L'objectif de cette thèse est de proposer de nouveaux algorithmes pour surmonter les limitations actuelles et de relever les défis ouverts dans le traitement de l'imagerie spectroscopique par résonance magnétique (ISRM). L'ISRM est une modalité non invasive capable de fournir la distribution spatiale des composés biochimiques (métabolites) utilisés comme biomarqueurs de la maladie. Les informations fournies par l'ISRM peuvent être utilisées pour le diagnostic, le traitement et le suivi de plusieurs maladies telles que le cancer ou des troubles neurologiques. Cette modalité se montre utile en routine clinique notamment lorsqu'il est possible d'en extraire des informations précises et fiables. Malgré les nombreuses publications sur le sujet, l'interprétation des données d'ISRM est toujours un problème difficile en raison de différents facteurs tels que le faible rapport signal sur bruit des signaux, le chevauchement des raies spectrales ou la présence de signaux de nuisance. Cette thèse aborde le problème de l'interprétation des données d'ISRM et la caractérisation de la rechute des patients souffrant de tumeurs cérébrales. Ces objectifs sont abordés à travers une approche méthodologique intégrant des connaissances a priori sur les données d'ISRM avec une régularisation spatio-spectrale. Concernant le cadre applicatif, cette thèse contribue à l'intégration de l'ISRM dans le workflow de traitement en radiothérapie dans le cadre du projet européen SUMMER (Software for the Use of Multi-Modality images in External Radiotherapy) financé par la Commission européenne (FP7-PEOPLE-ITN). / The aim of this thesis is to propose new algorithms to overcome the current limitations and to address the open challenges in the processing of magnetic resonance spectroscopic imaging (MRSI) data. MRSI is a non-invasive modality able to provide the spatial distribution of relevant biochemical compounds (metabolites) commonly used as biomarkers of disease. Information provided by MRSI can be used as a valuable insight for the diagnosis, treatment and follow-up of several diseases such as cancer or neurological disorders. Obtaining accurate and reliable information from in vivo MRSI signals is a crucial requirement for the clinical utility of this technique. Despite the numerous publications on the topic, the interpretation of MRSI data is still a challenging problem due to different factors such as the low signal-to-noise ratio (SNR) of the signals, the overlap of spectral lines or the presence of nuisance components. This thesis addresses the problem of interpreting MRSI data and characterizing recurrence in tumor brain patients. These objectives are addressed through a methodological approach based on novel processing methods that incorporate prior knowledge on the MRSI data using a spatio-spectral regularization. As an application, the thesis addresses the integration of MRSI into the radiotherapy treatment workflow within the context of the European project SUMMER (Software for the Use of Multi-Modality images in External Radiotherapy) founded by the European Commission (FP7-PEOPLE-ITN framework).

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.

The neurophysiological basis of cognition changes with age is relatively unexplained, with most studies reporting weak relationships between cognition and measures of brain function, such as event related potentials, brain size and cerebral blood flow. Proton magnetic resonance spectroscopy (1H-MRS) is an in vivo method used to detect metabolites within the brain that are relevant to certain brain processes. Recent studies have shown that these metabolites, in particular N-acetyl aspartate (NAA), which is associated with neuronal viability, correlate with performance on neuropsychological tests or other measures of cognitive function in patients with a variety of cognitive disorders associated with ageing and in normal ageing subjects. We have studied the relationship between metabolites and cognitive function in elderly patients 3 months and 3 years after a stroke or transient ischemic attack (TIA) and in an ageing comparison group. Metabolites were no different between stroke/TIA patients and elderly controls, however, there were significant metabolite differences between stroke/TIA patients with cognitive impairment (Vascular Cognitive Impairment and Vascular Dementia) and those without. Frontal measures of NAA and NAA/Cr predicted cognitive decline over 12 months and 3 years in stroke/TIA patients and elderly controls, and these measures were superior predictors than structural MRI measures. Longitudinal stability of metabolites in ageing over 3 years was associated with stability of cognitive function. The results indicate that 1H-MRS is a useful tool in differentiating stroke/TIA patients with and without cognitive impairment, with possibly superior predictive ability than structural MRI for assessing future cognitive decline. The changes in 1H-MRS that occur with ageing and cognitive decline have implications for the neurophysiological mechanisms and processes that are occurring in the brain, as well as application to clinical diagnosis, the early detection of pathology and the examination of longitudinal change.

