Performance analysis and tuning in multicore environments

Performance analysis is the task of monitor the behavior of a program execution. The main goal is to find out the possible adjustments that might be done in order improve the performance. To be able to get that improvement it is necessary to find the different causes of overhead. Nowadays we are already in the multicore era, but there is a gap between the level of development of the two main divisions of multicore technology (hardware and software). When we talk about multicore we are also speaking of shared memory systems, on this master thesis we talk about the issues involved on the performance analysis and tuning of applications running specifically in a shared Memory system. We move one step ahead to take the performance analysis to another level by analyzing the applications structure and patterns. We also present some tools specifically addressed to the performance analysis of OpenMP multithread application. At the end we present the results of some experiments performed with a set of OpenMP scientific application.

Bihippocampal damage with emotional dysfunction: impaired auditory recognition of fear.

A right-handed man developed a sudden transient, amnestic syndrome associated with bilateral hemorrhage of the hippocampi, probably due to Urbach-Wiethe disease. In the 3rd month, despite significant hippocampal structural damage on imaging, only a milder degree of retrograde and anterograde amnesia persisted on detailed neuropsychological examination. On systematic testing of recognition of facial and vocal expression of emotion, we found an impairment of the vocal perception of fear, but not that of other emotions, such as joy, sadness and anger. Such selective impairment of fear perception was not present in the recognition of facial expression of emotion. Thus emotional perception varies according to the different aspects of emotions and the different modality of presentation (faces versus voices). This is consistent with the idea that there may be multiple emotion systems. The study of emotional perception in this unique case of bilateral involvement of hippocampus suggests that this structure may play a critical role in the recognition of fear in vocal expression, possibly dissociated from that of other emotions and from that of fear in facial expression. In regard of recent data suggesting that the amygdala is playing a role in the recognition of fear in the auditory as well as in the visual modality this could suggest that the hippocampus may be part of the auditory pathway of fear recognition.

Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations.

Calcium is vital to the normal functioning of multiple organ systems and its serum concentration is tightly regulated. Apart from CASR, the genes associated with serum calcium are largely unknown. We conducted a genome-wide association meta-analysis of 39,400 individuals from 17 population-based cohorts and investigated the 14 most strongly associated loci in ≤ 21,679 additional individuals. Seven loci (six new regions) in association with serum calcium were identified and replicated. Rs1570669 near CYP24A1 (P = 9.1E-12), rs10491003 upstream of GATA3 (P = 4.8E-09) and rs7481584 in CARS (P = 1.2E-10) implicate regions involved in Mendelian calcemic disorders: Rs1550532 in DGKD (P = 8.2E-11), also associated with bone density, and rs7336933 near DGKH/KIAA0564 (P = 9.1E-10) are near genes that encode distinct isoforms of diacylglycerol kinase. Rs780094 is in GCKR. We characterized the expression of these genes in gut, kidney, and bone, and demonstrate modulation of gene expression in bone in response to dietary calcium in mice. Our results shed new light on the genetics of calcium homeostasis.

Mise en oeuvre de protocoles spatiaux pour analyser la modulation de processus cognitifs en fonction de la dimension émotionnelle chez le rongeur

