A Bioacoustica oferece ferramentas úteis para diversas ciências e práticas na utilização acadêmica, científica, aplicada e conservação da vida animal. Nossa hipótese é que as chamadas naturais, como o rugido de longo alcance do bugios preto, atuam como elemento de enriquecimento ambiental, se a sua execução aumenta a exibição de um comportamento natural em cativeiro. O bugio faz um uso diário do rugido e sua emissão é conhecida por evocar respostas de outros bandos de bugio em vida livre. Para testar a eficácia dos rugidos em melhorar o bem-estar foi realizado um experimento no Bosque e Zoológico Fábio Barreto, no município de Ribeirão Preto, onde treze indivíduos (6 fêmeas e 7 machos) viviam em cinco recintos adjacentes. Eles tiveram contato visual e acústico entre eles e com outras duas espécies de primatas e outros grupos de vida livre de bugio preto. Adotoamos o delineamento experimental ABABA, em que fases controle A foram intercaladas com o tratamento (playback de rugido) nas fases B, duas vezes ao dia (manhã e tarde). Na primeira fase B, o estímulo foi sempre tocado no mesmo horário (previsível) e, na segunda fase tratamento, horários aleatórios foram adotados (imprevisível). Nós avaliamos as alterações na duração relativa de 6 comportamentos entre as fases A e B, entre sexo e em ambos os períodos, com o teste ANOVA de medidas repetidas. Nós notamos um aumento no comportamento natural da espécie em fases de tratamento, como alerta, atenção dirigida, e interações sociais, juntamente com a diminuição de comportamentos estereotipados, sugerindo melhoria do bem-estar. As emissões naturais de rugidos também aumentaram. Concluímos que ambos os tratamentos, previsível e imprevisível, melhoraram o bem-estar e propomos a utilização da reprodução de chamadas específicas de especies como uma nova categoria de enriquecimento ambiental. A resposta dos outros primatas nos levou a concluir que houve um efeito sobre animais vizinhos que pode ser benéfico ou prejudicial de acordo com a espécie e a condição psicológica dos animais. / The Bioacoustics offers useful tools for diverse academic, scientific and applied sciences and practices in use and conservation of animal life. We hypothesized that natural call, as the loud roar of the black-howler monkey, would act as environmental enrichment element if its execution increased the display of natural behavior in captivity. The howler-monkey makes an everyday use of the roar and its emission is known to evoke free-living howler-monkeys to call back in response. To test the effectiveness of roars in improving welfare we conducted an experiment in Bosque e Zoológico Fábio Barreto, in the municipality of Ribeirão Preto where thirteen individuals (6 females and 7 males) were living in five adjacent enclosures. They had visual and acoustic contact between them and with two other primate species and a free-living black-howler monkey group. We adopted the ABABA experimental design, in which control phases A were interspersed with treatment (roar playback) phases B, two times a day (morning and afternoon). In the first B phase, the stimulus was always played at the same time (predictable) and, in the other different random schedules were adopted (unpredictable). We evaluate changes in relative duration of 6 behaviors from A to B phases, between sex and in both periods with a repetitive factorial ANOVA. We reported increase in natural behavior of the species in treatment phases, as alert, oriented attention, and social interactions, coupled with the decrease of stereotyped behaviors, suggesting welfare improvement. Thus, natural emissions of roars also increased. We concluded that both predictable and unpredictable routines improved welfare and we propose the use of playback of specie-specific calls as a new category of environmental enrichment. The answer of the other primates led us to conclude that there was a neighborhood effect that can be beneficial or harmful according to the species and the psychological condition of the animals.