Ce travail de thèse a pour but d'étudier la structure et la dynamique du plasma induit par une impulsion laser nanoseconde d'éclairement d'une dizaine de GW cm-2, sur la surface d'une cible métallique plongée dans un gaz ambiant d'argon à pression atmosphérique. Comme source d'émission spectroscopique, un tel plasma constitue la base de l'approche laser-induced breakdown spectroscopy (LIBS), une technique d'analyse chimique en plein développement mais dont la maturation nécessite une compréhension approfondie des mécanismes mis en jeu dans la détente du plasma. Cependant la phase d'émission spectroscopique du plasma intéressante pour la technique LIBS n'occupe qu'un intervalle de temps limité dans la durée de vie de celui-ci, typiquement entre une centaine de nanosecondes et quelques microsecondes après l'impact de l'impulsion laser sur la cible. Au temps très courts, et notamment en présence de l'impulsion laser, la détente du plasma fait intervenir un grand nombre de processus physiques. Ces derniers sont largement partagés par des plasmas beaucoup plus énergétiques qui peuvent être soit produits artificiellement par des lasers hors norme, tels qu'un laser Mégajoule, soit présents dans des milieux difficilement accessibles, tels que le milieu interstellaire. L'étude du plasma à l'échelle du laboratoire peut donc fournir un système-modèle qui pourrait permettre des études fines et systématiques à moindre coût. Enfin, la phase de détente du plasma peut conduire à la formation de nanoparticules par recondensation ultrarapide. L'étude de la structure et la dynamique de la phase gazeuse facilitera ainsi la compréhension des mécanismes impliqués dans la condensation du plasma. Ce travail a été rendu possible avec l'utilisation des techniques de diagnostics reposant sur la spectroscopie d'émission et l'imagerie spectrale rapide du plasma. Cette approche expérimentale constitue aussi une des originalités de ce travail de thèse. Grâce à l'application de telles techniques, plutôt classiques, couplées avec un moyen de détection offrant une grande résolution temporelle et un montage expérimental à précision et à stabilité mécaniques extrêmement poussées, la structure d'un plasma a été révélée jusqu'à un degré de détail rarement atteint auparavant. La dynamique de la propagation du plasma dans un gaz ambiant a été ainsi étudiée en fonction du régime de l'onde d'absorption soutenue par laser. Un contrôle sur le régime de propagation a été notamment réalisé par ablations avec le fondamental et la troisième harmonique d'un laser Nd:YAG à 1064 nm et 355 nm / The purpose this PhD work is to study the structure and the dynamics of the plasma induced by a nanosecond laser pulse with irradiance in the range of 10 GW cm-2, on the surface of a metallic target surrounded by an ambient gas of argon at the atmospheric pressure. As a spectroscopic emission source, such plasma is the basis of laser-induced breakdown spectroscopy (LIBS), a rapidly developing analytical technique. The maturation of this technique requires today a deeper understanding of the mechanisms involved in the expansion of the plasma. However the spectroscopic emission phase of the plasma, interesting for LIBS, occupies only a limited time interval in the lifetime of the plume, typically between a few hundred nanoseconds and several microseconds after the impact of the laser pulse on the target. At very short delay, especially in the presence of the laser pulse, the plasma expansion involves physical processes which are often shared by plasmas with much higher energies which can be either artificially produced by unconventional lasers, such as a megajoule laser, or present in hostile environments such as interstellar media. The study of the plasma at the laboratory scale may therefore provide a model system that could allow detailed and systematic studies of the plasma with a modest cost. Finally, the condensation phase of the plasma could lead to the formation of nanoparticles. The study of the structure and the dynamics of the gas phase can facilitate the understanding of the mechanisms involved in the condensation of the plasma. This PhD thesis work has been made possible with the use of the diagnostics techniques based on emission spectroscopy and fast spectroscopic imaging of the plasma. Such experimental approach is also one of the originalities of this work. Thanks to the use of such techniques, rather classical in a general way, coupled with a detection providing high temporal resolution and an experimental setup with advanced mechanical precision and stability, the structure of the plasma has been revealed with a level of detail rarely achieved so far. The dynamics of the plasma during its expansion in an ambient gas has been thus studied as a function of the regime of the laser-supported absorption wave. A control of the propagation regime was achieved by ablations with the fundamental and the third harmonics of a Nd:YAG laser at 1064 nm and 355 nm respectively

