This thesis investigated the effect of visuomotor and working memory 1) task difficulty and 2) multitasking on dynamic functional connectivity in the brain. Studies have only recently begun to investigate functional connectivity within the scope of concurrent dual task or varying task difficulty conditions (Cocchi, Zalesky, et al. 2011; Rietschel et al. 2012). A series of EEG recordings were conducted during execution of visuomotor or working memory tasks within a novel paradigm using BCI2VR custom MATLAB toolbox. Functional connectivity was correlated with task-related coherence (TRCoh) analysis between two task conditions involving either variation in task difficulty or concurrent execution during multitasking within the delta (0 – 4 Hz), theta (4 – 8 Hz), alpha (8 – 12 Hz), beta1 (12-16 Hz), beta2 (16 – 20 Hz) and beta3 (20 – 24 Hz) frequency bands. An increase in coherence was observed with increased cognitive load, during both increased task difficulty and multitasking, in all frequency bands except beta1 and beta2. This may suggest that the psychomotor efficiency hypothesis also applies to multitasking as well as task difficulty. Decreases in beta coherence were observed with increased performance error, indicating that interregional beta coherence may not follow the PEH trend. The increased coherence between brain regions in the alpha, delta and theta bands contributes to the growing volume of research on quantifying cognitive workload and may serve as a future basis on increasing multitasking efficiency during high stress environments. Further research recording multitasking effects on individuals over regular intervals during an extended period of time (months or years) will be required to better understand changes in functional connectivity within the brain.

The development of functional connectivity is often described as changing from local to distributed connections which give rise to the functional brain networks observed in adulthood. In contrast to the well-explored pattern found in functional connectivity, no research has been published describing effective connectivity development. Also, there is a plethora of literature describing functional connectivity patterns in a variety of neurodevelopmental and internalizing disorders, but there is little consistency in the connectivity patterns discovered for each disorder. Hence, this study aimed to describe functional and effective resting-state connectivity during adolescent development in a typically developing adolescent (TDA) group (n = 128) and to determine how adolescents with comorbid neurodevelopmental disorders (CND) (n = 46) differed. This was accomplished through functional and effective connectivity analysis within and between four networks: the Default Mode Network (DMN), the Salience Network (SN), the Dorsal Attention Network (DAN), and the Frontal Parietal Control Network (FPCN). The results from this study indicate that within-network connectivity decreased across age in the TDA group, which is in opposition to previous work which suggests strengthening within-network connectivity. The CND group displayed hyper-connectivity compared to the TDA group in between-network connectivity with no effect of age. The effective connectivity in the TDA group displayed decreasing connectivity within networks with increasing age, a novel effect not previously reported in the literature. The CND group’s effective connectivity was overall hyper-connected (for within- and between-networks). The functional connectivity patterns in the TDA group suggest that functional connectivity has subtle developmental change during adolescence. Further, the CND group consistently displayed hyper-connectivity in functional and effective connectivity. The CND group, and perhaps similar comorbid groups, may have less efficient networks which could contribute to their disorder(s).

Early brain development is characterized by rapid growth and perpetual reconfiguration, driven by a dynamic milieu of heterogeneous processes. Moreover, potent postnatal brain plasticity engenders increased vulnerability to environmental stimuli. However, little is known regarding the ontogeny and temporal manifestations of inter- and intra-regional functional connectivity that comprise functional brain networks. Recently, resting-state functional magnetic resonance imaging (fMRI) emerged as a promising non-invasive neuroinvestigative tool, measuring spontaneous fluctuations in blood oxygen level dependent (BOLD) signal at rest that reflect baseline neuronal activity. Its application has expanded to infant populations in the past decade, providing unprecedented insight into functional organization of the developing brain, as well as early biomarkers of abnormal/ disease states. However, rapid extension of the resting-state technique to infant populations leaves many methodological issues need to be resolved prior to standardization of the technique. The purpose of this thesis is to describe a protocol for intrinsic functional connectivity analysis, and extraction of resting-state networks in infants <12 months of age using the data-driven approach independent component analysis (ICA). To begin, we review the evolution of resting-state fMRI application in infant populations, including the biological premise for neural networks. Next, we present a protocol designed such that investigators without previous knowledge in the field can implement the analysis and reliably obtain viable results consistent with previous literature. Presented protocol provides detailed, albeit basic framework for RSN analysis, with interwoven discussion of basic theory behind each technique, as well as the rationale behind selecting parameters. The overarching goal is to catalyze efforts towards development of robust, infant-specific acquisition and preprocessing pipelines, as well as promote greater transparency by researchers regarding methods used. Finally, we review the literature, current methodological challenges and potential future directions for the field of infant resting-state fMRI.

