Bioinformatic analysis for exploring relationships between genes and gene products

To carry out their specific roles in the cell, genes and gene products often work together in groups, forming many relationships among themselves and with other molecules. Such relationships include physical protein-protein interaction relationships, regulatory relationships, metabolic relationships, genetic relationships, and much more. With advances in science and technology, some high throughput technologies have been developed to simultaneously detect tens of thousands of pairwise protein-protein interactions and protein-DNA interactions. However, the data generated by high throughput methods are prone to noise. Furthermore, the technology itself has its limitations, and cannot detect all kinds of relationships between genes and their products. Thus there is a pressing need to investigate all kinds of relationships and their roles in a living system using bioinformatic approaches, and is a central challenge in Computational Biology and Systems Biology. This dissertation focuses on exploring relationships between genes and gene products using bioinformatic approaches. Specifically, we consider problems related to regulatory relationships, protein-protein interactions, and semantic relationships between genes. A regulatory element is an important pattern or "signal", often located in the promoter of a gene, which is used in the process of turning a gene "on" or "off". Predicting regulatory elements is a key step in exploring the regulatory relationships between genes and gene products. In this dissertation, we consider the problem of improving the prediction of regulatory elements by using comparative genomics data. With regard to protein-protein interactions, we have developed bioinformatics techniques to estimate support for the data on these interactions. While protein-protein interactions and regulatory relationships can be detected by high throughput biological techniques, there is another type of relationship called semantic relationship that cannot be detected by a single technique, but can be inferred using multiple sources of biological data. The contributions of this thesis involved the development and application of a set of bioinformatic approaches that address the challenges mentioned above. These included (i) an EM-based algorithm that improves the prediction of regulatory elements using comparative genomics data, (ii) an approach for estimating the support of protein-protein interaction data, with application to functional annotation of genes, (iii) a novel method for inferring functional network of genes, and (iv) techniques for clustering genes using multi-source data.

Quantitative diatom-based reconstruction of paleoenvironmental conditions in Florida Bay and Biscayne Bay, U.S.A.

The spatial and temporal distribution of modern diatom assemblages in surface sediments, on the most dominant macrophytes, and in the water column at 96 locations in Florida Bay, Biscayne Bay and adjacent regions were examined in order to develop paleoenvironmental prediction models for this region. Analyses of these distributions revealed distinct temporal and spatial differences in assemblages among the locations. The differences among diatom assemblages living on subaquatic vegetation and sediments, and in the water column were significant. Because concentrations of salts, total phosphorus (WTP), total nitrogen (WTN) and total organic carbon (WTOC) are partly controlled by water management in this region, diatom-based models were produced to assess these variables. Discriminant function analyses showed that diatoms can also be successfully used to reconstruct changes in the abundance of diatom assemblages typical for different habitats and life habits. ^ To interpret paleoenvironmental changes, changes in salinity, WTN, WTP and WTOC were inferred from diatoms preserved in sediment cores collected along environmental gradients in Florida Bay (4 cores) and from nearshore and offshore locations in Biscayne Bay (3 cores). The reconstructions showed that water quality conditions in these estuaries have been fluctuating for thousands of years due to natural processes and sea-level changes, but almost synchronized shifts in diatom assemblages occurred in the mid-1960’s at all coring locations (except Ninemile Bank and Bob Allen Bank in Florida Bay). These alterations correspond to the major construction of numerous water management structures on the mainland. Additionally, all the coring sites (except Card Sound Bank, Biscayne Bay and Trout Cove, Florida Bay) showed decreasing salinity and fluctuations in nutrient levels in the last two decades that correspond to increased rainfall in the 1990’s and increased freshwater discharge to the bays, a result of increased freshwater deliveries to the Everglades by South Florida Water Management District in the 1980’s and 1990’s. Reconstructions of the abundance of diatom assemblages typical for different habitats and life habits revealed multiple sources of diatoms to the coring locations and that epiphytic assemblages in both bays increased in abundance since the early 1990’s. ^

Obesity and Serum High Sensitivity C-Reactive Protein Levels Among Elderly Turkish Immigrants in the Netherlands with Type 2 Diabetes