Résumé : Emotion et cognition sont deux termes généralement employés pour désigner des processus psychiques de nature opposée. C'est ainsi que les sciences cognitives se sont longtemps efforcées d'écarter la composante «chaude »des processus «froids »qu'elles visaient, si ce n'est pour montrer l'effet dévastateur de la première sur les seconds. Pourtant, les processus cognitifs (de collecte, maintien et utilisation d'information) et émotioAnels (d'activation subjective, physiologique et comportementale face à ce qui est attractif ou aversif) sont indissociables. Par l'approche neuro-éthologique, à l'interface entre le substrat biologique et les manifestations comportementales, nous nous sommes intéressés à une fonction cognitive essentielle, la fonction mnésique, classiquement exprimée chez le rongeur par l'orientation spatiale. Au niveau du substrat, McDonald et White (1993) ont montré la dissociation de trois systèmes de mémoire, avec les rôles de l'hippocampe, du néostriatum et de l'amygdale dans l'encodage des informations respectivement épisodiques, procédurales et émotionnelles. Nous nous sommes penchés sur l'interaction entre ces systèmes en fonction de la dimension émotionnelle par l'éclairage du comportement. L'état émotionnel de l'animal dépend de plusieurs facteurs, que nous avons tenté de contrôler indirectement en comparant leurs effets sur l'acquisition, dans diverses conditions, de la tâche de Morris (qui nécessite la localisation dans un bassin de la position d'une plate-forme submergée), ainsi que sur le style d'exploration de diverses arènes, ouvertes ou fermées, plus ou moins structurées par la présence de tunnels en plexiglas transparent. Nous avons d'abord exploré le rôle d'un composant du système adrénergique dans le rapport à la difficulté et au stress, à l'aide de souris knock-out pour le récepteur à la noradrénaline a-1 B dans un protocole avec 1 ou 4 points de départ dans un bassin partitionné. Ensuite, nous nous sommes penchés, chez le rat, sur les effets de renforcement intermittent dans différentes conditions expérimentales. Dans ces conditions, nous avons également tenté d'analyser en quoi la situation du but dans un paysage donné pouvait interférer avec les effets de certaines formes de stress. Finalement, nous avons interrogé les conséquences de perturbations passées, y compris le renforcement partiel, sur l'organisation des déplacements sur sol sec. Nos résultats montrent la nécessité, pour les souris cont~ô/es dont l'orientation repose sur l'hippocampe, de pouvoir varier les trajectoires, ce qui favoriserait la constitution d'une carte cognitive. Les souris a->B KO s'avèrent plus sensibles au stress et capables de bénéficier de la condition de route qui permet des réponses simples et automatisées, sous-tendues par l'activité du striatum. Chez les rats en bassin 100% renforcé, l'orientation apparaît basée sur l'hippocampe, relayée par le striatum pour le développement d'approches systématiques et rapides, avec réorientation efficace en nouvelle position par réactivation dépendant de l'hippocampe. A 50% de renforcement, on observe un effet du type de déroulement des sessions, transitoirement atténué par la motivation Lorsque les essais s'enchaînent sans pause intrasession, les latences diminuent régulièrement, ce qui suggère une prise en charge possible par des routines S-R dépendant du striatum. L'organisation des mouvements exploratoires apparaît dépendante du niveau d'insécurité, avec différents profils intermédiaires entre la différentiation maximale et la thigmotaxie, qui peuvent être mis en relation avec différents niveaux d'efficacité de l'hippocampe. Ainsi, notre travail encourage à la prise en compte de la dimension émotionnelle comme modulatrice du traitement d'information, tant en phase d'exploration de l'environnement que d'exploitation des connaissances spatiales. Abstract : Emotion and cognition are terms widely used to refer to opposite mental processes. Hence, cognitive science research has for a long time pushed "hot" components away from "cool" targeted processes, except for assessing devastating effects of the former upon the latter. However, cognitive processes (of information collection, preservation, and utilization) and emotional processes (of subjective, physiological, and behavioral activation roue to attraction or aversion) are inseparable. At the crossing between biological substrate and behavioral expression, we studied a chief cognitive function, memory, classically shown in animals through spatial orientation. At the substrate level, McDonald et White (1993) have shown a dissociation between three memory systems, with the hippocampus, neostriatum, and amygdala, encoding respectively episodic, habit, and emotional information. Through the behavior of laboratory rodents, we targeted the interaction between those systems and the emotional axis. The emotional state of an animal depends on different factors, that we tried to check in a roundabout way by the comparison of their effects on acquisition, in a variety of conditions, of the Morris task (in which the location of a hidden platform in a pool is required), as well as on the exploration profile in different apparatus, open-field and closed mazes, more or less organized by clear Plexiglas tunnels. We first tracked the role, under more or less difficult and stressful conditions, of an adrenergic component, with knock-out mice for the a-1 B receptor in a partitioned water maze with 1 or 4 start positions. With rats, we looked for the consequences of partial reinforcement in the water maze in different experimental conditions. In those conditions, we further analyzed how the situation of the goal in the landscape could interfere with the effect of a given stress. At last, we conducted experiments on solid ground, in an open-field and in radial mazes, in order to analyze the organization of spatial behavior following an aversive life event, such as partial reinforcement training in the water maze. Our results emphasize the reliance of normal mice to be able to vary approach trajectories. One of our leading hypotheses is that such strategies are hippocampus-dependent and are best developed for of a "cognitive map like" representation. Alpha-1 B KO mice appear more sensitive to stress and able to take advantage of the route condition allowing simple and automated responses, most likely striatum based. With rats in 100% reinforced water maze, the orientation strategy is predominantly hippocampus dependent (as illustrated by the impairment induced by lesions of this structure) and becomes progressively striatum dependent for the development of systematic and fast successful approaches. Training towards a new platform position requires a hippocampus based strategy. With a 50% reinforcement rate, we found a clear impairment related to intersession disruption, an effect transitorily minimized by motivation enhancement (cold water). When trials are given without intrasession interruption, latencies consistently diminish, suggesting a possibility for striatum dependent stimulus-response routine to occur. The organization of exploratory movements is shown to depend on the level of subjective security, with different intermediary profiles between maximum differentiation and thigmotaxy, which can be considered in parallel with different efficiency levels of the hippocampus dependent strategies. Thus, our work fosters the consideration of emotion as a cognitive treatment modulator, during spatial exploration as well as spatial learning. It leads to a model in which the predominance of hippocampus based exploration is challenged by training conditions of various nature.

