Grande parte do sucesso do Google provêm do algoritmo Page Rank, que avalia quantitativamente a importância de cada página na web. Esta ordenação é obtida através do vetor estacionário de uma matriz estocástica específica, utilizando o Método das Potências. A velocidade de convergência deste método será avaliada em detalhe, já que se trata de uma resposta imediata da pesquisa do usuário. Afim de entender as diferentes situações que o modelo pode enfrentar, diversas simulações são apresentadas neste trabalho. Em particular, estamos interessados nos fatores que influenciam a velocidade de convergência. Para tanto, o número de páginas total e de cada conjunto fechado, bem como o número de conjuntos fechados e de nós pendentes foram estudados. / Great part of Google\'s success comes from the Page Rank algorithm, wich quantitatively evaluates the importance of each page on the web. This sort is achieved through a specific stochastic matrix stationary vector, using the Power Method. The convergency speed of this method will be evaluated in details, since this is a imediate response for the user search. In order to understand the diferent situations the model can confront, several simulations are shown in this work. In particular, we are interested in the factors which influences the convergency speed. For that, the total and inside each closed set number of pages and also the closed sets and dangling nodes numbers were studied.

O câncer colorretal (CCR) é a segunda de causa morte relacionada ao câncer, com aproximadamente 500.000 mortes por ano em países desenvolvidos. Os pacientes com doença localmente avançada ou metastática possuem um prognóstico ruim e, desta forma, a detecção precoce é necessária para reduzir a alta mortalidade associada à essa doença. Ainda, os métodos de rastreamento utilizados no momento apresentam boa exatidão, porém são de alto custo, consomem muito tempo e são incômodos para os pacientes. A colonoscopia é o método mais comumente utilizado para a detecção de CCR. Entretanto, apresentam duas limitações importantes: i) necessidade da luz intestinal estar limpa, sem resíduos fecais, o que só é conseguido após um preparo rigoroso, com dieta e laxativos, nos dias que antecedem a realização do exame, e, ii) é examinador-dependente, ou seja, dependem da experiência do profissional em localizar as alterações anatômicas, e ainda da habilidade em selecionar o melhor local para a realização da biópsia. Portanto, o desenvolvimento de um método rápido e sensível para o diagnóstico do câncer colorretal é extremamente importante.<br /> A proposta desta dissertação foi desenvolver um método eficaz para o preparo dos tecidos parafinizados e extração de proteínas para experimentos em eletroforese bidimensional (2DE). Tecidos fixados em formaldeído e embebidos em parafina apresentam como vantagens a preservação da qualidade morfológica, abundância e facilidade de armazenamento, o que permite estudos futuros. Entretanto, para análises proteômicas, a recuperação do material biológico é ineficiente. A partir deste estudo, 156 proteínas foram obtidas de tecidos parafinizados, sendo possível identificar por espectrometria de massas, levando a estudos posteriores para identificação de possíveis biomarcadores relacionados ao CCR. / Colorectal cancer (CRC) is the second cause of cancer-related death, with approximately 500,000 deaths per year in developed countries. Patients with locally advanced or metastatic disease have a poor prognosis and, thus, early detection is needed to reduce the high mortality associated with this disease. Yet, the screening methods used at the time have good accuracy, but are expensive, time consuming and are uncomfortable for patients. Colonoscopy is the most commonly used method for the detection of CRC. However, present two major limitations: i) the need to be clean intestinal lumen without fecal waste, which is achieved only after rigorous preparation with laxatives and diet, in the days before the exam, and ii) it is examiner-dependent, i.e., depends on the professional\'s experience in locating anatomical changes, and even the ability to select the best site for biopsy. Therefore, the development of a rapid and sensitive method for the diagnosis of colorectal cancer is extremely important. The purpose of this dissertation was to develop an effective method for the preparation of tissues and protein extraction experiments for two-dimensional electrophoresis (2DE). Tissues fixed in formaldehyde and embedded in paraffin have the advantage of preserving the morphological quality, abundance and storage facility, which allows for further studies. However, for proteomic analysis, the recovery of biological material is inefficient. From this study, 156 proteins were obtained from paraffinized tissues, and can be identified by mass spectrometry, leading to further studies to identify potential biomarkers related to CCR.

