Eukaryotic genomes contain a large number of repetitive structures. Their detection and assembly today are the main challenges of bioinformatics. This work includes a classification of repetitive DNA and represents an implementation of a novel de novo assembler focusing on searching and constructing LTR retrotransposons and satellite DNA. Assembler accepts on his input short reads (single or pair-end), obtained from next-generation sequencing machines (NGS). This assembler is based on Overlap Layout Consensus approach.

A descrição dum subgénero dentro da ficção histórica que se distinguiu pela sua distanciação do Romance Histórico Tradicional em vários aspetos, o chamado Novo Romance Histórico, ocupou muitos estudiosos nas últimas décadas. Mais recentemente, o catedrático português Carlos Reis realçou a importância da personagem como categoria narrativa na literatura, opondo-se às tendências estruturalistas que marcam os estudos literários modernos. Na nossa pesquisa, rastreamos o processo da figuração duma personagem coletiva no romance Mad Maria do escritor brasileiro Márcio Souza: os trabalhadores barbadianos. Por um lado, observamos como o autor usou dados historiográficos para a figuração duma personagem coletiva baseada num grupo de trabalhadores caribenhos, cuja participação nas obras da ferrovia Madeira-Mamoré no início do século passado é bem documentada. Pelo outro lado, consideramos a relevância desta personagem em relação à ideologia do escritor, posto que uma das características fundamentais do Novo Romance Histórico é a narração do passado histórico através de personagens pertencentes a grupos marginais, cuja voz não faz parte do discurso historiográfico tradicional. La descripción de un subgénero de la ficción histórica, el cual se destaca por alejarse en varios aspectos de la Novela Histórica Tradicional, a saber, la llamada Nueva Novela Histórica, ha ocupado a muchos estudiosos en las últimas décadas. Más recientemente, el catedrático portugués Carlos Reis realzó la importancia del personaje como categoría narrativa en la literatura, en oposición a las tendencias estructuralistas que marcan los estudios literarios modernos. En nuestras investigaciones, vamos rastreando el proceso de figuración de un personaje colectivo en la novela Mad Maria del escritor brasileño Márcio Souza: los trabajadores barbadenses. Por un lado, observamos como el autor empleó datos biográficos para la figuración de un personaje colectivo inspirado en un grupo de trabajadores caribeños, cuyo papel en la construcción de la vía férrea Madeira-Mamoré a principios del siglo pasado está bien documentado. Por otro lado, consideramos la relevancia de dicho personaje respecto a la ideología del escritor, habida cuenta que un rasgo diferencial de la Nueva Novela Histórica es la narración del pasado histórico por medio de personajes de proveniencia marginal, cuya voz no forma parte del discurso historiográfico tradicional. The task of describing a subgenre of historical fiction which clearly sets itself apart in many respects from the Traditional Historical Novel, namely, the so-called New Historical Novel, has occupied a number of scholars in the past few decades. More recently, the Portuguese university professor Carlos Reis has emphasized the character's importance as a narrative category within literature, in contrast to the structuralist tendencies which characterize modern literary studies. In our research, we trace the representational process of a collective character - the Barbadian labourers - in the Brazilian authorMárcio Souza's novel Mad Maria. First of all, we analyze the author's use of historiographical data in the depiction of a collective character based on a group of Caribbean labourers, whose role in constructing the Madeira-Mamoré railroad early in the last century is well documented. Second of all, we consider this character's relevance to the writer's ideological profile, since one of the New Historical Novel's distinguishing features is the narration of historical events through characters belonging to marginal groups whose voice has been excluded from traditional historiographical discourse.

<div>Deep neural networks (DNNs) have gained tremendous attention over the recent years due to their outstanding performance in solving many problems in different fields of science and technology. Currently, this field is of interest to many researchers and growing rapidly. The ability of DNNs to learn new concepts with minimal instructions facilitates applying current DNN-based methods to new problems. Here in this dissertation, three methods based on DNNs are discussed, tackling different problems in the field of computer-aided drug design.</div><div><br></div><div>The first method described addresses the problem of prediction of hydration properties from 3D structures of proteins without requiring molecular dynamics simulations. Water plays a major role in protein-ligand interactions and identifying (de)solvation contributions of water molecules can assist drug design. Two different model architectures are presented for the prediction the hydration information of proteins. The performance of the methods are compared with other conventional methods and experimental data. In addition, their applications in ligand optimization and pose prediction is shown.</div><div><br></div><div>The design of de novo molecules has always been of interest in the field of drug discovery. The second method describes a generative model that learns to derive features from protein sequences to design de novo compounds. We show how the model can be used to generate molecules similar to the known for the targets the model have not seen before and compare with benchmark generative models.</div><div><br></div><div>Finally, it is demonstrated how DNNs can learn to predict secondary structure propensity values derived from NMR ensembles. Secondary structure propensities are important in identifying flexible regions in proteins. Protein flexibility has a major role in drug-protein binding, and identifying such regions can assist in development of methods for ligand binding prediction. The prediction performance of the method is shown for several proteins with two or more known secondary structure conformations.</div>

