Modelos de fragilidade com aplicações em analise de ligação

Orientador : Hildete Prisco PinheiroDissertação (mestrado) - Universidade Estadual de Campinas. Instituto de Matematica, Estatistica e Computação CientificaMestradoMestre em Estatístic

Rqc: A Bioconductor Package for Quality Control of High-Throughput Sequencing Data

As sequencing costs drop with the constant improvements in the field, next-generation sequencing becomes one of the most used technologies in biological research. Sequencing technology allows the detailed characterization of events at the molecular level, including gene expression, genomic sequence and structural variants. Such experiments result in billions of sequenced nucleotides and each one of them is associated to a quality score. Several software tools allow the quality assessment of whole experiments. However, users need to switch between software environments to perform all steps of data analysis, adding an extra layer of complexity to the data analysis workflow. We developed Rqc, a Bioconductor package designed to assist the analyst during assessment of high-throughput sequencing data quality. The package uses parallel computing strategies to optimize large data sets processing, regardless of the sequencing platform. We created new data quality visualization strategies by using established analytical procedures. That improves the ability of identifying patterns that may affect downstream procedures, including undesired sources technical variability. The software provides a framework for writing customized reports that integrates seamlessly to the R/Bioconductor environment, including publication-ready images. The package also offers an interactive tool to generate quality reports dynamically. Rqc is implemented in R and it is freely available through the Bioconductor project (https://bioconductor.org/packages/Rqc/) for Windows, Linux and Mac OS X operating systems

Identification of common and divergent gene expression signatures in patients with venous and arterial thrombosis using data from public repositories.

STRENGTHS AND LIMITATIONS OF THIS STUDY:Our results represent the first comparison of venous and arterial thrombosis at the transcriptomic level.Our main result was the demonstration that immunothrombosis pathways are important to the pathophysiology of these conditions, also at the transcriptomic level.A specific signature for venous and arterial thrombosis was described, and validated in independent cohorts.The limited number of public repositories with gene expression data from patients with venous thromboembolism limits the representation of these patients in our analyses.In order to gather a meaningful number of studies with gene expression data we had to include patients in different time-points since the index thrombotic event, which might have increased the heterogeneity of our population

Cyclooxygenase-1 as a potential therapeutic target for seizure suppression: evidences from zebrafish pentylenetetrazole-seizure model

Cyclooxygenases (COX) -1 and -2 are isoenzymes that catalyze the conversion of arachidonic acid into prostaglandins (PGs). COX-2 and PGs are rapidly increased following seizures and are known to play important roles in the neuroinflammatory process. COX-2 isoform has been predominantly explored as the most suitable target for pharmacological intervention in epilepsy studies while COX-1 remains poorly investigated. In the present study, we evaluated the effects of selective cyclooxygenases (COX) -1 inhibitor or selective COX-2 inhibitor on seizure suppression in the zebrafish pentylenetetrazole (PTZ)-seizure model. Zebrafish larvae were incubated in 5 μM of SC-236 for 24 hours or 2.8 μM of SC-560 for 30 minutes, followed by exposure to 15 mM PTZ for 60 min. Real-time quantitative PCR analysis was carried out to investigate transcription levels of cox1 (ptgs1), as well as to determine cfos levels, used as a marker for neuronal activity. Effects of selective COX-2 or COX-1 inhibitors on locomotor activity response (velocity and distance moved) during PTZ exposure were evaluated using the Danio Vision video-tracking system. Our results showed an inducible expression of the cox1 gene after 60 minutes of PTZ exposure. Cox1 mRNA levels were upregulated compared with the control group. We found that COX-2 inhibition treatment had no effect on zebrafish PTZ-induced seizures. On the other hand, COX-1 inhibition significantly attenuated PTZ-induced increase of locomotor activity and reduced the c-fos mRNA expression. These findings suggest that COX-1 inhibition rather than COX-2 has positive effects on seizure suppression in the zebrafish PTZ-seizure model

Data from: Geographical and intrapopulation variation in the diet of a threatened marine predator, Pontoporia blainvillei (Cetacea)

Diet variation can occur in geographically structured populations due to variation in prey availability. Within locations, diet may vary due to effects of season, sex, age, and individual. Nevertheless, these sources of variation are seldom considered together in dietary studies. Major efforts are underway to investigate population and ecological traits of marine organisms to set guidelines for conservation and management. Examining diet variation is a major concern when developing conservation guidelines for threatened species, especially for marine predators whose prey availability can be reduced by commercial fisheries. We analyzed diet variation at the geographical and intrapopulation levels for detecting stocks of the franciscana dolphin (Pontoporia blainvillei) within São Paulo State coast. We analyzed samples of stomach contents of individuals incidentally caught by artisanal fisheries. We investigated the geographical (Northern, Central, and Southern regions of São Paulo State coast, Brazil) and intrapopulation effects of season, sex, and age. We used the leave-one-out cross validation method to test for significance of the proportional similarity index, which measures the overlap between diet compositions. We found diet variation in the franciscana dolphin across different levels, from the geographical to the individual level, including the effects of season, sex, and age. Diet variation as a function of age suggests an ontogenetic diet shift for the species. Our findings indicate that ecological processes within local stocks must drive management actions at local geographic scales. Evidence for ecological differences between franciscana stocks is of great significance for the conservation of this threatened species

Franciscana dolphin diet

Samples of franciscana dolphins (n = 58) incidentally caught by artisanal gillnet fisheries from the Northern (n = 11, municipalities of Ubatuba, Ilhabela, Caraguatatuba, and São Sebastião), Central (n = 40, municipalities of Bertioga, Guarujá, Santos, São Vicente, Praia Grande, Mongaguá, Itanhaém, and Peruíbe), and Southern regions (n = 7, Iguape, Ilha Comprida and Cananéia) of the São Paulo State coast in Brazil. Franciscana dolphins were classified into juveniles (n = 8), subadults (n = 18) or adults (n = 32) according to total length. For females (n = 34), juveniles were < 90 cm, subadults were > 90 cm and < 119 cm, and adults were > 119 cm. For males (n = 24), juveniles were < 90 cm, subadults were > 90 cm and < 107 cm, and adults were > 107 cm. The detailed distribution of specimens of franciscana dolphin bycaught according to region, season, sex, and age is shown in the table