A VDAC é a proteína mais abundante da membrana mitocondrial externa. Possui diversas funções, tais como o controle da troca de metabólitos, através da membrana, e a participação no maquinário apoptótico. Estudamos o interactoma da VDAC com as proteínas mitocondriais neuronais do cérebro bovino e murino, a fim de compreender se a expressão diferenciada da VDAC1 e VDAC2 verificada entre essas células estão associadas às diferenças nas interações da VDAC. Os complexos proteicos foram analisados por 2D Blue Native SDS-PAGE e identificados via MALDI-TOF TOF usando o software Mascot e o banco de dados NCBInr. Foram identificados 27 e 46 spots em murino e bovino, respectivamente. Nós identificamos proteínas solúveis e incorporadas na membrana que não são participantes da fosforilação oxidativa, dentre elas a aldeido deidrogenase e muitas outras constituintes de complexos mitocondriais já conhecidos tão bem como novos, tais como a putative stomatin-like protein 2 complex e a switch-associated protein 70. Nossos resultados mostraram que os neurônios bovinos possuem mais complexos (5) contendo a VDAC do que em ratos (1), os quais indicam uma cinética diferencial de acoplamento e desacoplamento. Interessantemente, a lista contendo as proteínas identificadas inclui algumas proteínas conhecidas ou supostamente localizadas em compartimentos não-mitocondriais, por exemplo, a myc-induced nuclear antigen. O interactoma diferencial da VDAC entre as espécies bovina e murina, evidencia a presença de uma base comum, porém com diferentes ambientes estruturais, as quais podem ser a base da diferença entre os sítios de ligação A e B observados nas diferentes espécies. / The voltage dependent anion channel (VDAC) is the most abundant protein of outer mitochondrial membrane. VDAC controls metabolite exchange through this membrane and the apoptosis machinery. We studied the interactome of VDAC with mitochondrial proteins of neuronal cells from rat and bovine brain. We wished to understand if the differential expression of VDAC1 and VDAC2 verified between these cells was linked to differences in the VDAC interactions. Protein complexes were analyzed by 2D Blue Native SDS-PAGE and were identified by MALDI-TOF TOF using Mascot software against the NCBInr database. Number of 27 e 46 spots were identified from rat and bovine brain, respectively. We identified soluble and membrane-embedded non-OXPHOS proteins, among them aldehyde dehydrogenase, and many as constituents of known mitochondrial complexes as well as novel ones such as putative stomatin-like protein 2 complex and switchassociated protein 70. Our results showed that bovine neurons had more protein complexes (5) containing VDAC than rat cells (1), which indicates a differential kinetics of assembly or disassembly. Interestingly, the identification list included some proteins known or presumed to be localized to nonmitochondrial compartments, for example, myc-induced nuclear antigen. Our results support evidences of differential apoptotic and energetic mechanisms verified in these brains. The differential VDAC interactome between bovine and murine, support evidences of a common base, but whith different structural environment, which may be the basis of the difference between the binding sites A and B observed in these brains.