A amostragem ambiental por esfregaço ou swipe samples é uma metodologia que vem sendo empregada rotineiramente pela Agência Internacional de Energia Atômica (AIEA) para verificar se os Estados signatários do Acordo de Salvaguardas estão realizando atividades nucleares não declaradas. A análise dessas amostras ambientais é complementar aos procedimentos de salvaguardas convencionais para a verificação das informações cedidas pelos Estados. Neste trabalho, foi descrita uma metodologia que visa a fortalecer os processos de salvaguarda nuclear e da ciência forense nuclear no país. A proposta é estudar e avaliar a técnica de ablação à laser acoplada a um espectrômetro de massa de alta resolução com fonte de plasma indutivamente acoplado (LA-HR-ICP-MS Laser Ablation High Resolution Inductively Coupled Plasma Mass Spectrometry), como técnica alternativa para a análise das amostras de esfregaço. Adicionalmente, foram empregadas outras técnicas complementares (atividade radioativa, microscopia eletrônica de varredura e espectroscopia de energia dispersiva) com o intuito de garantir maior segurança ao processo de inspeção de salvaguardas e investigações forenses nucleares. A precisão, medida através do desvio padrão relativo (DPR),dos resultados obtidos para as razões isotópicas 234U/238U, 235U/238U e 236U/238U do padrão analisado (CRM -125A) para a medida do fator de discriminação de massa foram, respectivamente, 1,3 %, 0,2 % e 7,6 %. Já as incertezas percentuais (u %), que também contemplam o DPR das medições, variaram de 3,5 % a 29,8 % para as medições da razão isotópica 235U/238U e de 16,6 % a 42,9 % para a razão isotópica 234U/238U. Esses valores mostraram-se compatíveis com outros estudos que utilizaram a mesma técnica para análise de amostras reais coletadas em uma instalação nuclear. As amostras coletadas apresentaram nível de enriquecimento que variou de (2,3 ± 0,7) % (amostra 3 corredor de acesso à instalação) a (17,3 ± 2,8) % (amostra 18 bancada de recuperação de UF4). A partir da coleta de amostras nesses diversos pontos, desde a entrada da instalação até a bancada em que se manuseia o urânio enriquecido, foi possível detectar diversos níveis de enriquecimento no isótopo 235U. / Environmental sampling performed by means of swipe samples is a methodology frequently employed by International Atomic Energy Agency (IAEA) to verify if the signatory States of the Safeguards Agreements are conducing unauthorized activities. Swipe samples analysis is complementary to the Safeguards ordinary procedures used to verify the information given by the States. In this work it was described a methodology intending to strengthen the nuclear safeguards and nuclear forensics procedures. The proposal is to study and evaluate the laser ablation high resolution inductively coupled plasma mass spectrometry (LA-HR-ICP-MS) technique as an alternative to analyze the real-life swipe samples. The precision achieved through the standard(CRM -125A)measurements, represented by the relative standard deviation (RSD), was respectively 1.3 %, 0.2 % e 7.6 %for the 234U/238U, 235U/238U e 236U/238Uisotopes ratios. The percent uncertainties (u %), which covers the RSD, ranged from 3.5 % to 29.8 % to the 235U/238U measurements and from 16.6 % to 42.9 % to the 234U/238U isotope ratio. These results were compatible with former studies performed by the LA-HR-ICP-MS that analyzed real-life swipe samples collected at a nuclear facility. Swipe samples collected from several points of the nuclear facility presented enrichment level ranging from (2.3 ± 0.7) % (sample 3) to (17.3 ± 2.8) % (sample18). They also allowed detecting different enrichment levels within the facility.

Atualmente, percebe-se o crescimento de consumidores preocupados com a qualidade dos produtos alimentares quando optam por ingerir carnes provenientes de animais criados em produções que valorizam o bem-estar animal e possuem um pensamento sustentável. Os animais são entidades psicológicas e instiga os pesquisadores a modificar, alterar e criar novas situações que proporcionem aos mesmos viverem, reproduzirem e crescerem de maneira agradável e de forma ética. O enriquecimento ambiental é considerado um tipo de manejo quando se busca melhorar a qualidade de vida dos animais por meio de estímulos ambientais. A música como um estímulo sensorial pode ser uma forma de enriquecer o ambiente. Ainda, a musicoterapia relaciona-se com a arte, a ciência e a educação e pode ser utilizada em diferentes metodologias e objetivos. Diante disto, a presente pesquisa propôs validar uma metodologia inédita e verificar se o agente sensorial música influenciou no comportamento, no bem-estar e no desempenho produtivo de suínos em fase de crescimento. Concluiu-se que a metodologia proposta em utilizar a música em instalações abertas foi eficaz para o desenvolvimento da pesquisa e que esse agente sensorial interviu positivamente nos comportamentos e proporcionou melhoria no bem-estar dos animais. / Nowadays, it is perceived the growth of consumers concerned about the quality of food products when choose to ingest meat from animals that were created in productions that value animal welfare and have a sustainable thinking. Animals are psychological entities and instigates researchers to modify, alter and create new situations that allow them to live, reproduce and grow in a pleasant and ethical way. Environmental enrichment can be considered a type of handling when improves quality life of the animals by environmental stimuli. Music as a sensory stimulus can be a way to enrich the environment. Also, music therapy is related to art, science and education and can be used in different methodologies and objectives. In this view, the present research proposed to validate an unpublished methodology and to verify if the sensory agent music influenced the behavior, wellfare and productive performance of growing pigs. It was concluded that the methodology proposed to use music in open facilities was effective for the development of the research and that this sensory agent intervened positively in the behaviors and provided improvement in the animal welfare.

