Biocuration is manual scientific collection, annotation and validation of literary information of biological and model organisms into a single database. Successful biocuration processes involve those with an extensive collection of literature, a user-friendly database interfaces for entering and analyzing data from published papers, and highly regulated training and quality assurance protocols. Due to the rapid expansion of biomedical literature, an efficient and accurate biocuration process has become more valuable due to the magnitude of data available in published literature. As the biocuration process incorporates undergraduates, it is critical that the medium for data collection is simple, ergonomic, and infallible. A reconstructed FileMaker Pro database was introduced to previously trained undergraduate students for process evaluation. Streamlining the biocuration process and grouping data structure to be more intuitive were two goals the new database interface hoped to achieve. The creation of a rigorous training program and strict quality management protocol is needed to prepare the lab for the introduction of efficient biocuration processes. Through the database designing process, training protocols were drafted to effectively call the biocurator’s attention to important changes in the interface design. Upon prototyping the database, entry errors were reviewed, training protocols were adjusted, and the quality protocols were drafted. When the combination of undergraduate biocurators and the reconstructed database under these new protocols was compared to statistics in the biocuration field, results proved to show increase in both productivity rates as well as accuracy rates. By having such efficiency at the undergraduate level, subject matter experts will no longer be required to perform this type of research and can focus on analysis. This will increase research productivity and reduce costs in the overall biocuration process. With over 12,000 published papers regarding Amyotrophic Lateral Sclerosis on Pubmed in 2014 alone, this revolutionary combination could lead to quickly finding a suitable cure for these patients.

Mesolimbic dopamine plays an important role in ethanol reinforcement, and studies have shown that accumbal dopamine increases during operant ethanol self-administration. However, no one has ever studied this dopaminergic response during the acquisition of ethanol self-administration. Furthermore, some studies have shown that the dopamine signal does not correlate with the pharmacological effects of ethanol, but with the time during which the animal consumes the majority of the ethanol solution and when the sensory stimuli of ethanol are strongest. However, there is currently no direct evidence showing that the sensory stimuli of ethanol is indeed what causes the brief increase in accumbal dopamine during ethanol self-administration. The studies in this dissertation attempted to elucidate these issues. We designed and tested a placebo spout, which was to be used to study the relationship between accumbal dopamine and the sensory stimuli of ethanol during self-administration. Unfortunately, the placebo designs were either not feasible for performing microdialysis or did not show promising behavioral data. We also developed and tested a self-administration protocol in which the concentrations of ethanol (10%) were kept constant throughout the study. The new protocol was successful in initiating and maintaining ethanol self-administration, and the animals doubled their intake from day 1 to day 2 of ethanol consumption. Using this protocol, we trained male Long Evans rats to self-administer ethanol and measured accumbal dopamine during the first two days of ethanol self-administration through microdialysis. The behavioral and neurochemical data matched. A single exposure to ethanol was sufficient for the animals to double their ethanol consumption by day 2 and to cause an increase in accumbal dopamine during the first 5 minutes of ethanol self-administration. The dopamine response was observed during the time when the sensory stimuli of ethanol were strongest, but before ethanol reached peak concentrations in the brain. Overall, these results suggest that the dopamine response to ethanol self-administration may not be solely pharmacological and that a single exposure to ethanol is sufficient to learn the association between ethanol and its cues. These findings give us greater insight into mesolimbic dopamine's role in the early stages of ethanol reinforcement. / text

Les Interfaces Cerveau Ordinateur Actives (ICOs) permettent à une personne d'exercer un contrôle direct et volontaire sur un système informatique par interprétation de son activité cérébrale : certains signaux du cerveau sont capturés afin que le système reconnaisse des actions imaginées spécifiques (mouvements, images, concepts). Les ICOs actives et leurs utilisateurs doivent être entrainés. Cet entraînement rend les signaux plus aisés à reconnaître par le système.Cependant, à l'heure actuelle les ICO servent principalement dans un contexte médical pour aider les personnes en situation de handicap (moteur, ou empêchant complètement la communication avec le monde extérieur) et se trouvent rarement en dehors de laboratoires spécialisés.Les ICO ont de nombreuses limitations :• La variabilité dans les signaux: les signaux sont différents d'une personne à l'autre voire même chez un même individu à des moments différents.• Des sessions d'entraînement longues et répétitives: entre dix minutes et deux mois, sont ennuyantes et désengagent les utilisateurs du processus d'apprentissage.