The study examined the associations of anthropometric measures of obesity with high sensitivity C-reactive protein (hs-CRP) levels in Turkish immigrants with type 2 diabetes (T2D) living in the Netherlands. A total of 110 participants, physician-diagnosed with T2D, aged 30 years and older were recruited from multiple sources from The Hague, Netherlands. Serum hs-CRP levels were measured with immunoturbidimetric assay. Glycated hemoglobin (A1C) was determined by high-pressure liquid chromatography. Measures of obesity: body weight, body mass index (BMI), waist circumference (WC), hip circumference (HC), waist-to-hip ratio (WHR), and waist-to-height ratio (WHtR) were determined. Statistical analysis included descriptive statistics, Pearson’s correlations and multiple linear regressions (MLR) stratified by gender. Hs-CRP was log transformed to achieve normality. Subjects with hs-CRP levels >10 mg/L (n = 17) were excluded from the analysis. Females had a higher BMI (p = 0.007), HC (p < 0.001), and WHtR (p = 0.011) as compared to males. Conversely, males had a higher weight (p = 0.007), and WHR (p < 0.001) than females. MLR showed that after controlling for covariates, log hs-CRP was positively associated with BMI (B = 0.039, SE = 0.019, β = 0.287, p < 0.05), WC (B = 0.025, SE = 0.011, β = 0.332, p < 0.05) and WHtR (B = 4.015, SE = 1.464, β = 0.376, p < 0.01) in females only. Gender-specific associations between obesity measures and hs-CRP level need to be further investigated in the Turkish immigrant population. Hs-CRP assessment may be added as a standard of care for T2D treatment within this population.

Embedded Heat Pipes in Cofired Ceramic Substrates for Enhanced Thermal Management of Electronics

A novel and new thermal management technology for advanced ceramic microelectronic packages has been developed incorporating miniature heat pipes embedded in the ceramic substrate. The heat pipes use an axially grooved wick structure and water as the working fluid. Prototype substrate/heat pipe systems were fabricated using high temperature co-fired ceramic (alumina). The heat pipes were nominally 81 mm in length, 10 mm in width, and 4 mm in height, and were charged with approximately 50-80 mL of water. Platinum thick film heaters were fabricated on the surface of the substrate to simulate heat dissipating electronic components. Several thermocouples were affixed to the substrate to monitor temperature. One end of the substrate was affixed to a heat sink maintained at constant temperature. The prototypes were tested and shown to successful and reliably operate with thermal loads over 20 Watts, with thermal input from single and multiple sources along the surface of the substrate. Temperature distributions are discussed for the various configurations and the effective thermal resistance of the substrate/heat pipe system is calculated. Finite element analysis was used to support the experimental findings and better understand the sources of the system's thermal resistance.

Uma plataforma adaptável para localização em ambientes internos

Location systems have become increasingly part of people's lives. For outdoor environments, GPS appears as standard technology, widely disseminated and used. However, people usually spend most of their daily time in indoor environments, such as: hospitals, universities, factories, buildings, etc. In these environments, GPS does not work properly causing an inaccurate positioning. Currently, to perform the location of people or objects in indoor environments no single technology could reproduce for indoors the same result achieved by GPS for outdoors environments. Due to this, it is necessary to consider use of information from multiple sources using diferent technologies. Thus, this work aims to build an Adaptable Platform for Indoor location. Based on this goal, the IndoLoR platform is proposed. This platform aims to allow information reception from diferent sources, data processing, data fusion, data storage and data retrieval for the indoor location context.

Uma plataforma adaptável para localização em ambientes internos

Location systems have become increasingly part of people's lives. For outdoor environments, GPS appears as standard technology, widely disseminated and used. However, people usually spend most of their daily time in indoor environments, such as: hospitals, universities, factories, buildings, etc. In these environments, GPS does not work properly causing an inaccurate positioning. Currently, to perform the location of people or objects in indoor environments no single technology could reproduce for indoors the same result achieved by GPS for outdoors environments. Due to this, it is necessary to consider use of information from multiple sources using diferent technologies. Thus, this work aims to build an Adaptable Platform for Indoor location. Based on this goal, the IndoLoR platform is proposed. This platform aims to allow information reception from diferent sources, data processing, data fusion, data storage and data retrieval for the indoor location context.