O zika é um arbovírus emergente. Há evidências para a relação entre o zika e a microcefalia congênita e também com a síndrome de Guillain-Barre. Várias características do vírus são importantes, como a persistência do vírus no sêmen por vários meses, transmissão sexual e evidência de transmissão pré-natal. As mães grávidas infectadas com zika podem dar à luz crianças aparentemente saudáveis que podem apresentar manifestações e complicações tardias. Existe uma clara necessidade de diagnosticar e sequenciar amostras clínicas do ZIKV que circulam na América do Sul, especificamente no Brasil. No entanto, as baixas cargas virais observadas que são observadas comumente em amostras humanas constituem um fator complicador para detecção, amplificação e sequenciamento. Neste projeto, propor projetar um fluxo de trabalho otimizado para o sequenciamento completo do genoma com base no pré-enriquecimento por PCR (reação em cadeia da polimerase) e pools de amplicons. / Zika is an emerging arbovirus. There is enough evidence for the relation between Zika and congenital microcephaly and also with the Guillain-Barre syndrome. Several characteristics of the virus are important, such as persistence of the virus in semen for several months, sexual transmission and evidence of prenatal transmission. Zika infected pregnant mothers may give birth to apparently healthy children that may show late manifestations and complications. There is a clear necessity of diagnosing and sequencing clinical samples of ZIKV circulating in South America, specifically in Brazil. Nevertheless, the observed low viral loads that are commonly in human samples constitute a complicating factor for detection, amplification and sequencing. In this project, we aim to design an optimized workflow for full genome sequencing based on pre-enrichment by PCR (polymerase chain reaction) and amplicon pools.

Ratos submetidos à desnutrição proteica apresentam elevada impulsividade e alterações em comportamentos de avaliação de risco no labirinto em cruz elevado (LCE). A desnutrição também pode influenciar a atividade do eixo hipotálamo-hipófise-adrenal (HPA). Alterações causadas pela desnutrição podem ser parcialmente revertidas pela estimulação ambiental; animais desnutridos e submetidos ao enriquecimento ambiental apresentaram maior locomoção e exploração no LCE, comparados com animais de mesma condição de dieta e que não foram estimulados. Demonstrou-se também que a estimulação pode influenciar os níveis de corticosterona plasmática evidenciando uma alteração da sensibilidade do eixo HPA. Este trabalho tem o objetivo de comparar, em ratos desnutridos (M) e bem nutridos (C), os efeitos do enriquecimento ambiental (E) em relação às concentrações de corticosterona plasmática, expressão de receptores de glicocorticóides (GR) no hipocampo e o desempenho no LCE aos 36 dias de idade. Ratos Wistar machos foram divididos em dois grupos de acordo com a dieta e subdivididos em subgrupos conforme a manipulação ambiental. A manipulação ambiental foi realizada no período de 8 a 35 dias (1 hora por dia). Após o teste no LCE os animais foram decapitados e tiveram o sangue coletado e o cérebro removido. Para a análise de corticosterona plasmática foi utilizada a técnica de radioimunoensaio. Para a quantificação dos receptores (GR) no hipocampo foi realizada uma análise quantitativa de expressão gênica por meio da reação em cadeia da polimerase (PCR) em tempo real. Ratos M apresentaram menor peso corporal quando comparados com os ratos C (p<0,001). Em relação ao LCE, ratos M permaneceram uma maior porcentagem de tempo [F(1,44)=9,08; p<0,01] e entraram mais [F(1,44)=9,01; p<0,01] nos braços abertos em relação a C. Animais ME apresentaram porcentagem de tempo nos braços abertos (6% ± 2%) próxima àquela dos animais CN (8% ± 2%). De acordo com a PCR em tempo real, o teste do LCE alterou a quantidade de receptores GR no hipocampo (t(10)=2,37; p<0,05) e essa adaptação ocorreu diferentemente em ratos M quando comparados com os C. Também foi possível observar que a quantidade de receptores GR após o teste do LCE é diferente entre os grupos M e ME (t(11)=4,48; p<0,05). Os dados do presente estudo sugerem que animais desnutridos se expõem a mais situações de risco que ratos bem nutridos. Quando o enriquecimento ambiental foi realizado no período crítico do desenvolvimento do sistema nervoso central observou-se um efeito de neuroproteção em relação às alterações produzidas pela desnutrição tanto na expressão de RNAm de receptores GR como no comportamento de avaliação de risco de ratos no LCE. Os dados do presente trabalho também mostraram que a desnutrição pode alterar a resposta de estresse mediada pelo eixo HPA após exposição ao teste do LCE, e que o enriquecimento ambiental possui efeito