<p>    </p> <p>Cerebrovascular diseases, such as stroke, constitute the most common life-threatening neurological disease in the United States. To support normal brain function, maintaining adequate brain perfusion (i.e., cerebral blood flow (CBF)) is important. Therefore, it is crucial to assess the brain perfusion so that early intervention in cerebrovascular diseases can be applied if abnormal perfusion is observed. The goal of my study is to develop metrics to measure the brain perfusion through modeling brain physiology using resting-state and task-based blood-oxygenation-level- dependent (BOLD) functional MRI (fMRI). My first and second chapters focused on deriving the blood arrival time using the resting-state BOLD signal. In the first chapters, we extracted the systemic low-frequency oscillations (sLFOs) in the fMRI signal from the internal carotid arteries (ICA) and the superior sagittal sinus (SSS). Consistent and robust results were obtained across 400 scans showing the ICA signals leading the SSS signals by about 5 seconds. This delay time could be considered as an effective perfusion biomarker that is associate with the cerebral circulation time (CCT). To further explore sLFOs in assessing dynamic blood flow changes during the scan, in my second chapter, a “carpet plot” (a 2-dimensional plot time vs. voxel) of scaled fMRI signal intensity was reconstructed and paired with a developed slope-detection algorithm. Tilted vertical edges across which a sudden signal intensity change took place were successfully detected by the algorithm and the averaged propagation time derived from the carpet plot matches the cerebral circulation time. Given that CO₂ is a vasodilator, controlling of inhaled CO₂ is able to modulate the BOLD signal, therefore, as a follow-up study, we focused on investigating the feasibility of using a CO₂ modulated sLFO signal as a “natural” bolus to track CBF with the tool developed from the second chapter. Meaningful transit times were derived from the CO₂-MRI carpet plots. Not only the timing, the BOLD signal deformation (the waveform change) under CO₂ challenge also reveals very useful perfusion information, representing how the brain react to stimulus. Therefore, my fourth chapter focused on characterizing the brain reaction to the CO₂ stimulus to better measure the brain health using BOLD fMRI. Overall, these studies deepen our understanding of fMRI signal and the derived perfusion parameters can potentially be used to assess some cerebrovascular diseases, such as stroke, ischemic brain damage, and steno-occlusive arterial disease in addition to functional activations. </p>

This qualitative study examines an asynchronous online course from a private university utilizing a template model for all online courses to provide students with consistent navigation and course structure throughout their degree program. The asynchronous online courses are purposely created using three criteria of quality course design: navigation is intuitive, information is chunked, and instructions are written clearly. A two-part usability test was conducted with three internal and three external participants. The two-part usability test focused on course navigation and examined the signaling, segmenting, and coherence principles applied to course content page layouts. Transcripts from the usability tests and observational field notes were coded through an iterative process in Nvivo. Through emic and etic coding, seven main categories were identified: user experience, cognitive load, multimedia learning principles, page design and layout attributes, course navigational attributes, course attributes and information, and participant navigational behavior. The findings for first-day navigation, general navigational behaviors, and perceptions of design elements used to implement the signaling, segmenting, and coherence principle are discussed. Course design recommendations for creating a positive usability experience and suggestions for future research are provided.

The physical complications of Type 1 diabetes mellitus (T1DM) have been understood as an accelerated ageing process (Morley, 2008). Do people with T1DM also experience accelerated cognitive and brain ageing? Using findings from research of the normal cognitive and brain ageing process and conceptualized in theories of the functional brain changes in cognitive ageing, a combination of cognitive testing and functional magnetic resonance imaging (fMRI) techniques were used to evaluate evidence of accelerated cognitive and brain ageing in middle-aged adults with T1DM. The first part of this thesis comprises a cognitive study of 94 adults (≥ 45 years of age) with long duration (≥ 10 years) of T1DM. Participants completed cognitive assessment and questionnaires on general mood and feelings about living with diabetes. Findings highlighted the importance of microvascular disease (specifically retinopathy) as an independent predictor of cognitive function. The incidence and predictors of mild cognitive impairment (MCI) were then explored. Results indicate a higher percentage of the group met criteria for MCI than expected based on incidence rates in the general population, providing initial evidence of accelerated cognitive ageing. Psychological factors were explored next. The relationship between the measures of well-being, diabetes health, and cognitive function highlighted the need for attention to patient's psychological well-being in diabetes care. Finally, a subgroup of 30 participants between the ages of 45 and 65 who differed on severity of retinopathy were selected to take part in an fMRI study. Blood oxygen level dependent (BOLD) activity was evaluated while participants were engaged in cognitive tasks and during rest. The findings provided evidence that the pattern of BOLD activation and functional connectivity for those with high severity of retinopathy are similar to patterns found in adults over the age of 65. In line with the theories of cognitive ageing, functional brain changes appear to maintain a level of cognitive function. Evidence of accelerated brain ageing in this primarily middle-aged group, emphasizes the importance of treatments and regimens to prevent or minimize microvascular complications.