Bactéria e fungos são as principais fontes de enzimas envolvidas na transformação de compostos chave para o fluxo de carbono em solos de manguezal, caracterizado por alta prevalência de anaerobiose, salinidade e elevado teor de matéria orgânica. A decomposição de plantas ou resíduos de animais nestas condições é muito lenta, devido à pressão seletiva sobre a evolução de enzimas envolvidas nos processos de mineralização de nutrientes. A metagenômica, permiti o acesso a grande maioria da diversidade microbiana no ambiente, por meio da geração de bibliotecas de clones, o que resulta em um cenário promissor para bioprospecção de novas atividades enzimáticas. Neste estudo, foi relatada a descrição e caracterização de uma nova ?-N-acetil-hexosaminidase (EC 3.2.1.52) da família GH3, envolvida na degradação da matéria orgânica em solo de manguezal contaminado por derramamento de óleo localizado no município de Bertioga-SP, por meio de uma triagem de 12.960 clones metagenômicos. O clone positivo para a atividade celulolítica foi sequenciado e um total de 1.175.586 reads foram gerados com tamanho médio de 198 pb. As sequencias foram trimadas com base na qualidade de índice PHRED >= 30.0, e remoção de sequencias do hospedeiro (E. coli) e do vetor (fosmídeo), originando um contig final com 39.586 Kb. Entre as ORF\'s anotadas a partir do contig gerado, uma sequencia de 1.065 nucleotídeos foi identificada como codificante para a enzima ?-N-acetil-hexosaminidase, evidenciando baixa similaridade (32 %) com as demais encontradas no bancos de dados comparativos. A enzima foi expressa e purificada, onde uma banda isolada foi visualizada por SDS-PAGE com massa molecular prevista de 43 kDa. Por fim, as atividades ótimas da enzima (30 °C; pH 5.0; 0.5 M de NaCl; diminuição de atividade após 3hs de incubação) foram caracterizadas por meio do indicador p-nitrophenol (pNP) ligados aos substratos GlNac, GalNac e Glc. A detecção da enzima por meio da metagenômica, evidenciou que os manguezais são reservatórios de novas enzimas com características diferenciadas e altos potenciais de aplicabilidades biotecnológicas / Bacteria and fungi are major sources of enzymes involved in the transformation of key compounds for the carbon fluxes on mangrove soils, characterized by the high prevalence of anaerobiosis salinity and high content of organic matter. The decomposition of plant or animals residues under these conditions is very slow, acting as a selective pressure on the evolution of enzymes involved in the mineralization process of nutrients. Metagenomics has provided access to the vast majority of the microbial diversity in the environment through the generation of fosmid libraries, resulting in a promising scenario for bioprospection enzymatic activities. In this study, we report the description and characterization of a novel ?-N-acetylhexosaminidase (EC 3.2.1.52) of GH3 family, involved in the degradation of organic matter in mangrove soils contaminated by oil spill located in the city of Bertioga-SP through of a screening of 12.960 metagenomic clones. The positive clone for cellulolytic activitie was sequenced and a total of 1.175.586 reads were generated with measuring size 198 bp. The sequences were trimmed based on the index of quality PHRED >= 30.0 and removing the sequences to host (E. coli) and vector (fosmid) resulting in a contig of 39.586 Kb. Between the anoted ORF\'s from generated contig a sequence of 1.065 nucleotides was identified coding for a ?-N-acetylhexosaminidase showing low similatrity (32 %) with the other found in comparatives databases. The enzyme was expressed and purified where an isolated band can be visualized by SDS-PAGE with molecular mass of 43 kDa. Finally, as optimum activity of the enzyme (30 °C; pH 5.0; 0.5M NaCl; decreased activity after 3 h incubation) were characterized by the indicator p-nitrophenol (pNP) linked to the substrates GlNac, GalNac and Glc. The detection of the enzyme through metagenomics indicated that mangroves are reservoirs of novel enzymes with different characteristics and high potential for biotechnological applicability

The purpose of this study is to investigate the influence of different types of web page design on browsers' attitudes, figure out if the information processing styles play the moderating roles, and examine the relationship between attitude towards the web page and visit intention. Three web pages are designed specially for this research. They are created in different types, words only, pictures only, and combination of words and pictures. Respondents are undergraduate students, and answer questionnaires online. SPSS 14 is used to perform statistical analyses. Principal findings are summarized as follows. First, there is no significant difference between high and low NFC individuals about attitude towards the web page when the tourism web page presents in words (all-verbal) design. However, when the web page is only composed of pictures without any written description, NFC individuals, without respect to high or low NFC, show much lower level of attitude towards the web page and no differences appear between them. Second, the statistical analysis shows a higher level of attitude towards the web page is associated to high PFA individuals, compared with low PFA individuals, when the tourism web page presents in pictures (all-visual) design. When the tourism web page presents in words design, high and low PFA individuals show much lower level of attitude towards the web page and no differences appear between them. Third, we find that individuals with high NFC and high PFA are significantly different from the other groups when the tourism web page presents in combination (words and pictures) design. They show higher level of attitude towards the web page, compared with the other processor groups. Lastly, result shows that there is a positive correlation between attitude towards the web page and visit intention. Attitude towards the web page has a significant impact on visit intention, namely, higher level of Awp, then higher level of VI.