protetor em relação os efeitos da desnutrição precoce sobre a atividade deste eixo / Rats subjected to protein malnutrition have high impulsivity and changes in risk-assessment behaviors in the elevated plus maze (EPM). Malnutrition can also influence the activity of the hypothalamic-pituitary-adrenal (HPA). Changes caused by malnutrition can be partly reversed by environmental stimulation; malnourished animals subjected to environmental enrichment had higher locomotion and exploration in the EPM compared with animals of the same condition and diet that were not stimulated. It was also demonstrated that stimulation can influence plasma corticosterone levels indicating a change in sensitivity of the HPA axis. This study aims to compare, in undernourished rats (M) and well nourished (C), the effects of environmental enrichment (E) in relation to plasma concentrations of corticosterone, expression of glucocorticoid receptors (GR) in the hippocampus and performance in EPM at 36 days of age. Male Wistar rats were divided into two groups according to diet and subdivided according handling environment. The environmental manipulation was performed within 8 to 35 days (1 hour per day). After testing in the EPM animals were decapitated and had their blood drawn and the brain removed. For the analysis of plasma corticosterone it was used the radioimmunoassay technique. For quantification of the glucocorticoid receptor (GR) in the hippocampus it was performed a quantitative analysis of gene expression by polymerase chain reaction (PCR) in real time. M rats showed lower body weight compared to C rats (p<0.001). In relation to the EPM, M rats showed higher number of entries [F(1,44)=9.01, p<0.01] and remain a higher percentage of time [F(1,44)=9.08, p<0.01] in the open arms as compared to C. ME rats presented a percentage of time in the open arms (6% ± 2%) similar to that of CN animals (8% ± 2%). According to the real time PCR, the EPM test changed the quantity of GR receptors in the hippocampus (t(10)=2.37, p<0.05), and that adaptation was different in M as compared with C rats. It was also observed that the amount of GR after EPM test was different between M and ME groups (t(11)=4.48, p<0.05). Data from the present study suggest that M animals are more likely to explore risk situations than C rats. It is also suggested that environmental enrichment imposed during the critical period of central nervous system development may have neuroprotective effects in both physiological and behavioral changes produced by early protein malnutrition. The data of this work also showed that malnutrition may alter the stress response mediated by the HPA axis after exposure to the EPM test and that environmental enrichment has a protective effect against the effects of malnutrition on the functioning of that axis.

O presente trabalho trata da aplicação do Método de Resíduos Ponderados, mais especificamente do Método dos Mínimos Quadrados, na obtenção de soluções aproximadas de problemas de estruturas em casca, em especial os reservatórios cilíndricos submetidos a carregamento hidrostático em regime de comportamento linear. Os meios empregados para a obtenção das soluções aproximadas referem-se à adoção de bases aproximativas lineares, polinomiais, além da possibilidade de enriquecimento da aproximação mediante a adição de funções com características similares à própria solução exata. Uma outra alternativa utilizada refere-se à aplicação do Método dos Mínimos Quadrados com divisão do domínio de integração. Tais procedimentos podem ser úteis na análise de estruturas por evitar, de modo significativo, a elevação do esforço computacional, mediante a utilização de uma base aproximativa que corresponda às características requeridas pela solução analítica do problema. / The present dissertation deals with the application of the Weighed Residual Method to analysis of cilindrical shells, more specifically of the Least Squared Method, in the attainment of approach solutions of shells structural problems, in special the cylindrical reservoirs submitted the hydrostatic shipment in regimen of linear behavior. The half employees for obtention of the approach solutions refer to adotion of linear, polynomial approaches bases, beyond the possibility of enrichment of the approach by means of the addition of functions with similar characteristics to the proper accurate solution.One another used alternative mentions the application to Least Squared Method with division of the integration domain. Such procedures can be useful in the analysis of structures for preventing, in significant way, the rise of the computational effort, by means of the use of a aproximativa base that correspond to the characteristics required for the analytical solution of the problem.

