la structure du plasma. Par ailleurs, les mécanismes microscopiques conduisant à l'onde de détonation soutenue par laser dans argon ou dans l'air sont aussi étudiés. Lors du refroidissant du plasma dans l'air, des oxydes métalliques peuvent se former. L'étude de la formation de molécules, au-delà de l'intérêt pratique pour la LIBS, fournit également un aperçu de la cinétique chimique dans le plasma, ce qui est intéressant pour l'étude de la transformation du plasma en phase gazeuse à une phase recondensée de nanoparticules / Laser-induced breakdown spectroscopy (LIBS) has been invented for more than 50 years, which analyzes the spectrum of the laser-induced plasma to determine the elemental composition of the ablated sample. Recently, LIBS technique has been well developed and applied in different domains, for example oceanic exploration, pollution monitoring in the environment. LIBS uses the ablation plasma as a light source that contains the elemental composition information of the sample. However, the laser-induced plasma exhibits a transient behavior. Although time-resolved and gated detection can greatly improve the performance of the LIBS technique especially that of calibration-free LIBS (CF-LIBS) with a better determination of plasma temperature, the temporal evolution of the plasma is correlated to its morphology and its spatial inhomogeneity. The determination of the morphology as well as the internal structure of the plasma together with their evolution during plasma expansion into the ambient gas is therefore crucial for the optimization of the use of ablation plasma as a spectroscopic emission source. Evolutions of the morphology and the internal structure of the ablation plasma are considered as the consequence of its hydrodynamic expansion into the ambient gas. Following the thesis of Qianli Ma which has studied the effect of laser wavelength on the behavior of the plasma induced in an ambient gas of argon, the present thesis has used the same diagnostic techniques (time- and space-resolved emission spectroscopy and fast spectroscopic images) together with 1064 nm ns laser pulse ablation of a target of aluminum to investigate the effects of other parameters, such as the fluence and the duration of laser pulse, the effect of different ambient gases (argon and air), on the morphology and internal structure of the plasma. Furthermore, in order to understand the effects of these parameters on the properties of the plasma, the microscopic mechanisms during post ablation and the propagation of the plasma are also studied. While the plasma cools down in air, molecules are formed, AlO for instance. So the thesis also studied the condition for the formation of the molecules in the plasma. Beyond the practical interest of this study for LIBS, it provides also insights to the kinetics of the AlO molecule formation in laserinduced plasma

La Spectroscopie et l'Imagerie Spectroscopique de Résonance Magnétique (ISRM) jouent un rôle émergent parmi les outils cliniques, en donnant accès, d'une manière complètement non-invasive, aux concentrations des métabolites in vivo. Néanmoins, les inhomogénéités du champ magnétique, ainsi que les courants de Foucault, produisent des distorsions significatives de la forme de raie des spectres, induisant des conséquences importantes en termes de biais lors de l'estimation des concentrations. Lors des traitements post-acquisition, cela est habituellement traité à l'aide des méthodes de pré-traitement, ou bien par l'introduction de fonctions analytiques plus complexes. Cette thèse se concentre sur la prise en compte de distorsions arbitraires de la forme de raie, dans le cas des méthodes qui utilisent une base de métabolites comme connaissance a priori. L'état de l'art est évalué, et une nouvelle approche est proposée, fondée sur l'adaptation de l'amortissement de la base des métabolites au signal acquis. La forme de raie présumée commune à tous les métabolites est estimée et filtrée à l'aide de la méthode LOWESS. L'approche est validée sur des signaux simulés, ainsi que sur des données acquises in vitro. Finalement, une deuxième approche novatrice est proposée, fondée sur l'utilisation des propriétés spectrales de la forme de raie commune. Le nouvel estimateur est testé seul, mais aussi associé avec l'estimateur classique de maximum de vraisemblance, démontrant une réduction significative du biais dans le cas des signaux à haut rapport signal-sur-bruit. / Magnetic Resonance Spectroscopy (MRS) and Spectroscopic Imaging (MRSI) play an emerging role in clinical assessment, providing in vivo estimation of disease markers while being non-invasive and applicable to a large range of tissues. However, static magnetic field inhomogeneity, as well as eddy currents in the acquisition hardware, cause important distortions in the lineshape of acquired NMR spectra, possibly inducing significant bias in the estimation of metabolite concentrations. In the post-acquisition stage, this is classically handled through the use of pre-processing methods to correct the dataset lineshape, or through the introduction of more complex analytical model functions. This thesis concentrates on handling arbitrary lineshape distortions in the case of quantitation methods that use a metabolite basis-set as prior knowledge. Current approaches are assessed, and a novel approach is proposed, based on adapting the basis-set lineshape to the measured signal.Assuming a common lineshape to all spectral components, a new method is derived and implemented, featuring time domain local regression (LOWESS) filtering. Validation is performed on synthetic signals as well as on in vitro phantom data. Finally, a completely new approach to MRS quantitation is proposed, centred on the use of the compact spectral support of the estimated common lineshape. The new metabolite estimators are tested alone, as well as coupled with the more common residual-sum-of-squares MLE estimator, significantly reducing quantitation bias for high signal-to-noise ratio data.