A Fuzzy Ontology-Driven Approach to Semantic Interoperability in e-Government Big Data

With the increasing production of information from e-government initiatives, there is also the need to transform a large volume of unstructured data into useful information for society. All this information should be easily accessible and made available in a meaningful and effective way in order to achieve semantic interoperability in electronic government services, which is a challenge to be pursued by governments round the world. Our aim is to discuss the context of e-Government Big Data and to present a framework to promote semantic interoperability through automatic generation of ontologies from unstructured information found in the Internet. We propose the use of fuzzy mechanisms to deal with natural language terms and present some related works found in this area. The results achieved in this study are based on the architectural definition and major components and requirements in order to compose the proposed framework. With this, it is possible to take advantage of the large volume of information generated from e-Government initiatives and use it to benefit society.

Influence of landscape evolution on the distribution of floristic patterns in northern Amazonia revealed by delta 13C data

The Amazonian lowlands include large patches of open vegetation which contrast sharply with the rainforest, and the origin of these patches has been debated. This study focuses on a large area of open vegetation in northern Brazil, where d13C and, in some instances, C/N analyses of the organic matter preserved in late Quaternary sediments were used to achieve floristic reconstructions over time. The main goal was to determine when the modern open vegetation started to develop in this area. The variability in d13C data derived from nine cores ranges from -32.2 to -19.6 parts per thousand, but with nearly 60% of data above -26.5 parts per thousand. The most enriched values were detected only in ecotone and open vegetated areas. The development of open vegetation communities was asynchronous, varying between estimated ages of 6400 and 3000 cal a BP. This suggests that the origin of the studied patches of open vegetation might be linked to sedimentary dynamics of a late Quaternary megafan system. As sedimentation ended, this vegetation type became established over the megafan surface. In addition, the data presented here show that the presence of C4 plants must be used carefully as a proxy to interpret dry paleoclimatic episodes in Amazonian areas. Copyright (c) 2012 John Wiley & Sons, Ltd.

Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes

The gecko genus Phyllopezus occurs across South America's open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p. przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a taxonomy that is isomorphic with phylogenetic history. We recovered multiple, deeply divergent, cryptic lineages within P. pollicaris. These cryptic lineages possessed mtDNA distances equivalent to distances among other gekkotan sister taxa. Described P. pollicaris subspecies are not reciprocally monophyletic and current subspecific taxonomy does not accurately reflect evolutionary relationships among cryptic lineages. We highlight the conservation significance of these results in light of the ongoing habitat loss in South America's open biomes. (C) 2011 Elsevier Inc. All rights reserved.

Comparison between endoscopic and open surgery in 37 patients with nasopharyngeal angiofibroma

Juvenile nasopharyngeal angiofibroma is a rare benign vascular tumor of the nasopharynx. Although the treatment of choice is surgery, there is no consensus on what is the best approach. Aim: To compare surgical time and intraoperative transfusion requirements in patients undergoing endoscopic surgery versus open / combined and relate the need for transfusion during surgery with the time between embolization and surgery. Material and Methods: Study descriptive, analytical, retrospective study with a quantitative approach developed in the Otorhinolaryngology department of a teaching hospital. Analyzed 37 patients with angiofibroma undergoing surgical treatment. Data obtained from medical records. Analyzed with tests of the Fisher-Freeman-Halton and Games-Howell. Was considered significant if p <0.05. Study design: Historical cohort study with cross-sectional. Results: The endoscopic approach had a shorter operative time (p <0.0001). There is less need for transfusion during surgery when the embolization was performed on the fourth day. Conclusion: This suggests that the period ahead would be ideal to perform the process of embolization and endoscopic surgery by demanding less time would be associated with a lower morbidity. This study, however, failed to show which group of patients according to tumor stage would benefit from specific technical.

Crossing over does occur in males of Drosophila ananassae from natural populations

Spontaneous crossing over in males of Drosophila ananassae has been well demonstrated using F-1 individuals from crosses between marker stocks and wild type strains. However, the question of its occurrence in males from natural populations remained open. Here we present the cytological evidence that crossing over does occur in males of D. ananassae from two Brazilian populations, sampled nearly 21 years apart, and in two recently sampled populations, one from Indonesia and one from Okinawa, Japan. Cytological analysis of meiosis in males collected from nature and in sons of females from the same population inseminated in nature revealed the presence of chiasmata, inversion chiasmata, and isosite chromosome breakages in the diplotene cells in all sampled populations. These data demonstrate that reciprocal and nonreciprocal exchanges and chromosome breakages, previously reported as related events of male crossing over, do occur at variable frequencies among males from natural populations.