The brain ages, and with it come alterations in its micro- and macro-structure which reflect in its morphology and functioning. Changes in the brain structure and functional coupling between regions can be assessed with neuroimaging, and, more specifically, magnetic resonance imaging (MRI). Using MRI data from two stages (Pilot and Enhanced) of the Nathan Kline Institute Rockland Sample (NKI-RS), totalling 613, free of neurodegenerative diseases, and right-handed, participants aged 18 to 85 years old, we measured gray-matter parameters such as cortical volume, cortical thickness, and cortical surface area, and also volume of subcortical structures. We also measured cortico-cortical functional connectivity, defined either as the Pearson correlation coefficient and partial correlation coefficient, bivariate instantaneous Granger causality and Granger causality, and generalized partial directed coherence (GPDC). GPDC was evaluated in five frequencies between the four pairs of regions displaying the strongest evidence for linear thinning, measured by their associated t-statistic, and its alterations alongside aging were assessed using a multivariate approach based on Dirichlet Regression. We also studied spatial associations between patterns of morphometric and connectivity alterations. We reproduced generalized age-related atrophy reported in the literature in cortical volume (90% of the studied structures), surface area (68%) and thickness (90%), and volumetric atrophy of several subocortical structures. We observe a positive association in the joint distribution of the expected cortical thickness at 18 years old and the yearly percentage reduction in cortical thickness. We showed, projecting these two quantitities into their principal axes and analyzing the spatial distribution of the scores, that the first principal component correlates with neocortical granularity while the second principal component represents cortical type admixture. On functional connectivity, we gathered evidence for overall increased Pearson correlation coefficient (6% of the connections in the Pilot NKI-RS and 2% in the Enhanced NKI-RS), with proportionally smaller number of decreases (0.1% in the Pilot NKI-RS and 0.3% in the Enhanced NKI-RS). The Pearson partial correlation coefficient between 12 out of 65 homotopic region pairs shows a pattern of decline with age, suggesting inter-hemispheric disconnection. However, predictive causality, as measured by both Granger causalities, do not share the same degree of changes observed in the correlational metrics. We observe increased GPDC from several regions to themselves in many frequencies (25% out of a total of 40 self-connections), indicating a degree of disconnection to the other regions. Given seed regions, we uncovered spatially distributed significant patterns of association between the standardized effect of age on the connectivity to its targets and on their targets thicknesses. Regions with smaller evidence for age-related thinning, such as several occipital areas, tend to have fewer alterations in functional connectivity than regions with greater evidence for age-related thinning, like many frontal regions. We hypothesize that regions showing a negative association (5% of the seed regions) are part of compensatory systems, being increasingly correlated with regions displaying most atrophy. Regions showing a positive association (5%) do not have compensatory mechanisms available, and therefore are losing connectivity to atrophyc regions. Overall, we found evidence for brainwide alterations in connectivity and cortical and subcortical morphometry throughout the human adult lifespan. We also found a specifc pattern of associations between the atrophic trends and age-related alterations in connectivity in the brain / O cérebro envelhece, e com isso vêm à tona alterações em sua micro e macroestrutura que se refletem em sua morfologia e funcionamento. Mudanças na estrutura cerebral e acoplamento funcional entre suas regiões podem ser averiguadas através da neuroimagem, e, mais especificamente, imagem por ressonância magnética (IRM). Usando dados de IRM das duas etapas (Pilot and Enhanced) do Nathan Kline Institute Rockland Sample (NKI-RS), totalizando 613 participantes destros, livres de doenças neurodegenerativas, com idade entre 18 e 85 anos, medimos parâmetros de substância cinzenta como volume, espessura, e área de superfície corticais, e também volume de estruturas subcorticais. Também medimos conectividade funcional cortico-cortical, definida como o coeficiente de correlação de Pearson, coeficiente de correlação parcial de Pearson, causalidade instântanea de Granger e causalidade de Granger bivariadas, e coerência parcial direcionada generalizada (GPDC). A GPDC foi medida em cinco frequências entre quatro pares de regiões que demonstraram a mais forte evidência para diminuição da espessura cortical linearmente, medido pela estatística-t associada, e suas