Les récents développements en RMN et IRM ont eu un impact spectaculaire sur l’imagerie médicale et aident à appréhender de manière fonctionnelle et non invasive de nombreux mécanismes cérébraux. L’imagerie par RMN de perfusion a notamment une importance primordiale en neuroimagerie clinique dans la caractérisation de nombreux désordres cérébrovasculaires (tumeurs cérébrales, AVC). Cependant il n’existe pour le moment aucune technique qui quantifie de manière non-invasive le bon fonctionnement du réseau microvasculaire cérébral. Cette thèse se concentre sur l’utilisation de la séquence FENSI en imagerie préclinique à haut et ultra haut champ magnétique pour caractériser et quantifier la dynamique des flux microvasculaires dans le cerveau du rat. Nous présentons les enjeux de l’IRM de perfusion en neuroimagerie, ainsi que les contraintes associées aux méthodes conventionnelles – méthode de marquage de spin artériel (ASL) et IRM dynamique de contraste de susceptibilité magnétique (DSC-MRI) – dont la technique FENSI peut d’affranchir. Cependant d’autres problèmes sont adressés. Les images acquises avec FENSI et pondérées en flux peuvent être contaminées par des effets de transferts d’aimantation (MT) qui empêchent de quantifier le débit sanguin cérébral. Une première technique de correction de ces effets par post-traitement est proposée. Nous dérivons les premières cartes de flux sanguin cérébral chez le rat à 7 tesla. Une seconde approche est considérée, où les effets MT dans les images acquises avec et sans saturation des spins circulant dans le réseau capillaire (tag/control) se compensent. Cette seconde approche permet une vraie quantification non-invasive du flux sanguin cérébral (CBFlux) in-vivo. Le réseau microvasculaire est caractérisé via FENSI à différents stages du développement tumoral dans un modèle de gliosarcome cérébral (9L) chez le rat. Les mesures de flux mettent en évidence une forte hétérogénéité de développement vasculaire des gliosarcomes peu avancés (diamètre inférieur à 3 mm). A un stade avancé, le flux sanguin est significativement plus faible dans la tumeur (-40 %) que dans le sous cortex, en bon accord avec la littérature sur ce type de gliosarcome. De plus, les cartes paramétriques de flux permettent de distinguer différents compartiments dans la tumeur. Une comparaison avec une méthode de marquage endothélial sur coupes histologiques suggère que le flux sanguin calculé avec FENSI est corrélé avec la concentration locale en micro-vaisseaux. Nous avons également tentés d’évaluer la dynamique temporelle de la réponse vasculaire à un stimulus et d’appliquer FENSI à l’IRM fonctionnelle (IRMf). Nous avons mis en place un protocole d’IRMf chez le rat à 7 tesla et caractérisé la réponse hémodynamique obtenue par contraste BOLD. A 7 tesla la technique FENSI souffre d’un faible SNR temporel et semble plus adaptée pour quantifier des changements métaboliques associées à de longues plages temporelles. L’implémentation de la séquence à ultra-haut champ (17.2 tesla) donne lieu à de sérieux espoirs en IRMf. De plus, nous mettons en évidence à 17.2 tesla des contrastes spécifiques à l’utilisation de différents anesthésiques