• Un feedback limité: les systèmes actuels proposent un feedback unimodal élémentaire qui est inadapté pour les nombreux utilisateurs. la communication est unidirectionnelle dans le sens où le système donne des instructions que l'utilisateur doit exécuter.L'objectif de cette thèse est de proposer des solutions aux problèmes sus décrits afin d'obtenir une architecture consistante qui rendra les ICO plus compatibles avec les applications d'IHM. L'idée principale est l'implantation du co-apprentissage dans la boucle ICO et l'exploration de la manière dont les utilisateurs et le système peuvent mutuellement se donner du feedback dans le but de l'amélioration de l'utilisabilité des ICO.Cette thèse se structure autour de trois innovations portant sur la boucle ICO :• Une architecture générale basée sur les principes des ICO asynchrones et sur l'entraînement incrémental combinés avec une séparation aveugle des sources et un classifieur à distance minimum. Nous évaluerons l'architecture sur une tache de pilotage de drone au long d'un mois et concluons qu'elle est en adéquation avec les besoins d'une utilisation quotidienne ludique.• Une modalité de visualisation plus intuitive pour les résultats de classification ainsi que pour les caractéristiques de distance sur la base d'une projection en coordonnées de Wachspress pour un nombre arbitraire de classes. Nous combinons la visualisation avec un feedback direct des utilisateurs leur permettant d'interactivement changer la marge de classification, le type de distance où encore de trier et de gérer les signaux d'entraînement en temps réel. Nous évaluons cette contribution sur un jeu de tir simple et découvrons qu'il y a une bonne synergie entre la modalité de visualisation et le feedback direct des utilisateurs et qu'une telle combinaison est bien plus agréable à utiliser qu'un entraînement d'ICO standard.• Enfin, nous développons une ICO fonctionnelle à base d'imagerie conceptuelle à l'aide de notre architecture ainsi que de nos systèmes de visualisation et de feedback, ce qui permet une interaction plus agréable au travers de l'imagination de catégories sémantiques et de concepts. Nous démontrons que ce type d'ICO détecte plus aisément les catégories sémantiques éloignées plutôt que les catégories sémantiques proches. Pour terminer, nous créons un nouveau protocole d'entraînement implicite pour les ICO à base d'Imagerie Conceptuelle basé sur l'amorçage sémantique et conceptuel, ce qui permet d'intégrer l'entraînement dans le scénario et l'environnement d'une jeu vidéo sans que l'utilisateur n'en soit conscient. Notre protocole mène à une meilleure immersion et à meilleur sentiment de flot vis à vis du jeu. / Active Brain Computer Interfaces (BCIs) allow people to exert direct voluntary control over a computer system: their brain signals are captured and the system recognizes specific imagined actions (movements, images, concepts). Active BCIs and their users must undergo training. This makes the signals easier to recognize by the system. This acquisition can take from 10 minutes up to 2 months. BCIs can thus be applied to many control and interaction scenarios of our everyday lives, especially in relation to entertainment (Wolpaw et al., 2002).BCIs are mostly used by disabled people in a medical setting and seldom leave the lab. First of all, high-grade equipment is expensive and non-portable. Although there are commercial ventures proposing BCI acquisition equipment to the general public, the quality is still insufficient to build accurate and robust BCIs.BCIs also suffer from numerous limitations:• Variability of the signals: signals different across people or within the same individual at different times.• Long and repetitive training sessions: between 10 minutes up to several months, disengage and bore users.• Limited feedback: simple unimodal feedback ill adapted for many users. Feedback is unidirectional and the user just has to follow instructions.All these issues limit the adoption of BCI, the lack of widespread commercial success and the use of BCI from human computer interaction applications.The objective of the thesis is to propose solutions to the above problems so as to obtain a consistent architecture that will allow BCIs to be better suitable to Human-Computer Interaction (HCI) applications. The idea is to implement co-learning in the BCI loop and to explore how users and system can give feedback to each other in order to improve BCI usability.This thesis is structured around three innovations surrounding the BCI loop:• A general architecture based on asynchronous BCI principles and on incremental training combined with an unsupervised blind-source separation filter and a minimum distance classifier. This architecture allows producing BCIs with minimal training session. We evaluate the architecture on a drone piloting task over a month and find that it is suitable for use in daily recreational applications.• A more intuitive visualization modality for classification outcomes and distance features using Wachspress coordinate projection for an arbitrary number of classes. We combine the visualization with direct feedback mechanism where users can interactively change the classification margin, change the types of features as well as edit the training trials in real-time. We evaluate our contribution on a simple shooter game and find there is a good synergy between our visualization modality and direct user feedback and that the combination is much more enjoyable to users than a standard BCI training.• Finally we develop an operational Conceptual Imagery BCI based on our architecture, visualization and feedback system that allow for more natural interactions through the imagination of sematic categories and concepts. We show that this type of BCI is more effective at detecting distinct semantic categories rather than close ones. Then, we build on this conceptual BCI to propose a smart home control system for healthy and disabled users. Finally we invent a new seamless training protocol for Conceptual Imagery that uses conceptual and semantic priming in order to integrate the training in the narrative and environment of the game without the realization of the user. Our technique leads to better flow and immersion of users in the game. We believe this training protocol can be extended to many tasks outside of games or even of Conceptual Imagery.