alterações ao longo do envelhecimento foram estudadas usando uma abordagem multivariada baseada na Regressão de Dirichlet. Também estudamos associações espaciais entre padrões de alterações morfométricas e na conectividade. Reproduzimos a atrofia generalizada devido à idade reportada na literatura no volume cortical (90% das estruturas estudadas), área de superfície (68%) e espessura (90%), e atrofia volumétrica de várias estruturas subcorticais. Observamos uma associação positiva na distribuição conjunta do valor esperado da espessura cortical aos 18 anos de idade e a redução percentual anual na espessura cortical. Mostramos, ao projetar ambos em seus eixos principais e analizar a distribuição espacial desses índices, que a primeira componente principal correlaciona-se com a granularidade neocortical enquanto que a segunda componente principal representa o tipo cortical. Sobre a conectividade funcional, colhemos evidências para um aumento geral no coeficiente de correlação de Pearson (6% das conexões no Pilot NKI-RS e 2% no Enhanced NKI-RS), com menor proporção de decréscimos (0.1% no Pilot NKI-RS e 0.3% no Enhanced NKI-RS). O coeficiente de correlação parcial de Pearson entre 12 de 65 pares de regiões homotópicas demonstra um padrão de declínio com a idade, sugerindo desconexão inter-hemisférica. No entanto, a causalidade preditiva, como medida através de ambas as métricas de causalidade de Granger, não aparenta o mesmo grau de mudanças observado nas medidas correlacionais. Observamos aumentos na GPDC de várias regiões para si próprias em muitas frequências (25% de um total de 40 auto-conexões), que indica um grau de disconexão às outras regiões. Dadas regiões semente, revelamos padrões significativos espacialmente distribuídos de associação entre efeitos padronizados da idade na conectividade para seus alvos e das espessuras dos alvos. Regiões com menor evidência para o desbastamento relacionado com a idade, como várias áreas occipitais, tendem a ter menos alterações em sua conectividade funcional que regiões com maior evidência suportando o desbastamento cortical relacionado à idade, como diversas regiões frontais. Hipotetizamos que regiões cuja associação é negativa (5% das regiões semente) são parte de sistemas compensatórios, estando correlacionadas com regiões que demonstram os maiores graus de atrofia de modo crescente. Regiões cuja associação é positiva (5%) não teriam mecanismos compensatórios à disposição, e portanto perdem conectividade para regiões atróficas. No geral, encontramos evidências para alterações na conectividade e na morfometria cortical e subcortical no cérebro todo ao longo da extensão da vida adulta humana. Também achamos um padrão específico de associações entre tendências atróficas e alterações na conectividade cerebral devido à idade

abstract: Neural interfacing applications have advanced in complexity, with needs for increasingly high degrees of freedom in prosthetic device control, sharper discrimination in sensory percepts in bidirectional interfaces, and more precise localization of functional connectivity in the brain. As such, there is a growing need for reliable neurophysiological recordings at a fine spatial scale matching that of cortical columnar processing. Penetrating microelectrodes provide localization sufficient to isolate action potential (AP) waveforms, but often suffer from recorded signal deterioration linked to foreign body response. Micro-Electrocorticography (μECoG) surface electrodes elicit lower foreign body response and show greater chronic stability of recorded signals, though they typically lack the signal localization necessary to isolate individual APs. This dissertation validates the recording capacity of a novel, flexible, large area μECoG array with bilayer routing in a feline implant, and explores the ability of conventional μECoG arrays to detect features of neuronal activity in a very high frequency band associated with AP waveforms. Recordings from both layers of the flexible μECoG array showed frequency features typical of cortical local field potentials (LFP) and were shown to be stable in amplitude over time. Recordings from both layers also showed consistent, frequency-dependent modulation after induction of general anesthesia, with large increases in beta and gamma band and decreases in theta band observed over three experiments. Recordings from conventional μECoG arrays over human cortex showed robust modulation in a high frequency (250-2000 Hz) band upon production of spoken words. Modulation in this band was used to predict spoken words with over 90% accuracy. Basal Ganglia neuronal AP firing was also shown to significantly correlate with various cortical μECoG recordings in this frequency band. Results indicate that μECoG surface electrodes may detect high frequency neuronal activity potentially associated with AP firing, a source of information previously unutilized by these devices. / Dissertation/Thesis / Doctoral Dissertation Biomedical Engineering 2018