Metronidazole Immediate Release Formulations: A Fasting Randomized Open-Label Crossover Bioequivalence Study in Healthy Volunteers

Metronidazole is a BCS (Biopharmaceutics Classification System) class 1 drug, traditionally considered the choice drug in the infections treatment caused by protozoa and anaerobic microorganisms. This study aimed to evaluate bioequivalence between 2 different marketed 250 mg metronidazole immediate release tablets. A randomized, open-label, 2 x 2 crossover study was performed in healthy Brazilian volunteers under fasting conditions with a 7-day washout period. The formulations were administered as single oral dose and blood was sampled over 48 h. Metronidazole plasma concentrations were determined by a liquid chromatography mass spectrometry (LC-MS/MS) method. The plasma concentration vs. time profile was generated for each volunteer and the pharmacokinetic parameters C-max, T-max, AUC(0-t), AUC(0-infinity), k(e), and t(1/2) were calculated using a noncompartmental model. Bioequivalence between pharmaceutical formulations was determined by calculating 90% CIs (Confidence Intervall) for the ratios of C-max, AUC(0-t), and AUC(0-infinity) values for test and reference using log-transformed data. 22 healthy volunteers (11 men, 11 women; mean (SD) age, 28 (6.5) years [range, 21-45 years]; mean (SD) weight, 66 (9.3) kg [range, 51-81 kg]; mean (SD) height, 169 (6.5) cm [range, 156-186 cm]) were enrolled in and completed the study. The 90% CIs for C-max (0.92-1.06), AUC(0-t) (0.97-1.02), and AUC(0-infinity) (0.97-1.03) values for the test and reference products fitted in the interval of 0.80-1.25 proposed by most regulatory agencies, including the Brazilian agency ANVISA. No clinically significant adverse effects were reported. After pharmacokinetics analysis, it concluded that test 250 mg metronidazole formulation is bioequivalent to the reference product according to the Brazilian agency requirements.

VVV DR1: The first data release of the Milky Way bulge and southern plane from the near-infrared ESO public survey VISTA variables in the Via Lactea

Context. The ESO public survey VISTA variables in the Via Lactea (VVV) started in 2010. VVV targets 562 sq. deg in the Galactic bulge and an adjacent plane region and is expected to run for about five years. Aims. We describe the progress of the survey observations in the first observing season, the observing strategy, and quality of the data obtained. Methods. The observations are carried out on the 4-m VISTA telescope in the ZYJHK(s) filters. In addition to the multi-band imaging the variability monitoring campaign in the K-s filter has started. Data reduction is carried out using the pipeline at the Cambridge Astronomical Survey Unit. The photometric and astrometric calibration is performed via the numerous 2MASS sources observed in each pointing. Results. The first data release contains the aperture photometry and astrometric catalogues for 348 individual pointings in the ZYJHK(s) filters taken in the 2010 observing season. The typical image quality is similar to 0 ''.9-1 ''.0. The stringent photometric and image quality requirements of the survey are satisfied in 100% of the JHK(s) images in the disk area and 90% of the JHK(s) images in the bulge area. The completeness in the Z and Y images is 84% in the disk, and 40% in the bulge. The first season catalogues contain 1.28 x 10(8) stellar sources in the bulge and 1.68 x 10(8) in the disk area detected in at least one of the photometric bands. The combined, multi-band catalogues contain more than 1.63 x 10(8) stellar sources. About 10% of these are double detections because of overlapping adjacent pointings. These overlapping multiple detections are used to characterise the quality of the data. The images in the JHK(s) bands extend typically similar to 4 mag deeper than 2MASS. The magnitude limit and photometric quality depend strongly on crowding in the inner Galactic regions. The astrometry for K-s = 15-18 mag has rms similar to 35-175 mas. Conclusions. The VVV Survey data products offer a unique dataset to map the stellar populations in the Galactic bulge and the adjacent plane and provide an exciting new tool for the study of the structure, content, and star-formation history of our Galaxy, as well as for investigations of the newly discovered star clusters, star-forming regions in the disk, high proper motion stars, asteroids, planetary nebulae, and other interesting objects.

Electronic Government Interoperability: Identifying the Barriers for Frameworks Adoption

Interoperability is a crucial issue for electronic government due to the need of agencies' information systems to be totally integrated and able to exchange data in a seamless way. A way to achieve it is by establishing a government interoperability framework (GIF). However, this is a difficult task to be carried out due not only to technological issues but also to other aspects. This research is expected to contribute to the identification of the barriers to the adoption of interoperability standards for electronic government. The article presents the preliminary findings from a case study of the Brazilian Government framework (e-PING), based on the analyses of documents and face-to-face interviews. It points out some aspects that may influence the establishment of these standards, becoming barriers to their adoption.

