Made available in DSpace on 2014-06-12T15:56:06Z (GMT). No. of bitstreams: 2 arquivo2739_1.pdf: 2586871 bytes, checksum: 3a0e10a22b131714039f0e8ffe875d80 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2010 / Nos sistemas de tagging social usuários atribuem tags (palavras-chave) a recursos (páginas Web, fotos, publicações, etc), criando uma estrutura conhecida como folksonomia, que possibilita uma melhora na navegação, organização e recuperação de informação. Atualmente, esses sistemas são muito populares na Web, portanto, melhorar sua qualidade e automatizar o processo de atribuição de tags é uma tarefa importante. Neste trabalho é proposto um sistema que automaticamente atribui tags a páginas, baseando-se em múltiplas fontes de conhecimento como o conteúdo textual, estrutura de hiperlinks e bases de conhecimento. A partir dessas fontes, vários atributos são extraídos para construir um classificador que decide que termos devem ser sugeridos como tag. Experimentos usando um dataset com tags e páginas extraídas do Delicious, um importante sistema de tagging social, mostram que nossos métodos obtém bons resultados de precisão e cobertura, quando comparado com tags sugeridas por usuários. Além disso, uma comparação com trabalhos relacionados mostra que nosso sistema tem uma qualidade de sugestão comparável a abordagens estado da arte na área. Finalmente, uma avaliação com usuários foi feita para simular um ambiente real, o que também produziu bons resultados