The impact of pre- and post-natal contexts on immunity, glucocorticoids and oxidative stress resistance in wild and domesticated grey partridges

Genetic background, prenatal and post-natal early-life conditions influence the development of interconnected physiological systems and thereby shape the phenotype. Certain combinations of genotypes and pre- and post-natal conditions may provide higher fitness in a specific environmental context. Here, we investigated how grey partridges Perdix perdix of two strains (wild and domesticated) cope physiologically with pre- and post-natal predictable vs. unpredictable food supply. Food unpredictability occurs frequently in wild environments and requires physiological and behavioural adjustments. Well-orchestrated and efficient physiological systems are presumably more vital in a wild environment as compared to captivity. We thus predicted that wild-strain grey partridges have a stronger immunity, glucocorticoid (GC) stress response and oxidative stress resistance (OSR) than domesticated birds, which have undergone adaptations to captivity. We also predicted that wild-strain birds react more strongly to environmental stimuli and, when faced with harsh prenatal conditions, are better able to prepare their offspring for similarly poor post-natal conditions than birds of domesticated origin. We found that wild-strain offspring were physiologically better prepared for stressful situations as compared to the domesticated strain. They had a high GC stress response and a high OSR when kept under predictable food supply. Wild-strain parents reacted to prenatal unpredictable food supply by lowering their offspring's GC stress response, which potentially lowered GC-induced oxidative pressure. No such pattern was evident in the domesticated birds. Irrespective of strain and prenatal feeding scheme, post-natal unpredictable food supply boosted immune indices, and GC stress response was negatively related to antibody response in females and to mitochondrial superoxide production. Wild-strain grey partridge showed fitness-relevant physiological advantages and appeared to prepare their offspring for the prospective environment. Negative relationships between GC stress response, immunity and oxidative indices imply a pivotal role of an organism's oxidative balance and support the importance of considering multiple physiological systems simultaneously.

Pain, frailty and comorbidity on older men: the CHAMP study.

Intrusive pain is likely to have a serious impact on older people with limited ability to respond to additional stressors. Frailty is conceptualised as a functional and biological pattern of decline accumulating across multiple physiological systems, resulting in a decreased capacity to respond to additional stressors. We explored the relationship between intrusive pain, frailty and comorbid burden in 1705 community-dwelling men aged 70 or more who participated in the baseline phase of the CHAMP study, a large epidemiological study of healthy ageing based in Sydney, Australia. 9.4% of men in the study were frail (according to the commonly-used Cardiovascular Health Study frailty criteria).Using a combination of self-report and clinical measures, we found an association between frailty and intrusive pain that remained after accounting for demographic characteristics, number of comorbidities, self-reported depressed mood and arthritis (adjusted odds ratio 1.7 (95% confidence interval (CI) 1.1-2.7), p=0.0149). The finding that adjusting for depressed mood, but not a history of arthritis, attenuated the relationship between frailty and intrusive pain points to a key role for central mechanisms. Additionally, men with the highest overall health burden (frail plus high comorbid burden) were most likely to report intrusive pain (adjusted odds ratio 3.0 (95% CI 1.6-5.5), p=0.0004). These findings provide support for the concept that intrusive pain is an important challenge for older men with limited capacity to respond to additional physical stressors. To our knowledge, this is the first study to explore specifically the relationship between pain and frailty.