[pt] Este trabalho se propõe investigar a trajetória do novo trabalhismo a partir da experiência do Partido Democrático Trabalhista (PDT). O estudo percorre as origens, as negociações e conflitos, a formação identitária, o desempenho político, bem como os desafios enfrentados ao longo da década de 1980, período que abrange o fim da ditadura militar e a reorganização político-partidária do Brasil. Durante quase vinte anos, o trabalhismo, que era uma tradição hegemônica no país desde Vargas, ficou relegado ao ostracismo. O PTB foi extinto, os petebistas cassados e exilados. É o caso de Leonel Brizola, principal herdeiro do getulismo, que viveu como exilado no Uruguai e depois em Portugal. A pesquisa mostra como Brizola, da capital portuguesa, liderou o processo de reorganização do novo trabalhismo - um projeto gestado em meio ao exílio. Por fim, o estudo enfatiza o peso da tradição política no Brasil, investigando como o PDT buscou resgatar o trabalhismo do pré-1964 e ressignificá-lo no contexto da redemocratização. / [en] This study aims to analyze the new laborism s project conducted by the Democratic Labour Party (PartidoDemocráticoTrabalhista). It addresses the political party s origins, identity formation, negotiations and conflicts, political performance, as well as the challenges faced throughout the 1980s. This is the period of the end of the military dictatorship (1964-1985) and the political-party reorganization in Brazil. For almost twenty years, laborism (trabalhismo), a hegemonic tradition in the country since Getúlio Vargas regime (1930s), was left to ostracism. PTB, Brazilian Laborism Party, was extinct, party members were persecuted and went to exiled. It was the case of Leonel Brizola, the main inheritor of getulism, who lived in exiled in Uruguay and later in Portugal. From the Portuguese capital, Brizola lead the process of the new laborism project. Finally, this study emphasizes the weight of political tradition in Brazil by investigating how the PDT sought to rescue pre-1964 labor political ideology. In doing so, Brizola gave new meanings to laborism (trabalhismo) in the context of the Brazilian redemocratization.

[pt] Nesse artigo, apresentamos um modelo Novo Keynesiano de economia aberta com dois países, taxação distorciva e gasto governamental estocástico. Nessa modelagem comparamos, em uma base de bem-estar, diferentes regras monetária e fiscal com uma referência constituída pelo equilíbrio cooperativo da política de Ramsey. / [en] In this paper, we present a New Keynesian two-country open economy model featuring distortionary taxation and stochastic government spending. Within this modeling we compare, in a welfare-sense, different fiscal and monetary rules with a benchmark constituted by a cooperative Ramseypolicy equilibrium.

Peptide binders are short proteins that bind to larger proteins. Due to peptide binders having high specificity and being cheap to synthesize, they are a prime candidate for drug design. Creating new proteins in silico can be divided into three steps: protein backbone generation, sequence design, and computational filtering. With the release of AlphaFold2 (AF2), protein structure prediction is possible with atomic accuracy, even for peptide-protein complexes. Structure predictions enables some important computational filtering, which saves time and resources before doing experimental validation. After the release of AF2 together with the advancements in generative AI, new computational methods for the first two design steps have been developed. In this report, three different methods for backbone generation and sequence design were evaluated and compared: EvoBind, RFdiffusion, and ProteinMPNN. The latter two were developed solely for protein design. However, their broad application capabilities allowed for peptide development, which was implemented in this report. In total, 5500 peptides for 55 different protein targets were designed by each method, with the purpose to evaluate the performance and identify advantages of the methods. Combining the three methods in unexplored ways allowed for additional evaluation as well as gaining deeper understanding of how the methods worked. Whilst not being one-shot design approaches, all methods used in the report showed potential of being able to design de novo peptide binders with varying degree of in silico success. The methods’ peptide design success rate ranged from 16% to 2.6%. The direct evolution approach applied with EvoBind generated most peptide binder backbones with close binding to the specified interfaces. Using the message passing neural network (MPNN) in ProteinMPNN, the sequences designed were optimized for binding affinity and resulted in sequences that were easier for AF2 to predict. The methods allow for the potential development of peptide binder therapeutics to become more cost- and time efficient, on the basis that AF2’s predictions are aligned with the expressed peptides’ bindings and structures.

[pt] A presente tese tem como finalidade realizar um estudo teológico-pastoral da Igreja Batista Memorial de Alphaville no contexto da missão na cidade. A pesquisa descreve elementos caracteristicos do objeto de pesquisa e traz uma descrição da eclesiologia neotestamentária que serve de criteriologia para que se analise o objeto pesquisado. O atual trabalho é composto por cinco capítulos. O primeiro deles contém aspectos introdutórios. O segundo é de natureza narrativa, onde descrevemos o objeto de estudo, apresentando as suas características essenciais e experiências históricas. O terceiro traz uma exposição da eclesiologia da Igreja do Novo Testamento e tem por objetivo examinar a eclesiologia fundante. O quarto capítulo é uma análise crítica de alguns elementos notórios da Igreja Batista Memorial de Alphaville realizada a partir da experiência eclesial fundante vivida pelas igrejas locais do Novo Testamento. No quinto e último capítulo é apresentada uma conclusão baseada nas informações e reflexões dos capítulos anteriores. / [en] The present thesis aims to carry out a theological-pastoral study of the Memo-rial Baptist Church of Alphaville in the context of mission in the city. The research describes characteristic elements of the research object and provides a description of the New Testament ecclesiology that serves as a criteriology to analyze the object researched. The present work consists of five chapters. The first of them contains introductory aspects. The second is narrative in nature, where we describe the object of study, presenting its essential characteristics and historical experiences. The third brings an exposure of the ecclesiology of the New Testament Church and aims to examine founding ecclesiology. The fourth chapter is a critical analysis of some char-acteristic elements of the Alphaville Memorial Baptist Church carried out from the founding ecclesial experience lived by the local New Testament churches. In the fifth and final chapter a conclusion is presented based on the information and reflections of the previous chapters.

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