Cette thèse d’épistémologie et d’histoire des sciences cognitives est consacrée à son niveau le plus général au problème de l’instrument scientifique, parent pauvre de la réflexion sur l’investigation scientifique, et se concentre à titre particulier sur le développement des techniques d’imagerie cérébrale fonctionnelle et leur introduction dans le domaine cognitif au cours des années 1980-1990. Un choix motivé notamment par la nouveauté et l’importance de ce nouvel instrument, dont l’émergence est régulièrement comparée à celle du télescope au moment de la Révolution scientifique du XVIIe siècle. La première partie est ainsi consacrée à une analyse générale de l’instrument scientifique et des problèmes essentiels qu’il soulève. Elle propose un certain nombre d’hypothèses en réponse, et en examine les enjeux théoriques. La deuxième partie défend une interprétation historique de l’émergence des deux technologies d’imagerie fonctionnelle que sont la tomographie par émission de positons et l’imagerie par résonance magnétique fonctionnelle. En reprenant dans le détail certains éléments d’invention et de diffusion de ces techniques, elle montre notamment l’intrication des procédures de validation des instruments et des divers mécanismes scientifiques et sociétaux qui poussent à les développer puis à les utiliser. A la lumière des analyses théoriques et générales de la première, et sur la base de l’interprétation historique de la seconde, la troisième partie est dédiée à l’examen des implications de ces nouvelles technologies d’imagerie sur l’évolution du champ des sciences cognitives et de la reprise de leurs résultats dans d’autres domaines, tant scientifiques que technologiques ou pratiques. A ce double égard, elle défend la thèse générale que l’introduction de l’imagerie agit beaucoup moins comme un facteur de résolution de certaines questions que comme un facteur de déplacement de la problématique et de l’impact théorique et sociétal des sciences cognitives. / At a general level, this dissertation in philosophy and history of cognitive science is devoted to the underestimated problem of scientific instruments. It is focused on some functional brain imaging techniques introduced in the field of cognitive studies during the 1980’s and 1990’s, the impact of such new technologies being sometimes compared to an instrumental revolution, in a way similar to the impact of the invention of the telescope on post-Galilean astronomy. The first part consists in a philosophical and historical analysis of the notion of scientific instrument. In this regard, some issues are raises and some hypotheses are formulated. The second part presents an interpretation of the historical emergence of Positron Emission Tomography and functional Magnetic Resonance Imaging. Dealing with details of the invention and circulation of those techniques, it shows in particular the entanglement of the validation procedures of instruments with the various scientific and societal mechanisms driving to their development and use. Taking its roots in the general analysis of the first part and the historical interpretation of the second part, the third part looks into the impact of the new functional brain imaging technologies on the evolution of cognitive science and the diffusion of its results in other domains. Concerning both cognitive science and larger aspects, it is argued that brain imaging is less a factor of resolution of specific questions than a factor of shifting in the problematics and the theoretical and societal significance of cognitive science.

Functional connectivity is a field within neuroscience where measurements of co-activation between brain regions are used to test various hypotheses or explore how the brain activates depending on a given situation or task. After analysis, the underlying data in the field consists of a n by n adjacency matrix where each cell represents a correlation value between two regions in the brain. Depending on the research question the number of regions and matrices incorporated varies and new visualizations are needed in order to portray them. In this thesis the design of an interactive web based visualization tool for functional connectivity was explored through an iterative design process. The design of the tool was based on existing guidelines, interviews and best practices in data visualization as well as an analysis of current visualization solutions used in functional connectivity. The final concept and prototype uses a network plot for functional connectivity called the connectogram as well as a grouped bar graph to provide an intuitive and accessible way of comparing functional connectivity data by interacting with and highlighting networks and specific network data through direct manipulation. Results of qualitative evaluations of a prototype using data from a concurrent scientific project is presented. The prototype was found to be useful, engaging, easily perceivable and offered an easy and quick way of exploring data sets.

