Expression, purification and structural analysis of the Pyrococcus abyssi RNA binding protein PAB1135

<p>Abstract</p> <p>Background</p> <p>The gene coding for the uncharacterized protein PAB1135 in the archaeon <it>Pyrococcus abyssi </it>is in the same operon as the ribonuclease P (RNase P) subunit Rpp30.</p> <p>Findings</p> <p>Here we report the expression, purification and structural analysis of PAB1135. We analyzed the interaction of PAB1135 with RNA and show that it binds efficiently double-stranded RNAs in a non-sequence specific manner. We also performed molecular modeling of the PAB1135 structure using the crystal structure of the protein Af2318 from <it>Archaeoglobus fulgidus </it>(<ext-link ext-link-id="2OGK" ext-link-type="pdb">2OGK</ext-link>) as the template.</p> <p>Conclusions</p> <p>Comparison of this model has lead to the identification of a region in PAB1135 that could be involved in recognizing double-stranded RNA.</p

Usabilidade e experiência do usuário de sistemas de informação: em busca de limites e relações

A Usabilidade e a Experiência do usuário de sistemas de informação são aspectos de grande relevância no processo de desenvolvimento de interfaces digitais. Cada um desses elementos contribui, objetiva e/ou subjetivamente, para a identificação de aspectos fundamentais para a criação de interfaces de sistemas de informação. Nessa perspectiva, o referido estudo tem o objetivo de apresentar reflexões acerca dos possíveis limites e relações entre esses dois elementos. Trata-se de uma pesquisa qualitativa, baseada em pesquisa bibliográfica sobre as temáticas usabilidade e experiência do usuário em bases de dados internacionais (Scopus e Web of Science), sem delimitação de área do conhecimento e recorte temporal, destacando, especialmente, os termos de forma relacional. A partir do referido estudo, foi possível evidenciar a carência de estudos capazes de unificar o significado desses conceitos e, consequentemente promover o avanço e aprofundamento de estudos dessas temáticas. Assim, o estudo evidenciou que usabilidade e a experiência do usuário possuem numerosas características, o que salienta a necessidade de um entendimento mais aprofundado por parte dos pesquisadores interessados nas referidas temáticas, devido à ausência de consenso sobre essas questões

Comparison of Sentiment Analysis and User Ratings in Venue Recommendation

Venue recommendation aims to provide users with venues to visit, taking into account historical visits to venues. Many venue recommendation approaches make use of the provided users’ ratings to elicit the users’ preferences on the venues when making recommendations. In fact, many also consider the users’ ratings as the ground truth for assessing their recommendation performance. However, users are often reported to exhibit inconsistent rating behaviour, leading to less accurate preferences information being collected for the recommendation task. To alleviate this problem, we consider instead the use of the sentiment information collected from comments posted by the users on the venues as a surrogate to the users’ ratings. We experiment with various sentiment analysis classifiers, including the recent neural networks-based sentiment analysers, to examine the effectiveness of replacing users’ ratings with sentiment information. We integrate the sentiment information into the widely used matrix factorization and GeoSoCa multi feature-based venue recommendation models, thereby replacing the users’ ratings with the obtained sentiment scores. Our results, using three Yelp Challenge-based datasets, show that it is indeed possible to effectively replace users’ ratings with sentiment scores when state-of-the-art sentiment classifiers are used. Our findings show that the sentiment scores can provide accurate user preferences information, thereby increasing the prediction accuracy. In addition, our results suggest that a simple binary rating with ‘like’ and ‘dislike’ is a sufficient substitute of the current used multi-rating scales for venue recommendation in location-based social networks

Nanostructured 3D Constructs Based on Chitosan and Chondroitin Sulphate Multilayers for Cartilage Tissue Engineering

