Molecular analysis of the dengue virus type 1 and 2 in Brazil based on sequences of the genomic envelope-nonstructural protein 1 junction region

The genomic sequences of the Envelope-Non-Structural protein 1 junction region (E/NS1) of 84 DEN-1 and 22 DEN-2 isolates from Brazil were determined. Most of these strains were isolated in the period from 1995 to 2001 in endemic and regions of recent dengue transmission in São Paulo State. Sequence data for DEN-1 and DEN-2 utilized in phylogenetic and split decomposition analyses also include sequences deposited in GenBank from different regions of Brazil and of the world. Phylogenetic analyses were done using both maximum likelihood and Bayesian approaches. Results for both DEN-1 and DEN-2 data are ambiguous, and support for most tree bipartitions are generally poor, suggesting that E/NS1 region does not contain enough information for recovering phylogenetic relationships among DEN-1 and DEN-2 sequences used in this study. The network graph generated in the split decomposition analysis of DEN-1 does not show evidence of grouping sequences according to country, region and clades. While the network for DEN-2 also shows ambiguities among DEN-2 sequences, it suggests that Brazilian sequences may belong to distinct subtypes of genotype III.

Reconstrução/processamento de imagem médica com GPU em tomossíntese

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Comparing the performance of geostatistical models with additional information from covariates for sewage plume characterization

In this work, kriging with covariates is used to model and map the spatial distribution of salinity measurements gathered by an autonomous underwater vehicle in a sea outfall monitoring campaign aiming to distinguish the effluent plume from the receiving waters and characterize its spatial variability in the vicinity of the discharge. Four different geostatistical linear models for salinity were assumed, where the distance to diffuser, the west-east positioning, and the south-north positioning were used as covariates. Sample variograms were fitted by the Mat`ern models using weighted least squares and maximum likelihood estimation methods as a way to detect eventual discrepancies. Typically, the maximum likelihood method estimated very low ranges which have limited the kriging process. So, at least for these data sets, weighted least squares showed to be the most appropriate estimation method for variogram fitting. The kriged maps show clearly the spatial variation of salinity, and it is possible to identify the effluent plume in the area studied. The results obtained show some guidelines for sewage monitoring if a geostatistical analysis of the data is in mind. It is important to treat properly the existence of anomalous values and to adopt a sampling strategy that includes transects parallel and perpendicular to the effluent dispersion.

Land cover dynamics in Savanna Ecosystem of Borena Ethiopia

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Assessing the impacts of land use and land cover change on hydrology of watershed: a case study on Gigel-Abbay Watershed, Lake Tana Basin, Ethiopia

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Natural transovarial transmission of dengue virus 4 in Aedes aegypti from Cuiabá, State of Mato Grosso, Brazil

INTRODUCTION: Dengue is the most prevalent arboviral disease in tropical areas. In Mato Grosso, outbreaks are reported every year, but studies on dengue in this state are scarce. METHODS: Natural transovarial infection of Aedes aegypti by a flavivirus was investigated in the Jardim Industriário neighborhood of Cuiabá, Mato Grosso. Eggs were collected with ovitraps during the dry, intermediate, and rainy seasons of 2012. After the eggs hatched and the larvae developed to adulthood, mosquitoes (n = 758) were identified and allocated to pools of 1-10 specimens according to the collection location, sex, and climatic period. After RNA extraction, multiplex semi-nested RT-PCR was performed to detect the four dengue virus (DENV) serotypes, yellow fever virus, West Nile virus and Saint Louis encephalitis virus. RESULTS: DENV-4 was the only flavivirus detected, and it was found in 8/50 pools (16.0%). Three of the positive pools contained females, and five contained males. Their nucleotide sequences presented 96-100% similarity with DENV-4 genotype II strains from Manaus, Amazonas. The minimum infection rate was 10.5 per 1000 specimens, and the maximum likelihood estimator of the infection rate was 11.6 (95% confidence interval: 4.8; 23.3). CONCLUSIONS: This study provides the first evidence of natural transovarial infection by DENV-4 in Ae. Aegypti in Mato Grosso, suggesting that this type of infection might serve as a mechanism of virus maintenance during interepidemic periods in Cuiabá, a city where dengue epidemics are reported every year. These results emphasize the need for efficient vector population control measures to prevent arbovirus outbreaks in the state.

