Showing papers by "Federal University of Rio de Janeiro published in 2010"

Preexposure Chemoprophylaxis for HIV Prevention in Men Who Have Sex with Men

Abstract: The study subjects were followed for 3324 person-years (median, 1.2 years; maximum, 2.8 years). Of these subjects, 10 were found to have been infected with HIV at en rollment, and 100 became infected during follow-up (36 in the FTC–TDF group and 64 in the placebo group), indicating a 44% reduction in the incidence of HIV (95% confidence interval, 15 to 63; P = 0.005). In the FTC–TDF group, the study drug was detected in 22 of 43 of seronegative subjects (51%) and in 3 of 34 HIV-infected subjects (9%) (P<0.001). Nausea was reported more frequently during the first 4 weeks in the FTC–TDF group than in the placebo group (P<0.001). The two groups had similar rates of serious adverse events (P = 0.57). Conclusions Oral FTC–TDF provided protection against the acquisition of HIV infection among the subjects. Detectable blood levels strongly correlated with the prophylactic effect. (Funded by the National Institutes of Health and the Bill and Melinda Gates Foun dation; ClinicalTrials.gov number, NCT00458393.)

The ATLAS Simulation Infrastructure

Abstract: The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.

Evolution of the Raman spectra from single-, few-, and many-layer graphene with increasing disorder

Abstract: We report on the micro-Raman spectroscopy of monolayer, bilayer, trilayer, and many layers of graphene (graphite) bombarded by low-energy argon ions with different doses. The evolution of peak frequencies, intensities, linewidths, and areas of the main Raman bands of graphene is analyzed as function of the distance between defects and number of layers. We describe the disorder-induced frequency shifts and the increase in the linewidth of the Raman bands by means of a spatial-correlation model. Also, the evolution of the relative areas ${A}_{D}/{A}_{G}$, ${A}_{{D}^{\ensuremath{'}}}/{A}_{G}$, and ${A}_{{G}^{\ensuremath{'}}}/{A}_{G}$ is described by a phenomenological model. The present results can be used to fully characterize disorder in graphene systems.

Virus-like particles in vaccine development

Abstract: Virus-like particles (VLPs) are multiprotein structures that mimic the organization and conformation of authentic native viruses but lack the viral genome, potentially yielding safer and cheaper vaccine candidates. A handful of prophylactic VLP-based vaccines is currently commercialized worldwide: GlaxoSmithKline's Engerix (hepatitis B virus) and Cervarix (human papillomavirus), and Merck and Co., Inc.'s Recombivax HB (hepatitis B virus) and Gardasil (human papillomavirus) are some examples. Other VLP-based vaccine candidates are in clinical trials or undergoing preclinical evaluation, such as, influenza virus, parvovirus, Norwalk and various chimeric VLPs. Many others are still restricted to small-scale fundamental research, despite their success in preclinical tests. This article focuses on the essential role of VLP technology in new-generation vaccines against prevalent and emergent diseases. The implications of large-scale VLP production are discussed in the context of process control, monitorization and optimization. The main up- and down-stream technical challenges are identified and discussed accordingly. Successful VLP-based vaccine blockbusters are briefly presented concomitantly with the latest results from clinical trials and the recent developments in chimeric VLP-based technology for either therapeutic or prophylactic vaccination.

Observation of a centrality-dependent dijet asymmetry in lead-lead collisions at √sNN=2.76 Tev with the ATLAS detector at the LHC

Abstract: By using the ATLAS detector, observations have been made of a centrality-dependent dijet asymmetry in the collisions of lead ions at the Large Hadron Collider. In a sample of lead-lead events with a per-nucleon center of mass energy of 2.76 TeV, selected with a minimum bias trigger, jets are reconstructed in fine-grained, longitudinally segmented electromagnetic and hadronic calorimeters. The transverse energies of dijets in opposite hemispheres are observed to become systematically more unbalanced with increasing event centrality leading to a large number of events which contain highly asymmetric dijets. This is the first observation of an enhancement of events with such large dijet asymmetries, not observed in proton-proton collisions, which may point to an interpretation in terms of strong jet energy loss in a hot, dense medium.

