Latest trend in multi core architectures is to integrate heterogeneouscores on a single chip in order to achieve task and threadlevel parallelism, high performance and energy efficiency. Someexamples of heterogeneous multi cores processors include (Tegraby NVIDIA,Cell by IBM and Fusion by AMD). The goal of this thesis work is to design a heterogeneous (2x2)network on chip which can run different tasks in parallel on allthe four cores in the network. Development steps of heterogeneousnetwork on chip include integration of Leon3 -a soft core processorby AeroFlex Gaisler which conforms with IEEE 1754 (SPARCV8) architecture- at one of the nodes of a homogeneous networkon chip incorporating four NiosII/s cores -soft core processor byAltera.This integration involves replacing a NiosII/s processor fromone of the four nodes of the homogeneous network by Leon3 processor.To translate the signals between the resource to networkinterface of the node and the Leon3 processor an AMBA bus1 toAvalon bus2 signal translation wrapper was designed. All processorsin the network on chip communicate by message passing interface.To exploit the potential of heterogeneous network on chipthree applications including sparse LU factorization, nqueens andFibonacci numbers calculation were run on it. These applicationwere run on Leon3 SPARC which generated a number of tasks thatcan run in parallel on all cores of the network simultaneously. Thisparallel execution of nqueens and fibonacci numbers calculationhas resulted in speed up as compared to the serial execution ofthese applications on Leon3 SPARC only. Because of the limitedsize of the on chip memory available for the Leon3 processor, itwas not possible to run sparse LU factorization for bigger matrixsizes and this constraint has resulted in no speed up in case ofsparse LU factorization.

L’objectif de ce travail était d’examiner la spécificité fonctionnelle du traitement et des représentations des hauteurs musicales. À cette fin, ce traitement a été comparé à celui des phonèmes de la parole, d’une part, et aux associations spatiales évoquées par des séquences ordonnées, d’autre part. Nos quatre études avaient pour point commun d’adapter à un nouvel objet de recherche des méthodes bien établies en psychologie cognitive. Ainsi, nous avons exploité la tâche de classification accélérée (Etude 1) de Garner (1974), l’analyse des conjonctions illusoires en mémoire (Etude 2), l’additivité de la composante mismatch negativity (MMN) des potentiels évoqués (Etude 3) et l’observation d’associations spatiales de codes de réponse (Etude 4). Les trois premières études, menées chez des participants non-musiciens, portaient sur la spécificité de traitement des hauteurs par rapport à celui des phonèmes au sein de stimuli chantés. Les deux premières études ont mis en évidence un effet surprenant de la nature des phonèmes sur leurs interactions avec le traitement des mélodies : les voyelles apparaissaient plus intégrées à la mélodie que les consonnes. Ceci était vrai à la fois lors du traitement en temps réel de non-mots chantés (Etude 1) et au niveau des traces en mémoire de ces mêmes non-mots (Etude 2, utilisant une tâche de reconnaissance à choix forcé permettant la mise en évidence de conjonctions illusoires). Cette dissociation entre voyelles et consonnes quant à leur intégration avec les traitements mélodiques ne semblait pas causée par des caractéristiques acoustico-phonétiques telles que la sonorité. Les résultats de la troisième étude indiquaient que les MMNs en réponse à des déviations de hauteur et de voyelle n’étaient pas additives et que leur distribution topographique ne différait pas selon le type de déviation. Ceci suggère que, même au niveau pré-attentionnel, le traitement des voyelles n’est pas indépendant de celui des hauteurs. Dans la quatrième étude, nous avons comparé le traitement des hauteurs musicales à un autre domaine : la cognition spatiale. Nous avons ainsi montré que les non-musiciens comme les musiciens associent les notes graves à la partie inférieure et les notes aiguës à la partie supérieure de l’espace. Les deux groupes liaient aussi les notes graves au côté gauche et les notes aiguës au côté droit, mais ce lien n’était automatique que chez les musiciens. Enfin, des stimuli musicaux plus complexes (intervalles mélodiques) n’évoquaient ces associations spatiales que chez les musiciens et ce, uniquement sur le plan horizontal. Ces recherches contribuent de plusieurs manières à la compréhension de la cognition musicale. Premièrement, nous avons montré