Background Power, sprint and agility abilities are important capacities in modern soccer and are often decisive for the outcome of the game. Finding ways to develop these as effective as possible and improve game related performance is important to optimize further physical development. Aim The aim of the present study was to investigate the effect of a five-week strength (SG) versus an agility training program (AG) regarding power, sprinting and agility performance in youth postpubertal soccer players. The purpose with the study plan was to be able to implement the results in training programs among the tested population.  Methods 15 post-pubertal non-elite male soccer players participated in the study; average age 16.6 ± 0.6 years, weight 65.8 ± 5.8 kg and height 176.4 ± 5.7 cm. Participants were randomized in two groups and followed science based training programs for five weeks. Power development, sprint and agility performance were tested through a test battery of four tests: drop jump (DJ), countermovement jump (CMJ), sprint 20-m (S-20) and T-test. Reactive strength index (RSI) was calculated by dividing DJ height (cm) with contact time (s). The tests were conducted before and after the training programs to evaluate the efficiency of the training programs.  Results The results demonstrated no significant difference between the groups. No significant improvement was measured for DJ in any group. Though significant improvements in CMJ for both groups (p &gt; 0.05). Significant improvements were also noted for sprint ability for AG (p &lt; 0.01) while moderate and non-significant changes for SG (p = 0.05). Significant improvements were measured in agility for both groups (p &gt; 0.01). Further, significant improvements in calculated RSI were noted for AG (p &lt; 0.05) but not for SG (p &lt; 0.05).  Conclusion The implementation of a five week strength training program induces a significant improvement in power development through CMJ and agility ability. The implementation of a five week agility training program induces a significant improvement on jumping, sprint and agility abilities. The practical implication is that since both training programs brought improvements, you as a coach can apply what best suits your group and resources. / Bakgrund Effektutveckling, sprint- och agilityförmåga är centrala, ofta matchavgörande förmågor inom dagens fotboll. Att hitta sätt att utveckla dessa förmågor så effektivt som möjligt och förbättra matchrelaterad prestationsförmåga blir viktigt för att optimera fortsatt fysisk utveckling. Syfte Syftet med studien var att undersöka effekten av ett femveckors styrke- (SG) kontra ett agilityträningsprogram (AG) gällande hopp-, sprint- och agilityförmåga hos unga fotbollsspelare. Avsikten med studiens upplägg var att det med enkelhet ska kunna implementeras i träningsplaneringen för den undersökta populationen. Metod 15 postpubertala fotbollsspelande pojkar på breddnivå deltog i studien; medelålder 16,6 ± 0,6 år, vikt 65,8 ± 5,8 kg och längd 176,4 ± 5,7 cm. Deltagarna randomiserades i två grupper och fick i fem veckor följa vetenskapligt förankrade träningsprogram. Effektutveckling, sprintoch agilityförmåga testades genom ett testbatteri av fyra tester: drop jump (DJ), counter movement jump (CMJ), sprint 20-m och T-test. Reaktiv styrkeindex (RSI) beräknades genom att dividera hopphöjd i DJ (cm) med markkontakttiden (s). Testerna genomfördes innan och efter genomförandet av träningsprogrammen för att utvärdera träningsprogrammen. Resultat Resultatet påvisade ingen signifikant skillnad mellan grupperna. Ingen signifikant förbättring uppmättes för DJ i någon av grupperna. Däremot en signifikant förbättring av CMJ för båda grupperna (p &gt; 0.05). Signifikanta förbättringar noterades även på sprintförmåga för AG (p &lt; 0.01) medan måttliga, och icke-signifikanta förändringar för SG (p = 0.051). Signifikanta förbättringar uppmättes i agilityförmåga för båda grupper (p &lt;0.01). Vidare noterades signifikanta förbättringar i beräknat RSI för AG (p &lt; 0.05) men ej för SG (p &lt; 0.05). Slutsats Genomförandet av ett femveckors styrketräningsprogram ger signifikanta förbättringar på effektutveckling genom CMJ och agilityförmåga genom t-test på unga fotbollsspelare. Ett femveckors agilityträningsprogram ger signifikanta förbättringar på hopp-, sprint- och agilityförmåga. Den praktiska implikationen är att då båda träningsprogrammen medförde förbättringar kan man som tränare tillämpa det som passar bäst in för sin grupp och resurser. / <p>Ämneslärarprogrammet, Specialidrott</p>