Effectiveness and safety of bronchial thermoplasty in the treatment of severe asthma: A multicenter, randomized, double-blind, sham-controlled clinical trial

Abstract: RATIONALE: Bronchial thermoplasty (BT) is a bronchoscopic procedure in which controlled thermal energy is applied to the airway wall to decrease smooth muscle. OBJECTIVES: To evaluate the effectiveness and safety of BT versus a sham procedure in subjects with severe asthma who remain symptomatic despite treatment with high-dose inhaled corticosteroids and long-acting beta(2)-agonists. METHODS: A total of 288 adult subjects (Intent-to-Treat [ITT]) randomized to BT or sham control underwent three bronchoscopy procedures. Primary outcome was the difference in Asthma Quality of Life Questionnaire (AQLQ) scores from baseline to average of 6, 9, and 12 months (integrated AQLQ). Adverse events and health care use were collected to assess safety. Statistical design and analysis of the primary endpoint was Bayesian. Target posterior probability of superiority (PPS) of BT over sham was 95%, except for the primary endpoint (96.4%). MEASUREMENTS AND MAIN RESULTS: The improvement from baseline in the integrated AQLQ score was superior in the BT group compared with sham (BT, 1.35 +/- 1.10; sham, 1.16 +/- 1.23 [PPS, 96.0% ITT and 97.9% per protocol]). Seventy-nine percent of BT and 64% of sham subjects achieved changes in AQLQ of 0.5 or greater (PPS, 99.6%). Six percent more BT subjects were hospitalized in the treatment period (up to 6 wk after BT). In the posttreatment period (6-52 wk after BT), the BT group experienced fewer severe exacerbations, emergency department (ED) visits, and days missed from work/school compared with the sham group (PPS, 95.5, 99.9, and 99.3%, respectively). CONCLUSIONS: BT in subjects with severe asthma improves asthma-specific quality of life with a reduction in severe exacerbations and healthcare use in the posttreatment period. Clinical trial registered with www.clinialtrials.gov (NCT00231114).

Chagas disease: a new worldwide challenge

Abstract: Endemic Chagas disease began as a neglected disease of poor, rural and forgotten populations. Its spread from Latin America to non-endemic countries is a new worldwide challenge, say Jose Rodrigues Coura and Pedro Albajar Vinas.

Does the type of matrix matter? A quantitative review of the evidence

Abstract: It has been increasingly recognized that the type of matrix surrounding habitat patches can affect biodiversity in landscapes, but there were only qualitative reviews of the subject focused on particular taxonomic groups. We present a quantitative review of studies from 1985 to 2008 that compared effects of different matrix types on individuals, populations and communities. We compiled 104 studies, most on animals, covering a broad range of landscape types and spatial scales. Most studies were empirical, focused on individuals and communities, and evaluated abundance/richness in the patch as the dependent variable. The type of matrix surrounding habitat patches influenced the studied parameters in 95% of the studies, but such effects were overall smaller compared to patch size or isolation effects. Matrix type effects were strongly species-specific, with different species responding differently to matrix type in 96% of studies comparing species or group of species. In 88% of studies, matrix types more similar in structure to the patch had higher quality for the studied organisms from the point of view of functional connectivity. Overall, the type of matrix is important, but patch size and isolation are the main determinants of ecological parameters in landscapes. Matrix quality generally increases with increasing structural similarity with habitat patches, a pattern that could be used as a general guideline for management of the matrix in fragmented landscapes.

