Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Assessment of Preclinical Learning on Oral Surgery Using Three Instructional Strategies

The purpose of this investigation was to evaluate three learning methods for teaching basic oral surgical skills Thirty predoctoral dental students without any surgical knowledge or previous surgical experience were divided Into three groups (n=10 each) according to instructional strategy Group 1, active learning Group 2, text reading only, and Group 3, text reading and video demonstration After instruction, the apprentices were allowed to practice incision dissection and suture maneuvers in a bench learning model During the students' performance, a structured practice evaluation test to account for correct or incorrect maneuvers was applied by trained observers Evaluation tests were repeated after thirty and sixty days Data from resulting scores between groups and periods were considered for statistical analysis (ANOVA and Tukey Kramer) with a significant level of a=0 05 Results showed that the active learning group presented the significantly best learning outcomes related to immediate assimilation of surgical procedures compared to other groups All groups results were similar after sixty days of the first practice Assessment tests were fundamental to evaluate teaching strategies and allowed theoretical and proficiency learning feedbacks Repetition and interactive practice promoted retention of knowledge on basic oral surgical skills

Evaluation of flow patterns and elongated bubble characteristics during the flow boiling of halocarbon refrigerants in a micro-scale channel

In the present study, quasi-diabatic two-phase flow pattern visualizations and measurements of elongated bubble velocity, frequency and length were performed. The tests were run for R134a and R245fa evaporating in a stainless steel tube with diameter of 2.32 mm, mass velocities ranging from 50 to 600 kg/m(2) s and saturation temperatures of 22 degrees C, 31 degrees C and 41 degrees C. The tube was heated by applying a direct DC current to its surface. Images from a high-speed video-camera (8000 frames/s) obtained through a transparent tube just downstream the heated sections were used to identify the following flow patterns: bubbly, elongated bubbles, churn and annular flows. The visualized flow patterns were compared against the predictions provided by Barnea et al. (1983) [1], Felcar et al. (2007) [10], Revellin and Thome (2007) [3] and Ong and Thome (2009) [11]. From this comparison, it was found that the methods proposed by Felcar et al. (2007) [10] and Ong and Thome (2009) [1] predicted relatively well the present database. Additionally, elongated bubble velocities, frequencies and lengths were determined based on the analysis of high-speed videos. Results suggested that the elongated bubble velocity depends on mass velocity, vapor quality and saturation temperature. The bubble velocity increases with increasing mass velocity and vapor quality and decreases with increasing saturation temperature. Additionally, bubble velocity was correlated as linear functions of the two-phase superficial velocity. (C) 2010 Elsevier Inc. All rights reserved.

Investigation of Normal Force and Moment Coefficients for an AUV at Nonlinear Angle of Attack and Sideslip Range

This paper presents a comparative study of computational fluid dynamics (CFD) and analytical and semiempirical (ASE) methods applied to the prediction of the normal force and moment coefficients of an autonomous underwater vehicle (AUV). Both methods are applied to the. bare hull of the vehicle and to the body-hydroplane combination. The results are validated through experiments in a towing tank. It is shown that the CFD approach allows for a good prediction of the coefficients over the range of angles of attack considered. In contrast with the traditional ASE formulations used in naval and aircraft fields, an improved methodology is introduced that takes advantage of the qualitative information obtained from CFD flow visualizations.

The effect of the dibenzylbutyrolactolic lignan (-)-cubebin on doxorubicin mutagenicity and recombinogenicity in wing somatic cells of Drosophila melanogaster

The dibenzylbutyrolactolic lignan (-)-cubebin was isolated from dry seeds of Piper cubeba L (Piperaceae). (-)-Cubebin possesses anti-inflammatory, analgesic and antimicrobial activities. Doxorubicin (DXR) is a topoisomerase-interactive agent that may induce single- and double-strand breaks, intercalate into the DNA and generate oxygen free radicals. Here, we examine the mutagenicity and recombinogenicity of different concentrations of (-)-cubebin alone or in combination with DXR using standard (ST) and high bioactivation (HB) crosses of the wing Somatic Mutation And Recombination Test in Drosophila melanogaster. The results from both crosses were rather similar. (-)-Cubebin alone did not induce mutation or recombination. At lower concentrations, (-)-cubebin statistically reduced the frequencies of DXR-induced mutant spots. At higher concentrations, however, (-)-cubebin was found to potentiate the effects of DXR, leading to either an increase in the production of mutant spots or a reduction, due to toxicity. These results suggest that depending on the concentration, (-)-cubebin may interact with the enzymatic system that catalyzes the metabolic detoxification of DXR, inhibiting the activity of mitochondria! complex 1 and thereby scavenging free radicals. Recombination was found to be the major effect of the treatments with DXR alone. The combined treatments reduced DXR mutagenicity but did not affect DXR recombinogenicity. (C) 2011 Elsevier Ltd. All rights reserved.