Orientador: Anete Pereira de Souza. / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T14:31:52Z (GMT). No. of bitstreams: 1 DaSilva_CarlaCristina_D.pdf: 7310053 bytes, checksum: 1acc7f4e6eb7811b25670f85f9563217 (MD5) Previous issue date: 2014 / Resumo: A seringueira (Hevea brasiliensis), espécie nativa da Amazônia, é a maior fonte de borracha natural do mundo. Programas de melhoramento genético da seringueira têm sido cruciais para a obtenção de caracteres desejáveis. Entretanto, o ciclo de melhoramento da seringueira é muito longo (cerca de 30 anos), tornando-se essencial o desenvolvimento de novas técnicas de avaliação precoce. As bibliotecas de cDNA e Expressed Sequence Tags (ESTs) são ferramentas muito importantes em biologia molecular: possibilitam identificar genes preferencialmente expressos em tecidos ou tipos celulares e também são valiosas fontes de marcadores polimórficos, instrumentos poderosos para genotipagem e mapeamento molecular. O uso de marcadores derivados de ESTs permite construir mapas funcionais, nos quais são posicionados genes transcritos ou regiões próximas aos genes. Este tipo de mapeamento é importante para estudos de associação gene-característica, e identificação de genes candidatos. Este trabalho objetivou a construção de bibliotecas de cDNA de diferentes tecidos (painel, látex e folha) e tratamentos (exposição ao frio e infecção controlada por Microcyclus ulei) de seringueira para desenvolver sequências EST e marcadores moleculares gene-direcionados a partir destas sequências, para aumentar a saturação de um mapa integrado baseado em microssatélites, no qual identificaram 18 quantitative trait loci (QTLs) para características de crescimento, construído previamente em nosso laboratório. Foram sequenciados 10.464 clones, gerando 8.551 ESTs de alta qualidade que agrupadas formaram 5.211 unigenes. Destes, 3.582 (68,7%) apresentam similaridade com uma proteína hipotética ou expressa. Foram desenvolvidos 173 marcadores EST-SSR e 43 marcadores SNP para H. brasiliensis. 150 EST-SSRs (87%) podem estar associados a genes funcionais, e 98,8% foram transferidos para outras espécies de Hevea, sugerindo que o gênero seja um complexo formado pelas diferentes espécies. Os SNPs foram identificados em 13 ESTs similares a proteínas de resposta a estresse, desenvolvimento e síntese de látex. Seis sequências foram abundantes nas bibliotecas de exposição ao frio e análises de expressão demonstraram que a expressão de cinco sequências aumentou durante o experimento, principalmente a expressão de duas sequências que foi aumentada mais de 70 vezes. Dos EST-SSRs desenvolvidos, 46 foram genotipados na população segregante F1 com 270 indivíduos, e estes marcadores foram adicionados ao mapa genético de seringueira, totalizando 330 marcadores. O programa OneMap foi usado para a construção do mapa que possui 3.068,9 cM de extensão e 22 grupos de ligação (LGs). Cinco locos foram mapeados em regiões QTL, e os transcritos de três são similares a proteínas de resposta a estresse e desenvolvimento. Estes locos podem ser genes candidatos para estudos relacionados a características de crescimento em seringueira. Até o momento, este é o primeiro trabalho em seringueira que combina análises de ESTs de diferentes tecidos e tratamentos, e análises sobre a exposição a baixas temperaturas, em vários genótipos de seringueira. Os novos marcadores adicionados ao mapa poderão auxiliar na identificação de genes de interesse e de QTLs para outras características de importância agronômica. Os vários marcadores gene-direcionados desenvolvidos serão utilizados para mapeamento e posicionamento de possíveis genes em outras populações de mapeamento que estão sendo avaliadas no Laboratório de Análise Genética e Molecular / Abstract: Rubber tree (Hevea brasiliensis), native species of the Amazon, is world¿s major source of natural rubber. Rubber tree breeding programs have been fundamental for the selection of desirable traits. However, the breeding cycle is time consuming (around 30 years), which makes the development of new techniques for early evaluation a necessity. cDNA libraries and Expressed Sequence Tags (ESTs) are very important tools in molecular biology: they enable the identification of genes preferentially expressed in tissues or cellular types and are also a valuable resource of polymorphic markers, powerful instruments for genotyping and molecular mapping. The use of EST-derived markers allows the construction of functional maps, wherein expressed genes or regions near genes are positioned. This type of mapping is important for gene-trait association studies and candidate genes identification. The present study aimed at the construction of cDNA libraries from different tissues (panel, latex and leave) and treatments (cold exposure and Microcyclus ulei controlled infection) of rubber tree for the development of EST sequences and gene-targeted molecular markers, to raise the saturation of a microsatellite-based integrated genetic map previously constructed in our laboratory, in which 18 quantitative trait loci (QTLs) related to growth traits were identified. Sequencing of 10.464 clones generated 8,551 high quality ESTs that were clustered into 5,211 unigenes. Among these, 3,582 (68.7%) showed similarity to a hypothetical or expressed protein. A total of 173 EST-SSR and 43 SNP markers were developed for H. brasiliensis. 150 SSRs (87%) could be associated with functional genes, and 98.8% were transferred to other Hevea species, suggesting that the genus is a complex formed by different species. The SNP markers were identified in 13 ESTs that showed similarity to stress response, development and latex biosynthesis proteins. Six sequences were highly abundant in the cold exposure libraries and expression analyses demonstrated that five sequences were up-regulated during the exposure, with emphasis to two sequences with more than 70-fold increase in expression. From the developed EST-SSRs, 46 were genotyped in the segregating F1 population comprised of 270 plants. These markers were added to the genetic map, which know contains a total of 330 markers. The OneMap software was used for the map construction that now has 3,068.9 cM and 22 linkage groups. Five loci were mapped into QTLs, and transcripts of three of them present similarity to proteins involved in stress response and developmental processes. These loci may be candidate genes for studies related to rubber tree growth traits. To our knowledge, this is the first work in rubber tree that combines analyses of ESTs from different tissues and treatments, and to analyze sequences under cold stress, in several H. brasiliensis genotypes. The new positioned markers may help in the identification of genes of interest and QTLs for other agronomic important traits. The several gene-targeted markers developed here will be used in the mapping and positioning of possible genes in other mapping populations that are now being evaluated at Genetics and Molecular Analysis Laboratory / Doutorado / Genetica Vegetal e Melhoramento / Doutora em Genética e Biologia Molecular