Mapping the Pasture Steppe in Bayankhongor, Mongolia: comparison of classification methods, using Landsat-8 and geophysical data

Grasslands in semi-arid regions, like Mongolian steppes, are facing desertification and degradation processes, due to climate change. Mongolia’s main economic activity consists on an extensive livestock production and, therefore, it is a concerning matter for the decision makers. Remote sensing and Geographic Information Systems provide the tools for advanced ecosystem management and have been widely used for monitoring and management of pasture resources. This study investigates which is the higher thematic detail that is possible to achieve through remote sensing, to map the steppe vegetation, using medium resolution earth observation imagery in three districts (soums) of Mongolia: Dzag, Buutsagaan and Khureemaral. After considering different thematic levels of detail for classifying the steppe vegetation, the existent pasture types within the steppe were chosen to be mapped. In order to investigate which combination of data sets yields the best results and which classification algorithm is more suitable for incorporating these data sets, a comparison between different classification methods were tested for the study area. Sixteen classifications were performed using different combinations of estimators, Landsat-8 (spectral bands and Landsat-8 NDVI-derived) and geophysical data (elevation, mean annual precipitation and mean annual temperature) using two classification algorithms, maximum likelihood and decision tree. Results showed that the best performing model was the one that incorporated Landsat-8 bands with mean annual precipitation and mean annual temperature (Model 13), using the decision tree. For maximum likelihood, the model that incorporated Landsat-8 bands with mean annual precipitation (Model 5) and the one that incorporated Landsat-8 bands with mean annual precipitation and mean annual temperature (Model 13), achieved the higher accuracies for this algorithm. The decision tree models consistently outperformed the maximum likelihood ones.

Search for s-channel single top-quark production in proton-proton collisions at s√=8 TeV with the ATLAS detector

This Letter presents a search at the LHC for s-channel single top-quark production in proton-proton collisions at a centre-of-mass energy of 8 TeV. The analyzed data set was recorded by the ATLAS detector and corresponds to an integrated luminosity of 20.3 fb−1. Selected events contain one charged lepton, large missing transverse momentum and exactly two b-tagged jets. A multivariate event classifier based on boosted decision trees is developed to discriminate s-channel single top-quark events from the main background contributions. The signal extraction is based on a binned maximum-likelihood fit of the output classifier distribution. The analysis leads to an upper limit on the s-channel single top-quark production cross-section of 14.6 pb at the 95% confidence level. The fit gives a cross-section of σs=5.0±4.3 pb, consistent with the Standard Model expectation.

Extreme value Birnbaum-Saunders regression models applied to environmental data

Extreme value models are widely used in different areas. The Birnbaum–Saunders distribution is receiving considerable attention due to its physical arguments and its good properties. We propose a methodology based on extreme value Birnbaum–Saunders regression models, which includes model formulation, estimation, inference and checking. We further conduct a simulation study for evaluating its performance. A statistical analysis with real-world extreme value environmental data using the methodology is provided as illustration.

Spatial and temporal evolution of family-farming land use in the Tapajós region of the Brazilian Amazon

Pressures on the Brazilian Amazon forest have been accentuated by agricultural activities practiced by families encouraged to settle in this region in the 1970s by the colonization program of the government. The aims of this study were to analyze the temporal and spatial evolution of land cover and land use (LCLU) in the lower Tapajós region, in the state of Pará. We contrast 11 watersheds that are generally representative of the colonization dynamics in the region. For this purpose, Landsat satellite images from three different years, 1986, 2001, and 2009, were analyzed with Geographic Information Systems. Individual images were subject to an unsupervised classification using the Maximum Likelihood Classification algorithm available on GRASS. The classes retained for the representation of LCLU in this study were: (1) slightly altered old-growth forest, (2) succession forest, (3) crop land and pasture, and (4) bare soil. The analysis and observation of general trends in eleven watersheds shows that LCLU is changing very rapidly. The average deforestation of old-growth forest in all the watersheds was estimated at more than 30% for the period of 1986 to 2009. The local-scale analysis of watersheds reveals the complexity of LCLU, notably in relation to large changes in the temporal and spatial evolution of watersheds. Proximity to the sprawling city of Itaituba is related to the highest rate of deforestation in two watersheds. The opening of roads such as the Transamazonian highway is associated to the second highest rate of deforestation in three watersheds.