A Formação de professores nas tramas do virtual

This study aims to reflect on the cultural and aesthetics formation of teacher, and how they act as a co-author in the virtual environment. The reflection permeates on topics such as: The Information Age and the challenges of the teacher in the twenty-first century; teacher professional development and the multiple personal identities; the importance of cultural repertoire for teaching practice and the role of the teacher as co-author in the informational network. In addition to the theoretical reflections were conducted two focus groups with the participation of teachers with different graduations and working in various levels of education to discuss the presented topics. It was proposed to create a website for the teacher to sail and collaborate with posts on many cultural artifacts. For the construction of the content for the site, it developed a “daily creation”, which is the search information storage from multiple sources, such as academic papers, songs, websites, magazines, comics, blogs, books, photographs, advertisements, finally everything that can increase imagination and serve for the production of content. Data analysis of the focus group showed that teachers recognize the varied cultural repertoire makes for a good professional aplomb, but cannot actively participate in the local culture. It was also found that the teacher has difficulty manipulating information technology and communication and therefore, distance themselves from an active production network. The focus group contributed to building a website and posts on cultural artifacts. Production can be accessed at www.digitaldoprofessor.com.

PRODUÇÃO DE SENTIDOS NA INFÂNCIA: MEDIAÇÕES NA RECEPÇÃO DA SÉRIE DE ANIMAÇÃO DOUG FUNNIE

Esta pesquisa propõe uma reflexão a respeito dos processos de recepção de produtos culturais por parte do telespectador infantil. A problematização está em investigar, valendo-se dos referenciais teóricos das mediações comunicativas da cultura e do enfoque integral da audiência, como as crianças com idade entre 7 e 12 anos interagem com as narrativas audiovisuais, especialmente com a série de animação televisiva, para desta perspectiva compreender como se dão a apropriação e a produção de sentidos no cotidiano, tomando-se por base a interpretação do desenho animado Doug Funnie. O estudo emprega como metodologia a revisão de literatura combinada ao grupo de discussão norteado pelo modelo teórico-metodológico da mediação múltipla formulado por Guillermo Orozco Gómez, com base no paradigma das mediações de Jesús Martín-Barbero. A pesquisa de recepção, realizada em ambiente escolar, constatou que a comunicação midiática é de natureza dialógica e implica em reconhecimento e projeção do interlocutor no universo da ficção, assim, a produção de sentidos em relação ao desenho animado não está contida no audiovisual, mas no contexto sociocultural no qual interlocutores relacionam-se entre si e com os meios. E desta interação emergem a compreensão e a recriação dos produtos culturais, sinalizando que as interpretações do telespectador infantil revelam a sua maneira de ver o mundo.

Stimulus Integration and Parsing in the Primate Auditory Midbrain

Integrating information from multiple sources is a crucial function of the brain. Examples of such integration include multiple stimuli of different modalties, such as visual and auditory, multiple stimuli of the same modality, such as auditory and auditory, and integrating stimuli from the sensory organs (i.e. ears) with stimuli delivered from brain-machine interfaces.

The overall aim of this body of work is to empirically examine stimulus integration in these three domains to inform our broader understanding of how and when the brain combines information from multiple sources.

First, I examine visually-guided auditory, a problem with implications for the general problem in learning of how the brain determines what lesson to learn (and what lessons not to learn). For example, sound localization is a behavior that is partially learned with the aid of vision. This process requires correctly matching a visual location to that of a sound. This is an intrinsically circular problem when sound location is itself uncertain and the visual scene is rife with possible visual matches. Here, we develop a simple paradigm using visual guidance of sound localization to gain insight into how the brain confronts this type of circularity. We tested two competing hypotheses. 1: The brain guides sound location learning based on the synchrony or simultaneity of auditory-visual stimuli, potentially involving a Hebbian associative mechanism. 2: The brain uses a ‘guess and check’ heuristic in which visual feedback that is obtained after an eye movement to a sound alters future performance, perhaps by recruiting the brain’s reward-related circuitry. We assessed the effects of exposure to visual stimuli spatially mismatched from sounds on performance of an interleaved auditory-only saccade task. We found that when humans and monkeys were provided the visual stimulus asynchronously with the sound but as feedback to an auditory-guided saccade, they shifted their subsequent auditory-only performance toward the direction of the visual cue by 1.3-1.7 degrees, or 22-28% of the original 6 degree visual-auditory mismatch. In contrast when the visual stimulus was presented synchronously with the sound but extinguished too quickly to provide this feedback, there was little change in subsequent auditory-only performance. Our results suggest that the outcome of our own actions is vital to localizing sounds correctly. Contrary to previous expectations, visual calibration of auditory space does not appear to require visual-auditory associations based on synchrony/simultaneity.