Abstract Atlantic salmon is one of the most widely known migratory fish species whose populations have declined because of hydropower installations. Attempts have been made to preserve salmon stocks in regulated rivers by building fishways for adult fish migrating upstream, but downstream migration of salmon smolts has been almost totally ignored. Instead, captive breeding programmes and extensive stocking of hatchery-reared salmon smolts have been initiated to compensate for highly reduced natural production and to maintain salmon yields. In recent decades, demands to reduce the environmental effects of hydropower production, together with public awareness of decreasing recapture rate and yield of stocked salmon, have increased calls for rebuilding wild salmon stocks in rivers modified for hydropower production. As a consequence, survival of salmon smolts during downstream migration and the effects of hatchery rearing and stocking methods are now research topics of high importance. This thesis examined the need for modifications to the current standard hatchery rearing and release methods, determined the effects of commonly used tagging methods and investigated the impacts of river regulation on the survival and behaviour of downstream migrating smolts by applying telemetry techniques. Modifications made to the standard rearing processes noticeably affected the physiology, behaviour and survival of salmon smolts. In addition, the timing of release was shown to be a key factor for the survival of released smolts. Therefore, comprehensive rearing of smolts, and improving current release methods, especially to match the timing of release to the migration window of wild smolts, are high priorities. Observations in semi-natural environments indicated that commonly used tagging methods had only slight effects on the survival of smolts, so they can be freely used to examine smolt performance. However, more information on rearing and stocking processes and tagging methods is still needed to fully verify the present findings in field conditions. Finally, increasing smolt survival during their downstream migration in regulated rivers is an urgent issue, as survival of smolts was found to be six-fold lower within a river section with five hydropower dams than in a corresponding section of a free-flowing river. In future salmon stock rebuilding actions in regulated rivers, safeguarding downstream migration of smolts should be considered as an equally important issue to safeguarding upstream migration of spawners. / Tiivistelmä Lohen kannat ovat taantuneet jokien vesivoimarakentamisen seurauksena. Rakennettujen jokien katkenneita vaellusyhteyksiä on pyritty avaamaan rakentamalla kalateitä ylävirtaan vaeltavia aikuisia lohia varten, mutta alavirtaan vaeltavat kalat ovat jääneet lähes huomiotta. Samanaikaisesti kalankasvatus ja massiiviset poikasistutukset ovat olleet suuressa roolissa lohikantojen ylläpitämisessä. Viime vuosikymmeninä istutustulosten heikkeneminen ja toisaalta yleisemminkin lisääntynyt kiinnostus ympäristöasioita kohtaan ovat lisänneet halukkuutta palauttaa lohikantojen luontaista lisääntymistä rakennettuihin jokiin. Tämän seurauksena kasvatus- ja istutusmenetelmien vaikutukset lohen poikasiin sekä vaelluksen onnistuminen rakennetuilla joilla ovatkin nousseet tärkeiksi tutkimusaiheiksi. Väitöskirjani tavoitteena oli selvittää telemetriatekniikoiden avulla nykyisin käytössä olevien kasvatus- ja istutusmenetelmien, yleisesti käytössä olevien kalamerkintätapojen sekä joen patoamisen vaikutusta lohen vaelluspoikasten jokivaelluksen onnistumiseen. Poikaskasvatuksen aikaiset muutokset vaikuttivat vaelluspoikasten kokoon, fysiologiaan ja käyttäytymiseen. Lisäksi kasvatuskäytäntöjä muuttamalla saatiin tuotettua enemmän luonnonpoikasia muistuttavia istukkaita kuin perinteisellä kasvatusmenetelmällä. Istutusajankohta osoittautui myös tärkeäksi selittäjäksi vaelluspoikasten eloonjäännissä. Kasvatusmenetelmien muuttaminen paremmin luonnonolosuhteita vastaaviksi ja istutusajankohdan sovittaminen luonnonpoikasten luonnolliseen vaellusaikaan olisivat tarpeellisia muutoksia nykyisiin kasvatus- ja istutuskäytäntöihin. Yleisesti käytössä olevat kalamerkintätavat soveltuvat vaelluspoikastutkimuksiin, sillä eri merkintämenetelmien vaikutukset vaelluspoikasten kasvuun ja käyttäytymiseen olivat vähäisiä kokeellisissa olosuhteissa tehdyssä tutkimuksessa. Lisää tietoa kuitenkin tarvitaan kasvatus- ja istutusmenetelmien sekä merkintätapojen vaikutuksista luonnonolosuhteissa. Lohen vaelluspoikasten selviytymistä alasvaelluksesta rakennetuilla joilla tulee parantaa merkittävästi, sillä vapaasti virtaavassa joessa vaelluspoikasten selviytymisen havaittiin olevan kuusinkertainen rakennettuun jokeen verrattuna. Lohikantojen palauttamishankkeissa on palaavien aikuislohien kutuvaelluksen rinnalla kiinnitettävä erityistä huomiota myös vaelluspoikasten jokivaelluksen onnistumiseen.