que les consonnes et les voyelles diffèrent dans leurs interactions avec la musique, une idée à mettre en perspective avec les rôles différents de ces phonèmes dans l’évolution du langage. Ensuite, les travaux sur les représentations spatiales des hauteurs musicales ouvrent la voie à un courant de recherche qui aidera à dévoiler les liens potentiels entre habiletés musicales et spatiales. / The purpose of this work was to examine the functional specificity of musical pitch processing and representation. To this aim, we compared musical pitch processing to (1) the phonological processing of speech and (2) the spatial associations evoked by ordered sequences. The four studies described here all use classical methods of cognitive psychology, which have been adapted to our research question. We have employed Garner’s (1974) speeded classification task (Study 1), the analysis of illusory conjunctions in memory (Study 2), the additivity of the mismatch negativity (MMN) component of event-related potentials (Study 3), as well as the observation of spatial associations of response codes (Study 4). The three first studies examined, in non-musician participants, the specificity of pitch processing compared to phoneme processing in songs. Studies 1 and 2 revealed a surprising effect of phoneme category on their interactions with melodic processing: vowels were more integrated with melody than were consonants. This was true for both on-line processing of sung nonwords (Study 1) and for the memory traces of these nonwords (Study 2, using a forced-choice recognition task allowing the occurrence of illusory conjunctions). The difference between vowels and consonants was not due to acoustic-phonetic properties such as phoneme sonority. The results of the third study showed that the MMN in response to pitch and to vowel deviations was not additive and that its brain topography did not differ as a function of the kind of deviation. This suggests that vowel processing is not independent from pitch processing, even at the pre-attentive level. In the fourth study, we compared pitch processing to another domain: spatial cognition. We showed that both musicians and non-musicians map pitch onto space, in that they associate low-pitched tones to the lower spatial field and high-pitched tones to the higher spatial field. Both groups of participants also associated low pitched-tones with the left and high-pitched tones with the right, but this association was automatic only in musicians. Finally, more complex musical stimuli such as melodic intervals evoked these spatial associations in the horizontal plane only in musicians. This work contributes to the understanding of music cognition in several ways. First, we have shown that consonants and vowels differ in their interactions with music, an idea related to the contrasting roles of these phonemes in language evolution. Second, the work on the spatial representation of pitch opens the path to research that will help uncover the potential links between musical and spatial abilities.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

O reparo cardíaco pós-infarto do miocárdio (IM) continua sendo um desafio, apesar do grande progresso no tratamento clínico e na redução da mortalidade. Nesse sentido, estudos com modelos pré-clínicos têm demonstrado que o transplante de células-tronco adultas, como as células-tronco derivadas de tecido adiposo (ASCs), preserva a função ventricular após IM. Esta melhora não está relacionada à mecanismos de substituição tecidual, mas a ação parácrina através da liberação de moléculas bioativas pleiotrópicas. No presente estudo, nós procuramos identificar proteínas-alvo importantes relacionadas com a resposta pleiotrópica benéfica associada ao uso de ASC pós-IM. Foram realizadas análises de bioinformática do secretoma de mASC submetida à hipóxia e stretch, mimetizando o microambiente do IM, para encontrar novos alvos. Uma rede de interações incluindo três candidatos que interagem entre si: SPARC, MMP-3 e Osteopontina, foi gerada. Padronizamos o modelo de morte celular por H2O2 em cardiomiócitos, fibroblastos cardíacos e células endoteliais, os três tipos celulares principalmente encontrados no coração, e avaliamos a expressão desses fatores nessas células. Os dados mostram que o peróxido de hidrogênio altera a expressão desses fatores de forma heterogênea nessas células e induz a produção e secreção de colágeno em fibroblastos. Entretanto, o tratamento com SPARC, Osteopontina e MMP-3 não melhorou a viabilidade das células tratadas com H2O2 