Sabe-se que diversas regiões do cérebro humano trabalham em sincronia, mesmo anatomicamente separadas, sugerindo conexões funcionais e estruturais. Dessa forma, nosso cérebro pode ser considerado uma rede que pode ser estudada para diferenças entre indivíduos e entre tarefas, em que os nodos podem ser diferentes regiões e as arestas podem ser medidas de conectividade funcional entre séries temporais de um sinal de ressonância magnética de cada região. Neste estudo, propomos analisar como conectividade funcional e parâmetros de rede cerebral se relacionam com desempenho intelectual e um estado de atenção sustentada. Foram adquiridas imagens de ressonância magnética de 30 indivíduos saudáveis jovens em estado de repouso e de atenção sustentada, a partir delas foram calculadas as conexões funcionais entre 90 regiões cerebrais usando o coeficiente de correlação entre pares de series temporais. Destes sujeitos foram estimados sete índices de inteligência a partir da aplicação do teste WAIS-III. As matrizes de conectividade evidenciariam um comportamento de rede complexa de mundo pequeno para limiares entre 0,2 e 0,5. Não foram encontradas associações entre parâmetros globais das redes ponderadas em estado de repouso e os índices de inteligência. Conectividade funcional e alguns parâmetros de rede locais evidenciaram correlações com pontuações de inteligência, principalmente nas regiões frontal, pré-central, parietal e occipital, giro fusiforme e supramarginal e caudado. Embora o p-valor não-corrigido seja bem pequeno e/ou haja simetria entre hemisférios em alguns resultados, ao ser considerado o efeito de múltiplas comparações para análise inteira não foram encontradas associações estatisticamente significativas, por isso as análises foram corrigidas para cada região (p-valor corrigido pelo FDR<0,05). Ainda assim, possivelmente um aumento do número de sujeitos levaria a resultados mais conclusivos. Não foram encontrados resultados que confirmassem a hipótese de que, para indivíduos normais, haveria uma maior anti-correlação de redes extrínsecas e intrínsecas como um todo para o estado de atenção focada em relação ao estado de repouso. Entretanto, durante o estado de atenção sustentada, foram encontradas algumas diferenças estatisticamente significantes nas conexões locais dentro das redes positivas e negativas à tarefa, evidenciadas por um aumento na magnitude das correlações positivas ou negativas durante a atenção sustentada, além de uma tendência de anti-correlação em conexões entre regiões positivas e negativas à tarefa. / It\'s known that some regions of the human brain work synchronously, even if they are anatomically separated, suggesting functional and structural connections. In this way, our brain can be considered a network that can be studied for individual or task differences and in which nodes can be the different regions and edges can be the measurements of functional connectivity between blood oxygen level-dependent signal time series from each region. In this study, we aim to analyze how functional connectivity and brain network parameters relate to intellectual performance and to sustained attention state. Resonance Magnetic images were acquired in 30 healthy young volunteers in resting and attentional state. The functional connections between 90 brain regions were computed from them using correlation coefficient between pairs of temporal series. Seven intelligence indices were estimated from these subjects through WAIS-III test application and associations between functional connectivity values or brain network parameters were sought. Connectivity matrices evidenced a small-world complex network behavior for thresholds between 0.2 and 0.5. No associations between global parameters using weighted networks were found. Functional connectivity and network parameters have evidenced some correlations with intelligence scores, mainly in frontal, pre-central, parietal, occipital regions, fusiform and supramarginal gyrus and caudate nucleus. Even that the uncorrected p-value was small and/or there was symmetry between hemispheres in several results, statistical significant associations were not found considering multiple comparisons correction for the entire analysis, therefore the analysis were corrected for each region (FDR corrected p-value <0.05). Even, increasing the number of subjects possibly would get more conclusive results. Results corroborant to the initial hypothesis of greater anti-correlation between default mode network and task-positive regions were not found for the sustained attention state. However, during sustained attention state, some statistically significant differences in local connections within task-positive and negative regions were found, evidenced by the increase of the strength of positive and negative correlations, besides of a trend of anti-correlation in connections between task-positive and negative regions.