Det här arbetet innefattar html 5 i avseendet beträffande användning av dess nya taggar/attribut redan nu, även fastän år som 2022 eller 2014 har nämnts av vissa när det gäller utvecklingsspråkets färdigställande. Intresset bakom arbetet uppstod baserat på några olika saker. Först och främst vid studerandet inom kursen "Webbteknisk Introduktion" (som läses i samband med Webbprogrammerare-programmets första år (hösten 2009), hos Linnéuniversitet) där användning av nya taggar, och påståenden avseende att språket redan då kunde börja användas, samt även utvecklingsspråkets namn (eftersom innefattningen av språket består av mycket mer än taggar/attribut) bidrog. Av de nytillkomna taggarna/attributen, har automatiska tester (via Javascript) gentemot de senaste versionerna av webbläsarna (Maj 2011 samt Augusti 2011) bestående av Internet Explorer, Opera, Mozilla Firefox, Apples Safari och Google Chrome genomförts. Operativsystemen webbläsarna körts under består av Mac OS X Server 10.6.7 och Windows 7 Professional (x86). Avseende resultatet visar det att webbläsarna överlag har omkring 80 till 90 % stöd för de nytillkommna taggarna, även fastän alla nya attribut stöds olika i webbläsarna. Slutsatsen av testerna visar därmed att det blir en övervägning i avseendet beträffande vad som kan/bör/skall brukas. / This essay is about html 5 and its tags/attributes can be used right now, even if years like 2022 or 2014 has been talked about for dates when the new language can be completely done. The interest behind the essay arose when I’ve studied in a computer course named “Webbteknisk Introduktion” at the Linnaeus University the autumn of 2009, inside the program: “Webbprogrammerare-programmet”. The course was mainly about html, but at one point we’ve also got to have our hands on the new thing – html 5. It was said at the same point in the course, that html 5 was more or less ready to use. Which caught my interest and wanted to get evidence about it. New tags/attributes have in this work been tested with JavaScript towards the latest web browsers (as of May 2011 and August 2011) consisting of: Internet Explorer, Opera, Mozilla Firefox, Apple Safari and Google Chrome. On top of Mac OS X Server 10.6.7 and Windows 7 Professional (x86). According to the final results, it shows that the tested browsers had about 80 to 90 percent support for the new tags, even if the attributes may vary. The final conclusion about the completed tests would then be that it’s more or less a choice of the things in the language he/she wants, or need to use, and so on.

This thesis is focused on using social applications from practical point of view in a real business environment. In fact, it is focused more on using them than dealing with hypothesis. There are two main objectives covering developing social application add-on and implementation of another type of social application in a company. The first objective is to develop social system, which provides functionality to fulfill team agenda for most of teams created within of scope on University of Economics. The second main objective is to describe important aspects of implementation Wiki system to one of departments in CSOB Company, the Bikipedia Project.

Dada a grande quantidade de conteúdo criado por usuários na Web, uma proposta para ajudar na busca e organização é a criação de sistemas de anotações (tagging systems), normalmente na forma de palavras-chave, extraídas do próprio conteúdo ou sugeridas por visitantes. Esse trabalho aplica um algoritmo de mineração de dados em um banco de dados RDF, contendo instâncias que podem fazer referências à rede Linked Data do DBpedia, para recomendação de tags utilizando as medidas de similaridade taxonômica, relacional e literal de descrições RDF. O banco de dados utilizado é o Arquigrafia, um sistema de banco de dados na Web cujo objetivo é catalogar imagens de projetos arquitetônicos, e que permite que visitantes adicionem tags às imagens. Foram realizados experimentos para a avaliação da qualidade das recomendações de tags realizadas considerando diferentes modelos do Arquigrafia incluindo o modelo estendido do Arquigrafia que faz referências ao DBpedia. Os resultados mostram que a qualidade da recomendação de determinadas tags pode melhorar quando consideramos diferentes modelos (com referências à rede Linked Data do DBpedia) na fase de aprendizado. / Given the huge content created by users in the Web, a way to help in search and organization is the creation of tagging systems, usually in a keyword form (extracted from the Web content or suggested by users). This work applies a data mining algorithm in a RDF database, which contain instances that can reference the DBpedia Linked Data repository, to recommend tags using the taxonomic, relational and literal similarities from RDF descriptions. The database used is the Arquigrafia, a database system available in the Web which goal is to catalog architecture projects, and it allows a user to add tags to images. Experiments were performed to evaluate the quality of the tag recommendations made considering differents models of Arquigrafia\'s database, including an extended model which has references to DBpedia. The results shown that the quality of the recommendations of some tags can be improved when we consider different models (with references to DBpedia Linked Data repository) in the learning phase.