My next line of research examines how electrical stimulation of the inferior colliculus influences perception of sounds in a nonhuman primate. The central nucleus of the inferior colliculus is the major ascending relay of auditory information before it reaches the forebrain, and thus an ideal target for understanding low-level information processing prior to the forebrain, as almost all auditory signals pass through the central nucleus of the inferior colliculus before reaching the forebrain. Thus, the inferior colliculus is the ideal structure to examine to understand the format of the inputs into the forebrain and, by extension, the processing of auditory scenes that occurs in the brainstem. Therefore, the inferior colliculus was an attractive target for understanding stimulus integration in the ascending auditory pathway.

Moreover, understanding the relationship between the auditory selectivity of neurons and their contribution to perception is critical to the design of effective auditory brain prosthetics. These prosthetics seek to mimic natural activity patterns to achieve desired perceptual outcomes. We measured the contribution of inferior colliculus (IC) sites to perception using combined recording and electrical stimulation. Monkeys performed a frequency-based discrimination task, reporting whether a probe sound was higher or lower in frequency than a reference sound. Stimulation pulses were paired with the probe sound on 50% of trials (0.5-80 µA, 100-300 Hz, n=172 IC locations in 3 rhesus monkeys). Electrical stimulation tended to bias the animals’ judgments in a fashion that was coarsely but significantly correlated with the best frequency of the stimulation site in comparison to the reference frequency employed in the task. Although there was considerable variability in the effects of stimulation (including impairments in performance and shifts in performance away from the direction predicted based on the site’s response properties), the results indicate that stimulation of the IC can evoke percepts correlated with the frequency tuning properties of the IC. Consistent with the implications of recent human studies, the main avenue for improvement for the auditory midbrain implant suggested by our findings is to increase the number and spatial extent of electrodes, to increase the size of the region that can be electrically activated and provide a greater range of evoked percepts.

My next line of research employs a frequency-tagging approach to examine the extent to which multiple sound sources are combined (or segregated) in the nonhuman primate inferior colliculus. In the single-sound case, most inferior colliculus neurons respond and entrain to sounds in a very broad region of space, and many are entirely spatially insensitive, so it is unknown how the neurons will respond to a situation with more than one sound. I use multiple AM stimuli of different frequencies, which the inferior colliculus represents using a spike timing code. This allows me to measure spike timing in the inferior colliculus to determine which sound source is responsible for neural activity in an auditory scene containing multiple sounds. Using this approach, I find that the same neurons that are tuned to broad regions of space in the single sound condition become dramatically more selective in the dual sound condition, preferentially entraining spikes to stimuli from a smaller region of space. I will examine the possibility that there may be a conceptual linkage between this finding and the finding of receptive field shifts in the visual system.

In chapter 5, I will comment on these findings more generally, compare them to existing theoretical models, and discuss what these results tell us about processing in the central nervous system in a multi-stimulus situation. My results suggest that the brain is flexible in its processing and can adapt its integration schema to fit the available cues and the demands of the task.

Optimal Capital Requirements in Financial Networks with Fire Sales

I explore and analyze a problem of finding the socially optimal capital requirements for financial institutions considering two distinct channels of contagion: direct exposures among the institutions, as represented by a network and fire sales externalities, which reflect the negative price impact of massive liquidation of assets.These two channels amplify shocks from individual financial institutions to the financial system as a whole and thus increase the risk of joint defaults amongst the interconnected financial institutions; this is often referred to as systemic risk. In the model, there is a trade-off between reducing systemic risk and raising the capital requirements of the financial institutions. The policymaker considers this trade-off and determines the optimal capital requirements for individual financial institutions. I provide a method for finding and analyzing the optimal capital requirements that can be applied to arbitrary network structures and arbitrary distributions of investment returns.