abstract: Electromagnetic fields (EMFs) generated by biologically active neural tissue are critical in the diagnosis and treatment of neurological diseases. Biological EMFs are characterized by electromagnetic properties such as electrical conductivity, permittivity and magnetic susceptibility. The electrical conductivity of active tissue has been shown to serve as a biomarker for the direct detection of neural activity, and the diagnosis, staging and prognosis of disease states such as cancer. Magnetic resonance electrical impedance tomography (MREIT) was developed to map the cross-sectional conductivity distribution of electrically conductive objects using externally applied electrical currents. Simulation and in vitro studies of invertebrate neural tissue complexes demonstrated the correlation of membrane conductivity variations with neural activation levels using the MREIT technique, therefore laying the foundation for functional MREIT (fMREIT) to detect neural activity, and future in vivo fMREIT studies. The development of fMREIT for the direct detection of neural activity using conductivity contrast in in vivo settings has been the focus of the research work presented here. An in vivo animal model was developed to detect neural activity initiated changes in neuronal membrane conductivities under external electrical current stimulation. Neural activity was induced in somatosensory areas I (SAI) and II (SAII) by applying electrical currents between the second and fourth digits of the rodent forepaw. The in vivo animal model involved the use of forepaw stimulation to evoke somatosensory neural activations along with hippocampal fMREIT imaging currents contemporaneously applied under magnetic field strengths of 7 Tesla. Three distinct types of fMREIT current waveforms were applied as imaging currents under two inhalants – air and carbogen. Active regions in the somatosensory cortex showed significant apparent conductivity changes as variations in fMREIT phase (φ_d and ∇^2 φ_d) signals represented by fMREIT activation maps (F-tests, p <0.05). Consistent changes in the standard deviation of φ_d and ∇^2 φ_d in cortical voxels contralateral to forepaw stimulation were observed across imaging sessions. These preliminary findings show that fMREIT may have the potential to detect conductivity changes correlated with neural activity. / Dissertation/Thesis / Doctoral Dissertation Biomedical Engineering 2020

Le but de ce travail est d’étudier deux dimensions sémiologiques, identifiées dans la littérature comme associées au trouble dépressif résistant, l’anxiété et l’apathie. Ces marqueurs cliniques et leurs corrélats radiologiques seront ensuite testés dans une analyse longitudinale du pronostic à 6 mois d’une cohorte de patients souffrant de dépression. Les données originales de ce travail sont issues de la cohorte LONGIDEP. Cette étude prospective, naturalistique, a été menée chez des patients souffrant d’un épisode dépressif majeur qui bénéficiaient, dans le cadre des soins courants, d’une évaluation clinique, neuropsychologique et d’une imagerie cérébrale à l’inclusion. Une nouvelle évaluation a été proposée à 6 mois de l’inclusion. Cette étude nous a permis de montrer que 1) l’apathie dans la dépression est associée à un profil clinique et physiopathologique spécifique, 2) l’analyse catégorielle et sémiologique de l’anxiété dans une population de sujet déprimés résistants n’étaient pas concordantes. Les déprimés résistants présentaient une hyperperfusion amygdale centro-médiane, 3) l’anxiété trait, un pattern cognitif associé à la mémoire visuo-spatiale étaient prédictifs d’une évolution péjorative de la dépression. Des anomalies structurales de régions impliquées dans la régulation émotionnelle et plus précisément l’adaptation au danger/peur, étaient associées à une évolution péjorative de la dépression. Des deux dimensions sémiologiques étudiées, l’anxiété apparaît être impliquées dans le pronostic de la dépression. L’étude des liens entre l’anxiété et les troubles de la motivation est une perspective de recherche pour la dépression résistante. / The aim of this work is to study anxiety and apathy in treatment resistant depression. These clinical factors and its imaging correlates will be tested in prediction of outcome in a 6-months follow-up. Original data were retrieved in LONGIDEP cohort. This is a prospective study conducted in routine care. Patients suffering from a mood depressive episode benefited from a clinical, neuropsychological and brain imaging. They were assessed once again at 6 months. Our study has shown that 1) apathy in depression is associated with specific clinical and pathophysiological patterns, 2) categorical and dimensional approach of anxiety in treatment resistant depression are not convergent. This latter population exhibited higher brain perfusion of centro-medial amygdala, 3) trait anxiety, cognitive patterns of visuospatial memory were predictive of pejorative outcome. Structural abnormalities in key regions involved in emotion regulation were associated with pejorative outcome of depression. Only anxiety was involved in outcome of depression. The link between anxiety and motivation should be studied in further works.