utilisés en routine à l’hôpital. La méthode que nous avons mise en place peut être sensibilisée à de nombreuses vitesses, augmentant le nombre de ses applications potentielles. Ainsi, un choix judicieux de paramètres permet d’explorer le volume sanguin ou l’orientation du débit ciblé. Les forces et faiblesses de la méthode sont détaillées. L’utilisation de FENSI n’est en général pas justifiée par un gain de signal par rapport à des séquences ASL optimisées, mais bénéficie de l’actuelle montée en champ des imageurs cliniques pour être étudiée. Les applications potentielles varient de l’IRMf et l’imagerie de diffusion au suivi pharmacologique et diagnostic de désordres cérébrovasculaires, dont l’étude via ASL est limitée dû à l’allongement des temps de transit sanguins. / The discoveries, implementations and developments of NMR and MRI have had a major impact in medical imaging. Compared to other imaging modalities (PET, SPECT, CT), current MRI research helps to further and better understand the inner mechanisms of the human body in a less invasive manner. In clinical neuroimaging, perfusion MRI is of spectacular importance to study cerebrovascular diseases and cancer. However, at the moment, there is no perfusion MRI sequence that allows for a complete, non-invasive and precise quantification of microvascular flow dynamics. This work focuses on the use of the recently introduced Flow Enhanced Signal Intensity method (FENSI) to characterize and quantify vasculature at capillary level, at high and ultra high magnetic field (7 and 17.2 tesla). For that purpose, the possible quantification of blood flux with FENSI is explored in vivo. The combination of flux quantification and flow-enhanced signal (compared to Arterial Spin Labeling) can make of FENSI an ideal method to characterize in a complete non-invasive way the brain microvasculature. After removal of magnetization transfer (MT) effects, the blood flow dynamics are studied with FENSI in a very aggressive and propagative rat brain tumor model: the 9L gliosarcoma. The objective is to assess whether FENSI is suitable for a longitudinal non-invasive characterization of microvascular changes associated with tumor growth. The results obtained with FENSI are compared with literature on 9L perfusion and immuno-histochemistry. In the first paper published on FENSI, a first glance was also casted on the potential of the flow enhanced technique when applied to fMRI. The results obtained at the time were contaminated by MT effects. With the implementation of a new MT-free FENSI technique, the possibility to map the brain cerebral functioning based on a quantitative physiological parameter (CBFlux) more directly related to neuronal activity than the usual BOLD signal is within reach. At ultra high field, the influence of different anesthetics on the rat brain microvascular network and BOLD contrast is also considered. After many developments around the FENSI technique, the method is compared to classical ASL and DSC perfusion MRI sequences. The strengths and weaknesses of the FENSI method, its characteristics, ‘precautions for use’, and potential main applications are detailed and discussed.