A morphological classification capturing functional variation in phytoplankton

Abstract: 1. A logical way of distinguishing functional groups of phytoplankton is to cluster species according to their functional traits, such as growth rate and nutrient assimilation constants. However, data for such an approach are lacking for the vast majority of the species. 2. In this study, we show that a classification based on simple morphological traits may capture much of the variability in functional properties among the phytoplankton. We used information on more than 700 freshwater species, from more than 200 lakes situated in climate zones ranging from subpolar to tropical. 3. Morphological characteristics correlated well with functional properties, such as growth rate and sinking rate, and also with the population size and biomass attained in the field. This suggests that morphology is a good predictor of the functional characteristics of species. 4. Cluster analysis was used to define seven species groups based on morphology. Although some of the clusters are taxonomically homogeneous, others include species of several separate divisions. Functional traits (not used for the classification) differed significantly among the clusters, suggesting that the clusters may indeed represent meaningful functional groups. 5. Advantages of our morphological approach to classification include its objectivity, its independence from taxonomic affiliations, and the relative ease of its application to the majority of species for which physiological traits are unknown and are not readily determined.

Using pedotransfer functions to estimate the van Genuchten-Mualem Soil Hydraulic Properties: a review.

Abstract: We reviewed the use of the van Genuchten–Mualem (VGM) model to parameterize soil hydraulic properties and for developing pedotransfer functions (PTFs). Analysis of literature data showed that the moisture retention characteristic (MRC) parameterization by setting shape parameters m = 1 − 1/ n produced the largest deviations between fitted and measured water contents for pressure head values between 330 (log10 pressure head [pF] 2.5) and 2500 cm (pF 3.4). The Schaap–van Genuchten model performed best in describing the unsaturated hydraulic conductivity, K . The classical VGM model using fixed parameters produced increasingly higher root mean squared residual, RMSR, values when the soil became drier. The most accurate PTFs for estimating the MRC were obtained when using textural properties, bulk density, soil organic matter, and soil moisture content. The RMSR values for these PTFs approached those of the direct fit, thus suggesting a need to improve both PTFs and the MRC parameterization. Inclusion of the soil water content in the PTFs for K only marginally improved their prediction compared with the PTFs that used only textural properties and bulk density. Including soil organic matter to predict K had more effect on the prediction than including soil moisture. To advance the development of PTFs, we advocate the establishment of databases of soil hydraulic properties that (i) are derived from standardized and harmonized measurement procedures, (ii) contain new predictors such as soil structural properties, and (iii) allow the development of time-dependent PTFs. Successful use of structural properties in PTFs will require parameterizations that account for the effect of structural properties on the soil hydraulic functions.

The Fluorescence Detector of the Pierre Auger Observatory

Abstract: The Pierre Auger Observatory is a hybrid detector for ultra-high energy cosmic rays. It combines a surface array to measure secondary particles at ground level together with a fluorescence detector to measure the development of air showers in the atmosphere above the array. The fluorescence detector comprises 24 large telescopes specialized for measuring the nitrogen fluorescence caused by charged particles of cosmic ray air showers. In this paper we describe the components of the fluorescence detector including its optical system, the design of the camera, the electronics, and the systems for relative and absolute calibration. We also discuss the operation and the monitoring of the detector. Finally, we evaluate the detector performance and precision of shower reconstructions.

Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

Abstract: Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes.

Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish

Abstract: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.

Water ice and organics on the surface of the asteroid 24 Themis

Abstract: Two groups, both using the NASA Infrared Telescope Facility (IRTF) on Mauna Kea in Hawaii but independently, have obtained infrared spectra of the main-belt asteroid 24 Themis consistent with the widespread presence of a frosty coating containing water ice and organics. Although the presence of water on the surface of some asteroids had been inferred from the comet-like activity of several small asteroids, these are the first actual measurements of water and organics in the asteroid belt. The presence of surface ice is particularly surprising because of the relatively short lifetime that exposed ice has at this distance from the Sun — between the orbits of Mars and Jupiter. It has been suggested that Earth's current supply of water was delivered by asteroids. The presence of water on the surface of some asteroids has been inferred from the comet-like activity of several small asteroids, including two members of the Themis dynamical family, but hitherto has not been measured. Here, infrared spectra of the asteroid 24 Themis are reported; the results show that ice and organic compounds are not only present, but also prevalent, on its surface. It has been suggested1,2,3 that Earth’s current supply of water was delivered by asteroids, some time after the collision that produced the Moon (which would have vaporized any of the pre-existing water). So far, no measurements of water ice on asteroids4,5 have been made, but its presence has been inferred from the comet-like activity of several small asteroids, including two members of the Themis dynamical family6. Here we report infrared spectra of the asteroid 24 Themis which show that ice and organic compounds are not only present on its surface but also prevalent. Infrared spectral differences between it and other asteroids make 24 Themis unique so far, and our identification of ice and organics agrees with independent results7 that rule out other compounds as possible sources of the observed spectral structure. The widespread presence of surface ice on 24 Themis is somewhat unexpected because of the relatively short lifetime of exposed ice at this distance (∼3.2 au) from the Sun. Nevertheless, there are several plausible sources, such as a subsurface reservoir that brings water to the surface through ‘impact gardening’ and/or sublimation.