Ce travail est conçu dans le panorama de développement rapide de grandes bases de données qui rassemblent des ensembles de résultats expérimentaux sur l’organisation anatomo-fonctionnelle du cerveau humain à différentes échelles; l’abondance d’informations demande un effort intra et interdisciplinaire pour les synthétiser de façon cohérente. Le but de cette thèse est de contribuer à cet effort de synthèse. Le travail suit deux chemins: intra disciplinaire pour relier et synthétiser les résultats produits par la communauté de l’imagerie cérébrale, avec une focalisation particulière sur les Réseaux de Repos et les Réseaux Cognitifs; inter-disciplinaire pour relier l’organisation anatomo-fonctionnelle du cortex cérébral (résultats en imagerie cérébrale), et les expressions des gènes révélées par les bases de données publiées très récemment sur le transcriptome humain.Cette thèse est organisée en trois parties: dans Partie I nous étudions l’organisation anatomo-fonctionnelle du cortex à partir des études d’imagerie cérébrale. Dans la Partie II, nous étudions les liens entre l’expression corticale des gènes et l’organisation anatomo-fonctionnelle du cortex, à la fois en termes de similitude topographique et de congruence de fonction, en se focalisant en particulier sur le traitement de l’information et la mémorisation. Dans la Partie III, nous présentons une plate-forme pour intégrer dans une même représentation les données d’imagerie cérébrale et d’expression génétique.En perspective, nous montrons comment notre approche pourrait donner des nouveaux points de vu au débat sur les maladies neurodégénératives et psychiatriques, et sur les modelés des dynamiques corticales. / This work is conceived in the present panorama of fast development of large databases gathering experimental results about the organization of the human brain at different scales. This abundance of information calls for an intra and inter-disciplinary effort aimed to synthesize this information in a coherent way.The aim of this thesis was to contribute to this effort for knowledge synthesis to better understand the multiscale organization of the cerebral cortex. The work followed two paths: an intra-disciplinary effort to bring together results produced by the brain imaging community with particular focus on Resting State and Task Based MRI experiments; an inter-disciplinary attempt to draw a link between the anatomo-functional organization of the cortex as emerging from brain imaging studies and the cortical patterns of gene expression as revealed by recently published atlases of the adult human brain transcriptome.The thesis is organized into three parts: In Part I studied the anatomo-functional organization of the human cortex starting from brain imaging studies. In Part II we studied the link between cortical gene expression and the anatomo-functional organization of the cortex both in term of their topography and in term of their function, focusing in particular on information processing and memory formation. In Part III we present a platform that we developed to favor knowledge integration between cognitive networks and gene expression databases.In perspective we show how our approach may provide new insights to the debate about neurodegenerative and psychiatric diseases on one hand, modeling of dynamical processes in different areas of the cortex on the other.

Indiana University-Purdue University Indianapolis (IUPUI) / Although cancer and treatment-associated cognitive dysfunction has been well-documented in the literature, much work remains to elucidate the biological mechanisms driving this effect, hampering current therapeutic efforts. To address this gap, we first reviewed studies utilizing neuroimaging to characterize cognitive dysfunction in cancer, as studies of neurodegenerative diseases point to neuroimaging as a sensitive measure of cognitive dysfunction. This review highlighted the need for longitudinal imaging studies of cancer and treatment-related changes in cerebral structure and function. Subsequently, we utilized multimodal neuroimaging techniques in a female breast cancer cohort to investigate the longitudinal impact of cancer and chemotherapy treatment on cerebral perfusion and gray matter. Our findings indicate that chemotherapy is associated with elevated perfusion, primarily in posterior brain regions, as well as depressed frontal perfusion associated with decreased frontal gray matter density. This pattern of results suggests the involvement of multiple mechanisms of chemotherapy-induced cognitive dysfunction. We also investigated the relationship of cognitive dysfunction and chemotherapy-induced peripheral neuropathy (CIPN), another type of chemotherapy-related nervous system sequelae, again utilizing multimodal, longitudinal neuroimaging, and found that peripheral neuropathy symptoms following chemotherapy were associated with changes in cerebral perfusion and gray matter density. Together, these findings support the hypothesis that multiple biological mechanisms drive cancer and treatment-related cognitive dysfunction. Interestingly, although cancer is associated with cognitive dysfunction, epidemiological studies have shown that cancer and Alzheimer's disease (AD) are inversely correlated. To extend our imaging analysis beyond breast cancer, we leveraged the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort to investigate the inverse relationship of cancer and AD and investigate the impact of both of these diseases on gray matter density. We found that though the inverse relationship of these diseases was replicated in the ADNI cohort, cancer history was associated with lower gray matter density, similar to findings from breast cancer studies, independent of AD diagnostic group. Finally, we reviewed microRNA studies, as microRNAs are important regulators of many cell signaling pathways and have been actively investigated in relation to both diseases. This review suggests several pathways that may be driving the inverse association and may contribute to cognitive dysfunction.