Deux méthodes d'imagerie par résonance magnétique sont proposées pour analyser in vivo le tissu cérébral de la matière blanche. La première méthode permet l'acquisition ultra-rapide de cartes des métabolites cérébraux par une lecture de l'espace réciproque répétée à des intervalles de quelques millisecondes à l'aide d'une nouvelle trajectoire excentrée, combinée à un gradient de retour. Une procédure de correction de phase, pour prévenir la formation d'artéfacts de repliement dans l'image et le spectre, est introduite sur la base de paramètres déterminés à partir du signal des protons de l'eau. Une acquisition des cartes métaboliques tridimensionnelles de la créatine, de la choline, du N-acétylaspartate, du glutamate et du myo-inositol ont été déterminées de manière fiable dans la substance blanche humaine à 3 Tesla avec une matrice de taille 32 × 32 × 16 et une résolution isotropique de 7 mm. La deuxième méthode permet l'acquisition d'un train de 32 images échantillonnées géométriquement le long d'une courbe de recroissance, en employant une série d'échos de gradient excités par un angle de bascule de 5° pour éviter des effets de saturation. Après transformée inverse de Laplace utilisant une régularisation spatiale, on obtient une distribution continue des temps de relaxation spin-réseau, T1. Dans la région de T1 entre 100 ms et 230 ms, on distingue un pic attribué à l'eau hydratant les membranes de la myéline. La fraction apparente de cette composante de l'eau de myéline augmente en fonction de l'intensité du champ magnétique, de 8,3 % à 3 Tesla, à 11,3 % à 4 Tesla, pour atteindre 15,0 % à 7 Tesla / Two magnetic resonance imaging methods are proposed for the in vivo investigation of human brain white matter tissue. The first method allows the ultra-fast acquisition of maps of brain metabolites by repeating the sampling of k-space at intervals of a few milliseconds, with a center-out trajectory combined with flyback gradients. A phase-correction procedure is introduced to prevent the formation of aliasing artifacts in the image and in the spectrum, on the basis of parameters determined from the signal of the ubiquitous water protons. An acquisition of threedimensional metabolite maps of creatine, choline, N-acetylaspartate, glutamate, and myo-inositol were determined reliably in human brain white matter at 3 Tesla with a 32 × 32 × 16 matrix and a 7-mm isotropic resolution. The second method enables the acquisition of a train of 32 images geometrically sampled along an inversion-recovery curve, using a series of gradient echoes excited by a low 5° flip angle to avoid saturation effects. After inverse Laplace transform, using a spatial regularization, a continuous distribution of the spin-lattice relaxation times, T1, is obtained. In the region of T1 between 100 ms and 230 ms, a small component is attributed to water hydrating myelin membranes. The apparent fraction of this myelin water component increases with the strength of the magnetic field, from 8.3% at 3 Tesla, to 11.3% at 4 Tesla, and 15.0% at 7 Tesla

Breast cancer is a global public health problem since it is the most frequently diagnosed cancer in women in Western countries. Clinical guidelines for breast cancer prognosis/diagnosis are currently based on tumour size, histological type and grade, lymph node status as well as the expression of various cellular receptors. Yet, current predictions remain unsatisfactory to identify the best treatment for the individual patient. The search for identifying new predictive and prognostic factors is ongoing. Furthermore, compelling evidences have solidified the notion that the evolving epithelial cells, founders of the breast disease, are helped in their malignant course by the tumour microenvironment. Better characterizing the dual effect of the immune regulation but also the epithelial-stromal cross-talk on both tumour-promotion and -suppression is essential for understanding patient uniqueness and their implication in disease outcome. Because of its potential to probe tissues and cells at the molecular level without requirement for extrinsic