Neuromorphic information processing systems mimic the dynamics of neurons and synapses, and the architecture of biological nervous systems. By using a combination of sub-threshold analog circuits, and fast programmable digital circuits, spiking neural networks with co-localized memory and computation can be implemented, enabling more energy-efficient information processing than conventional von Neumann digital computers. When configuring such a spiking neural network, the variability caused by device mismatch of the analog electronic circuits must be managed and exploited. While pre-trained spiking neural networks have been approximated in neuromorphic processors in previous work, configuration methods and tools need to be developed that make efficient use of the high number of inhomogeneous analog neuron and synapse circuits in a systematic manner. The aim of the work presented here is to investigate such automatic configuration methods, focusing in particular on Monte Carlo methods, and to develop software for training and configuration of the Dynap-SE neuromorphic processor, which is based on the Dynamic Neuromorphic Asynchronous Processor (DYNAP) architecture. A Monte Carlo optimization method enabling configuration of spiking neural networks on the Dynap-SE is developed and tested with the Metropolis-Hastings algorithm in the low-temperature limit. The method is based on a hardware-in-the-loop setup where a PC performs online optimization of a Dynap-SE, and the resulting system is tested by reproducing properties of small neural networks in the auditory system of field crickets. It is shown that the system successfully configures two different auditory neural networks, consisting of three and four neurons respectively. However, appropriate bias parameter values defining the dynamic properties of the analog neuron and synapse circuits must be manually defined prior to optimization, which is time consuming and should be included in the optimization protocol in future work.

Estudos epidemiológicos vêm demonstrando que quantidades apropriadas de atividade física regular estão associadas a significativa redução do risco para o desenvolvimento de câncer de cólon em até 40% entre os indivíduos mais fisicamente ativos. Por outro lado, tem sido observado que o exercício físico exaustivo aumenta a produção sistêmica de radicais livres, com concomitante aumento dos danos oxidativos ao DNA, além de deprimir a função imune global, eventos relacionados ao aumento do risco para o desenvolvimento de câncer. Relativamente, poucos estudos experimentais exploram essas relações, principalmente no que concerne ao exercício exaustivo e o câncer. A taxa de proliferação celular epitelial, os focos de criptas aberrantes (FCAs) e as criptas com acúmulo de beta-catenina (CABC) têm sido marcadores biológicos (biomarcadores) usados para a identificação precoce de fatores que poderiam influenciar a carcinogênese colônica em ratos. Através da aplicação do carcinógeno químico 1,2dimetilhidrazina (DMH), logo após os protocolos de exercício, foram estudados quatro grupos principais de ratos previamente sedentários (grupo-controle, e três grupos submetidos, respectivamente, ao treinamento crônico de natação, à natação até a exaustão, e à natação até a exaustão após treinamento crônico), sendo sacrificados quinze dias após a injeção da DMH. Após análise histológica e imunohistoquímica, os biomarcadores estudados mostraram resultados coerentes nas diferentes situações experimentais aferidas. Foi observada uma diminuição estatisticamente significante da resposta hiperproliferativa, do número de FCAs e de CABC no grupo que realizou o treinamento crônico, enquanto o grupo submetido ao exercício exaustivo apresentou aumento estatisticamente significante dos parâmetros citados, quando comparados ao grupo-controle. No grupo submetido à associação dos dois protocolos de exercício, quando comparado ao grupo-controle, não houve alterações significantes nos biomarcadores de transformação neoplásica estudados. Nesse estudo experimental, o treinamento físico crônico teve efeito protetor contra o desenvolvimento dos biomarcadores precoces de transformação neoplásica do cólon, enquanto o exercício físico exaustivo aumentou a prevalência destes em ratos sedentários. O treinamento físico crônico, quando associado ao exercício físico exaustivo, não alterou a prevalência dos biomarcadores estudados. Desse achado, acrescido do que se pode encontrar na literatura científica atual, levanta-se a hipótese de que, de maneira similar à relação entre exercício físico e infecções, também o exercício poderia ou proteger contra o desenvolvimento, ou aumentar o risco para o câncer, dependendo do tipo, intensidade e duração da atividade desenvolvida. / Ephitelial cell proliferation, aberrant crypt foci (ACF) and â-catenin-accumulated crypts (BCAC) have been used for early detection of factors that influence colorectal carcinogenesis in rats. It has been observed that moderate and regular physical activity may prevent colon cancer up to 40% in humans. However, exhaustive exercise increases free radical DNA oxidative damage and depresses immune function, events also related to the increased risk for cancer development. Fifteen days after either a single exhaustive swimming bout or a swimming physical training for 8 weeks, or both, in untrained rats treated with a colon carcinogen, we observed a statistically significant decreased number of those biomarkers in rats under training protocol, and a statistically significant increased number of them in rats under exhaustive protocol, when compared to the non-exercised group. For the rats under exhaustive protocol after being trained, data was not evident. Thus, we concluded that training protected against the biomakers development and exhaustive exercise improved colorectal carcinogenesis biomarkers development in sedentary rats. From our finding and literature data, we hypothesize that, similarly to the suggested relationship between exercise and infections, exercise could be protective against cancer or it could increase the risk for this disease depending on its type, dose and duration.