Evaluating different methods of microarray data normalization

Abstract Background With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration. Results Here, we considered three commonly used normalization approaches, namely: Loess, Splines and Wavelets, and two non-parametric regression methods, which have yet to be used for normalization, namely, the Kernel smoothing and Support Vector Regression. The results obtained were compared using artificial microarray data and benchmark studies. The results indicate that the Support Vector Regression is the most robust to outliers and that Kernel is the worst normalization technique, while no practical differences were observed between Loess, Splines and Wavelets. Conclusion In face of our results, the Support Vector Regression is favored for microarray normalization due to its superiority when compared to the other methods for its robustness in estimating the normalization curve.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

A feature selection approach for identification of signature genes from SAGE data

Abstract Background One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements. Results A new framework to select specific genes that distinguish different biological states based on the analysis of SAGE data is proposed. The new framework applies the bolstered error for the identification of strong genes that separate the biological states in a feature space defined by the gene expression of a training set. Credibility intervals defined from a probabilistic model of SAGE measurements are used to identify the genes that distinguish the different states with more reliability among all gene groups selected by the strong genes method. A score taking into account the credibility and the bolstered error values in order to rank the groups of considered genes is proposed. Results obtained using SAGE data from gliomas are presented, thus corroborating the introduced methodology. Conclusion The model representing counting data, such as SAGE, provides additional statistical information that allows a more robust analysis. The additional statistical information provided by the probabilistic model is incorporated in the methodology described in the paper. The introduced method is suitable to identify signature genes that lead to a good separation of the biological states using SAGE and may be adapted for other counting methods such as Massive Parallel Signature Sequencing (MPSS) or the recent Sequencing-By-Synthesis (SBS) technique. Some of such genes identified by the proposed method may be useful to generate classifiers.

Simcluster: clustering enumeration gene expression data on the simplex space

Abstract Background Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space. Results Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster. Conclusion Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data.

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Interferon-gamma alters the phagocytic activity of the mouse trophoblast

Interferon-gamma (IFN-gamma) mediates diverse functions in bone marrow-derived phagocytes, including phagocytosis and microbe destruction. This cytokine has also been detected at implantation sites under both physiological and pathological conditions in many different species. At these particular sites, the outermost embryonic cell layer in close contact with the maternal tissues, the trophoblast exhibits intense phagocytic activity. To determine whether IFN-gamma affects phagocytosis of mouse-trophoblast cells, ectoplacental cone-derived trophoblast was cultured and evaluated for erythrophagocytosis. Phagocytic activity was monitored ultrastructurally and expressed as percentage of phagocytic trophoblast in total trophoblast cells. Conditioned medium from concanavalin-A-stimulated spleen cells significantly enhanced trophoblast phagocytosis. This effect was blocked by pre-incubation with an anti-IFN-gamma neutralizing antibody. Introduction of mouse recombinant IFN-gamma (mrIFN-gamma) to cultures did not increase cell death, but augmented the percentage of phagocytic cells in a dose-dependent manner. Ectoplacental cones from mice deficient for IFN-gamma receptor alpha-chain showed a significant decrease of the phagocytosis, even under mrIFN-gamma stimulation, suggesting that IFN-gamma-induced phagocytosis are receptor-mediated. Reverse transcriptase-PCR analyses confirmed the presence of mRNA for IFN-gamma receptor alpha and beta-chains in trophoblast cells and detected a significant increase in the mRNA levels of IFN-gamma receptor beta-chain, mainly, when cultured cells were exposed to IFN-gamma. Immunohistochemistry and Western blot analyses also revealed protein expression of the IFN-gamma receptor alpha-chain. These results suggest that IFN-gamma may participate in the phagocytic activation of the mouse trophoblast, albeit the exact mechanism was not hereby elucidated. Protective and/or nutritional fetal benefit may result from this physiological response. In addition, our data also shed some light on the understanding of trophoblast tolerance to inflammatory/immune cytokines during normal gestation.

New insights about host response to smallpox using microarray data

Abstract Background Smallpox is a lethal disease that was endemic in many parts of the world until eradicated by massive immunization. Due to its lethality, there are serious concerns about its use as a bioweapon. Here we analyze publicly available microarray data to further understand survival of smallpox infected macaques, using systems biology approaches. Our goal is to improve the knowledge about the progression of this disease. Results We used KEGG pathways annotations to define groups of genes (or modules), and subsequently compared them to macaque survival times. This technique provided additional insights about the host response to this disease, such as increased expression of the cytokines and ECM receptors in the individuals with higher survival times. These results could indicate that these gene groups could influence an effective response from the host to smallpox. Conclusion Macaques with higher survival times clearly express some specific pathways previously unidentified using regular gene-by-gene approaches. Our work also shows how third party analysis of public datasets can be important to support new hypotheses to relevant biological problems.