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Function prediction of transcription start site associated RNAs (TSSaRNAs) in Halobacterium salinarum NRC-1 / Predição de função para TSSaRNAs (transcritos associados a sitios de início de transcrição) em Halobacterium salinarum NRC-1Adam, Yagoub Ali Ibrahim 07 February 2019 (has links)
The Transcription Start Site Associated non-coding RNAs (TSSaRNAs) have been predicted across the three domain of life. However, still, there are no reliable annotation efforts to identify their biological functions and their underline molecular machinery. Therefore, this project addresses the question of what are the potential functions of TSSaRNAs regarding their roles in addressing the cellular functions. To answer this question, we aimed to accurately identify TSSaRNAs in the model organism Halobacterium salinarum NRC-1 (an Archean microorganism) that incubated at the standard growth condition. Consequently, we aimed to investigate TSSaRNAs structural stability in the term of the thermodynamic energies. Moreover, we attempted to functionally annotate TSSaRNAs based on Rfam functional classification of non-coding RNAs. Based on the statistical approach we developed an algorithm to predict TSSaRNA using next-generation RNA sequencing data (RNA-Seq). To perform structural annotation of TSSaRNAs, we investigated the structural stability of TSSaRNAs by modeling the secondary structures by minimizing the thermodynamic free energy. We simulated TSSaRNAs tertiary structures based on the secondary structures constrain using the Rosetta-Common RNA tool. The structures of the minimum free energy supposed to be biophysically stable structures. To investigate the higher order structures of TSSaRNAs, we studied the hybridization between TSSaRNAs and their cognate genes as part of RNA based regulation system. Also, based on our hypothesis that TSSaRNAs may bind to protein to trigger their function, we have investigated the interaction between TSSaRNAs and Lsm protein which known as a chaperone protein that mediates RNA function and involved in RNA processing. Our pipeline to perform the functional annotation of TSSaRNAs aimed to classify TSSaRNAs into their corresponding Rfam families based on two steps: either through querying TSSaRNAs sequences against the co-variance models of Rfam families or by querying the Rfam sequences against the co-variance models of the consensus secondary structures in TSSaRNAs. The results showed that the prediction algorithm has succeeded to identify a total of 224 TSSaRNAs that expressed in the same strand of the mRNAs and 58 TSSaRNAs that expressed as antisense of the mRNAs. The identified TSSaRNAs molecules showed a median length of 25 nucleotides. Regarding the structural annotation of TSSaRNAs, the results showed that most of TSSaRNAs possessed thermodynamically stable secondary structures and their tertiary structures were capable of forming more complex structures through binding with other biomolecules. About the formation of higher-order structures, we have observed that most of TSSaRNAs (92.2%) were capable of hybridizing into their cognate genes also 55 TSSaRNAs indicated putative interactions with Lsm protein. Furthermore, the computation docking experiments demonstrated the TSSaRNAs-Lsm complexes associated with favorable binding energy of a median of -542900 kcal mole -¹. Regarding the functional annotation of TSSaRNAs, the results showed that the majority of TSSaRNAs (42.05%) considered as potential cis-acting regulators such as cis-regulatory element and sRNAs, but still, there are potential trans-acting regulators to regulate distant molecules such as CRISPR and antisense RNA. Moreover, the results indicated that TSSaRNAs could trigger more complex function as a catalytic function such as Riboswitch or to play a role in the defense against a virus such as CRISPR. As a conclusion; based on the results of this study we could state that TSSaRNAs have several potential functions opening the experimental validation perspective. / Os RNA não codificantes