In this thesis we were interested in combining functional connectivity (from functional Magnetic Resonance Imaging) and structural connectivity (from Diffusion Tensor Imaging) with a data fusion approach. While data fusion approaches provide an abundance of information they are underutilized due to their complexity. To solve this problem, we integrated the ease of a neuroimaging toolbox, known as the Functional And Tractographic Analysis Toolbox (FATCAT) with a data fusion approach known as the anatomically weighted functional connectivity (awFC) approach - to produce a practical and more efficient pipeline. We studied the connectivity within resting-state networks of different populations using this novel pipeline. We performed separate analyses with traditional structural and functional connectivity for comparison with the awFC findings - across all three projects. In the first study we evaluated the awFC of participants with major depressive disorder compared to controls. We observed significant connectivity differences in the default mode network (DMN) and the ventral attention network (VAN). In the second study we studied the awFC of MDD remitters compared to non-remitters at baseline and week-8 (post antidepressant), and evaluated awFC in remitters longitudinally from baseline to to week-8. We found significant group differences in the DMN, VAN, and frontoparietal network (FPN) for remitters and non-remitters at week-8. We also found significant awFC longitudinally from baseline to week-8 in the dorsal attention network (DAN) and FPN. We also tested the associations between connectivity strength and cognition. In the third study we studied the awFC in children exposed to pre- and postnatal adversity compared to controls. We observed significant differences in the DMN, FPN, VAN, DAN, and limbic network (LIM). We also assessed the association between connectivity strength in middle childhood and motor and behavioural scores at age 3. Therefore, the FATCAT-awFC pipeline, we designed was capable of identifying group differences in RSN in a practical and more efficient manner. / Thesis / Doctor of Philosophy (PhD)

Children and adolescents with concussion display aberrant functional connectivity in some of the major neurocognitive networks. This includes the Default Mode Network, Central Executive Network and Salience Network. Using resting state fMRI, the purpose of this thesis was to explore the functional connectivity of cognition-related networks in youth experiencing concussion. With a prospective cohort study, the functional connectivity (defined as the temporal coherence between spatially separated brain regions) of children and adolescents ages 10-18 years old was evaluated in relation to a number of demographic and injury-specific factors including recovery length, age at the time of injury, symptom severity, and neurocognitive performance. The results showed two general trends: (1) a reduction in connectivity (i.e., hypoconnectivity) between the regions of the Default Mode Network, and (2) an increase in connectivity (i.e., hyperconnectivity) between additional sensory-related regions like the cerebellum and hippocampus. The Default Mode Network, which processes self-referential information, has a long-protracted development across childhood through adulthood. Given that the participants in this cohort exhibited reduced functional connectivity within the Default Mode Network and between the Default Mode Network and other neurocognitive networks suggests that this is an area of vulnerability in youth in the event of concussion. Increased connectivity between the Central Executive Network and Salience Network, and between cognitive- and sensory-related regions such as the hippocampus and cerebellum might be interpreted as a compensatory mechanism to supplement deficits of the Default Mode Network. This thesis sheds light on important concussion-related regions for future research to investigate further and delves into the possible neural mechanisms contributing to the cognitive, sensory, mood, and sleep disturbances in children and adolescents with concussion. / Dissertation / Doctor of Philosophy (PhD) / Your brain at rest is not resting. In fact, your many brain regions are continuously communicating even during rest to maintain important communication between them. This communication between brain regions is termed functional connectivity. When you receive a blow to the head, face, neck, or another part of your body that senses a biomechanical force to your brain, the functional connectivity (i.e., communication lines) between your brain regions may be altered. A blow of this nature is considered a concussion, also known as a mild traumatic brain injury. With disruptions to the typical functional connectivity between your brain regions following a concussion, you may experience difficulty in managing cognitive tasks, emotions, and body coordination. Among those most vulnerable to the effects of concussion are children and adolescents whose brains have yet to develop fully. The goal of this thesis was to evaluate the functional connectivity between brain regions of children and adolescents to determine how brain communication might be disrupted following concussion. These evaluations were done using functional magnetic resonance imaging (fMRI) of the brains of children and adolescents ages 10-18 years old. It was discovered that the functional connectivity of the frontal lobe is related severity of post-concussion symptoms such that individuals with worse symptoms had reduced functional connectivity in the frontal lobe compared to individuals who reported less severe symptoms. Further, children and adolescents with longer recovery periods have a different level of functional connectivity in the temporal lobe compared to youth with relatively shorter recovery periods. This might suggest that both of these regions could provide prognostic value in determining who might have worse symptoms or a longer recovery time following injury. In comparison to children and adolescents who have not had a concussion, children and adolescents experiencing a concussion are more likely to have abnormal functional connectivity between the hippocampus and cerebellum, which are particularly involved in processing sensory information and navigation. This was interpreted to mean that the brain responded to the concussion by increasing the communication between regions that might help a child with a concussion coordinate their bodies so that they can move from place to place. This was additionally supported by a further investigation which showed that children and adolescents have reduced communication between areas of the brain that might allow them to process information about the self (e.g., memories, sensations, relationships with others, etc.). Overall, the results demonstrated that following a concussion, children and adolescents may have a deficit in the functioning of the frontal lobe in a specific region that allows them to process cognitive and sensory information. This might explain why concussion leads to poor memory, body coordination, sensitivity to light and sounds, and even difficulty sleeping. Their brains might then compensate for the disruption by increasing alternate pathways of communication. Together these findings open gateways for future researchers to look more deeply at the specific regions affected by concussion in youth. It draws attention to the many neurocognitive, emotional, and somatic symptoms a child with a concussion exhibits and their symptoms’ underlying neurological processes.