contrast agents, infrared spectroscopy was seen as an attractive tool for clinical and diagnostic analysis in order to complement the existing methods. <p>In a first step, recording and processing methodology had to be defined in order to optimally compare IR spectra. The methodology developed and the analysis tools tested on carcinoma cell lines, demonstrated that spectra could be distinguished based on the cell line phenotypic nature. <p>The potential of IR imaging for breast tissular structure differentiation was highlighted in this thesis, demonstrating that spectral signature can be correlated with the major histological cell types observed in breast disease tissues. In order to develop a robust algorithm translating spectral data into helpful histopathological information, a spectral database of histologically well-defined breast tissues was built and used for the development of a cell type classifier. This latter one was extensively validated on independent clinical cases. Firstly, the IR-based histopathological classifier correctly assigned spectra acquired on eleven breast disease samples based on their histological nature. Secondly, lymphocyte and Collagen & Fibroblasts spectral signatures were demonstrated to be independent from tissue type and organ since, although trained on reference spectra recorded into breast disease samples, the cell type classifier correctly assigned spectra acquired on lymph nodes/tonsils and scar tissues respectively. Thirdly, we concluded that spectroscopically, breast carcinoma cell lines in culture are well-suited tumour models since spectra acquired on these carcinoma cell lines were correctly recognized as epithelium by the IR-based histological classifier. <p>By spectral characterizing lymphocytes from lymph nodes and tonsils, we demonstrated that the spectra acquired contained enough information to statistically discriminate them according to their lymphocyte activation states. Although considered as activated, the breast disease lymphoid infiltrates were found to present distinct spectral signature from lymphocytes acquired on activated lymph nodes and tonsils. Furthermore, tumour microenvironment, characterized by IR-imaging was demonstrated to exhibit a distinct spectral signature from wound healing tissues. These studies proved the uniqueness of the signature of both lymphoid infiltrate and tumour microenvironment in breast disease context. Correlating these specific spectral signatures to patient outcome and therapeutics response could help better consider the uniqueness of the patient. In a last step, considering the epithelial signature of carcinomas of both low and high grades, we demonstrated that the biochemical information reflected in the IR micro-spectra was clinically relevant for grading purpose.<p><p> <p><p>Le cancer du sein est le cancer le plus fréquemment diagnostiqué chez les femmes dans les pays occidentaux. Jusqu’à peu, les cellules épithéliales tumorales étaient vues comme les seuls acteurs de la carcinogenèse ;processus se déroulant dans un milieu extracellulaire considéré au pire comme passif ou permissif à l’évolution tumorale des cellules épithéliales adjacentes. Cependant, de nombreuses études ont montré que ce microenvironnement tumoral pouvait soit promouvoir le processus de carcinogenèse soit le combattre empêchant par la même, l’occurrence de la maladie. <p>Ce projet de thèse s’inscrit dans une problématique actuelle, à savoir une meilleure compréhension de la maladie mais également une prise en charge plus individualisée des patientes. Nous abordons ici une voie de recherche novatrice basée sur la signature globale des molécules cellulaires via leur spectre infrarouge. La technologie utilisée, à savoir la spectroscopie infrarouge, nous fournit une observation quantitative et qualitative de milliers de vibrations moléculaires. L’adaptation de réseaux de plusieurs milliers de détecteurs indépendants aux microscopes infrarouges permet, grâce aux méthodes statistiques multivariées, d’investiguer l’architecture macromoléculaire des cellules au sein d’une coupe tissulaire et de corréler les informations spectrales ainsi obtenues à l’histopathologie des tissus. Par cette technologie, nous visons à mettre au point un outil diagnostique et pronostique pour le cancer du sein basé sur l’imagerie IR. <p>Durant ce projet, nous avons montré que les différents types cellulaires observés dans les carcinomes mammaires pouvaient être distingués par le biais de leur spectre IR, qu’un modèle de reconnaissance histologique