Using page rank and semantic information are frequently used techniques in next page prediction systems. In our work, we extend the use of Page Rank algorithm for next page prediction with several navigational attributes, which are size of the page, duration of the page visit and duration of transition (two page visits sequentially), frequency of page and transition. In our model, we define popularity of transitions and pages by using duration information, use it in a relation with page size, and visit frequency factors. By using the popularity value of pages, we bias conventional Page Rank algorithm and model a next page prediction system that produces page recommendations under given top-n value. Moreover, we extract semantic terms from web URLs in order to tag pages semantically. The extracted terms are mapped into web URLs with different level of details in order to find semantically similar pages for next page recommendations. With this tagging, we model another next page prediction method, which uses Semantic Tagging (ST) similarity and exploits PPR values as a supportive method. Moreover, we model a Hybrid Page Rank (HPR) algorithm that uses both Semantic Tagging based approach and Popularity Based Page Rank values of pages together in order to investigate the effect of PPR and ST with equal weights. In addition, we investigate the effect of local (a synopsis of directed web graph) and global (whole directed web graph) modeling on next page prediction accuracy.

The development of metal-tolerance and antibiotic resistance in bacteria may be caused by metals polluting a particular environment. During mining and mineral processing activities, large quantities of metals are deposited into the soil. These high concentrations of metals are evolutionary pressures selecting for microorganisms tolerant to these metals. Metaltolerance maybe conferred to these organisms by mobile genetic elements such as plasmids. This study describes the characteristics of plasmids isolated from various bacteria that displayed an ability to withstand high metal concentrations. The isolated plasmids were individually transformed into Escherichia coli JM109. Transformants were then evaluated for metal-tolerant capabilities using a microdilution approach. Plasmids were then isolated from the transformants and the concentration of the plasmid DNA ranged between 11.75 – 118.06 ng/μl. These plasmids were of the same size as the original ones. This demonstrated that successful transformations with plasmid DNA were conducted. In order to determine the compatibility group, plasmids were subjected to PCR amplification using IncQ, IncP-9 and IncW specific primers. Only the IncW provided positive results. To demonstrate that the plasmids were free of genomic DNA, a 16S rDNA PCR test was included. The plasmids that were positive for IncW PCRs were all negative for the rDNA PCRs. Plasmids were stably inherited and at least three, isolated from three different Gram positive species, belonged to the Inc W group of plasmids. These were originally isolated from Paenibacillus ginsingari, Paenibacillus lautus and Bacillus cereus. Minimum inhibition concentrations (MICs) were carried out to determine the ability of transformed E. coli JM109 to tolerate metals at varying concentrations. Results indicated that transformed E. coli JM109 developed ability to grow in the presence of several heavy metals. Some strains were resistant to high concentrations (+10 mM) of Ni2+/Al3+, Pb2+ and Ba2+. The order of metal resistance was Ni/Al=Pb>Ba>Mn>Cr>Cu>Co=Hg. All the x transformants were sensitive to 1 mM of Co2+ and Hg2+. Moreover, protein profiling was used to determine the impact of plasmids on E. coli JM109. Proteins were extracted from both transformed and un-transformed E. coli JM109 using acetone-SDS protocol and subjected to one-dimensional (1D) and two-dimensional (2D) Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS- PAGE). Transformed E. coli JM109 were grown under the metal stress. One dimension SDS-PAGE illustrated general similarity of the profiles except for two banding positions in the 30 to 35 kDa region where bands were present in the transformants that were grown in the Ni/Al alloy containing media. Twodimensional electrophoresis PAGE