In particular, I first consider a network model consisting only of direct exposures and show that the optimal capital requirements can be found by solving a stochastic linear programming problem. I then extend the analysis to financial networks with default costs and show the optimal capital requirements can be found by solving a stochastic mixed integer programming problem. The computational complexity of this problem poses a challenge, and I develop an iterative algorithm that can be efficiently executed. I show that the iterative algorithm leads to solutions that are nearly optimal by comparing it with lower bounds based on a dual approach. I also show that the iterative algorithm converges to the optimal solution.

Finally, I incorporate fire sales externalities into the model. In particular, I am able to extend the analysis of systemic risk and the optimal capital requirements with a single illiquid asset to a model with multiple illiquid assets. The model with multiple illiquid assets incorporates liquidation rules used by the banks. I provide an optimization formulation whose solution provides the equilibrium payments for a given liquidation rule.

I further show that the socially optimal capital problem using the ``socially optimal liquidation" and prioritized liquidation rules can be formulated as a convex and convex mixed integer problem, respectively. Finally, I illustrate the results of the methodology on numerical examples and

discuss some implications for capital regulation policy and stress testing.

Predicting Forest Responses to Changing Environmental Conditions

Forests change with changes in their environment based on the physiological responses of individual trees. These short-term reactions have cumulative impacts on long-term demographic performance. For a tree in a forest community, success depends on biomass growth to capture above- and belowground resources and reproductive output to establish future generations. Here we examine aspects of how forests respond to changes in moisture and light availability and how these responses are related to tree demography and physiology.

First we address the long-term pattern of tree decline before death and its connection with drought. Increasing drought stress and chronic morbidity could have pervasive impacts on forest composition in many regions. We use long-term, whole-stand inventory data from southeastern U.S. forests to show that trees exposed to drought experience multiyear declines in growth prior to mortality. Following a severe, multiyear drought, 72% of trees that did not recover their pre-drought growth rates died within 10 years. This pattern was mediated by local moisture availability. As an index of morbidity prior to death, we calculated the difference in cumulative growth after drought relative to surviving conspecifics. The strength of drought-induced morbidity varied among species and was correlated with species drought tolerance.

Next, we investigate differences among tree species in reproductive output relative to biomass growth with changes in light availability. Previous studies reach conflicting conclusions about the constraints on reproductive allocation relative to growth and how they vary through time, across species, and between environments. We test the hypothesis that canopy exposure to light, a critical resource, limits reproductive allocation by comparing long-term relationships between reproduction and growth for trees from 21 species in forests throughout the southeastern U.S. We found that species had divergent responses to light availability, with shade-intolerant species experiencing an alleviation of trade-offs between growth and reproduction at high light. Shade-tolerant species showed no changes in reproductive output across light environments.

Given that the above patterns depend on the maintenance of transpiration, we next developed an approach for predicting whole-tree water use from sap flux observations. Accurately scaling these observations to tree- or stand-levels requires accounting for variation in sap flux between wood types and with depth into the tree. We compared different models with sap flux data to test the hypotheses that radial sap flux profiles differ by wood type and tree size. We show that radial variation in sap flux is dependent on wood type but independent of tree size for a range of temperate trees. The best-fitting model predicted out-of-sample sap flux observations and independent estimates of sapwood area with small errors, suggesting robustness in new settings. We outline a method for predicting whole-tree water use with this model and include computer code for simple implementation in other studies.

Finally, we estimated tree water balances during drought with a statistical time-series analysis. Moisture limitation in forest stands comes predominantly from water use by the trees themselves, a drought-stand feedback. We show that drought impacts on tree fitness and forest composition can be predicted by tracking the moisture reservoir available to each tree in a mass balance. We apply this model to multiple seasonal droughts in a temperate forest with measurements of tree water use to demonstrate how species and size differences modulate moisture availability across landscapes. As trees deplete their soil moisture reservoir during droughts, a transpiration deficit develops, leading to reduced biomass growth and reproductive output.