Das Ziel der Untersuchungen bestand darin, mit Hilfe objektiv messbarer Verhaltensreaktionen von Schweinen deren essentielle Ansprüche und Präferenzen zu ermitteln. Der Versuchsaufbau ermöglicht eine permanente Erfassung der Verhaltensabläufe von 22 Mastschweinen über den gesamten Haltungszeitraum. Dies erfolgt durch Anwendung einer elektronischen Identifikation, die Aufenthaltsort, -dauer und -frequenz von jedem Tier erfasst. Als Aufenthaltsorte standen den Tieren ein Bereich zur Nahrungsaufnahme, ein Bereich Ruhen und zwei Beschäftigungsbereiche zur Verfügung. Beide Futterautomaten und Tränken waren mit einer Tieridentifikation ausgestattet. Durch das sensorgestützte System konnten in den zwei Versuchen im Mittel über 6000 Datensätze je Tier erhoben werden. Der Auswertungsschwerpunkt wurde auf die Analyse von Präferenz und Nutzungsstruktur der Beschäftigungsbereiche gelegt. Als Beschäftigung standen den Schweinen Sand, eine neuartige Wühlmatte und Stroh zur Verfügung. Wühlen schien für die Tiere ein wichtiges Verhaltenselement zu sein. Die Nutzungshäufigkeit der Beschäftigung betrug 6-11 Besuche je Tier und Tag. Die potentielle Nutzungsdauer der Beschäftigungsangebote erreichte im Mittel höchstens 3,4 Stunden je Tier und Tag. Die Unterschiede zwischen den Angeboten waren signifikant. Die Individualität der Schweine ist sowohl in der Nutzungsfrequenz als auch - dauer stark ausgeprägt. Der Neuigkeitswert der Beschäftigung gewinnt mit zunehmendem Alter an Bedeutung. Durch eine Modellierung der sensorgestützt erfassten Parameter Nutzungshäufigkeit und Aufenthaltsdauer zu den Beschäftigungsangeboten ist es gelungen, eine objektive Bewertung tierindividueller Präferenz zu zwei Angeboten in einer Indexzahl zu erreichen. Unter Berücksichtigung des Adaptationsprozesses auf veränderte Umweltbedingungen im zeitlichen Verlauf kann mittels des Modells außerdem eine Aussage zur Affinität und Kompensationsmöglichkeit von Angeboten vorgenommen werden. / This study analyses individual requirements and preferences of pigs by measuring objective parameters of their behaviour. In contrary to previous approaches the generated experimental setup enabling long term investigation of 22 pigs behaviour during the whole fattening period. Using sensorbased identification of every single pig it was possible to record habitation, duration of stay and the frequency of attendance in distinct area of the facility namely feeding and drinking area, resting area as well as two areas with environmental enrichment. Furthermore two automatic feeders and the drinkers were equipped with the animal identification system. More than 6000 data sets for each animal were recorded in two independent experimental series. The evaluation focused on the analysis of both preference and utilisation of environmental enrichments such as sand, novel nuzzle mat and straw. It seemed that nuzzling turned out to be essential for the animals, as six to eleven visits per day and animal were recorded. Pigs attended to the respective elements up to 3.4 hours per day. Significant preferences for specific elements could be observed. For individual study animals both frequency and duration of stay were markedly variable. Attractiveness of novel environmental enrichments increased with increasing age of the pigs. By modelling frequency of use and duration of stay, both recorded sensor-based, it was possible to accomplish an objective analysis of the individual preference for specific offers which is represented by an index number. This number supported the results obtained by complex measurements precisely yet in a simplified manner. Taking into account the adaptation process to changing environmental conditions the generated model permits a conclusion regarding affinity and compensation of the offerings.