analysis showed that some of the proteins were upregulated while others were down-regulated. The largest numbers of proteins were from 15 – 75 kDa. The majority of these proteins had isoelectric points (pI) between 5 and 6. It was concluded that plasmids isolated from various heavy metal-tolerant bacterial species were successfully transformed into E. coli JM109 rendering various new metal-tolerant E. coli JM109 strains. Furthermore, the study showed that metal resistance was due to the presence of the plasmids. Two-dimensional SDS-PAGE resolved more differences in the protein expression profiles. Since the plasmids rendered the E. coli JM109 tolerant to metals tested, it also can be concluded that the change in the protein profiles was due to the effects of the plasmids. Furthermore, plasmids were also re-isolated from the transformants and these plasmids were of the same size as the original ones.. All the plasmids in this study were also stably inherited, a feature associated with IncW plasmids. More detailed genetic characterization of these plasmids is required. Plasmids isolated and characterized in this study may hold biotechnology potential. Such features should be exploited in follow-up experiments. / Thesis (Master of Environmental Sciences)--North-West University, Potchefstroom Campus, 2013.

The development of metal-tolerance and antibiotic resistance in bacteria may be caused by metals polluting a particular environment. During mining and mineral processing activities, large quantities of metals are deposited into the soil. These high concentrations of metals are evolutionary pressures selecting for microorganisms tolerant to these metals. Metaltolerance maybe conferred to these organisms by mobile genetic elements such as plasmids. This study describes the characteristics of plasmids isolated from various bacteria that displayed an ability to withstand high metal concentrations. The isolated plasmids were individually transformed into Escherichia coli JM109. Transformants were then evaluated for metal-tolerant capabilities using a microdilution approach. Plasmids were then isolated from the transformants and the concentration of the plasmid DNA ranged between 11.75 – 118.06 ng/μl. These plasmids were of the same size as the original ones. This demonstrated that successful transformations with plasmid DNA were conducted. In order to determine the compatibility group, plasmids were subjected to PCR amplification using IncQ, IncP-9 and IncW specific primers. Only the IncW provided positive results. To demonstrate that the plasmids were free of genomic DNA, a 16S rDNA PCR test was included. The plasmids that were positive for IncW PCRs were all negative for the rDNA PCRs. Plasmids were stably inherited and at least three, isolated from three different Gram positive species, belonged to the Inc W group of plasmids. These were originally isolated from Paenibacillus ginsingari, Paenibacillus lautus and Bacillus cereus. Minimum inhibition concentrations (MICs) were carried out to determine the ability of transformed E. coli JM109 to tolerate metals at varying concentrations. Results indicated that transformed E. coli JM109 developed ability to grow in the presence of several heavy metals. Some strains were resistant to high concentrations (+10 mM) of Ni2+/Al3+, Pb2+ and Ba2+. The order of metal resistance was Ni/Al=Pb>Ba>Mn>Cr>Cu>Co=Hg. All the x transformants were sensitive to 1 mM of Co2+ and Hg2+. Moreover, protein profiling was used to determine the impact of plasmids on E. coli JM109. Proteins were extracted from both transformed and un-transformed E. coli JM109 using acetone-SDS protocol and subjected to one-dimensional (1D) and two-dimensional (2D) Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS- PAGE). Transformed E. coli JM109 were grown under the metal stress. One dimension SDS-PAGE illustrated general similarity of the profiles except for two banding positions in the 30 to 35 kDa region where bands were present in the transformants that were grown in the Ni/Al alloy containing media. Twodimensional electrophoresis PAGE analysis showed that some of the proteins were upregulated while others were down-regulated. The largest numbers of proteins were from 15 – 75 kDa. The majority of these proteins