Le débit sanguin et sa régulation sont des indicateurs importants de la santé des tissus. Leur mesure a de nombreuses applications en recherche fondamentale et clinique. Certaines techniques optiques constituent un moyen intéressant pour la mesure du débit sanguin, car en général elles sont peu invasives et relativement abordables car elles utilisent des systèmes d'illumination continus. Pendant ma thèse, j'ai contribué au développement de techniques de suivi de la circulation sanguine dans des modèles animaux avec la construction d'un dispositif multimodal basé sur la fluxmétrie laser et sur l'imagerie des signaux optiques intrinsèques, capable de mesurer les paramètre hémodynamiques microvasculaire au niveau superficiel du cerveau. Ce dispositif, testé sur des modèles animaux d'accident vasculaire cérébral, est adaptable et peut être utilisé à d'autres fins. En parallèle, j'ai mis au point des nouvelles méthodes expérimentales et des protocoles de traitement d'images qui ont permis de réaliser des études longitudinales. En outre, ce dispositif a été utilisé dans une étude multidisciplinaire pour comprendre le rôle d'une protéine impliquée dans le cas de lésions de reperfusion après un accident vasculaire cérébral ischémique dans des modèles animaux. Ma contribution majeure réside dans le développement de l'imagerie de contraste de speckle spectroscopique et tomographique, nouvelle technique d'imagerie 3D non invasive pour la mesure du débit sanguin en profondeur. Dans l'ensemble, ces contributions permettront le développement de méthodes tomographiques non invasives rentables pour la mesure du débit sanguin chez l'homme. / Blood flow and its regulation are important for the health of tissues and its measurement has many applications in research and clinical environments. Optical techniques are often attractive for the non- or minimally-invasive, continuous and relatively inexpensive measurement of blood flow. This work contributes to the monitoring of blood flow in translational research with the construction of a multimodal device, based on laser speckle flowmetry and optical intrinsic signals, capable of measuring superficial microvascular cerebral blood flow, blood oxygenation and blood volume. This device was applied in animal models of ischemic stroke and is flexible to be modified and used for other purposes. In doing so, I have developed new experimental methods and image processing protocols that allowed us to perform longitudinal studies where the animal can be removed from the device several times. This device has also been used to elucidate the role of the Mannose-binding lectin protein in reperfusion injury after an ischemic stroke in animal models. This led to the main contribution of this work: the development of the speckle contrast optical spectroscopy and tomography, a new non-invasive, optical technique for deep blood flow measurement that paves the way for deeper and three dimensional imaging of blood flow. This new method was first developed from a theoretical perspective. Then it was validated in tissue simulating phantoms and demonstrated to be feasible in measurements on the human arm muscle. Overall, these contributions will allow the development of cost-effective, non-invasive tomographic methods for the measurement of blood flow even in humans.

Near infrared spectroscopy (NIRS) is an emerging neuroimaging modality with high temporal and good spatial resolution. In this thesis, NIRS was applied to understand functionality of the fronto-temporal cortex in response to language-related tasks. A 32-channel NIRS system (Imagent ISS Inc.) was used to perform experimental studies on 15 right-handed normal adults. Block-design based Word Expression and Word Reception paradigms were independently presented to participants. Activation, functional connectivity and cortical lateralization analyses were performed. From word expression studies, results showed left anterior region (encompassing Broca) is majorly involved over right homologue and posterior regions. From the word reception studies, results showed that right posterior region (encompassing right homologue of Wernicke) is highly involved in language reception, with right anterior region (encompassing right homologue of Broca) also involved. The current study has potential future applications in surgical evaluation of language regions in populations with neurological disorders such as epilepsy, and schizophrenia.