<div>The family Flaviviridae includes important genera such as flavivirus and hepacivirus which comprise significant human pathogens that affect hundreds of millions annually. The understanding of these viruses, the viral life cycle, and pathogenicity is vital when it comes to developing therapeutics. Flavivirus virions undergo major conformational rearrangements during the life cycle, including the assembly and maturation steps. In order to create a reagent to investigate these processes, luminescent reporter viruses have been constructed. Luminescent reporter tags have yet to be incorporated into the structural proteins of dengue virus (DENV) without significantly affecting replication or infectivity and successful tagging would allow for targeted studies examining access to specific structural epitopes. Engineering tags in DENV structural proteins is particularly difficult because most reporter tags involve large insertions which may create steric hindrance and inhibit proper protein folding. However, the reporter system described here, developed by Promega, is much smaller than a full-size luciferase protein. It involves an eleven amino acid subunit (HiBiT) tagged to a viral protein that creates measurable luminescence when incubated with the larger subunit (LgBiT). Using the structure of the virion as a guide, the HiBiT reporter tag was incorporated into the structural region of the DENV genome including sites in capsid (C) as well as the glycoproteins membrane (M) and envelope (E). Resulting recombinant viruses were characterized and tag sites within the C protein membrane anchor as well as the transmembrane domain of M protein were found to tolerate HiBiT insertion and produce infectious particles. The recombinant virus possessing HiBiT in C protein was found to be stable over three rounds of serial passaging while virus containing the M protein tag site was found to be unstable. HiBiT activity of the capsid tagged virus was also found to directly correlate with purified infectious particles, suggesting the capsid membrane anchor may remain associated with the virus even after polyprotein processing. Additionally, insert composition was found to be a key determinant for the production of infectious virus. The lessons learned from engineering HiBiT in the DENV system were then applied to hepatitis C virus (HCV). </div><div>The highly lipophilic and pleiomorphic nature of HCV has made structural studies particularly difficult. However, by constructing multi-tagged reporter viruses containing both HiBiT and various purification tags, researchers will save time and resources in preparation for structural studies which are vital for vaccine development. In this study, HiBiT was incorporated into sites within HCV previously shown to tolerate tags of various sizes. Different insert compositions were engineered within the genome and the construct containing both FLAG and HiBiT tags within the N-terminus of E2 yielded highly infectious and quantifiable, luminescent virus. The recombinant HCV containing FLAG and HiBiT displayed similar peak titer as compared to WT while also demonstrating HiBiT activity. Furthermore, the FLAG peptide was found to be partially surface exposed and capable of being used for virus purification purposes. The multi-tagged reporter virus characterized in this study provides a robust platform for quantification and purification of HCV, two facets of research that are critical for the determination of viral structure via cryo-EM and other imaging techniques. The findings from both the DENV and HCV studies provide a robust foundation for future tagging of viruses within the family Flaviviridae and offer insight on the structural proteins that compose the virion.</div>

The thesis is focused on design of self-location and navigation of small mobile robot inside buildings. It contents a description of collecting and processing data from laser scanner and their application for wall following algorithms. Designed algorithm was tested on real mobile robot. It describes system of visual tags and algorithms for their detection and decoding. Visual tags are used for indication of checkpoints used for navigation of mobile robot. It also describes method for route planning between this checkpoints.

This master’s thesis deals with using Text mining as a method to predict tags of articles. It describes the iterative way of handling big data files, parsing the data, cleaning the data and scoring of terms in article using TF-IDF. It describes in detail the flow of program written in programming language Python 3.4.3. The result of processing more than 1 million articles from Wikipedia database is a dictionary of English terms. By using this dictionary one is capable of determining the most important terms from article in corpus of articles. Relevancy of consequent tags proves the method used in this case.

α-Synuclein (AS) is a small intrinsically disordered protein expressed in neurons and abundantly present in synapses where it is involved in regulation of synaptic vesicle-mediated protein trafficking. Misfolding of AS into amyloid fibrils is a key process in progression of Parkinson's disease (PD), the second most common neurodegenerative disorder which has no cure to date. Inhibition of AS aggregation and blocking of cell-to-cell spreading of AS fibrils is a promising strategy for PD treatment. However, rational design of inhibitors of this type remains complicated due to the lack of thorough knowledge about the mechanisms of aggregation. Therefore, the aim of this thesis was to gain deeper knowledge about AS aggregation and to apply it for developing inhibitors of AS fibrillization. In my work on the mechanisms of AS aggregation, I first determined that the concentration of AS that enables the fibril growth is an order of magnitude lower than the concentration of AS required for initial fibril formation from monomers. I explored fibril disaggregation at AS concentrations below its Kd value, and characterized AS aggregation at low micromolar concentrations. I then investigated how different modifications of AS C-terminus (namely, extensions of various sizes and charges) affect fibril growth and...