Teknologiat ja toteutustavat palvelukeskeiseen arkkitehtuuriin perustuvassa Internet-pohjaisessajärjestelmässä

Palvelukeskeiseen arkkitehtuuriin perustuvia järjestelmiä voidaan kehittää käyttämällä useita vaihtoehtoisia teknologioita. Toteuttamiseen parhaiten soveltuvia teknologioita ovat erilaiset standardikokoelmat, jotka tukevat useiden toisistaan toteutustavaltaan poikkeavien järjestelmien yhdistämistä käyttämällä standardeihin perustuvia rajapintoja. Täten kyseiset kokoelmat tukevat laajojen, useista erillisistä osista koostuvien palvelujärjestelmien kehittämistä. Tässä työssä selvitetään mikä palvelukeskeinen arkkitehtuuri on sekä millaisia komponentteja ja teknologioita kyseiseen arkkitehtuuriin perustuvan palvelujärjestelmän toteuttamiseen tarvitaan. Tavoitteena on esitellä palvelukeskeinen arkkitehtuuri ja siihen liittyvät teknologiat sekä suunnitella korkealla tasolla kyseisiä teknologioita hyödyntävä integraatioalusta käyttäjien ja useiden palvelun tarjoajien yhdistämiseksi. Työn tuloksena syntyvän teknologiaselvitysraportin selvitysluonteen vuoksi työssä ei suunnitella tarkasti toteutettavaa järjestelmää vaan ainoastaanpohjustetaan järjestelmän suunnittelua sekä esitellään siihen liittyviä arkkitehtuuri- ja toteutusmahdollisuuksia. Internet-pohjainen palvelukeskeiseen arkkitehtuuriin perustuva järjestelmä voi perustua suoriinverkon välisiin yhteyksiin tai vaihtoehtoisesti erityyppisiin välitason sovelluksiin. Välitason sovellukset mahdollistavat niiden tyypistä riippuen järjestelmän erilaisten lisäominaisuuksien toteuttamisen ja tukevat useita yleisimpiä palvelukeskeisiä teknologioita. Työn tuloksena syntyneen teknologiaselvityksen perusteella näistä teknologioista Web-palvelu -arkkitehtuuri ja siihen liittyvät menetelmät soveltuvat parhaiten suunniteltavan järjestelmän rakenneosiksi. Järjestelmän tarkemmat toteutustavat riippuvat myöhemmin määriteltävistä yksityiskohtaisista vaatimuksista sekä valittavasta välitason ohjelmiston toteutuksesta.

Plataforma eMovie : xarxa social de pel·lícules

En aquest treball s'han estudiat diferents sistemes de recomanació, i s'han utilitzat per a veure com podrien arribar a recomanar pel·lícules als usuaris. Això s'ha realitzat dins del context de la recomanació web, un sistema mitjançant el qual es poden obtenir moltes dades dels usuaris, però que per altra banda requereix de temps de resposta ràpids.

Turbulent shallow-water model for orographic subgrid-scale perturbations

A parallel pseudo-spectral method for the simulation in distributed memory computers of the shallow-water equations in primitive form was developed and used on the study of turbulent shallow-waters LES models for orographic subgrid-scale perturbations. The main characteristics of the code are: momentum equations integrated in time using an accurate pseudo-spectral technique; Eulerian treatment of advective terms; and parallelization of the code based on a domain decomposition technique. The parallel pseudo-spectral code is efficient on various architectures. It gives high performance onvector computers and good speedup on distributed memory systems. The code is being used for the study of the interaction mechanisms in shallow-water ows with regular as well as random orography with a prescribed spectrum of elevations. Simulations show the evolution of small scale vortical motions from the interaction of the large scale flow and the small-scale orographic perturbations. These interactions transfer energy from the large-scale motions to the small (usually unresolved) scales. The possibility of including the parametrization of this effects in turbulent LES subgrid-stress models for the shallow-water equations is addressed.