Distance Education in Another Register: Uses and Appropriation of Technologies in Teacher Education

The article explores the relationships between distance education, information and communication technologies and teacher education. Its focus is on the interactive media and its uses in an in-service teacher education program, in Brazil, and on the ways the teachers used the technologies doing their own appropriateness. It departs from the presuppositions of the society of knowledge, that is, the close relationships between new technologies, continuing professional development and social inclusion, arguing that this paradigm is an ideological discourse. The article shows how the teachers have used the technologies in creative ways, calling the attention to the importance of this teachers` abilities as a basic skill to facing the challenges of the society of knowledge itself.

Using multidimensional projection techniques for reaching a high distinguishing ability in biosensing

Recent advances in the control of molecular engineering architectures have allowed unprecedented ability of molecular recognition in biosensing, with a promising impact for clinical diagnosis and environment control. The availability of large amounts of data from electrical, optical, or electrochemical measurements requires, however, sophisticated data treatment in order to optimize sensing performance. In this study, we show how an information visualization system based on projections, referred to as Projection Explorer (PEx), can be used to achieve high performance for biosensors made with nanostructured films containing immobilized antigens. As a proof of concept, various visualizations were obtained with impedance spectroscopy data from an array of sensors whose electrical response could be specific toward a given antibody (analyte) owing to molecular recognition processes. In addition to discussing the distinct methods for projection and normalization of the data, we demonstrate that an excellent distinction can be made between real samples tested positive for Chagas disease and Leishmaniasis, which could not be achieved with conventional statistical methods. Such high performance probably arose from the possibility of treating the data in the whole frequency range. Through a systematic analysis, it was inferred that Sammon`s mapping with standardization to normalize the data gives the best results, where distinction could be made of blood serum samples containing 10(-7) mg/mL of the antibody. The method inherent in PEx and the procedures for analyzing the impedance data are entirely generic and can be extended to optimize any type of sensor or biosensor.

Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial

Background Homozygous familial hypercholesterolaemia is a rare genetic disorder in which both LDL-receptor alleles are defective, resulting in very high concentrations of LDL cholesterol in plasma and premature coronary artery disease. This study investigated whether an antisense inhibitor of apolipoprotein B synthesis, mipomersen, is effective and safe as an adjunctive agent to lower LDL cholesterol concentrations in patients with this disease. Methods This randomised, double-blind, placebo-controlled, phase 3 study was undertaken in nine lipid clinics in seven countries. Patients aged 12 years and older with clinical diagnosis or genetic confirmation of homozygous familial hypercholesterolaemia, who were already receiving the maximum tolerated dose of a lipid-lowering drug, were randomly assigned to mipomersen 200 mg subcutaneously every week or placebo for 26 weeks. Randomisation was computer generated and stratified by weight (<50 kg vs >= 50 kg) in a centralised blocked randomisation, implemented with a computerised interactive voice response system. All clinical, medical, and pharmacy personnel, and patients were masked to treatment allocation. The primary endpoint was percentage change in LDL cholesterol concentration from baseline. Analysis was by intention to treat. This trial is registered with ClinicalTrials.gov, number NCT00607373. Findings 34 patients were assigned to mipomersen and 17 to placebo; data for all patients were analysed. 45 patients completed the 26-week treatment period (28 mipomersen, 17 placebo). Mean concentrations of LDL cholesterol at baseline were 11.4 mmol/L (SD 3.6) in the mipomersen group and 10.4 mmol/L (3.7) in the placebo group. The mean percentage change in LDL cholesterol concentration was significantly greater with mipomersen (-24.7%, 95% CI 31.6 to 17.7) than with placebo (-3.3%, 12.1 to 5.5; p=0.0003). The most common adverse events were injection-site reactions (26 [76%] patients in mipomersen group vs four [24%] in placebo group). Four (12%) patients in the mipomersen group but none in the placebo group had increases in concentrations of alanine aminotransferase of three times or more the upper limit of normal. Interpretation Inhibition of apolipoprotein B synthesis by mipomersen represents a novel, effective therapy to reduce LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia who are already receiving lipid-lowering drugs, including high-dose statins.