e nem modulou a resposta antigênica. No que se refere à produção de colágeno, a proteína SPARC conseguiu reduzir esta a níveis basais, semelhante ao que ocorreu com as células tratadas com o meio condicionado de ASC. Em conjunto, os resultados mostram que a proteína SPARC reduz a produção de colágeno assim como o meio condicionado, consistente com a ideia de que a SPARC participa, pelo menos em parte, da resposta benéfica associada ao transplante de ASC pós-infarto do miocárdio / Cardiac repair post-myocardial infarction (MI) remains a challenge despite great progress in clinical management and mortality reduction. In this sense, studies with pre-clinical models have shown that the transplantation of adult stem cells, such as stem cells derived from adipose tissue (ASCs), preserves ventricular function after MI. This improvement is not related to mechanisms of tissue replacement and cell transdifferentiation, but the paracrine action through the release of pleiotropic bioactive molecules. In the present study we tried to identify key proteins related with the beneficial pleiotropic response associated with ASC transplantation post-MI. We perform bioinformatic analyses of the proteins released by mASC subjected to stretch and hypoxia, mimmiking the MI microenvironment, to find novel targets. The network of interactions includes three candidates that interact with each other: SPARC, MMP-3 and Osteopontin. We standardized the model of cell death by H2O2 in cardiomyocytes, cardiac fibroblasts and endothelial cells, the three major cell types that form the heart, and evaluate the expression of these factors. The data show that hydrogen peroxide alters the expression of these factors heterogeneously in these cells and induces collagen production and secretion in fibroblasts. However, treatment with SPARC, Osteopontin and MMP-3 did not improve the viability of cells treated with H2O2 and does not influence the angiogenic response. Concerning to the production of collagen, SPARC protein could reduce this to basal levels, similar to what happened with the cells treated with conditioned medium of ASC. Together, these results showed that SPARC protein reduces collagen production similarly to the conditioned medium treatment, which is consistent with the idea that SPARC is responsible, at least in part, for the beneficial effects associated with the transplanted ASC post-MI

O câncer de mama triplo negativo (TNBC) é um dos tumores mais agressivos, muitas vezes resistentes à terapia sistêmica e com evolução para doença metastática. O entendimento de sua biologia e a concepção de novos tratamentos são essenciais para melhorar o seu prognóstico. Atualmente, as opções de tratamento são reduzidas e a quimioterapia ainda é o tratamento padrão. A expressão de SPARC (secreted protein acidic and rich in cysteine) é supostamente alterada em várias doenças malignas. No entanto, pouco se sabe sobre o valor prognóstico do SPARC em pacientes com TNBC. Usando uma pequena coorte de descoberta de TNBC muito bem caracterizada em relação à expressão do SPARC e comportamento clínico, conseguimos identificar vários genes como diferencialmente expressos na comparação entre amostras de TNBC / SPARC negativo vs. TNBC / SPARC positivo. Cinco desses genes diferencialmente expressos, SOHLH2, DNAJC12, LIM-1, CEACAM-5 e CTAG1A foram escolhidos para serem validados por imuno-histoquímica (IHC) em tissue microarrays (TMAs) contendo uma coorte independente de TNBC. Para acessar o valor prognóstico desses potenciais novos biomarcadores, avaliamos a associação entre a expressão de IHC e os resultados das pacientes pela análise de Kaplan-Meier para a coorte de validação. Foi observado que a coloração negativa da expressão de SOHLH2 e coloração positiva de DNAJC12 e LIM1 mostrou uma tendência a ser correlacionada com um pior prognóstico tanto para a sobrevida livre de doença quanto para sobrevida global. Nossos resultados fornecem novas informações sobre alterações transcriptômicas associadas ao comportamento clínico de TNBC que podem servir como ferramenta potencial para a identificação e caracterização de novos biomarcadores candidatos como fatores prognósticos e preditivos para pacientes com TNBC no futuro / Triple-negative breast cancer (TNBC) is one of the most aggressive, therapy-resistant, and metastatic tumors. Understanding of its biology and designing new treatments are essential to improve its prognosis. Currently, treatment options are reduced, and chemotherapy is still the standard treatment. SPARC (secreted protein acidic