In tropical seascapes, coral reefs often exist in proximity to marine vegetated habitats such as seagrass, mangroves, and macroalgae. This habitat mosaic offers the possibility for connection and exchange of both organisms and nutrition between habitats, mediated by biological and physical processes. This dissertation examines flows of organisms and nutrition between coral reefs and tropical vegetated habitats in the central Red Sea through 3 different mechanisms: 1) Use of multiple habitat types by tropical marine fishes, 2) Transport of algal material to coral reefs via the foraging behavior and movements of herbivorous fishes, and 3) Physical flow of water between coastal habitats. The results of this thesis suggest that coastal tropical habitats maintain a variety of ecological links at different spatial and temporal scales. A large fraction (36%) of fish species found on coral reefs are also found in at least one marine vegetated habitat in the central Red Sea, with many species mainly living in vegetated habitats as juveniles. This demonstrates the value of mangrove, seagrass, and macroalgae habitats to coral reef fishes, and suggests that many species make ontogenetic migrations between reef and non-reef habitats through their lives. Two species of herbivorous reef fishes (Naso elegans and N. unicornis) were found on coral reefs with algae in their guts which likely originated from nearby Sargassum-dominated macroalgae canopies, representing a fish-mediated, cross-habitat flux of nutrition from macroalgae habitats to coral reefs. Finally, we used a combination of remote sensing, a dye tracer study, and in-water measurements to observe water movement from shallow seagrass and mangrove habitats to nearby lagoon and coral reef habitats. Water exiting seagrass and mangrove habitats had altered concentrations of various nutrients (such as increased particulate organic carbon or decreased dissolved nutrients), suggesting that Red Sea mangroves and seagrasses change nutrient concentrations in water and the movement of water from these habitats to coral reefs could supply reefs with an allochthonous source of nutrition. These various linkages, controlled by a range of physical and biological processes, highlight the interconnected nature of tropical coastal ecosystems, and thereby the need to conserve whole habitat mosaics in the pursuit to protect coral reefs and maintain healthy and functioning coastal ecosystems.

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