associados ao sítio de início da transcrição - em inglês, transcription start site associated non-coding RNAs (TSSaRNA) - foram observados nos três domínios da vida. No entanto, sem esforço confiável de anotação para identificar suas funções biológicas e seus mecanismos moleculares. Portanto, esse projeto levanta a questão de quais são as funções em potencial dos TSSaRNAs a respeito de seus papeis nas funções celulares. Para responder esta questão, nós objetivamos em identificar de forma eficaz os TSSaRNAs no organismo modelo Halobacterium salinarum NRC-1 (um microrganismo do domínio Arqueia) encubado em uma condição de crescimento padrão. Consequentemente, nós investigamos a estabilidade estrutural dos TSSaRNAs em relação a energias termodinâmicas. Ainda, fizemos a anotação funcional dos TSSaRNAs baseado na classificação funcional Rfam dos RNAs não-codificantes. Baseada em uma abordagem estatística nós desenvolvemos um algoritmo para predizer TSSaRNA usando dados de sequenciamento de RNA de nova geração (RNA-Seq). Para investigar a estabilidade estrutural dos TSSaRNAs nós modelamos as estruturas secundárias minimizando a energia livre termodinâmica para alcançar a estrutura mais estável biofisicamente. Nós simulamos estruturas terciárias de TSSaRNAs baseado nas restrições das estruturas secundárias usando a ferramenta Rosetta-Common RNA. As estruturas de energia livre mínima seriam supostamente estruturas estáveis biofisicamente. Para investigar as estruturas de ordem superior (quaternária) dos TSSaRNAs, nós estudamos a hibridização entre os TSSaRNAs e seus genes cognatos como parte de um possível sistema de regulação baseado em RNA. Ainda, baseada na hipótese que os TSSaRNAs podem ligar à proteína para habilitar sua função, nós investigamos a interação entre TSSaRNAs e proteína Lsm que é conhecida por ser uma proteína chaperone que media função do RNA e está envolvida no processamento do RNA. Nosso pipeline para executar a anotação funcional dos TSSaRNAs objetivou classificar as TSSaRNAs em suas correspondentes classes Rfam baseado em dois passos: por meio de consulta das sequências TSSaRNA em relação a modelos de covariância de famílias Rfam ou por consulta de sequências Rfam em relação a modelos de covariância das estruturas de secundárias de consenso das estruturas secundárias nos TSSaRNAs. Os resultados mostraram que o algoritmo de detecção teve sucesso em identificar um total de 224 TSSaRNAs que expressaram na mesma direção dos mRNAs e 58 TSSaRNAs que expressaram no sentido oposto (antisenso) dos mRNAs. As moléculas TSSaRNAs identificadas mostraram um comprimento mediano de 25 nucleotídeos. A respeito da anotação estrutural dos TSSaRNAs, os resultados mostraram que a maioria dos TSSaRNAs possuíam estruturas secundárias estáveis termodinamicamente e suas estruturas terciárias foram capazes de formar estruturas mais complexas por meio de vínculos com outras biomoléculas. Quanto à formação de estruturas de maior de estruturas de alta ordem nos observamos que a maioria dos TSSaRNAs (92.2%) são capazes, pelo menos em princípio, de hibridizar em seus genes cognatos e, também, 55 TSSaRNAs evidenciaram interagir com a proteína Lsm. Além disso, os experimentos computacionais de docking demonstratam os complexos TSSaRNAs-Lsm associados com energia de ligação favorável com uma média de - 542900 kcal mole -¹. Quanto à anotação funcional dos TSSaRNAs, os resultados mostraram que a maioria dos TSSaRNAs (42.05%) podem ser consideradas potenciais reguladores atuando em cis tais como elemento cis-regulamentar e sRNAs, mas ainda há pontenciais reguladores atuando em trans para regular moléculas em loci distantes, tais como CRISPR e RNA antisense. Além disso, os resultados mostraram que TSSaRNAs podem potencialmente ativar funções mais complexas como uma função catalítica, tal como Riboswitch ou executar um papel de defesa contra vírus, tal como CRISPR. Como conclusão; baseado nos resultados desse estudo, nós podemos afirmar que TSSaRNAs possuem várias funções em potencial abrindo a perspecitiva de validação experimental.