Die Phosphorylierung als posttranslationale Modifikation von Proteinen spielt bei Signalwegen in Zellen eine große Rolle. Für die Entschlüsselung des molekularen Mechanismus der circadianen Uhr ist es daher von Interesse, die Phosphorylierungsstellen beteiligter Proteine zu identifizieren. Im Rahmen dieser Arbeit wurden die Proteine Period I und II mittels Flüssigkeitschromatographie und Tandemmassenspektrometrie (LC-MS/MS) auf Phosphorylierungsstellen untersucht. Hierbei lag der Fokus auf der Verbesserung bestehender Methoden, um eine bessere und umfassendere Identifizierung der Phosphorylierungsstellen, insbesondere in Bezug auf mehrfach phosphorylierte Peptide, zu erreichen. Der Arbeitsablauf beinhaltete die Verwendung mehrerer Proteasen, um eine hohe Sequenzabdeckung des Proteins zu erreichen. Nach der Proteolyse wurden die Phosphopeptide mittels Titandioxid angereichert. Hierbei und bei der LC-MS/MS-Analyse wurde Citrat als Additiv verwendet, welches eine bessere Chromatographie multiphosphorylierter Peptide ermöglicht. Bei der MS/MS-Analyse wurden CID und ETD als Fragmentierungsmethoden eingesetzt. Es konnten durch diese Methodik 30 bzw. 42 Phosphorylierungsstellen an den Proteinen Period I und II identifiziert werden, von denen 26 bzw. 14 zuvor nicht beschrieben waren. Nach der qualitativen Identifizierung wurden quantitative Varianten der optimierten Analytik untersucht, um die biologische Funktion der gefundenen Phosphorylierungsstellen untersuchen zu können. Hierbei wurden das metabolische Labeling der Zellen mit 15N-stickstoffhaltigen Aminosäuren und die säurekatalysierte Isotopenmarkierung auf Peptidebene mit 18O-Sauerstoff untersucht. Mit einer optimierten Variante der säurekatalysierten Isotopenmarkierung mit 18O-Sauerstoff lassen sich die Carboxygruppen der Peptide in 5h 30min mit einer Rate von >97% 18O-Sauerstoff markieren. Mit dieser Methode können weitere funktionelle Untersuchungen der Phosphorylierung an den Period-Proteinen durchgeführt werden. / Protein phosphorylation, a posttranslational modification, plays an important role in signal cascades in cells. In order to understand the molecular mechanism of the circadian clock, it is thus of interest to identify the phosphorylation sites on proteins contributing to the system. During the work for this thesis, the proteins Period I and II were analyzed for phosphorylation sites with liquid chromatography and tandem mass spectrometry (LC-MS/MS). Hereby the focus was on improving existing methods in order to better identify multi-phosphorylated peptides. In the workflow, the Period proteins were digested with several proteases in order to archive a high sequence coverage for analysis. After proteolysis the phosphopeptides were subsequently enriched with titanium dioxide. During phosphopeptide enrichment and reversed phase chromatography, citrate was used as an additive for a better chromatography and recovery of multiphosphorylated peptides. During LC-MS/MS analysis, CID and ETD were used as fragmentation mechanisms in the mass spectrometer. Using these methods, 30 and 42 phosphorylation sites could be identified on the proteins Period I and II, respectively, including 26 and 14 which were previously unpublished. In order to unravel the biological function of these phosphorylation sites, quantitative methods for the optimized LC-MS approach were investigated. This included the metabolic labeling of cells with amino acids containing 15N-nitrogen as well as acid catalyzed 18O-oxygen labeling on peptide level. The developed optimized variant of acid catalyzed 18O-oxygen labeling achieves an inclusion of 18O-oxygen at the peptide carboxy groups with a rate of >97% in 5h 30min. This method can be used for further investigation of the biological function of the phosphorylation on the Period proteins.