Thesis (MSc (Radiography))--Cape Peninsula University of Technology, 2019 / Introduction: Traumatic brain injury (TBI) is frequently associated with mortality and morbidity in low-income countries. Computed Tomography Brain (CTB) imaging aid in the management of patients by accurately exploring primary and secondary brain injuries following trauma. However, there is controversy among researchers on the benefits of follow-up CTB imaging (FCTBI) amongst patients presenting with TBI showing a normal baseline scan. As such, in an attempt to address the contention, the primary focus of this research study was to explore the role of FCTBI with regards to the clinical status of such patients. The secondary focus was to determine the timing of performing FCTBI post TBI. Method: A retrospective cross sectional quantitative design was conducted for this research study. A total sampling strategy was employed on medical records of 85 patients treated at the research site in Zimbabwe. Data were collected over a two year period. Adult patients between the ages of 18 and 75, with TBI and who had a normal first CTBI1 (primary scan done upon hospital admission) were included in this research study. The evolution of different types of brain pathology diagnosed on FCTBI in affected patients were recorded on data collection sheets. An analysis then followed to establish whether the sample patients had developed any neurological complications. Results: The study showed that in 85 patients with TBI, 36% recorded abnormal radiological findings on FCTBI with subdural haematoma (19%) being the most common intracranial lesion followed by intracerebral haemorrhage (8%), subarachnoid haemorrhage (6%) and lastly, pneumocephalus and epidural haematoma (1% respectively). The most frequent causal mechanism of trauma was road traffic accidents (RTAs) at 58%. Males with TBI comprised a higher proportion (53%) than did females (47%). The performance of CTBI1 at 8 hours post trauma occurrence, within a recommended hospital observation period of 20 hours post trauma occurrence, may provide sufficient time for lesions to evolve and thus determine the appropriate patient management. The young adult age group of 26-35 years was found to be more susceptible to TBI. Conclusion: FCTBI was found to be of value in timely detection of evolving intracranial lesions which enabled appropriate management of patients. The current study recommends that patients who exhibit a declining Glasgow Coma Scale (GCS) score and deteriorating neurological status undergo a FCTBI.

Le système des noyaux de la base est principalement impliqué dans le contrôle et l'apprentissage moteur.Le rôle de la voie cortico-striatale a été et est toujours fortement étudié mais le striatum reçoit aussides afférences excitatrices du thalamus, souvent considéré comme un simple relais entre les noyaux dela base et le cortex, formant ainsi des boucles de structures sous-corticales. Les principales afférencesthalamostriatales glutamatergiques proviennent des noyaux thalamiques intralaminaires et forment descontacts synaptiques avec les deux types de neurones efférents GABAergiques du striatum (i- et d-MSNs) et les interneurones cholinergiques (INCs). Le complexe thalamique intralaminaire peut sedistinguer en une partie rostrale (ILTr) contenant les noyaux centrolatéral (CL), paracentral (PC) etcentral médial (CeM) et une partie caudale (ILTc) formée du noyau parafasciculaire (Pf) chez lerongeur (équivalent du complexe parafasciculaire-centromedian chez le primate). Le complexe thalamiqueintralaminaire est souvent considéré comme une structure fonctionnelle homogène, cependant de plus enplus d’études mettent en évidence des différences anatomiques, électrophysiologiques et fonctionnelles desparties rostrales et caudales de l’intralaminaire. Le noyau intralaminaire caudal est de mieux en mieuxdécrit et sa projection striatale se montre impliquée principalement dans la réponse aux stimuli sensorielsainsi que dans la flexibilité motrice. Des données obtenues par Marco Diana et collaborateurs à l’EcoleNationale Supérieure (Paris) apportent un éclairage nouveau sur l'importance du noyau intralaminairerostral, en particulier le noyau centrolatéral, dans le contrôle du mouvement, en montrant que la stimulationoptogénétique de la projection glycinergique/GABAergique ponto-intralaminaire thalamique inhibe les neu-rones thalamiques et provoque une hypolocomotion. Ces résultats indiquent que la suppression de laprojection thalamique sur le striatum mène à une perturbation de la fonction des ganglions de la base.Cette dernière décennie se caractérise par une explosion de nouvelles techniques aussi bien dans lesdomaines d’imagerie que dans les techniques de manipulation génique d’animaux permettant de répondreà certaines questions qui ne pouvaient techniquement pas trouver de réponse jusqu’ici. Ce travail dethèse a pour but de mieux comprendre l’importance des afférences du thalamus intralaminaire sur lestriatum, en particulier sa partie rostrale, qui, de manière surprenante, sont très mal caractérisées. Deplus, les noyaux thalamiques intralaminaires sont un relais entre le cervelet et le striatum, par conséquent,l'analyse de ces connexions pourrait améliorer notre compréhension des maladies neurodégénératives tellesque la maladie de Parkinson impliquant à la fois les noyaux gris centraux et le cervelet, mais dont lesinteractions fonctionnelles n'ont pas encore été décryptées.La première partie de ce travail de thèse consiste en une étude anatomique détaillée des projections duthalamus intralaminaire sur le striatum, en particulier sur ses principales sous-populations (d- et i-MSNs,INCs) et sous-régions (dorso-latéral=DLS, dorso-médian=DMS), par l’utilisation combinée d’un marquagerétrograde monosynaptique et d’une technique de transparisation (« clearing ») permettant par la suitede réaliser une imagerie complète du cerveau à l’aide d’un microscope à feuille de lumière. Les analysesanatomiques réalisées ont permis de confirmer l’existence de projections directes des noyaux thalamiquesintralaminaires sur le striatum dorsal, celles-ci présentant un pattern d’innervation préférentiel pour lesINCs (DMS>DLS) suivi par les dMSNs (DLS>DMS). Les cibles postsynaptiques des projectionsthalamostriatales sont similaires aux projections dopaminergiques, suggérant une interaction étroite entreces afférences.La seconde partie de cette thèse, vise a mieux comprendre l’importance fonctionnelle des connexionsthalamostriatales mises en évidence précédemment dans la locomotion spontanée. Pour cela deux ap-proches seront utilisées: une approche modifiant l’activité de ces neurones par l’utilisation de techniquescomme l’optogénétique et la chémogénétique et une approche descriptive par une technique d’imageriecalcique permettant d’enregistrer l’activité neuronale en temps réel sur des animaux libres de se mouvoir.Les résultats obtenus montrent que l’inhibition de l’ensemble des neurones de l’ILTr est nécessaire pourobserver un phénotype moteur d’hypolocomotion. La mise en place d’un système de détection de motricitéfine et l’enregistrement de l’activité calcique des neurones striataux, nous permettront, à l’avenir, de mieux identifier le type de comportement moteur impliqué dans cette hypolocomotion ainsi que d’évaluer l’impactde cette inhibition thalamique sur l’activité des neurones striataux. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

