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What is in a rumour: combined visual analysis of rumour flow and user activity
No full textDue to the rapid propagation of rumours in Online Social Networks (OSNs), identifying and understanding characteristic patterns, evolution and user behaviours behind this activity is essential. Yet, there are few tools that can support analysing rumours and activities of players in their propagation. In this paper we propose a visual analysis approach to explore rumour components and life cycles as well as their association with user actions. The approach is realized by the implementation of a prototype system, called RumourFlow. Our framework designs, adopts and implements multiple visualizations and modeling tools that are integrated to reveal rumour contents and participants' activity, both within a rumour and across different rumours. The approach supports analysts in drawing hypotheses regarding rumour propagation. This paper presents the various models, algorithms and visualizations employed for rumour strength, rumour contents, user participation, as well as the core role of the visualizations in studying this phenomenon. The effectiveness of the approach is illustrated by a use case highlighting relevant insight into rumour spreading, most of which could not otherwise be observed.CNPqFAPESPNatural Sciences and Engineering Research Council of CanadaInternational Development Research Centre, Ottawa, Canad
Data-intensive analysis of HIV mutations
No full textAbstract\ud
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Background\ud
In this study, clustering was performed using a bitmap representation of HIV reverse transcriptase and protease sequences, to produce an unsupervised classification of HIV sequences. The classification will aid our understanding of the interactions between mutations and drug resistance. 10,229 HIV genomic sequences from the protease and reverse transcriptase regions of the pol gene and antiretroviral resistant related mutations represented in an 82-dimensional binary vector space were analyzed.\ud
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Results\ud
A new cluster representation was proposed using an image inspired by microarray data, such that the rows in the image represented the protein sequences from the genotype data and the columns represented presence or absence of mutations in each protein position.The visualization of the clusters showed that some mutations frequently occur together and are probably related to an epistatic phenomenon.\ud
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Conclusion\ud
We described a methodology based on the application of a pattern recognition algorithm using binary data to suggest clusters of mutations that can easily be discriminated by cluster viewing schemes.The authors are grateful for FAPESP grant #11/50761-2, and to CNPq, CAPES\ud
and PRP-USP for financial support
Bayesian reversible-jump for epistasis analysis in genomic studies
No full textAbstract\ud
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Background\ud
The large amount of data used in genomic analysis has allowed geneticists to achieve some understanding of the genetic architecture of complex traits. Although the information gathered by molecular markers has permitted gains in predictive accuracy and gene discovery, epistatic effects have been ignored based on exhaustive searches requesting estimates of its effects on the whole genome. In this work, we propose the reversible-jump technique to estimate epistasis in the genome without drastically altering the model dimension. To this end, we used a real maize dataset based on 256 F2:3 progenies plus a simulation data set based on 300 F2 individuals. In the simulation scenario, six QTL presenting main effects (additive and dominance) were combined with seven other epistatic effects totaling 13 QTL controlling the trait.\ud
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Results\ud
Our model explored 18,624 candidate epistases, but even in this vast space, only one spurious interaction was found. The three epistases selected by our model, named here as 18x26, 56x68 and 59x93, were very close to simulated ones (19x25, 54x72, 59x91 and 59x94). In the real dataset, we estimate 33,024 epistatic effects, and several minor epistatic combinations were found to explain a significant proportion of the genetic variance. The broad participation of epistasis in the real dataset may indicate the presence of pervasive epistasis acting on maize grain yield.\ud
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Conclusions\ud
The power of selecting true epistasis in thousands of possible combinations suggests the attractiveness of our model to handle genomic dataThis research was supported by Fundação de Amparo a Pesquisa do\ud
Estado de Minas Gerais for supporting this research through Grant\ud
No. APQ-01745-1
A visão de um americano a respeito do sistema das artes no Brasil nos anos 1940: relatos de Lincoln Kirstein a Nelson Rockefeller e Alfred Barr Jr.
No full textMelittin induces in vitro death of Leishmania (Leishmania) infantum by triggering the cellular innate immune response
No full textAbstract\ud
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Background\ud
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Apis mellifera venom, which has already been recommended as an alternative anti-inflammatory treatment, may be also considered an important source of candidate molecules for biotechnological and biomedical uses, such as the treatment of parasitic diseases.\ud
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Methods\ud
Africanized honeybee venom from Apis mellifera was fractionated by RP-C18-HPLC and the obtained melittin was incubated with promastigotes and intracellular amastigotes of Leishmania (L.) infantum. Cytotoxicity to mice peritoneal macrophages was evaluated through mitochondrial oxidative activity. The production of anti- and pro-inflammatory cytokines, NO and H2O2 by macrophages was determined.\ud
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Results\ud
Promastigotes and intracellular amastigotes were susceptible to melittin (IC50 28.3 μg.mL−1 and 1.4 μg.mL−1, respectively), but also showed mammalian cell cytotoxicity with an IC50 value of 5.7 μg.mL−1. Uninfected macrophages treated with melittin increased the production of IL-10, TNF-α, NO and H2O2. Infected melittin-treated macrophages increased IL-12 production, but decreased the levels of IL-10, TNF-α, NO and H2O2.\ud
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Conclusions\ud
The results showed that melittin acts in vitro against promastigotes and intracellular amastigotes of Leishmania (L.) infantum. Furthermore, they can act indirectly on intracellular amastigotes through a macrophage immunomodulatory effect.The authors would like to thank the State of São Paulo Research\ud
Foundation (FAPESP, proc. n. 2011/23236-4 and n. 2009/53846-9), the National Council for Scientific and Technological Development (CNPq, proc. n. 563582/2010-3), the Coordination for the Improvement of Higher Education Personnel (CAPES, AUXPE Toxinologia 1219/2011, proc. n. 23038.000823/2011-21 and AUXPE proc. n. 23038.005536/2012-31) and FINEP (protocol number 01.12.0450.01). DCP (306066/2011-4), RSFJr and AGT are CNPq research fellows
Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases
No full textAbstract\ud
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Background\ud
Sugarcane has been used as the main crop for ethanol production for more than 40 years in Brazil. Recently, the production of bioethanol from bagasse and straw, also called second generation (2G) ethanol, became a reality with the first commercial plants started in the USA and Brazil. However, the industrial processes still need to be improved to generate a low cost fuel. One possibility is the remodeling of cell walls, by means of genetic improvement or transgenesis, in order to make the bagasse more accessible to hydrolytic enzymes. We aimed at characterizing the cell wall proteome of young sugarcane culms, to identify proteins involved in cell wall biogenesis. Proteins were extracted from the cell walls of 2-month-old culms using two protocols, non-destructive by vacuum infiltration vs destructive. The proteins were identified by mass spectrometry and bioinformatics.\ud
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Results\ud
A predicted signal peptide was found in 84 different proteins, called cell wall proteins (CWPs). As expected, the non-destructive method showed a lower percentage of proteins predicted to be intracellular than the destructive one (33 % vs 44 %). About 19 % of CWPs were identified with both methods, whilst the infiltration protocol could lead to the identification of 75 % more CWPs. In both cases, the most populated protein functional classes were those of proteins related to lipid metabolism and oxido-reductases. Curiously, a single glycoside hydrolase (GH) was identified using the non-destructive method whereas 10 GHs were found with the destructive one. Quantitative data analysis allowed the identification of the most abundant proteins.\ud
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Conclusions\ud
The results highlighted the importance of using different protocols to extract proteins from cell walls to expand the coverage of the cell wall proteome. Ten GHs were indicated as possible targets for further studies in order to obtain cell walls less recalcitrant to deconstruction. Therefore, this work contributed to two goals: enlarge the coverage of the sugarcane cell wall proteome, and provide target proteins that could be used in future research to facilitate 2G ethanol production
Amino acid supplementation and impact on immune function in the context of exercise
No full textAbstract
Moderate and chronic bouts of exercise may lead to positive metabolic, molecular, and morphological adaptations, improving health. Although exercise training stimulates the production of reactive oxygen species (ROS), their overall intracellular concentration may not reach damaging levels due to enhancement of antioxidant responses. However, inadequate exercise training (i.e., single bout of high-intensity or excessive exercise) may result in oxidative stress, muscle fatigue and muscle injury. Moreover, during the recovery period, impaired immunity has been reported, for example; excessive-inflammation and compensatory immunosuppression. Nutritional supplements, sometimes referred to as immuno-nutrients, may be required to reduce immunosuppression and excessive inflammation. Herein, we discuss the action and the possible targets of key immuno-nutrients such as L-glutamine, L-arginine, branched chain amino acids (BCAA) and whey protein
Impact of the radiographic examination on diagnosis and treatment decision of caries lesions in primary teeth – the Caries Detection in Children (CARDEC-01) trial: study protocol for a randomized controlled trial
No full textAbstract\ud
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Background\ud
Although most clinical guidelines throughout the world indicate that clinicians take two bitewings for detecting caries lesions in primary molars of all children, evidence for this recommendation is essentially based on cross-sectional studies performed in laboratory settings or using convenience samples. The benefits and impact of performing radiographs on diagnosis and treatment decision of caries lesions in primary teeth, mainly considering relevant outcomes for patients, have not been evaluated yet. Thus, the aim of this randomized clinical trial will be to evaluate the impact of performing radiographic examination adjunct to the visual inspection for detecting and making treatment decision regarding caries lesions in primary teeth compared with visual inspection performed alone. We will consider different outcomes related to children's health and welfare.\ud
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Methods/Design\ud
To reach this objective, 250 children ages 3 to 6 years who sought dental treatment in our dental school will be randomly allocated in two groups according to the diagnostic strategy used for caries detection: visual inspection performed alone or visual inspection associated to radiographic examination. Two trained and calibrated examiners will carry out the examinations and elaborate the treatment decision plan. Then, children will be treated and followed up for 2 years, with evaluations after 12 and 24 months after the inclusion of children in the study. Children will also return after 6 and 18 months to reinforce the preventive orientations. Primary outcome will be the number of dental surfaces in need of dental treatment at the follow-up. Secondary outcomes will be the components of the primary outcome separately, as well as, proportion of false-positive results, the oral health-related quality of life, cost-efficacy, cost-adjusted life years, and number of new lesions in the first permanent molars.\ud
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Discussion\ud
Our working hypothesis is that radiographic examination would actually exert little influence on patient-centered outcomes, and visual inspection would be enough as diagnostic strategy for caries detection in primary teeth.\ud
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Trial registration\ud
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NCT02078453\ud
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. Registered 4 March 2015.This trial is funded by the Fundação de Amparo à Pesquisa do Estado de\ud
São Paulo – FAPESP (Grant # 2012/24243-7), CNPQ (Grants # 471817/2012-0\ud
and 471817/2012-0) and CAPES, Brazilian funding agencies. The authors\ud
wish to thank the participants of the Post-Graduation in Pediatric Dentistry\ud
Seminar of FOUSP for the critical comments
Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila
No full textAbstract
Background
We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the Drosophila buzzatii cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the D. buzzatii species cluster in order to assess the concordance of CHC differentiation with species divergence.
Results
Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C29 to C39, including methyl-branched alkanes, n-alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of D. serido suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived period (per) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only per + inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of D. serido significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal.
Conclusions
CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species