This thesis deals with the analysis of brain function in Magnetic Resonance Imaging (MRI) using two sequences: BOLD functional MRI (fMRI) and Arterial Spin Labelling (ASL). In this context, group statistical analyses are of great importance in order to understand the general mechanisms underlying a pathology, but there is also an increasing interest towards patient-specific analyses that draw conclusions at the patient level. Both group and patient-specific analyses are studied in this thesis. We first introduce a group analysis in BOLD fMRI for the study of specific language impairment, a pathology that was very little investigated in neuroimaging. We outline atypical patterns of functional activity and lateralisation in language regions. Then, we move forward to patient-specific analysis. We propose the use of robust estimators to compute cerebral blood flow maps in ASL. Then, we analyse the validity of the assumptions underlying standard statistical analyses in the context of ASL. Finally, we propose a new locally multivariate statistical method based on an a contrario approach and apply it to the detection of atypical patterns of perfusion in ASL and to activation detection in BOLD functional MRI.

L’action des conseillers du roi de France dans le domaine artistique, et notamment architectural, au tournant des XIIIe et XIVe siècles, a été abordée dans le cadre d’études monographiques, mais n’a jamais été envisagée dans un souci de synthèse. Recenser les bâtiments et les œuvres d’art réalisés à l’initiative de ces individus dans l’ancien royaume de France, les confronter avec les entreprises et les commandes royales permet de comprendre les motivations et l’impact d’un milieu alors en plein essor, celui des grands officiers royaux et des hommes de confiance qui assistaient quotidiennement le roi et l’aidaient à gouverner. L’époque retenue couvre les règnes des derniers Capétiens, Philippe le Bel (1285-1314) et ses trois fils (1314-1328). Il a semblé souhaitable d’étendre l’étude en amont au règne de Philippe le Hardi (1270-1285), afin de prendre en compte les prémices d’un véritable phénomène, par ailleurs très diversifié : lancement de projets architecturaux de grande ampleur destinés à l’usage propre du conseiller et de sa famille, embellissement d’édifices existants, participation à de grands chantiers en cours (cathédrales), commandes de tombeaux, d’œuvres d’art destinées à orner des fondations pieuses, réalisation d’hôpitaux ou d’édifices utilitaires ; beaucoup d’exemples témoignent de l’ambition comme de la piété de ces hommes. Dans les textes mais également dans le paysage monumental français actuel, il a été possible de retrouver de nombreuses traces de cette action, dont une typologie a été établie. L’étude a pour but de répondre aux questions suivantes : les conseillers du roi partageaient-ils le même mode de vie et avaient-ils des goûts communs ? Leur action fut-elle en tout point semblable à celle des membres de la famille royale et de la haute noblesse ? Peut-on mesurer la portée de ces réalisations ? / The action of the councillors of the French king in the artistic domain, particularly architectural, at the turn of the XIIIth and XIVth centuries, aroused a large number of monographic studies, but has never been envisaged in a concern of synthesis. Listing buildings and works of art commissioned by these individuals in the realm of France, confronting them with those patronized by the king, let us understand the motivations and the influence of an environment then in full development, that of the royal officers who assisted the king and helped him to govern. The chosen period covers the reigns of the last Capetians, Philip the Fair (1285-1314) and his three sons (1314-1328). It seemed worthwhile to widen the study area to include the reign of Philip the Bold (1270-1285) in order to take into account the beginnings of the phenomenon, besides very diversified : launch of large-scale architectural projects intended for the councillor and his family, embellishment of existing buildings (like cathedrals), production of gravestones, execution of works of art made to “decorate” pious foundations, construction of hospitals or utilitarian buildings ; many examples show the ambition as the devotion of these men. In texts but also in current French architectural landscape, it has been possible to find numerous traces of this action, a typology of which has been proposed. The study aims at answering the following questions : did the king’s councillors share the same lifestyle, the same tastes ? Was their action completely similar to that of the members of the royal family and the nobility ? Can we measure the reach of these creations ?

The aim of the thesis is to define the dependency of the classification of patients affected by neurodegenerative diseases on the choice of the parcellation atlas. Part of this thesis is the application of the functional connectivity analysis and the calculation of graph metrics according to the method published by Olaf Sporns and Mikail Rubinov [1] on fMRI data measured at CEITEC MU. The application is preceded by the theoretical research of parcellation atlases for brain segmentation from fMRI frames and the research of mathematical methods for classification as well as classifiers of neurodegenerative diseases. The first chapters of the thesis brings a theoretical basis of knowledge from the field of magnetic and functional magnetic resonance imaging. The physical principles of the method, the conditions and the course of acquisition of image data are defined. The third chapter summarizes the graph metrics used in the diploma thesis for analyzing and classifying graphs. The paper presents a brief overview of the brain segmentation methods, with the focuse on the atlas-based segmentation. After a theoretical research of functional connectivity methods and mathematical classification methods, the findings were used for segmentation, calculation of graph metrics and for classification of fMRI images obtained from 96 subjects into the one of two classes using Binary classifications by support vector machines and linear discriminatory analysis. The data classified in this study was measured on patiens with Parkinson’s disease (PD), Alzheimer’s disease (AD), Mild cognitive impairment (MCI), a combination of PD and MCI and subjects belonging to the control group of healthy individuals. For pre-processing and analysis, the MATLAB environment, the SPM12 toolbox and The Brain Connectivity Toolbox were used.