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

Abstract: Background: Epigenetic modifications, such as cytosine methylation, are inherited in plant species and may occur in response to biotic or abiotic stress, affecting gene expression without changing genome sequence. Laguncularia racemosa, a mangrove species, occurs in naturally contrasting habitats where it is subjected daily to salinity and nutrient variations leading to morphological differences. This work aims at unraveling how CpG-methylation variation is distributed among individuals from two nearby habitats, at a riverside (RS) or near a salt marsh (SM), with different environmental pressures and how this variation is correlated with the observed morphological variation. Principal Findings: Significant differences were observed in morphological traits such as tree height, tree diameter, leaf width and leaf area between plants from RS and SM locations, resulting in smaller plants and smaller leaf size in SM plants. Methyl-Sensitive Amplified Polymorphism (MSAP) was used to assess genetic and epigenetic (CpG-methylation) variation in L. racemosa genomes from these populations. SM plants were hypomethylated (14.6% of loci had methylated samples) in comparison to RS (32.1% of loci had methylated samples). Within-population diversity was significantly greater for epigenetic than genetic data in both locations, but SM also had less epigenetic diversity than RS. Frequency-based (GST) and multivariate (bST) methods that estimate population structure showed significantly greater differentiation among locations for epigenetic than genetic data. Co-Inertia analysis, exploring jointly the genetic and epigenetic data, showed that individuals with similar genetic profiles presented divergent epigenetic profiles that were characteristic of the population in a particular environment, suggesting that CpG-methylation changes may be associated with environmental heterogeneity. Conclusions: In spite of significant morphological dissimilarities, individuals of L. racemosa from salt marsh and riverside presented little genetic but abundant DNA methylation differentiation, suggesting that epigenetic variation in natural plant populations has an important role in helping individuals to cope with different environments.

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Abstract: Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.

STROBE initiative: guidelines on reporting observational studies

Abstract: Reporting of observational studies is often inadequate, hampering the assessment of their strengths and weaknesses and, consequently, the generalization of study results. The initiative named Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) developed a checklist of 22 items, the STROBE Statement, with recommendations about what should be included in a more accurate and complete description of observational studies. Between June and December 2008, a group of Brazilian researchers was dedicated to the translation and adaptation of the STROBE Statement into Portuguese. The present study aimed to show the translation into Portuguese, introduce the discussion on the context of use, the potential and limitations of the STROBE initiative.

Iniciativa STROBE: subsídios para a comunicação de estudos observacionais

Abstract: Frequentemente, a descricao de pesquisas de natureza observacional e inadequada, dificultando a avaliacao de seus pontos fracos e fortes e, em consequencia, a generalizacao de seus resultados. A iniciativa denominada Strengthening the Reporting of Observational Studies in Epidemiology (STROBE), formulou uma lista de verificacao que contem 22 itens, denominada STROBE Statement ("Declaracao STROBE"), com recomendacoes sobre o que deveria ser incluido em uma descricao mais precisa e completa de estudos observacionais. Entre junho e dezembro de 2008, um grupo de pesquisadores brasileiros dedicou-se a traducao e adaptacao da "Declaracao STROBE" para o portugues. O objetivo do estudo foi apresentar a traducao para o portugues, bem como introduzir a discussao sobre o contexto de utilizacao, as potencialidades e limitacoes da Iniciativa STROBE.