No description available.

Borderline intellectual functioning (BIF) is a multifactorial condition in which both genetic and environmental factors are likely to contribute to the clinical outcome. Abnormal cortical development and lower IQ scores were shown to be correlated in BIF children, but the genetic components of this condition and their possible connection with intelligence and brain morphology have never been investigated in BIF. The synaptosomal-associated protein of 25 kD (SNAP-25) is involved in synaptic plasticity, neural maturation, and neurotransmission, affecting intellectual functioning. We investigated SNAP-25 polymorphisms in BIF and correlated such polymorphisms with intelligence and cortical thickness, using socioeconomic status and environmental stress as covariates as a good proxy of the variables that determine intellectual abilities. Thirty-three children with a diagnosis of BIF were enrolled in the study. SNAP-25 polymorphisms rs363050, rs363039, rs363043, rs3746544, and rs1051312 were analyzed by genotyping; cortical thickness was studied by MRI; intelligence was measured using the WISC-III/IV subscales; environmental stressors playing a role in neuropsychiatric development were considered as covariate factors. Results showed that BIF children carrying the rs363043(T) minor allele represented by (CT C TT) genotypes were characterized by lower performance Perceptual Reasoning Index and lower full-scale IQ scores (p = 0.04) compared to those carrying the (CC) genotype. This association was correlated with a reduced thickness of the left inferior parietal cortex (direct effect = 0.44) and of the left supramarginal gyrus (direct effect = 0.56). These results suggest a link between SNAP-25 polymorphism and intelligence with the mediation role of brain morphological features in children with BIF.

No description available.