Nanostructured three-dimensional constructs combining layer-by-layer technology (LbL) and template leaching were processed and evaluated as possible support structures for cartilage tissue engineering. Multilayered constructs were formed by depositing the polyelectrolytes chitosan (CHT) and chondroitin sulphate (CS) on either bidimensional glass surfaces or 3D packet of paraffin spheres. 2D CHT/CS multi-layered constructs proved to support the attachment and proliferation of bovine chondrocytes (BCH). The technology was transposed to 3D level and CHT/CS multi-layered hierarchical scaffolds were retrieved after paraffin leaching. The obtained nanostructured 3D constructs had a high porosity and water uptake capacity of about 300%. Dynamical mechanical analysis (DMA) showed the viscoelastic nature of the scaffolds. Cellular tests were performed with the culture of BCH and multipotent bone marrow derived stromal cells (hMSCs) up to 21 days in chondrogenic differentiation media. Together with scanning electronic microscopy analysis, viability tests and DNA quantification, our results clearly showed that cells attached, proliferated and were metabolically active over the entire scaffold. Cartilaginous extracellular matrix (ECM) formation was further assessed and results showed that GAG secretion occurred indicating the maintenance of the chondrogenic phenotype and the chondrogenic differentiation of hMSCs

Doppler findings in a rare Coronary Artery Fistula

One of the primary forms of congenital anomalies of the coronary arteries is coronary artery fistula (CAF). It is defined as a direct communication between the coronary artery and any surrounding cardiac chamber or vascular structure, which bypasses the myocardial capillary bed. We present a newborn baby with a large coronary artery fistula connecting the left anterior descending (LAD) artery to the left ventricular (LV) apex. Associated cardiac abnormalities were found: a ventricular septal defect (diameter 4 mm), a patent foramen ovale as well as trivial tricuspid and mitral regurgitation. Here we demonstrate the echocardiograms of an extremely rare form of CAF diagnosed within the first days of postnatal life

A Rationale for Schistosomiasis Control in Elementary Schools of the Rainforest Zone of Pernambuco, Brazil

In 2001, a World Health Assembly resolution urged member states to ensure treatment against schistosomiasis and soil-transmitted helminthiasis in endemic areas with the goal of attaining a minimum target of at least 75% of all school-aged children by 2010. In the highly endemic Rainforest Zone of Pernambuco (ZMP), northeast Brazil, the Schistosomiasis Control Program has registered a cumulative coverage of only 20% of the population at risk, which jeopardizes the accomplishment of the minimum target for that area. Demographic and parasitological data from a representative municipality of the ZMP provide evidence that the current, community-based approach to control can be complemented with school-based actions. In the most troubled municipalities, individual diagnosis and treatment could be focused on school-aged children rather than whole populations without compromising the principles of the primary health care system. Local health and education teams should be encouraged to include school-based interventions to scale up coverage and achieve a rapid impact on infection

Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis

<p>Abstract</p> <p>Background</p> <p>Affymetrix GeneChips and Illumina BeadArrays are the most widely used commercial single channel gene expression microarrays. Public data repositories are an extremely valuable resource, providing array-derived gene expression measurements from many thousands of experiments. Unfortunately many of these studies are underpowered and it is desirable to improve power by combining data from more than one study; we sought to determine whether platform-specific bias precludes direct integration of probe intensity signals for combined reanalysis.</p> <p>Results</p> <p>Using Affymetrix and Illumina data from the microarray quality control project, from our own clinical samples, and from additional publicly available datasets we evaluated several approaches to directly integrate intensity level expression data from the two platforms. After mapping probe sequences to Ensembl genes we demonstrate that, ComBat and cross platform normalisation (XPN), significantly outperform mean-centering and distance-weighted discrimination (DWD) in terms of minimising inter-platform variance. In particular we observed that DWD, a popular method used in a number of previous studies, removed systematic bias at the expense of genuine biological variability, potentially reducing legitimate biological differences from integrated datasets.</p> <p>Conclusion</p> <p>Normalised and batch-corrected intensity-level data from Affymetrix and Illumina microarrays can be directly combined to generate biologically meaningful results with improved statistical power for robust, integrated reanalysis.</p