had isoelectric points (pI) between 5 and 6. It was concluded that plasmids isolated from various heavy metal-tolerant bacterial species were successfully transformed into E. coli JM109 rendering various new metal-tolerant E. coli JM109 strains. Furthermore, the study showed that metal resistance was due to the presence of the plasmids. Two-dimensional SDS-PAGE resolved more differences in the protein expression profiles. Since the plasmids rendered the E. coli JM109 tolerant to metals tested, it also can be concluded that the change in the protein profiles was due to the effects of the plasmids. Furthermore, plasmids were also re-isolated from the transformants and these plasmids were of the same size as the original ones.. All the plasmids in this study were also stably inherited, a feature associated with IncW plasmids. More detailed genetic characterization of these plasmids is required. Plasmids isolated and characterized in this study may hold biotechnology potential. Such features should be exploited in follow-up experiments. / Thesis (Master of Environmental Sciences)--North-West University, Potchefstroom Campus, 2013.

This thesis is focussed on detailed processing of the optimization of web pages for web search engines (SEO). It describes the functionality of full text search engines considering the order of search results. The thesis also presents the most often myths and problems from the field of optimization which are supplemented by the right procedures according to the currently used methods and processes. Further on, the thesis is supplemented by the general outline of the process of optimization which is furthermore used and explained in detail in a practical case study. There is also mentioned the point on the issue of scoring the rate of return in optimiza-tion.

Páginas-objeto são páginas que representam exatamente um objeto inerente do mundo real na web, considerando um domínio específico, e a busca por essas páginas é chamada de busca-objeto. Os motores de busca convencionais (do Inglês, General Search Engine - GSE) conseguem responder, de forma satisfatória, à maioria das consultas realizadas na web atualmente, porém, isso dificilmente ocorre no caso de buscas-objeto, uma vez que, em geral, a quantidade de páginas-objeto recuperadas é bastante limitada. Essa dissertação propõe um novo método para a identificação e a busca de páginas-objeto, denominado OPIS (acrônimo para Object Page Identifying and Searching). O cerne do OPIS está na adoção de técnicas de realimentação de relevância e aprendizagem de máquina na tarefa de classificação, baseada em conteúdo, de páginas-objeto. O OPIS não descarta o uso de GSEs e, ao invés disso, em sua etapa de busca, propõe a integração de um classificador a um GSE, adicionando uma etapa de filtragem ao processo de busca tradicional. Essa abordagem permite que somente páginas identificadas como páginas-objeto sejam recuperadas pelas consultas dos usuários, melhorando, assim, os resultados de buscas-objeto. Experimentos, considerando conjuntos de dados reais, mostram que o OPIS supera o baseline com ganho médio de 47% de precisão média. / Object pages are pages that represent exactly one inherent real-world object on the web, regarding a specific domain, and the search for these pages is named as object search. General Search Engines (GSE) can satisfactorily answer most of the searches performed in the web nowadays, however, this hardly occurs with object search, since, in general, the amount of retrieved object pages is limited. This work proposes a method for both identifying and searching object pages, named OPIS (acronyms to Object Page Identifying and Searching). The kernel of OPIS is to adopt relevance feedback and machine learning techniques in the task of content-based classification of object pages. OPIS does not discard the use of GSEs and, instead, in his search step, proposes the integration of a classifier to a GSE, adding a filtering step to the traditional search process. This simple approach allows that only pages identified as object pages are retrieved by user queries, improving the results for object search. Experiments with real datasets show that OPIS outperforms the baseline with average boost of 47% considering the average precision.