Indiana University-Purdue University Indianapolis (IUPUI) / A Multigraph is a set of graphs with a common set of nodes but different sets of edges. Multigraph visualization has not received much attention so far. In this thesis, I will introduce an interactive application in brain network data analysis that has a strong need for multigraph visualization. For this application, multigraph was used to represent brain connectome networks of multiple human subjects. A volumetric data set was constructed from the matrix representation of the multigraph. A volume visualization tool was then developed to assist the user to interactively and iteratively detect network features that may contribute to certain neurological conditions. I applied this technique to a brain connectome dataset for feature detection in the classification of Alzheimer's Disease (AD) patients. Preliminary results showed significant improvements when interactively selected features are used.

Indiana University-Purdue University Indianapolis (IUPUI) / Aniridia, a congenital ocular disorder caused by haploinsufficiency of transcription factor PAX6, is characterized by complete or partial iris hypoplasia with associated foveal hypoplasia. Brain imaging performed in patients heterozygous for PAX6 mutations often reveal absence of the brain anterior or posterior commissure, absence of the pineal gland, and a present but reduced in size corpus callosum. Renal coloboma syndrome, another autosomal dominant inherited disease, is characterized by hypodysplastic kidneys and optic nerve defects, and is caused by haploinsufficiency of transcription factor PAX2. In the first part of this thesis we investigated the role of these Pax genes in neural development, by generating an allelic series of knock-in models at the Pax6 locus. We showed that Pax6(5a) and Pax2 could not replace Pax6 for its auto-regulation in lens induction or for neural differentiation in retina. In brain development, however, we demonstrated that cell proliferation in the cerebral cortex and dorsoventral patterning of the telencephalon and neural tube was partially rescued in either knock-in mutant. We believe our novel findings not only reveal Pax-protein functional specificity during neural development, but may also be utilized to understand the aberrant molecular mechanism that result in aniridia and/or renal coloboma syndrome. Aphakia (lack of lens) is a rare human congenital disorder with its genetic etiology largely unknown. In the second part of this thesis, we show that homozygous deletion of Nf1, the Ras GTPase gene underlying human neurofibromatosis type 1 syndrome, caused lens dysgenesis in mouse. While early lens specification proceeded normally in Nf1 mutants, lens induction was disrupted due to deficient cell proliferation. Further analysis showed that ERK signaling was initially elevated in invaginating lens placode, but by lens vesicle stage, Ras signaling antagonist Sprouty2 was up regulated, followed by rapid decrease in ERK phosphorylation. Only after intraperitoneal treatment of U0126, an inhibitor of ERK phosphorylation, was lens development restored in Nf1 mutants. Hyperactive RAS-MAPK signaling is known to cause neuro-cardiofacial-cutaneous (NCFC) syndromes in human. As a member of NCFC family genes, Nf1 represents the first example that attenuation of Ras-MAPK kinase signaling pathway is essential for normal lens development.