Résumé Les premières études électrophysiologiques et anatomiques ont établi le rôle crucial du cortex somatosensoriel primaire et secondaire (SI et SII) dans le traitement de l'information somatosensorielle. Toutefois, les récentes avancées en techniques d’imagerie cérébrale ont mis en question leur rôle dans la perception somatosensorielle. La réorganisation du cortex somatosensoriel est un phénomène qui a été proposé comme cause de la douleur du membre fantôme chez les individus amputés. Comme la plupart des études se sont concentrées sur le rôle du SI, une étude plus approfondie est nécessaire. La présente série d'expériences implique une exploration du rôle des régions somatosensorielles dans la perception des stimuli douleureux et non-douleureux chez des volontaires sains et patients avec des douleurs de membre fantôme. La première étude expérimentale présentée dans le chapitre 3 est une méta-analyse des études de neuro-imagerie employant des stimuli nociceptifs chez des volontaires sains. En comparaison aux précédentes, la présente étude permet la génération de cartes quantitatives probabilistes permettant la localisation des régions activées en réponse à des stimuli nociceptifs. Le rôle du cortex somatosensoriel dans la perception consciente de stimuli chauds a été étudié dans le chapitre 4 grâce à une étude d'imagerie par résonance magnétique fonctionnelle, dans laquelle des stimuli thermiques douloureux et non-douloureux ont été administrés de manière contrebalancée. Grâce à cette procédure, la perception de la chaleur fut atténuée par les stimuli douloureux, ce qui permit la comparaison des stimuli consciemment perçus avec ceux qui ne le furent pas. Les résultats ont montrés que les stimulations chaudes perçues ont engendré l’activation de l’aire SI controlatérale, ainsi que de la région SII. Grâce à l’évaluation clinique de patients amputés présentant une altération de leurs perceptions somatosensorielles, il est également possible de dessiner un aperçu des régions corticales qui sous-tendent ces modifications perceptuelles. Dans le chapitre 5 nous avons émis l'hypothèse proposant que les sensations du membre fantôme représentent un corrélat perceptuel de la réorganisation somatotopique des représentations sensorielles corticales. En effet, la réorganisation des sensations peut donner des indices sur les régions impliquées dans la genèse des sensations référées. Ainsi, un protocole d’évaluation sensoriel a été administré à un groupe de patients affligés de douleur au niveau du membre fantôme. Les résultats ont montré que, contrairement aux études précédentes, les sensations diffèrent grandement selon le type et l'intensité des stimuli tactiles, sans évidence de la présence d’un modèle spatialement localisé. Toutefois, les résultats actuels suggèrent que les régions corticales à champs récepteurs bilatéraux présentent également des modifications en réponse à une déafférentation. Ces études présentent une nouvelle image des régions corticales impliquées dans la perception des stimuli somatosensoriels, lesquelles comprennent les aires SI et SII, ainsi que l'insula. Les résultats sont pertinents à notre compréhension des corrélats neurologiques de la perception somatosensorielle consciente. / Abstract Early anatomical and single-unit recording studies established a crucial role for the primary and secondary somatosensory cortices (SI & SII) in processing somatosensory information. However, recent advances in brain imaging and analysis techniques have called into question their role in somatosensation. Findings from this recent research are relevant to the study of the reorganizational changes occurring in the somatosensory cortices that have been causally linked to the genesis of pain in amputee patients. These patients continue to perceive and experience pain in the absent limb, which is usually referred to as phantom-limb pain; but little research on this phenomenon has focused on other regions outside SI, and further study is needed. The present series of experiments involve an exploration of the roles of the somatosensory cortices in the perception of noxious and innocuous tactile stimuli in healthy volunteers and patients with phantom-limb pain. The first experimental study in Chapter 3 is a meta-analytic review of neuroimaging studies examining noxious stimuli evoked activation in healthy volunteers. In comparison to previous reviews that have merely reported the prevalence of pain-related activation, the present study yields quantitative probabilistic maps that permit localization of the likelihood of obtaining activation in response to noxious stimuli within any brain region. The role of the somatosensory cortices in the conscious perception of brief warm stimuli was explored in Chapter 4 using functional magnetic resonance imaging, where noxious and innocuous thermal stimuli were counterbalanced within the experimental protocol. This procedure allowed a gating of the somatosensory system in which the perception of warm stimuli was attenuated by painful stimuli, thus permitting the comparison of detected with undetected stimuli. Results showed that detected warm stimuli significantly activated SI and SII. It is also possible to draw insight regarding which cortical regions subserve somatosensory processing and its organization by clinical assessment of amputee patients, who demonstrate altered somatosensation. To date, few studies have explored the relationship between referred sensations to the phantom and cortical reorganization. In Chapter 5 we hypothesized that referred sensations to phantom limbs are a perceptual correlates of a somatotopic reorganization of sensory representations. Derangements in referred sensations can give clues to the regions involved in referred sensations genesis. Thus, a quantitative sensory testing protocol was administered to a group of phantom-limb pain patients. Results showed that, contrary to previous reports, referred sensations to the phantom differed greatly based on the type and intensity of the tactile stimuli applied to the body, with no evidence of a spatially localized pattern. Previous reports of referred sensations have solely focused on plastic changes in SI. However, the present results suggest that other cortical regions with bilateral receptive fields also undergo reorganizational changes in response to deafferentation. These studies present an emerging picture of the cortical regions involved in the perception of somatosensory stimuli, which include SI and SII, as well as the insula. Findings are relevant to our understanding of the neural correlates of conscious perception of somatosensation and the formation of the mental representation of stimuli applied to the body.