Neural regulation of the stress response: glucocorticoid feedback mechanisms

The mammalian stress response is an integrated physiological and psychological reaction to real or perceived adversity. Glucocorticoids are an important component of this response, acting to redistribute energy resources to both optimize survival in the face of challenge and to restore homeostasis after the immediate challenge has subsided. Release of glucocorticoids is mediated by the hypothalamo-pituitary-adrenal (HPA) axis, driven by a neural signal originating in the paraventricular nucleus (PVN). Stress levels of glucocorticoids bind to glucocorticoid receptors in multiple body compartments, including the brain, and consequently have wide-reaching actions. For this reason, glucocorticoids serve a vital function in negative feedback inhibition of their own secretion. Negative feedback inhibition is mediated by a diverse collection of mechanisms, including fast, non-genomic feedback at the level of the PVN, stress-shut-off at the level of the limbic system, and attenuation of ascending excitatory input through destabilization of mRNAs encoding neuropeptide drivers of the HPA axis. In addition, there is evidence that glucocorticoids participate in stress activation via feed-forward mechanisms at the level of the amygdala. Feedback deficits are associated with numerous disease states, underscoring the necessity for adequate control of glucocorticoid homeostasis. Thus, rather than having a single, defined feedback ‘switch’, control of the stress response requires a wide-reaching feedback ‘network’ that coordinates HPA activity to suit the overall needs of multiple body systems.

Exploration du lien entre la qualité de la mentalisation et l'efficacité du rappel autobiographique

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

Modulation du système glutamatergique pendant l’apprentissage moteur : une étude de spectroscopie par résonance magnétique fonctionnelle

La présente étude avait pour but d’explorer les modulations fonctionnelles putaminales du signal de spectroscopie par résonance magnétique (SRM) combiné du glutamate et de la glutamine (Glx), ainsi que de l’acide γ-aminobutyrique (GABA) en lien avec l’apprentissage d’une séquence motrice. Nous avons émis l’hypothèse que les concentrations de Glx seraient spécifiquement augmentées pendant et après la pratique d’une telle tâche, et ce comparativement à une condition d’exécution motrice simple conçue pour minimiser l’apprentissage. La tâche d’appuis séquentiels des doigts (« finger taping task ») utilisée est connue pour induire un apprentissage moteur évoluant en phases, avec une progression initialement rapide lors de la première session d’entraînement (phase rapide), puis lente lors de sessions subséquentes (phase lente). Cet apprentissage est également conçu comme dépendant de processus « on-line » (pendant la pratique) d’acquisition et « off-line » (entre les périodes de pratique) de consolidation de la trace mnésique de l’habilité motrice. Une grande quantité de données impliquent le système de neurotransmission glutamatergique, principalement par l’action de ses récepteurs N-Méthyl-D-aspartate (NMDAR) et métabotropiques (mGluR), dans une multitude de domaine de la mémoire. Quelques-unes de ces études suggèrent que cette relation s’applique aussi à des mémoires de type motrice ou dépendante du striatum. De plus, certains travaux chez l’animal montrent qu’une hausse des concentrations de glutamate et de glutamine peut être associée à l’acquisition et/ou consolidation d’une trace mnésique. Nos mesures de SRM à 3.0 Tesla, dont la qualité ne s’est avérée satisfaisante que pour le Glx, démontrent qu’une telle modulation des concentrations de Glx est effectivement détectable dans le putamen après la performance d’une tâche motrice. Elles ne nous permettent toutefois pas de dissocier cet effet putativement attribuable à la plasticité du putamen associée à l’apprentissage moteur de séquence, de celui de la simple activation neuronale causée par l’exécution motrice. L’interprétation de l’interaction non significative, montrant une plus grande modulation par la tâche motrice simple, mène cependant à l’hypothèse alternative que la plasticité glutamatergique détectée est potentiellement plus spécifique à la phase lente de l’apprentissage, suggérant qu’une seconde expérience ainsi orientée et utilisant une méthode de SRM plus sensible au Glx aurait donc de meilleures chances d’offrir des résultats concluants.