This dissertation draws connections between the physiological condition of individual trees and their behavior in crowded, diverse, and continually-changing forest stands. The analyses take advantage of growing data sets on both the physiology and demography of trees as well as novel statistical techniques that allow us to link these observations to realistic quantitative models. The results can be used to scale up tree measurements to entire stands and address questions about the future composition of forests and the land’s balance of water and carbon.

Multipair massive MIMO full-duplex relaying with MRC/MRT processing

We consider a multipair relay channel, where multiple sources communicate with multiple destinations with the help of a full-duplex (FD) relay station (RS). All sources and destinations have a single antenna, while the RS is equipped with massive arrays. We assume that the RS estimates the channels by using training sequences transmitted from sources and destinations. Then, it uses maximum-ratio combining/maximum-ratio transmission (MRC/MRT) to process the signals. To significantly reduce the loop interference (LI) effect, we propose two massive MIMO processing techniques: i) using a massive receive antenna array; or ii) using a massive transmit antenna array together with very low transmit power at the RS. We derive an exact achievable rate in closed-form and evaluate the system spectral efficiency. We show that, by doubling the number of antennas at the RS, the transmit power of each source and of the RS can be reduced by 1.5 dB if the pilot power is equal to the signal power and by 3 dB if the pilot power is kept fixed, while maintaining a given quality-of-service. Furthermore, we compare FD and half-duplex (HD) modes and show that FD improves significantly the performance when the LI level is low.

Mécanismes psychophysiques et neuronaux de la compensation dynamique de multiples champs de force : facilitation et anticipation liée à des indices de couleur