Risk Factors for Visual Field Progression in Treated Glaucoma

Objective: To determine intraocular pressure (IOP)-dependent and IOP-independent variables associated with visual field (VF) progression in treated glaucoma. Design: Retrospective cohort of the Glaucoma Progression Study. Methods: Consecutive, treated glaucoma patients with repeatable VF loss who had 8 or more VF examinations of either eye, using the Swedish Interactive Threshold Algorithm (24-2 SITA-Standard, Humphrey Field Analyzer II; Carl Zeiss Meditec, Inc, Dublin, California), during the period between January 1999 and September 2009 were included. Visual field progression was evaluated using automated pointwise linear regression. Evaluated data included age, sex, race, central corneal thickness, baseline VF mean deviation, mean follow-up IOP, peak IOP, IOP fluctuation, a detected disc hemorrhage, and presence of beta-zone parapapillary atrophy. Results: We selected 587 eyes of 587 patients (mean [SD] age, 64.9 [13.0] years). The mean (SD) number of VFs was 11.1 (3.0), spanning a mean (SD) of 6.4 (1.7) years. In the univariable model, older age (odds ratio [OR], 1.19 per decade; P = .01), baseline diagnosis of exfoliation syndrome (OR, 1.79; P = .01), decreased central corneal thickness (OR, 1.38 per 40 mu m thinner; P < .01), a detected disc hemorrhage (OR, 2.31; P < .01), presence of beta-zone parapapillary atrophy (OR, 2.17; P < .01), and all IOP parameters (mean follow-up, peak, and fluctuation; P < .01) were associated with increased risk of VF progression. In the multivariable model, peak IOP (OR, 1.13; P < .01), thinner central corneal thickness (OR, 1.45 per 40 mu m thinner; P < .01), a detected disc hemorrhage (OR, 2.59; P < .01), and presence of beta-zone parapapillary atrophy (OR, 2.38; P < .01) were associated with VF progression. Conclusions: IOP-dependent and IOP-independent risk factors affect disease progression in treated glaucoma. Peak IOP is a better predictor of progression than is IOP mean or fluctuation.

Alcohol and tobacco, and the risk of cancers of the upper aerodigestive tract in Latin America: a case-control study

Cancers of the upper aerodigestive tract (UADT; including oral cavity, pharynx, larynx and oesophagus) have high incidence rates all over the world, and they are especially frequent in some parts of Latin America. However, the data on the role of the major risk factors in these areas are still limited. We have evaluated the role of alcohol and tobacco consumption, based on 2,252 upper aerodigestive squamous-cell carcinoma cases and 1,707 controls from seven centres in Brazil, Argentina, and Cuba. We show that alcohol drinkers have a risk of UADT cancers that is up to five times higher than that of never-drinkers. A very strong effect of aperitifs and spirits as compared to other alcohol types was observed, with the ORs reaching 12.76 (CI 5.37-30.32) for oesophagus. Tobacco smokers were up to six times more likely to develop aerodigestive cancers than never-smokers, with the ORs reaching 11.14 (7.72-16.08) among current smokers for hypopharynx and larynx cancer. There was a trend for a decrease in risk after quitting alcohol drinking or tobacco smoking for all sites. The interactive effect of alcohol and tobacco was more than multiplicative. In this study, 65% of all UADT cases were attributable to a combined effect of alcohol and tobacco use. In this largest study on UADT cancer in Latin America, we have shown for the first time that a prevailing majority of UADT cancer cases is due to a combined effect of alcohol and tobacco use and could be prevented by quitting the use of either of these two agents.

A university extension course in leprosy: telemedicine in the Amazon for primary healthcare

There is a high prevalence of leprosy in the Amazon region of Brazil. We have developed a distance education course in leprosy for training staff of the Family Health Teams (FHTs). The course was made available through a web portal. Tele-educational resources were mediated by professors and coordinators, and included the use of theoretical content available through the web, discussion lists, Internet chat, activity diaries, 3-D video animations (Virtual Human on Leprosy), classes in video streaming and case simulation. Sixty-five FHT staff members were enrolled. All of them completed the course and 47 participants received a certificate at the end of the course. At the end of the course, 48 course-evaluation questionnaires were answered. A total of 47 participants (98%) considered the course as excellent. The results demonstrate the feasibility of an interactive, tele-education model as an educational resource for staff in isolated regions. Improvements in diagnostic skills should increase diagnostic suspicion of leprosy and may contribute to early detection.

Cybertutor: a teaching tool in Dermatology

It was developed a teaching tool in Dermatology for undergraduate medical students, using an interactive website, the Cybertutor. Clinical cases, lectures and updated bibliography were selected. Photographies of dermatological lesions were taken from ambulatory patients. The topics of the lectures were based on the current curriculum of the Federal University of Rio Grande do Sul. The Cybertutor is a dynamic and modern teaching tool, allowing constant innovation.