and rich in cysteine) expression is reportedly altered in various malignancies. However, little is known regarding the prognostic value of SPARC in TNBC patients. Using a small discovered cohort of TNBC very well characterized regarding SPARC expression status and clinical behavior, we were able to identify several genes as differentially expressed in the comparison between TNBC/SPARC negative vs. TNBC/SPARC positive samples. Five of these differentially expressed genes, SOHLH2, DNAJC12, LIM, CEACAM-5 and CTAG1A were chosen to be validated by immunohistochemistry (IHC) on tissue microarrays (TMAs) containing an independent cohort of TNBC. To access the prognostic value of these potential new biomarkers, we evaluated the association between the IHC expression and patient\'s outcomes by Kaplan-Meier analysis for the validation cohort. We found that negative staining of SOHLH2 expression and positive staining of DNAJC12 and LIM1 showed a trend to be correlated with a poor prognosis for both disease-free survival and overall survival. Our findings provide new information on transcriptome changes associated the clinical behavior of TNBC that may serve as a potential tool for the identification and characterization of new candidate biomarkers as prognostic and predictive factors for patients with TNBC in the future

Le mélanome est le cancer de la peau le plus dangereux : il est capable de métastaser rapidement vers les ganglions et les viscères, et est réfractaire aux chimio/radiothérapies. De nouvelles thérapies ciblant la kinase BRAFV600 retrouvée dans 60% des mélanomes ont montré des effets spectaculaires en termes de survie globale et sans progression de la maladie. L’efficacité de ces thérapies est compromise par l’apparition fréquente de résistances. Les cellules cancéreuses sont ancrées au sein d’un microenvironnement avec lequel elles interagissent. Elles profitent de facteurs solubles du stroma et de l’adhésion à la matrice extracellulaire (MEC) pour survivre face aux thérapies. La protéine matricellulaire SPARC orchestre les interactions entre les cellules saines ou cancéreuses et leur microenvironnement. Absente dans les mélanocytes, son expression est initiée et augmentée dans les mélanomes, corrélée à la progression tumorale et à un mauvais pronostic clinique. Lorsqu’elle est sécrétée par les cellules de mélanome, elle active la kinase AKT, déstabilise le suppresseur de tumeur p53 et favorise la prolifération/survie tumorale. Nous avons montré que le module SPARC/AKT est un nouveau déterminant de la résistance innée ou acquise des mélanomes mutés BRAFV600 aux anti-BRAF, et mis en évidence l’intérêt du ciblage de SPARC en combinaison avec des anti-BRAF ou -MEK pour optimiser/restaurer la sensibilité des mélanomes à ces inhibiteurs. Nous avons aussi montré que les fibroblastes ganglionnaires ont des caractéristiques de fibroblastes activés, et confèrent une résistance aux anti-BRAF aux cellules de mélanomes en générant une MEC permissive à laquelle elles adhérent. / Melanoma is the most dangerous form of skin cancer due to its high metastatic potential and its resistance to both classical chemo- and radiotherapies. New targeted therapies directed against the V600E oncogenic form of BRAF found in about 60% of patients have demonstrated spectacular efficacy both in terms of progression free and overall survival. However most patients invariably relapse after a few months due to resistance mechanisms. Cancer cells are anchored and interact constantly with their microenvironment. Both soluble factors and the extracellular matrix produced by stromal cells have been shown to contribute to cancer cell resistance to therapies. SPARC is a matricellular protein that orchestrates interactions between normal and/or cancer cells and their microenvironment. While it is absent in melanocytes, SPARC expression increases in melanoma and is correlated with both tumoral progression and a bad prognosis. When SPARC is secreted by melanoma cells, it activates the AKT kinase, destabilizes the p53 tumor suppressor and promotes proliferation and survival. Here we identify the couple SPARC/AKT as a new actor contributing to both innate and acquired resistance to BRAFV600E inhibitors. In addition, we demonstrate that targeting SPARC in melanoma cells increases their sensitivity to both BRAF and MEK inhibitors. Finally we show that lymph node fibroblasts share features of activated fibroblasts and confer resistance to BRAF inhibitors to melanoma cells through the production of a permissive extracellular matrix.