Les traumatismes infantiles (TI) sont un facteur de vulnérabilité majeur à la schizophrénie. Nous avons ici choisi d'étudier l’impact des TI sur le cerveau dans la schizophrénie.Dans notre première étude, en voxel-based morphometry (VBM) et portant sur 21 schizophrènes et 30 contrôles, la négligence émotionnelle était associée à une diminution du volume total de matière grise dans les deux groupes. Cette association était plus marquée chez les schizophrènes. Chez les patients, la négligence émotionnelle était prédictive de la densité de matière grise du cortex préfrontal dorso-latéral, elle-même prédictive de la sévérité de la désorganisation.Dans notre seconde étude, nous avons utilisé une tâche émotionnelle en IRMf pour explorer les liens entre TI et connectivité fonctionnelle PPI (psychophysiological interaction) de l’amygdale chez 21 schizophrènes et 25 contrôles. Au cours de la tâche, chez les patients, la sévérité des abus sexuels et négligences physiques été associée à une diminution de connectivité entre l’amygdale et la région du cortex cingulaire postérieur/précunéus.Enfin le résultat le plus répliqué de notre revue de la littérature (15 articles d'imagerie) est l’association forte entre TI et diminution du volume total de matière grise. Chez les schizophrènes les TI étaient associés à des diminutions de matière grise au niveau du cortex préfrontal, à des altérations de l’intégrité de la matière blanche et à des altérations de connectivité fonctionnelle.Ainsi nos résultats suggèrent que les TI, interagissant avec d'autres facteurs de vulnérabilité, pourraient modeler la psychopathologie schizophrénique via des effets cérébraux neurodéveloppementaux. / Childhood trauma (CT) is a major risk afctir for schizophrenia. The aim of this work was to question the possible impact of CT on the brain of schizophrenia patients.In our first study, using voxel-based morphometry (VBM) in 21 patients with schizophrenia and 30 controls, childhood emotional neglect was associated with decreased total grey matter volume in both groups, with a stronger association in the patients group. In schizophrenia, emotional neglect predicted grey matter decrease in dorsolateral prefrontal cortex, which in turn predicted the severity of disorganization.In our second study, we used an fMRI emotional task with PPI (psychophysiological interaction) in 21 schizophrenia patients and 25 controls. During the emotional task, in schizophrenia group, sexual abuse and physical neglect during childhood were associated with decreased connectivity between the amygdala and the precuneus/posterior cingulate region.Finaly, the most replicated result in our review is the strong association between CT and decreased total grey matter volume. In addition, CT in schizophrenia patients is related to decreased prefrontal cortex grey matter, widespread alterations of white matter integrity and alterations of functional connectivity in a network including the amygdala, the anterior cingular cortex, the precuneus/posterior cingulate region and the temporo-parietal junction.Our findings suggest that CT, in interaction with other factors, could shape the psychopathology of schizophrenia through developmental effects on the brain, with predominent alterations in the prefrontal cortex, or in stress-related circuits affecting self-consciousness and social cognition.