De par leur grand nombre et leur sévérité, les maladies rares (MR) constituent un enjeu de santé majeur. Des bases de données de référence, comme Orphanet et Orphadata, répertorient les informations disponibles à propos de ces maladies. Cependant, il est difficile pour ces bases de données de proposer un contenu complet et à jour par rapport à ce qui est disponible dans la littérature. En effet, des millions de publications scientifiques sur ces maladies sont disponibles et leur nombre augmente de façon continue. Par conséquent, il serait très fastidieux d’extraire manuellement et de façon exhaustive des informations sur ces maladies. Cela motive le développement des approches semi-automatiques pour extraire l’information des textes et la représenter dans un format approprié pour son utilisation dans d’autres applications. Cette thèse s’intéresse à l’extraction de connaissances à partir de textes et propose d’utiliser les résultats de l’extraction pour enrichir une ontologie de domaine. Nous avons étudié trois directions de recherche: (1) l’extraction de connaissances à partir de textes, et en particulier l’extraction de relations maladie-phénotype (M-P); (2) l’identification d’entité nommées complexes, en particulier de phénotypes de MR; et (3) l’enrichissement d’une ontologie en considérant les connaissances extraites à partir de texte. Tout d’abord, nous avons fouillé une collection de résumés d’articles scientifiques représentés sous la forme graphes pour un extraire des connaissances sur les MR. Nous nous sommes concentrés sur la complétion de la description des MR, en extrayant les relations M-P. Cette trouve des applications dans la mise à jour des bases de données de MR telles que Orphanet. Pour cela, nous avons développé un système appelé SPARE* qui extrait les relations M-P à partir des résumés PubMed, où les phénotypes et les MR sont annotés au préalable par un système de reconnaissance des entités nommées. SPARE* suit une approche hybride qui combine une méthode basée sur des patrons syntaxique, appelée SPARE, et une méthode d’apprentissage automatique (les machines à vecteurs de support ou SVM). SPARE* bénéficié à la fois de la précision relativement bonne de SPARE et du bon rappel des SVM. Ensuite, SPARE* a été utilisé pour identifier des phénotypes candidats à partir de textes. Pour cela, nous avons sélectionné des patrons syntaxiques qui sont spécifiques aux relations M-P uniquement. Ensuite, ces patrons sont relaxés au niveau de leur contrainte sur le phénotype pour permettre l’identification de phénotypes candidats qui peuvent ne pas être références dans les bases de données ou les ontologies. Ces candidats sont vérifiés et validés par une comparaison avec les classes de phénotypes définies dans une ontologie de domaine comme HPO. Cette comparaison repose sur une modèle sémantique et un ensemble de règles de mises en correspondance définies manuellement pour cartographier un phénotype candidate extrait de texte avec une classe de l’ontologie. Nos expériences illustrent la capacité de SPARE* à des phénotypes de MR déjà répertoriés ou complètement inédits. Nous avons appliqué SPARE* à un ensemble de résumés PubMed pour extraire les phénotypes associés à des MR, puis avons mis ces phénotypes en correspondance avec ceux déjà répertoriés dans l’encyclopédie Orphanet et dans Orphadata ; ceci nous a permis d’identifier de nouveaux phénotypes associés à la maladie selon les articles, mais pas encore listés dans Orphanet ou Orphadata.Enfin, nous avons appliqué les structures de patrons pour classer les MR et enrichir une ontologie préexistante. Tout d’abord, nous avons utilisé SPARE* pour compléter les descriptions en terme de phénotypes de MR disponibles dans Orphadata. Ensuite, nous proposons de compter et grouper les MR au regard de leur description phénotypique, et ce en utilisant les structures de patron. [...] / Even if they are uncommon, Rare Diseases (RDs) are numerous and generally sever, what makes their study important from a health-care point of view. Few databases provide information about RDs, such as Orphanet and Orphadata. Despite their laudable effort, they are incomplete and usually not up-to-date in comparison with what exists in the literature. Indeed, there are millions of scientific publications about these diseases, and the number of these publications is increasing in a continuous manner. This makes the manual extraction of this information painful and time consuming and thus motivates the development of semi-automatic approaches to extract information from texts and represent it in a format suitable for further applications. This thesis aims at extracting information from texts and using the result of the extraction to enrich existing ontologies of the considered domain. We studied three research directions (1) extracting relationships from text, i.e., extracting Disease-Phenotype (D-P) relationships; (2) identifying new complex entities, i.e., identifying phenotypes of a RD and (3) enriching an existing ontology on the basis of the relationship previously extracted, i.e., enriching a RD ontology. First, we mined a collection of abstracts of scientific articles that are represented as a collection of graphs for discovering relevant pieces of biomedical knowledge. We focused on the completion of RD description, by extracting D-P relationships. This could find applications in automating the update process of RD databases such as Orphanet. Accordingly, we developed an automatic approach named SPARE*, for extracting D-P relationships from PubMed abstracts, where phenotypes and RDs are annotated by a Named Entity Recognizer. SPARE* is a hybrid approach that combines a pattern-based method, called SPARE, and