Estudos epidemiológicos vêm demonstrando que quantidades apropriadas de atividade física regular estão associadas a significativa redução do risco para o desenvolvimento de câncer de cólon em até 40% entre os indivíduos mais fisicamente ativos. Por outro lado, tem sido observado que o exercício físico exaustivo aumenta a produção sistêmica de radicais livres, com concomitante aumento dos danos oxidativos ao DNA, além de deprimir a função imune global, eventos relacionados ao aumento do risco para o desenvolvimento de câncer. Relativamente, poucos estudos experimentais exploram essas relações, principalmente no que concerne ao exercício exaustivo e o câncer. A taxa de proliferação celular epitelial, os focos de criptas aberrantes (FCAs) e as criptas com acúmulo de beta-catenina (CABC) têm sido marcadores biológicos (biomarcadores) usados para a identificação precoce de fatores que poderiam influenciar a carcinogênese colônica em ratos. Através da aplicação do carcinógeno químico 1,2dimetilhidrazina (DMH), logo após os protocolos de exercício, foram estudados quatro grupos principais de ratos previamente sedentários (grupo-controle, e três grupos submetidos, respectivamente, ao treinamento crônico de natação, à natação até a exaustão, e à natação até a exaustão após treinamento crônico), sendo sacrificados quinze dias após a injeção da DMH. Após análise histológica e imunohistoquímica, os biomarcadores estudados mostraram resultados coerentes nas diferentes situações experimentais aferidas. Foi observada uma diminuição estatisticamente significante da resposta hiperproliferativa, do número de FCAs e de CABC no grupo que realizou o treinamento crônico, enquanto o grupo submetido ao exercício exaustivo apresentou aumento estatisticamente significante dos parâmetros citados, quando comparados ao grupo-controle. No grupo submetido à associação dos dois protocolos de exercício, quando comparado ao grupo-controle, não houve alterações significantes nos biomarcadores de transformação neoplásica estudados. Nesse estudo experimental, o treinamento físico crônico teve efeito protetor contra o desenvolvimento dos biomarcadores precoces de transformação neoplásica do cólon, enquanto o exercício físico exaustivo aumentou a prevalência destes em ratos sedentários. O treinamento físico crônico, quando associado ao exercício físico exaustivo, não alterou a prevalência dos biomarcadores estudados. Desse achado, acrescido do que se pode encontrar na literatura científica atual, levanta-se a hipótese de que, de maneira similar à relação entre exercício físico e infecções, também o exercício poderia ou proteger contra o desenvolvimento, ou aumentar o risco para o câncer, dependendo do tipo, intensidade e duração da atividade desenvolvida. / Ephitelial cell proliferation, aberrant crypt foci (ACF) and â-catenin-accumulated crypts (BCAC) have been used for early detection of factors that influence colorectal carcinogenesis in rats. It has been observed that moderate and regular physical activity may prevent colon cancer up to 40% in humans. However, exhaustive exercise increases free radical DNA oxidative damage and depresses immune function, events also related to the increased risk for cancer development. Fifteen days after either a single exhaustive swimming bout or a swimming physical training for 8 weeks, or both, in untrained rats treated with a colon carcinogen, we observed a statistically significant decreased number of those biomarkers in rats under training protocol, and a statistically significant increased number of them in rats under exhaustive protocol, when compared to the non-exercised group. For the rats under exhaustive protocol after being trained, data was not evident. Thus, we concluded that training protected against the biomakers development and exhaustive exercise improved colorectal carcinogenesis biomarkers development in sedentary rats. From our finding and literature data, we hypothesize that, similarly to the suggested relationship between exercise and infections, exercise could be protective against cancer or it could increase the risk for this disease depending on its type, dose and duration.