Exploring the factor structure of neurocognitive measures in older individuals

Here we focus on factor analysis from a best practices point of view, by investigating the factor structure of neuropsychological tests and using the results obtained to illustrate on choosing a reasonable solution. The sample (n=1051 individuals) was randomly divided into two groups: one for exploratory factor analysis (EFA) and principal component analysis (PCA), to investigate the number of factors underlying the neurocognitive variables; the second to test the "best fit" model via confirmatory factor analysis (CFA). For the exploratory step, three extraction (maximum likelihood, principal axis factoring and principal components) and two rotation (orthogonal and oblique) methods were used. The analysis methodology allowed exploring how different cognitive/psychological tests correlated/discriminated between dimensions, indicating that to capture latent structures in similar sample sizes and measures, with approximately normal data distribution, reflective models with oblimin rotation might prove the most adequate.

Исследование возможной связи между изменениями электротеллурического поля и активацией сейсмотектонических процессов с использованием принципа максимального правдоподобия

ჩატარდა ელექტროტელურული ველის ცვალებადობის შესაძლო კავშირის კვლევა სეისმოტექტონიკური პროცესების აქტიურობასთან მიმართებაში მაქსიმალური დასაჯერებლობის პრინციპის გამოყენებით. 1982 წელს ელექტროტელურული ველის ურთიერთმართობული მდგენელების ინტენსივობის წლიურ-ყოველსაათიან ცვალებადობას და დუშეთიდან ასორმოცდაათი კილომეტრის რადიუსით შემოსაზღვრულ არეში მომხდარი არასუსტი მიწისძვრების მაგნიტუდების ცვალებადობას შორის არსებობს შესაძლო კავშირი.

Phylogeny of Thylamys (Didelphimorphia, Didelphidae) species, with special reference to Thylamys karimii

The genus Thylamys Gray, 1843 lives in the central and southern portions of South America inhabiting open and shrub-like vegetation, from prairies to dry forest habitats in contrast to the preference of other Didelphidae genera for more mesic environments. Thylamys is a speciose genus including T. elegans (Waterhouse, 1839), T. macrurus (Olfers, 1818), T. pallidior (Thomas, 1902), T. pusillus (Desmarest, 1804), T. venustus (Thomas, 1902), T. sponsorius (Thomas, 1921), T. cinderella (Thomas, 1902), T. tatei (Handley, 1957), T. karimii (Petter, 1968), and T. velutinus (Wagner, 1842) species. Previous phylogenetic analyses in this genus did not include the Brazilian species T. karimii, which is widely distributed in this country. In this study, phylogenetic analyses were performed to establish the relationships among the Brazilian T. karimii and all other previously analyzed species. We used 402-bp fragments of the mitochondrial cytochrome b gene, and the phylogeny estimates were conducted employing maximum parsimony (MP), maximum likelihood (ML), Bayesian (BY), and neighbor-joining (NJ). The topologies of the trees obtained in the different analyses were all similar and pointed out that T. karimii is the sister taxon of a group constituted of taxa from dry and arid environments named the dryland species. The dryland species consists of T. pusillus, T. pallidior, T. tatei, and T. elegans. The results of this work suggest five species groups in Thylamys. In one of them, T. velutinus and T. kariimi could constitute a sister group forming one Thylamys clade that colonized Brazil.

User-friendly parallel computations with econometric examples

This paper shows how a high level matrix programming language may be used to perform Monte Carlo simulation, bootstrapping, estimation by maximum likelihood and GMM, and kernel regression in parallel on symmetric multiprocessor computers or clusters of workstations. The implementation of parallelization is done in a way such that an investigator may use the programs without any knowledge of parallel programming. A bootable CD that allows rapid creation of a cluster for parallel computing is introduced. Examples show that parallelization can lead to important reductions in computational time. Detailed discussion of how the Monte Carlo problem was parallelized is included as an example for learning to write parallel programs for Octave.

A proposal for a new specification for a conditionally heteroskedastic variance model: the Quadratic Moving-Average Conditional Heteroskedasticity and an application to the D. Mark-U.S. dollar Exchange Rate

Ever since the appearance of the ARCH model [Engle(1982a)], an impressive array of variance specifications belonging to the same class of models has emerged [i.e. Bollerslev's (1986) GARCH; Nelson's (1990) EGARCH]. This recent domain has achieved very successful developments. Nevertheless, several empirical studies seem to show that the performance of such models is not always appropriate [Boulier(1992)]. In this paper we propose a new specification: the Quadratic Moving Average Conditional heteroskedasticity model. Its statistical properties, such as the kurtosis and the symmetry, as well as two estimators (Method of Moments and Maximum Likelihood) are studied. Two statistical tests are presented, the first one tests for homoskedasticity and the second one, discriminates between ARCH and QMACH specification. A Monte Carlo study is presented in order to illustrate some of the theoretical results. An empirical study is undertaken for the DM-US exchange rate.