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結構型金融商品之評價與分析-固定期限交換利率利差連動債券 / Evaluation and Analysis of Structured Financial Products-100% Principal Protected Leveraged Callable CMS Spread Note李健維 Unknown Date (has links)
次級房貸風暴使得包裝複雜的衍生性金融商品紛紛遭受波及後,目前結構型金融商品的條款設計將朝簡單化和透明化的趨勢發展,有助於全球金融市場的效率性、完整性與穩定性。本文從市場上選擇具代表性的利率結構型商品,應用模型來推導商品的價格,並深入分析商品的報酬與風險型態。
本文分析的個案商品為全球知名的匯豐銀行所發行之十年期「固定期限交換利率利差連動債券」,在評價上將採用LIBOR市場模型,利用市場上既有的資料求算出期初遠期利率,並校準模型所需的參數化波動度函數與相關係數函數,建立與市場一致的利率期間結構與利率波動度期間結構。模擬路徑時應用最小平方法蒙地卡羅來求得該商品發行之期初價格,此外,亦採用反向變異法加速收斂效果,並針對商品的條款設計作拆解與分析。最後,本文探討了發行機構發行商品之風險與避險策略,並且從投資人之報酬及風險層面作詳盡地剖析。
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Dimensions of the dining experience of academic employees at full-service restaurantsNaude, Petro 09 1900 (has links)
Full-service restaurants serve many different types of customers with preconceived ideas about what they want and expect to receive from the restaurant. During the dining experience, each customer experiences the service differently and subconsciously evaluates the experience differently. The purpose of this study is to determine the expectations and perceptions of customers regarding the dining experience dimensions at Full-Service Restaurants (FSRs). The dimensions relate to service quality, food quality and ambience quality expectations and perceptions of customers. Customer satisfaction was also analysed, as a satisfied customer will show return intentions and this customer will tell friends and family about this FSR. A self-administered survey of employees at a tertiary academic institution revealed that waiter professionalism, value for money and the atmosphere in the restaurant are the most important considerations when it comes to the expectations of the dining experience.
The findings of this study presented a demographic profile (gender, age, home language, highest education qualification, LSM) and it was found that demographic category groups differ in the way that they perceive the dining experience. The study reveals that males tends to be less critical than women, LSM 9 respondents are less critical than LSM 10 respondents and respondents with an undergraduate degree or less are less critical than respondents with a post-graduate degree. Respondents were satisfied overall with their dining experiences. Recommendations include that management must focus on pricing strategies, waiter training and the flow of communication between the restaurant and the customer. The recommendations made in this study will assist management of FSRs to understand the significance of the dining experience dimensions and to implement the required levels of service, food and ambience quality. With this knowledge, the management of FSRs can be assured of a satisfied customer and a competitive offering. / Business Management / M. Com. (Business Management)
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Conception optimale d’une gamme de moteurs synchrones à démarrage direct à haute performance énergétique / Optimal design of line-start permanent magnet synchronous motors of high efficiencyElistratova, Vera 06 November 2015 (has links)
Ce travail a pour objectif de développer un outil analytique multi-physiques de dimensionnement d’une gamme de moteurs « hybrides » à démarrage direct, intégrant les avantages des deux technologies : l’auto-démarrage de la technologie asynchrone et les bonnes performances énergétique en régime permanent de la technologie synchrone à aimants permanents en répondant aux nouveaux enjeux d’efficacité énergétique et en ajoutant à cela les aspects économiques.La validation de cet outil est effectuée par des modèles éléments finis créés avec un logiciel commercial ANSYS/Maxwell et par des essais expérimentaux réalisés à l’aide de deux prototypes LSPMSM 7.5kW. / This work aims to develop a multi-physical generic model (and a pre-design software) for a range of LSPMSMs which would integrate the advantages of both technologies: self-start asynchronous technology and good energy performance of synchronous permanent magnet technology. The validation of this model is carried out by finite element commercial software ANSYS / Maxwell and by experimental tests using two 7.5kW.LSPMSM prototypes.
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