No description available.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

O reparo cardíaco pós-infarto do miocárdio (IM) continua sendo um desafio, apesar do grande progresso no tratamento clínico e na redução da mortalidade. Nesse sentido, estudos com modelos pré-clínicos têm demonstrado que o transplante de células-tronco adultas, como as células-tronco derivadas de tecido adiposo (ASCs), preserva a função ventricular após IM. Esta melhora não está relacionada à mecanismos de substituição tecidual, mas a ação parácrina através da liberação de moléculas bioativas pleiotrópicas. No presente estudo, nós procuramos identificar proteínas-alvo importantes relacionadas com a resposta pleiotrópica benéfica associada ao uso de ASC pós-IM. Foram realizadas análises de bioinformática do secretoma de mASC submetida à hipóxia e stretch, mimetizando o microambiente do IM, para encontrar novos alvos. Uma rede de interações incluindo três candidatos que interagem entre si: SPARC, MMP-3 e Osteopontina, foi gerada. Padronizamos o modelo de morte celular por H2O2 em cardiomiócitos, fibroblastos cardíacos e células endoteliais, os três tipos celulares principalmente encontrados no coração, e avaliamos a expressão desses fatores nessas células. Os dados mostram que o peróxido de hidrogênio altera a expressão desses fatores de forma heterogênea nessas células e induz a produção e secreção de colágeno em fibroblastos. Entretanto, o tratamento com SPARC, Osteopontina e MMP-3 não melhorou a viabilidade das células tratadas com H2O2 e nem modulou a resposta antigênica. No que se refere à produção de colágeno, a proteína SPARC conseguiu reduzir esta a níveis basais, semelhante ao que ocorreu com as células tratadas com o meio condicionado de ASC. Em conjunto, os resultados mostram que a proteína SPARC reduz a produção de colágeno assim como o meio condicionado, consistente com a ideia de que a SPARC participa, pelo menos em parte, da resposta benéfica associada ao transplante de ASC pós-infarto do miocárdio / Cardiac repair post-myocardial infarction (MI) remains a challenge despite great progress in clinical management and mortality reduction. In this sense, studies with pre-clinical models have shown that the transplantation of adult stem cells, such as stem cells derived from adipose tissue (ASCs), preserves ventricular function after MI. This improvement is not related to mechanisms of tissue replacement and cell transdifferentiation, but the paracrine action through the release of pleiotropic bioactive molecules. In the present study we tried to identify key proteins related with the beneficial pleiotropic response associated with ASC transplantation post-MI. We perform bioinformatic analyses of the proteins released by mASC subjected to stretch and hypoxia, mimmiking the MI microenvironment, to find novel targets. The network of interactions includes three candidates that interact with each other: SPARC, MMP-3 and Osteopontin. We standardized the model of cell death by H2O2 in cardiomyocytes, cardiac fibroblasts and endothelial cells, the three major cell types that form the heart, and evaluate the expression of these factors. The data show that hydrogen peroxide alters the expression of these factors heterogeneously in these cells and induces collagen production and secretion in fibroblasts. However, treatment with SPARC, Osteopontin and MMP-3 did not improve the viability of cells treated with H2O2 and does not influence the angiogenic response. Concerning to the production of collagen, SPARC protein could reduce this to basal levels, similar to what happened with the cells treated with conditioned medium of ASC. Together, these results showed that SPARC protein reduces collagen production similarly to the conditioned medium treatment, which is consistent with the idea that SPARC is responsible, at least in part, for the beneficial effects associated with the transplanted ASC post-MI