published_or_final_version / Psychology / Master / Master of Philosophy

Confocal microscopes utilize point illumination and pinhole detection to reject out-of-focus light. Because of the point illumination and detection pinhole, confocal microscopes typically utilize point scanning for imaging, which limits the overall acquisition speed. Due to the excellent optical sectioning capabilities of confocal microscopes, they are excellent tools for the study of three-dimensional objects at the microscopic scale. Fluorescence confocal microscopy is especially useful in biomedical imaging due to its high sensitivity and specificity. However, all designs for confocal microscopes must balance tradeoffs between the numerical aperture (NA), field of view (FOV), acquisition speed, and cost during the design process. In this dissertation, two different designs for an array confocal microscope are proposed to significantly increase the acquisition speed of confocal microscopes. An array confocal microscope scans an array of beams in the object plane to parallelize the confocal microscope to significantly reduce the acquisition time. If N beams are used in the array confocal microscope, the acquisition time is reduced by a factor of N. The first design scans an array of miniature objectives over the object plane to overcome the trade-off between FOV and NA. The array of objectives is laterally translated and each objective scans a small portion of the total FOV. Therefore, the number of objectives used in the array limits the FOV, and the FOV is increased without sacrificing NA. The second design utilizes a single objective with a high NA, large FOV, and large working distance designed specifically for whole brain imaging. This array confocal microscope is designed to speed up the acquisition time required for whole brain imaging. Utilizing an objective with a large FOV and scanning using multiple beams in the array significantly reduces the time required to image large three-dimensional volumes. Both array confocal microscope designs use beam-splitting gratings to efficiently split one laser beam into a number of equal energy outgoing beams, so this dissertation explores design methods and analyses of beam-splitting gratings to fabrication errors. In this dissertation, an optimization method to design single layer beam-splitting gratings with reduced sensitivity to fabrication errors is proposed. Beam-spitting gratings are typically only designed for a single wavelength, so achromatic beam-splitting grating doublets are also analyzed for possible use in array confocal microscopes with multiple excitation wavelengths. An analysis of the lateral shift between grating layers in the achromatic grating doublet proves grating profiles with constant first spatial derivatives are significantly less sensitive than continuous phase profiles. These achromatic grating doublets have designed performance at two wavelengths, but the diffraction angles at the two wavelengths differ. To overcome that limitation, scale-invariant achromatic gratings are designed, which not only provide designed performance at two wavelengths, but also equal diffraction angles at two wavelengths.

A worldwide demographic shift is currently occurring, with rapidly increasing numbers of elderly individuals. Since the incidence of neurodegenerative disease generally increases with age, this entails an increase in dementia prevalence. There are several strong incentives for establishing robust and widely available imaging methods for the early diagnosis of these diseases. Atrophy patterns are evident only late in the disease process, and the distinction from healthy ageing can often be elusive. For early diagnosis, physiologic parameters such as perfusion or metabolism must be assessed. The available modalities all have restricted clinical usefulness. The main aim of this thesis was to advance the clinical usefulness of perfusion and metabolism imaging in patients with neurodegenerative dementia, with a focus on visual assessment. A cohort of patients with neurodegenerative dementia was included, along with an age-matched control group. All subjects underwent MRI, including a pseudocontinuous ASL sequence and FDG-PET. In papers II and III, a subgroup containing both patients and controls underwent a second FDG-PET with reduced dose. In paper IV, the material was combined with a similar cohort from Amsterdam. Paper I showed that spatial smoothing increased the correlation between visually assessed perfusion and metabolism levels as displayed with FDG-PET. However, the distinction between patients and healthy controls was less satisfactory due to false positives. Paper II showed that differences in regional standard uptake value ratios between normal- and low-dose FDG-PET were small and without clinically significant bias. Paper III showed that the diagnostic performance of Z-score maps showing regions of significant deficits in metabolism was highly similar in normal- and low-dose FDG-PET images.  Paper IV showed that ASL perfusion-based Z-score maps can be used for diagnostic purposes with high specificity, but inferior sensitivity, compared to FDG-PET. In conclusion, the included studies address aspects of the visual assessment of perfusion and metabolism neuroimaging, with a focus on clinical usefulness in diagnosing neurodegenerative dementia.

This thesis combines phenomenological and neuroscientific research to elucidate the effects of psychedelic agents on the human brain, mind and psychological well-being. Psychoactive plants have been used for thousands of years for ceremonial and ritual purposes. Psychedelics are psychoactive substances that affect cognitive processes and alter perception, thoughts, and mood. Illegalization of psychedelics in the 1960s rendered them impossible to study empirically but in the last couple of decades, relaxed legal restrictions regarding research purposes, renewed interest in the effects of psychedelic drugs and new brain imaging techniques have started to reveal the possibilities of these mind-altering substances. Psychedelics mainly affect the serotonin receptor 5-HT2A which in turn affect the functioning of largescale cortical areas by changing cerebral blood flow, alpha oscillations, and functional connectivity. These cortical changes not only induce immediate alterations in perception and cognition but have been shown to have positive effects in therapeutic interventions for depression, anxiety, and addiction, and also positively affect well-being in general. Although the pharmacology and neurobiology of psychedelics are still poorly understood, the potential benefits justify empirical research on psychedelics in humans.