The work describes the theoretical foundations of modern methods of creating new fonts, that is, using information technology, specifically vector programs. It also marginally shows the history of the font, Roman writing, the basic division of its compositions and describes its individual elements. The next part of the project focuses on creating digital fonts and continues with bringing it to live using algorithms and methods that can easily be processed in Matlab programming language. The method of implementation of the bringing the typeface to live is described and presentation of the generated results are then shown in few examples. Attention is also paid to the coordinates system, which is very important to solve geometric transformations, and two-dimensional vector graphics, which are widely used in the design and to render the fonts. Bézier curves and cubic Bézier curves are described in further detail along with vector graphics rasterization. One part of this text describes very important de Casteljau algorithm. The last chapter focuses on implementation in Matlab programming language, the creation of curves, that means single font characters, and the ways of how the algorithm works with transformations. Some sample images showing transformations using different input arguments are displayed in this section as well. There is evaluation of the contribution of this application and the possibilities of further expansion at the end.

Functional magnetic resonance imaging (fMRI) is recent important method, used in neuroimaging. The aim of this thesis is to develop software tool for comparison of two methods for functional and effective connectivity estimation. In this thesis are described the basics of magnetic resonance imaging, fMRI, basic terms of fMRI experiments and generally are described methods of functional and effective connectivity. Then are more detailed mentioned methods of dynamic causal modeling (DCM), Granger causal modeling (GCM) and independent component analysis (ICA). Practical implementation of DCM in toolbox SMP and ICA in toolbox GIFT is also mentioned. In purpose to describe behavior of DCM and GCM in dependence on several parameters are performed Monte Carlo simulations. Then the concept and realization of software tool for simulating connectivity and comparison of DCM and GCM are described. Finally results of DCM and GCM comparison and results of Monte Carlo simulations are discussed.

<p>Alzheimer’s disease (AD) is a degenerative disease with progressive deterioration of neural networks in the brain. Fractal dimension analysis (FD) of resting state blood oxygen level dependent (BOLD) signals acquired using functional magnetic resonance imaging (fMRI) allows us to quantify complex signalling in the brain and may offer a window into the network erosion. This novel approach can provide a sensitive tool to examine early stages of AD. As AD progresses, we expect to see a reduction in brain connectivity and signal complexity concurrent with biochemical changes (e.g. altered levels of N-acetyl aspartate (NAA), myoinositol (mI) and glutamate as measured using magnetic resonance spectroscopy, MRS), volumetric changes and abnormally high levels of brain iron.</p> <p>Over a series of 4 studies we examined the relationship of BOLD signal complexity and functional connectivity with documented MRI markers of pathology in AD (n=38) as compared to normal controls (NC) (n=16). AD subjects were in early stage of illness (mild to moderate impairment on the mini mental state exam, MMSE). We validated the temporal (short term (within minutes) and longer term (over a number of months)) consistency of FD measurement and choice of BOLD acquisition method (spiral vs. EPI), provided MRI sequence repeat time (TR) was kept constant. FD reduction (decrease in signal complexity) correlated with worsening pathological values on MRS (­NAA decrease and mI increase) and with a decrease in functional connectivity. This demonstrates that FD (signal complexity) reduces in proportion to AD severity. FD reduction is connected to functional connectivity measured through resting state network (RSN) analysis suggesting the reduction in FD relates to neuronal loss rather than altered vascularity. The narrow range of cognitive impairment (such as scores on the MMSE or the clinical dementia rating scale, CDR) likely precluded correlation between these measures and FD or RSN. Functional connectivity (RSN) was also reduced when brain iron levels were increased within certain network nodes (posterior cingulate cortex and lateral parietal cortex). Therefore iron deposition may play a role in network disruption of AD brains.</p> <p>The overall conclusion of this thesis is that signal complexity of BOLD fMRI signals, as measured with FD, may detect early pathology in the progression of AD. FD can detect neuronal changes in deep brain structures before volume loss in these structures and before significant changes in MRS markers were detectable between the AD and NC groups. An FD change mirrors disruptions in functional connectivity but detection is not limited to RSN nodes in the brain. This novel approach could further our understanding of AD and may be applied to other pathologies of the brain.</p> / Doctor of Philosophy (PhD)