a machine learning method (SVM). It benefited both from the relatively good precision of SPARE and from the good recall of the SVM. Second, SPARE* has been used for identifying phenotype candidates from texts. We selected high-quality syntactic patterns that are specific for extracting D-P relationships only. Then, these patterns are relaxed on the phenotype constraint to enable extracting phenotype candidates that are not referenced in databases or ontologies. These candidates are verified and validated by the comparison with phenotype classes in a well-known phenotypic ontology (e.g., HPO). This comparison relies on a compositional semantic model and a set of manually-defined mapping rules for mapping an extracted phenotype candidate to a phenotype term in the ontology. This shows the ability of SPARE* to identify existing and potentially new RD phenotypes. We applied SPARE* on PubMed abstracts to extract RD phenotypes that we either map to the content of Orphanet encyclopedia and Orphadata; or suggest as novel to experts for completing these two resources. Finally, we applied pattern structures for classifying RDs and enriching an existing ontology. First, we used SPARE* to compute the phenotype description of RDs available in Orphadata. We propose comparing and grouping RDs in regard to their phenotypic descriptions, and this by using pattern structures. The pattern structures enable considering both domain knowledge, consisting in a RD ontology and a phenotype ontology, and D-P relationships from various origins. The lattice generated from this pattern structures suggests a new classification of RDs, which in turn suggests new RD classes that do not exist in the original RD ontology. As their number is large, we proposed different selection methods to select a reduced set of interesting RD classes that we suggest for experts for further analysis

Submitted by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2017-06-05T14:03:37Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) JEFFERSON ROSA DE MENEZES.pdf: 2848766 bytes, checksum: e87a7c0a040b93eb5052a1ea902c099e (MD5) / Approved for entry into archive by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2017-06-05T14:03:52Z (GMT) No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) JEFFERSON ROSA DE MENEZES.pdf: 2848766 bytes, checksum: e87a7c0a040b93eb5052a1ea902c099e (MD5) / Made available in DSpace on 2017-06-05T14:03:52Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) JEFFERSON ROSA DE MENEZES.pdf: 2848766 bytes, checksum: e87a7c0a040b93eb5052a1ea902c099e (MD5) Previous issue date: 2017-02-22 / A deprivação maternal é um potente estressor na fase inicial da vida de mamíferos, ocasionando diversos déficits cognitivos que se mantêm na vida adulta. Dentre os mecanismos envolvidos nestes déficits estão o desiquilíbrio oxidativo e as alterações em determinadas proteínas, como o fator neurotrófico derivado do cérebro (do inglês Brain-Derived Neurotrophic Factor, BDNF). Estes eventos podem ocorrer em diferentes regiões do no cérebro, entre elas o hipocampo, principal região responsável pela formação e consolidação das memórias. Esta dissertação investigou os efeitos de diferentes estratégias neuroprotetoras (exercício físico, suplementação com chá verde, e, enriquecimento ambiental) nos déficits de memória advindos da deprivação maternal. Para avaliar a função mnemônica, foi utilizado um modelo animal de DM (em ratos Wistar) e os testes de reconhecimento de objetos, esquiva inibitória e labirinto aquático de Morris. Para avaliar o balanço redox hipocampal quantificamos espécies reativas de oxigênio (EROs), espécies reativas ao ácido tiobarbitúrico (TBARS), níveis de glutationa (GSH) e capacidade antioxidante total (FRAP), além disso, determinamos a atividade da enzima acetilcolinesterase e a quantificamos os níveis de BDNF. Nossos resultados demonstram que o exercício físico e o chá verde são estratégias antioxidantes eficazes de neuroproteção em um modelo de DM. Também demonstram que o enriquecimento ambiental é capaz de reverter os efeitos deletérios oriundos da DM por meio do incremento dos níveis de BDNF. Estes resultados revelam a possibilidade da utilização dessas intervenções como estratégia de neuroproteção. / Maternal deprivation is a potent stressor in the early life of mammalian, leading to several cognitive deficits that remain until adulthood. Among the mechanisms involved in these deficits are the oxidative imbalance and the alterations in some proteins, such as Brain-Derived Neurotrophic Factor (BDNF), events that can occur in different brain regions, as the hippocampus, the main region responsible for the memory formation and consolidation. This master thesis investigated the effects of different neuroprotective strategies (physical exercise, green tea supplementation, and environmental enrichment) on memory deficits related to maternal deprivation (MD). To evaluate the mnemonic function was used an animal model of MD (using Wistar rats) and the object recognition, inhibitory avoidance and Morris water maze memory tests. To evaluate hippocampal redox balance we quantified the reactive oxygen species (ROS), the thiobarbituric acid reactive species (TBARS), the glutathione levels (GSH) and the total antioxidant capacity (FRAP), as well as determine the acetylcholinesterase activity and the BDNF levels. Our results show that physical exercise and green tea are effective neuroprotective antioxidant strategies in a MD model. They also demonstrate that environmental enrichment is capable to reverse the deleterious effects of MD by increasing BDNF levels. These results reveal the possibility of using these interventions as a neuroprotection strategy.