pouvait être construit, validé et surtout automatisé et que ce modèle pouvait être transposé à l’étude d’autres tissus (ganglions, amygdales et cicatrices) et d’autres types d’échantillons (cellules épithéliales en culture). Nous avons également montré que les spectres de cellules épithéliales pouvaient être corrélés au grade histopathologique de la tumeur. Les spectres acquis de ganglions/amygdales ont montré que les profils spectraux pouvaient être corrélés à l’état d’activation lymphocytaire. De plus, l’étude de l’état d’activation lymphocytaire et fibroblastique a permis de mettre en avant un profil spectral propre et bien distinct des infiltrats lymphocytaires d’une part et de la matrice extracellulaire aux abords des tumeurs invasives d’autre part. <p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

<p>Lipids and sodium (²³Na) are two essential components of the human body. They play a role in almost all biological systems. However, an increase in their levels is associated with metabolic diseases. The elevation of their contents can cause similar health disorders. Examples of prevalent disorders that share an increase of musculoskeletal lipids and ²³Na are hypertension and diabetes. However, the relationship between in vivo lipid and sodium levels in pathophysiology has not been studied enough and therefore is still unclear. Additionally, the available quantification methods to facilitate such a study may not be practical. They are either invasive, not sensitive enough, or require an impractical measurement time.</p> <p>Therefore, in this work, our aims were to develop practical in vivo methods to quantify the absolute sodium concentration as well as the concentration of each lipid component individually, and to study the correlation between them within the skeletal muscles.</p> <p>Since lipids and ²³Na have different nuclear magnetic resonance properties, their quantification by magnetic resonance (MR) techniques face different challenges. Thus, we optimized different MR spectroscopic imaging (MRSI) techniques for lipids and ²³Na. </p> <p>Our proposed proton MRSI was able to provide eight lipid fat fraction (FF) maps representing each musculoskeletal lipid component (fatty acid) detected by our MRSI technique, and demonstrated a superior sensitivity compared to the conventional MR imaging methods.</p> <p>For ²³Na, our developed ²³Na-MRSI was able to measure and map the absolute ²³Na concentration with values agreeing with those reported previously in biopsy studies, and with a high repeatability (CV < 6 %) within significantly shorter acquisition time compared to other available techniques.</p> <p> Finally, the ²³Na concentration and the fat fractions of each lipid component within healthy skeletal muscles were measured and correlated using our developed MRSI methods. Our findings suggest a positive regional relationship between ²³Na and lipids and negative correlation between ²³Na and BMI under healthy conditions.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / Osteogenesis imperfecta is a rare congenital disease commonly characterized by brittle bones caused by mutations in the genes encoding Type I collagen, the single most abundant protein produced by the body. The murine model (oim) exists as a natural mutation of this protein, converting its heterotrimeric structure of two Col1a1 molecules and a single Col1a2 molecule into homotrimers composed of only the former. This defect impacts bone mechanical integrity, greatly weakening their structure. Femurs from male wild type (WT), heterozygous (oim/+), and homozygous (oim/oim) mice, all at 12 weeks of age, were assessed using assays at multiple length scales with minimal sample processing to ensure a near-physiological state. Atomic force microscopy (AFM) demonstrated detectable differences in the organization of collagen at the nanometer scale that may partially attribute to alterations in material and structural behavior obtained through mechanical testing and reference point indentation (RPI). Changes in geometric and chemical structure through the use of µ-Computed Tomography and Raman spectroscopy respectively indicate a smaller, brittle phenotype caused by oim. Changes within the periodic D-spacing of collagen point towards a reduced mineral nucleation site, supported by reduced mineral crystallinity, resulting in altered material and structural behavior in oim/oim mice. Multi-scale analyses of this nature offer much in assessing how molecular changes can compound to create a degraded, brittle phenotype.