The American alligator (Alligator mississippiensis) has been frequently studied in large reservoirs and coastal marshes. Large ontogenetic shifts in their diet and morphology have been linked with changes in habitat use, with adult males using deep, open water and juveniles and nesting females relying on vegetated marsh. In certain regions of the inland portion of the alligator’s range, these different aquatic habitats are represented by seasonal wetlands and riverine systems that are separated by a terrestrial matrix. Ontogenetic habitat shifts, therefore, would require overland movements between systems, which has important implications for conservation of the species. I tested several commonly used methods of surveying alligator populations to determine the most effective method of studying alligators in seasonal wetlands. I then used systematic trapping, nest surveys and radio telemetry to determine habitat use and overland movement rates by different sex and size classes. I found that seasonal wetlands provided nesting and nursery sites for these inland alligator populations, but that both juveniles undergoing an ontogenetic shift and nesting females move between the wetlands and riverine systems. Overland movements by alligators between the wetland and riverine habitats establish a level of functional connectivity between these aquatic ecosystems. I constructed a habitat suitability index of both the wetlands and the surrounding landscape to determine which patch and landscape characteristics were important to wetland use by alligators. I found that both descriptive wetland characteristics and the spatial relationships between wetlands were important predictors of alligator use. Overland movement was related to upland landuse as well as distance between aquatic habitats. Conserving a variety of wetland sizes and types within an intact upland matrix is critical to maintaining connectivity across the landscape. Furthermore, understanding how species may act as mobile links between ecosystems, particularly those with ontogenetic niche shifts, illustrates the importance of approaching conservation from a landscape perspective.

Functional MRI is a method of imaging changes in blood oxygenation that accompany neural activity in the brain. A specific area within fMRI studies investigates what the brain is doing when it is not being stimulated. It is postulated that there are distinctly separate regions of the brain that are connected based upon functional relations and that these connected regions synchronously communicate even during rest. Resting state connectivity has become a tool to investigate neurological disorders in humans without specific knowledge of the mechanisms that correlate neural activity with brain metabolism and blood flow. This work attempts to characterize resting state connectivity in the rat brain to establish a model that will help elucidate the relationship between functional connectivity, as measured with fMRI, and brain function. Four analysis techniques, power spectrum estimation, cross correlation analysis, principle component analysis, and independent component analysis, are employed to examine data acquired during a non-stimulation, single-slice, gradient echo EPI sequence in search of functionally connected, spatially distant regions of the rat brain.

The American alligator (Alligator mississippiensis) has been frequently studied in large reservoirs and coastal marshes. Large ontogenetic shifts in their diet and morphology have been linked with changes in habitat use, with adult males using deep, open water and juveniles and nesting females relying on vegetated marsh. In certain regions of the inland portion of the alligator’s range, these different aquatic habitats are represented by seasonal wetlands and riverine systems that are separated by a terrestrial matrix. Ontogenetic habitat shifts, therefore, would require overland movements between systems, which has important implications for conservation of the species. I tested several commonly used methods of surveying alligator populations to determine the most effective method of studying alligators in seasonal wetlands. I then used systematic trapping, nest surveys and radio telemetry to determine habitat use and overland movement rates by different sex and size classes. I found that seasonal wetlands provided nesting and nursery sites for these inland alligator populations, but that both juveniles undergoing an ontogenetic shift and nesting females move between the wetlands and riverine systems. Overland movements by alligators between the wetland and riverine habitats establish a level of functional connectivity between these aquatic ecosystems. I constructed a habitat suitability index of both the wetlands and the surrounding landscape to determine which patch and landscape characteristics were important to wetland use by alligators. I found that both descriptive wetland characteristics and the spatial relationships between wetlands were important predictors of alligator use. Overland movement was related to upland landuse as well as distance between aquatic habitats. Conserving a variety of wetland sizes and types within an intact upland matrix is critical to maintaining connectivity across the landscape. Furthermore, understanding how species may act as mobile links between ecosystems, particularly those with ontogenetic niche shifts, illustrates the importance of approaching conservation from a landscape perspective.