Design and Development of re configurable compact cross patch antenna for switchable polarization

Antennas are necessary and vital components of communication and radar systems, but sometimes their inability to adjust to new operating scenarios can limit system performance. Reconfigurable antennas can adjust with changing system requirements or environmental conditions and provide additional levels of functionality that may result in wider instantaneous frequency bandwidths, more extensive scan volumes, and radiation patterns with more desirable side lobe distributions. Their agility and diversity created new horizons for different types of applications especially in cognitive radio, Multiple Input Multiple Output Systems, satellites and many other applications. Reconfigurable antennas satisfy the requirements for increased functionality, such as direction finding, beam steering, radar, control and command, within a confined volume. The intelligence associated with the reconfigurable antennas revolved around switching mechanisms utilized. In the present work, we have investigated frequency reconfigurable polarization diversity antennas using two methods: 1. By using low-loss, high-isolation switches such as PIN diode, the antenna can be structurally reconfigured to maintain the elements near their resonant dimensions for different frequency bands and/or polarization. 2. Secondly, the incorporation of variable capacitors or varactors, to overcome many problems faced in using switches and their biasing. The performances of these designs have been studied using standard simulation tools used in industry/academia and they have been experimentally verified. Antenna design guidelines are also deduced by accounting the resonances. One of the major contributions of the thesis lies in the analysis of the designed antennas using FDTD based numerical computation to validate their performance.

Alteración de la atención y concentración en estudiantes de medicina que realizan turnos de noche

El sueño, es indispensable para la recuperación, física, mental y de procesos como la consolidación de memoria, atención y lenguaje. La privación de sueño (PS) incide en la atención y concentración. La PS es inherente a la formación médica, pero no es claro el papel de los turnos nocturnos en estudiantes, porque no cumplen con un objetivo académico, pero hay relación con disminución de la salud, productividad, accidentes, y alteraciones en diversas actividades. Está descrito el impacto de la PS sobre la capacidad de aprendizaje y aspectos como el ánimo y las relaciones interpersonales. MÉTODOS: Se realizó un estudio analítico observacional de cohorte longitudinal, con tres etapas de medición a 180 estudiantes de Medicina de la Universidad del Rosario, que evaluó atención selectiva y concentración mediante la aplicación de la prueba d2, validada internacionalmente para tal fin. RESULTADOS: Se estudiaron 180 estudiantes, 115 mujeres, 65 hombres, entre los 18 y 26 años (promedio 21). Al inicio del estudio dormían en promedio 7,9 horas, cifra que se redujo a 5,8 y 6,3 en la segunda y tercera etapa respectivamente. El promedio de horas de sueño nocturno, disminuyó en el segundo y tercer momento (p<0,001); Además se encontró mediante la aplicación de la prueba d2, que hubo correlación significativa directa débil, entre el promedio de horas de sueño, y el promedio del desempeño en la prueba (r=0.168, p=0.029) CONCLUSIONES: La PS, con períodos de sueño menores a 7,2 horas, impactan de manera importante la atención selectiva, la concentración

Efectividad del tratamiento con neurofeedback en trastornos del estado del ánimo, ansiedad y fibromialgia: una revisión de literatura

El neurofeedback es una técnica no invasiva en la que se pretende corregir, mediante condicionamiento operante, ondas cerebrales que se encuentren alteradas en el electroencefalograma. Desde 1967, se han conducido numerosas investigaciones relacionadas con los efectos de la técnica en el tratamiento de alteraciones psicológicas. Sin embargo, a la fecha no existen revisiones sistemáticas que reúnan los temas que serán aquí tratados. El aporte de este trabajo es la revisión de 56 artículos, publicados entre los años 1995 y 2013 y la evaluación metodológica de 29 estudios incluidos en la revisión. La búsqueda fue acotada a la efectividad del neurofeedback en el tratamiento de depresión, ansiedad, trastorno obsesivo compulsivo (TOC), ira y fibromialgia. Los hallazgos demuestran que el neurofeedback ha tenido resultados positivos en el tratamiento de estos trastornos, sin embargo, es una técnica que aún está en desarrollo, con unas bases teóricas no muy bien establecidas y cuyos resultados necesitan de diseños metodológicamente más sólidos que ratifiquen su validez.