Dans cette thèse, nous abordons le contrôle moteur du mouvement du coude à travers deux approches expérimentales : une première étude psychophysique a été effectuée chez les sujets humains, et une seconde implique des enregistrements neurophysiologiques chez le singe. Nous avons recensé plusieurs aspects non résolus jusqu’à présent dans l’apprentissage moteur, particulièrement concernant l’interférence survenant lors de l’adaptation à deux ou plusieurs champs de force anti-corrélés. Nous avons conçu un paradigme où des stimuli de couleur aident les sujets à prédire la nature du champ de force externe actuel avant qu’ils ne l’expérimentent physiquement durant des mouvements d’atteinte. Ces connaissances contextuelles faciliteraient l’adaptation à des champs de forces en diminuant l’interférence. Selon le modèle computationnel de l’apprentissage moteur MOSAIC (MOdular Selection And Identification model for Control), les stimuli de couleur aident les sujets à former « un modèle interne » de chaque champ de forces, à s’en rappeler et à faire la transition entre deux champs de force différents, sans interférence. Dans l’expérience psychophysique, quatre groupes de sujets humains ont exécuté des mouvements de flexion/extension du coude contre deux champs de forces. Chaque force visqueuse était associée à une couleur de l’écran de l’ordinateur et les deux forces étaient anti-corrélées : une force résistante (Vr) a été associée à la couleur rouge de l’écran et l’autre, assistante (Va), à la couleur verte de l’écran. Les deux premiers groupes de sujets étaient des groupes témoins : la couleur de l’écran changeait à chaque bloc de 4 essais, tandis que le champ de force ne changeait pas. Les sujets du groupe témoin Va ne rencontraient que la force assistante Va et les sujets du groupe témoin Vr performaient leurs mouvements uniquement contre une force résistante Vr. Ainsi, dans ces deux groupes témoins, les stimuli de couleur n’étaient pas pertinents pour adapter le mouvement et les sujets ne s’adaptaient qu’à une seule force (Va ou Vr). Dans les deux groupes expérimentaux, cependant, les sujets expérimentaient deux champs de forces différents dans les différents blocs d’essais (4 par bloc), associés à ces couleurs. Dans le premier groupe expérimental (groupe « indice certain », IC), la relation entre le champ de force et le stimulus (couleur de l’écran) était constante. La couleur rouge signalait toujours la force Vr tandis que la force Va était signalée par la couleur verte. L’adaptation aux deux forces anti-corrélées pour le groupe IC s’est avérée significative au cours des 10 jours d’entraînement et leurs mouvements étaient presque aussi bien ajustés que ceux des deux groupes témoins qui n’avaient expérimenté qu’une seule des deux forces. De plus, les sujets du groupe IC ont rapidement démontré des changements adaptatifs prédictifs dans leurs sorties motrices à chaque changement de couleur de l’écran, et ceci même durant leur première journée d’entraînement. Ceci démontre qu’ils pouvaient utiliser les stimuli de couleur afin de se rappeler de la commande motrice adéquate. Dans le deuxième groupe expérimental, la couleur de l’écran changeait régulièrement de vert à rouge à chaque transition de blocs d’essais, mais le changement des champs de forces était randomisé par rapport aux changements de couleur (groupe « indice-incertain », II). Ces sujets ont pris plus de temps à s’adapter aux champs de forces que les 3 autres groupes et ne pouvaient pas utiliser les stimuli de couleurs, qui n’étaient pas fiables puisque non systématiquement reliés aux champs de forces, pour faire des changements prédictifs dans leurs sorties motrices. Toutefois, tous les sujets de ce groupe ont développé une stratégie ingénieuse leur permettant d’émettre une réponse motrice « par défaut » afin de palper ou de sentir le type de la force qu’ils allaient rencontrer dans le premier essai de chaque bloc, à chaque changement de couleur. En effet, ils utilisaient la rétroaction proprioceptive liée à la nature du champ de force afin de prédire la sortie motrice appropriée pour les essais qui suivent, jusqu’au prochain changement de couleur d’écran qui signifiait la possibilité de changement de force. Cette stratégie était efficace puisque la force demeurait la même dans chaque bloc, pendant lequel la couleur de l’écran restait inchangée. Cette étude a démontré que les sujets du groupe II étaient capables d’utiliser les stimuli de couleur pour extraire des informations implicites et explicites nécessaires à la réalisation des mouvements, et qu’ils pouvaient utiliser ces informations pour diminuer l’interférence lors de l’adaptation aux forces anti-corrélées. Les résultats de cette première étude nous ont encouragés à étudier les mécanismes permettant aux sujets de se rappeler d’habiletés motrices multiples jumelées à des stimuli contextuels de couleur. Dans le cadre de notre deuxième étude, nos expériences ont été effectuées au niveau neuronal chez le singe. Notre but était alors d’élucider à quel point les neurones du cortex moteur primaire (M1) peuvent contribuer à la compensation d’un large éventail de différentes forces externes durant un mouvement de flexion/extension du coude. Par cette étude, nous avons testé l’hypothèse liée au modèle MOSAIC, selon laquelle il existe plusieurs modules contrôleurs dans le cervelet qui peuvent prédire chaque contexte et produire un signal de sortie motrice approprié pour un nombre restreint de conditions. Selon ce modèle, les neurones de M1 recevraient des entrées de la part de plusieurs contrôleurs cérébelleux spécialisés et montreraient ensuite une modulation appropriée de la réponse pour une large variété de conditions. Nous avons entraîné deux singes à adapter leurs mouvements de flexion/extension du coude dans le cadre de 5 champs de force différents : un champ nul ne présentant aucune perturbation, deux forces visqueuses anti-corrélées (assistante et résistante) qui dépendaient de la vitesse du mouvement et qui ressemblaient à celles utilisées dans notre étude psychophysique chez l’homme, une force élastique résistante qui dépendait de la position de l’articulation du coude et, finalement, un champ viscoélastique comportant une sommation linéaire de la force élastique et de la force visqueuse. Chaque champ de force était couplé à une couleur d’écran de l’ordinateur, donc nous avions un total de 5 couleurs différentes associées chacune à un champ de force (relation fixe). Les singes étaient bien adaptés aux 5 conditions de champs de forces et utilisaient les stimuli contextuels de couleur pour se rappeler de la sortie motrice appropriée au contexte de forces associé à chaque couleur, prédisant ainsi leur sortie motrice avant de sentir les effets du champ de force. Les enregistrements d’EMG ont permis d’éliminer la possibilité de co-contractions sous-tendant ces adaptations, étant donné que le patron des EMG était approprié pour compenser chaque condition de champ de force. En parallèle, les neurones de M1 ont montré des changements systématiques dans leurs activités, sur le plan unitaire et populationnel, dans chaque condition de champ de force, signalant les changements requis dans la direction, l’amplitude et le décours temporel de la sortie de force musculaire nécessaire pour compenser les 5 conditions de champs de force. Les changements dans le patron de réponse pour chaque champ de force étaient assez cohérents entre les divers neurones de M1, ce qui suggère que la plupart des neurones de M1 contribuent à la compensation de toutes les conditions de champs de force, conformément aux prédictions du modèle MOSAIC. Aussi, cette modulation de l’activité neuronale ne supporte pas l’hypothèse d’une organisation fortement modulaire de M1.