O câncer de mama triplo negativo (TNBC) é um dos tumores mais agressivos, muitas vezes resistentes à terapia sistêmica e com evolução para doença metastática. O entendimento de sua biologia e a concepção de novos tratamentos são essenciais para melhorar o seu prognóstico. Atualmente, as opções de tratamento são reduzidas e a quimioterapia ainda é o tratamento padrão. A expressão de SPARC (secreted protein acidic and rich in cysteine) é supostamente alterada em várias doenças malignas. No entanto, pouco se sabe sobre o valor prognóstico do SPARC em pacientes com TNBC. Usando uma pequena coorte de descoberta de TNBC muito bem caracterizada em relação à expressão do SPARC e comportamento clínico, conseguimos identificar vários genes como diferencialmente expressos na comparação entre amostras de TNBC / SPARC negativo vs. TNBC / SPARC positivo. Cinco desses genes diferencialmente expressos, SOHLH2, DNAJC12, LIM-1, CEACAM-5 e CTAG1A foram escolhidos para serem validados por imuno-histoquímica (IHC) em tissue microarrays (TMAs) contendo uma coorte independente de TNBC. Para acessar o valor prognóstico desses potenciais novos biomarcadores, avaliamos a associação entre a expressão de IHC e os resultados das pacientes pela análise de Kaplan-Meier para a coorte de validação. Foi observado que a coloração negativa da expressão de SOHLH2 e coloração positiva de DNAJC12 e LIM1 mostrou uma tendência a ser correlacionada com um pior prognóstico tanto para a sobrevida livre de doença quanto para sobrevida global. Nossos resultados fornecem novas informações sobre alterações transcriptômicas associadas ao comportamento clínico de TNBC que podem servir como ferramenta potencial para a identificação e caracterização de novos biomarcadores candidatos como fatores prognósticos e preditivos para pacientes com TNBC no futuro / Triple-negative breast cancer (TNBC) is one of the most aggressive, therapy-resistant, and metastatic tumors. Understanding of its biology and designing new treatments are essential to improve its prognosis. Currently, treatment options are reduced, and chemotherapy is still the standard treatment. SPARC (secreted protein acidic and rich in cysteine) expression is reportedly altered in various malignancies. However, little is known regarding the prognostic value of SPARC in TNBC patients. Using a small discovered cohort of TNBC very well characterized regarding SPARC expression status and clinical behavior, we were able to identify several genes as differentially expressed in the comparison between TNBC/SPARC negative vs. TNBC/SPARC positive samples. Five of these differentially expressed genes, SOHLH2, DNAJC12, LIM, CEACAM-5 and CTAG1A were chosen to be validated by immunohistochemistry (IHC) on tissue microarrays (TMAs) containing an independent cohort of TNBC. To access the prognostic value of these potential new biomarkers, we evaluated the association between the IHC expression and patient\'s outcomes by Kaplan-Meier analysis for the validation cohort. We found that negative staining of SOHLH2 expression and positive staining of DNAJC12 and LIM1 showed a trend to be correlated with a poor prognosis for both disease-free survival and overall survival. Our findings provide new information on transcriptome changes associated the clinical behavior of TNBC that may serve as a potential tool for the identification and characterization of new candidate biomarkers as prognostic and predictive factors for patients with TNBC in the future