A spiking neural network implementation of sound localisation

The focus of this paper is the implementation of a spiking neural network to achieve sound localization; the model is based on the influential short paper by Jeffress in 1948. The SNN has a two-layer topology which can accommodate a limited number of angles in the azimuthal plane. The model accommodates multiple inter-neuron connections with associated delays, and a supervised STDP algorithm is applied to select the optimal pathway for sound localization. Also an analysis of previous relevant work in the area of auditory modelling supports this research.

Putkien päittäishitsaaminen orbitaali-TIG-hitsauksella

Tämän kandidaatintyön tavoitteena oli esitellä orbitaali-TIG-hitsauksen käyttämistä putkien päittäishitsaamiseen. Työssä esitellään Suomesta saatavia orbitaali-TIG-laitteita ja TIG-hitsausprosessi pääperiaatteiltaan sekä prosessin käyttämistä orbitaalihitsaukseen. Myös orbitaali-TIG-hitsauksen tuottavuuteen ja laatuun liittyviä asioita käydään läpi. Suomesta saatavilla olevista laitteista valittiin toiminnallisten mittojen kannalta sopivimmat kandidaatintyötä varten suunniteltuun ripaputkilämmönvaihtimen hitsaukseen. Työ on pääasiallisesti tehty kirjallisuustutkimuksena käyttäen apuna orbitaalilaitteistojen valmistajien ja jälleenmyyjien haastatteluja. Kirjalliset lähteet koostuvat kotimaisesta ja kansainvälisestä hitsauksen alan kirjallisuudesta ja teksti on pyritty sitomaan yhteen käyttäen useaa eri lähdettä. Laitekohtaiset tiedot saatiin laitevalmistajien tuotetiedotteista ja sähköpostihaastatteluna laitteiden jälleenmyyjiltä ja laitevalmistajilta. Suomessa orbitaali-TIG-laitteita maahantuo ja jälleenmyy Masino Welding Oy ja Suomen Teknohaus Oy. Suomessa laitteita valmistaa Kemppi Oy, jonka orbitaalilaitteilla on useita jälleenmyyjiä. Masino Welding Oy myy saksalaisia Orbitalum GmbH:n laitteita ja Suomen Teknohaus Oy ranskalaisia Polysoude S.A.S.:n laitteita. Näiden laitevalmistajien joukosta suunnitellun ripaputkilämmönvaihtimen hitsaukseen soveltuu Orbitalumilta ja Polysoudelta yhdet sekä Kempiltä kaksi umpipihtimallista orbitaalihitsauspäätä. Orbitaali-TIG-hitsauslaitteissa virtalähteet ovat kehittyneet eniten vuosien aikana ja eri laitevalmistajien laitteistojen erot ovat pääasiassa virtalähteisiin liittyviä. Ripaputkilämmönvaihtimen hitsaamiseen sopivin hitsauspäämalli on umpipihti, sillä lämmönvaihtimen päädyt ovat hyvin ahtaita ja umpipihdit ovat orbitaalihitsauspäistä kaikkein kompakteimmat. Suomessa orbitaali-TIG-laitteita ei ole kauheasti tarjolla ja laitteiden markkinointi on jossain määrin kannattamatonta. Orbitaalihitsaus on kuitenkin varteenotettava vaihtoehto TIG-käsinhitsaukselle, jos hitsataan paljon samankaltaisia hitsejä.