Employing 2D Projections for Fast Visual Exploration of Large Fiber Tracking Data

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Relações entre estrutura sócio-espacial e fluxos gênicos em uma população de mouflons mediterrâneos (Ovis gmelini)

Pós-graduação em Genética e Melhoramento Animal - FCAV

Use of Poisson spatiotemporal regression models for the Brazilian Amazon Forest: malaria count data

INTRODUÇÃO: A malaria é uma doença endêmica na região da Amazônia Brasileira, e a detecção de possíveis fatores de risco pode ser de grande interesse às autoridades em saúde pública. O objetivo deste artigo é investigar a associação entre variáveis ambientais e os registros anuais de malária na região amazônica usando métodos bayesianos espaço-temporais. MÉTODOS: Utilizaram-se modelos de regressão espaço-temporais de Poisson para analisar os dados anuais de contagem de casos de malária entre os anos de 1999 a 2008, considerando a presença de alguns fatores como a taxa de desflorestamento. em uma abordagem bayesiana, as inferências foram obtidas por métodos Monte Carlo em cadeias de Markov (MCMC) que simularam amostras para a distribuição conjunta a posteriori de interesse. A discriminação de diferentes modelos também foi discutida. RESULTADOS: O modelo aqui proposto sugeriu que a taxa de desflorestamento, o número de habitants por km² e o índice de desenvolvimento humano (IDH) são importantes para a predição de casos de malária. CONCLUSÕES: É possível concluir que o desenvolvimento humano, o crescimento populacional, o desflorestamento e as alterações ecológicas associadas a estes fatores estão associados ao aumento do risco de malária. Pode-se ainda concluir que o uso de modelos de regressão de Poisson que capturam o efeito temporal e espacial em um enfoque bayesiano é uma boa estratégia para modelar dados de contagem de malária.

Genomic data as the hitchhiker's guide to cattle adaptation: tracking the milestones of past selection in the bovine genome

The bovine species have witnessed and played a major role in the drastic socio-economical changes that shaped our culture over the last 10,000 years. During this journey, cattle hitchhiked on human development and colonized the world, facing strong selective pressures such as dramatic environmental changes and disease challenge. Consequently, hundreds of specialized cattle breeds emerged and spread around the globe, making up a rich spectrum of genomic resources. Their DNA still carry the scars left from adapting to this wide range of conditions, and we are now empowered with data and analytical tools to track the milestones of past selection in their genomes. In this review paper, we provide a summary of the reconstructed demographic events that shaped cattle diversity, offer a critical synthesis of popular methodologies applied to the search for signatures of selection (SS) in genomic data, and give examples of recent SS studies in cattle. Then, we outline the potential and challenges of the application of SS analysis in cattle, and discuss the future directions in this field.

On determining spectral parameters, tracking jitter, and GPS positioning improvement by scintillation mitigation

A method of determining spectral parameters p (slope of the phase PSD) and T (phase PSD at 1 Hz) and hence tracking error variance in a GPS receiver PLL from just amplitude and phase scintillation indices and an estimated value of the Fresnel frequency has been previously presented. Here this method is validated using 50 Hz GPS phase and amplitude data from high latitude receivers in northern Norway and Svalbard. This has been done both using (1) a Fresnel frequency estimated using the amplitude PSD (in order to check the accuracy of the method) and (2) a constant assumed value of Fresnel frequency for the data set, convenient for the situation when contemporaneous phase PSDs are not available. Both of the spectral parameters (p, T) calculated using this method are in quite good agreement with those obtained by direct measurements of the phase spectrum as are tracking jitter variances determined for GPS receiver PLLs using these values. For the Svalbard data set, a significant difference in the scintillation level observed on the paths from different satellites received simultaneously was noted. Then, it is shown that the accuracy of relative GPS positioning can be improved by use of the tracking jitter variance in weighting the measurements from each satellite used in the positioning estimation. This has significant advantages for scintillation mitigation, particularly since the method can be accomplished utilizing only time domain measurements thus obviating the need for the phase PSDs in order to extract the spectral parameters required for tracking jitter determination.

Disparity between Multilocus Enzyme Electrophoresis, Microsatellite Markers and Pulsed-Field Gel Electrophoresis in epidemiological tracking of Candida albicans

Various molecular systems are available for epidemiological, genetic, evolutionary, taxonomic and systematic studies of innumerable fungal infections, especially those caused by the opportunistic pathogen C. albicans. A total of 75 independent oral isolates were selected in order to compare Multilocus Enzyme Electrophoresis (MLEE), Electrophoretic Karyotyping (EK) and Microsatellite Markers (Simple Sequence Repeats - SSRs), in their abilities to differentiate and group C. albicans isolates (discriminatory power), and also, to evaluate the concordance and similarity of the groups of strains determined by cluster analysis for each fingerprinting method. Isoenzyme typing was performed using eleven enzyme systems: Adh, Sdh, M1p, Mdh, Idh, Gdh, G6pdh, Asd, Cat, Po, and Lap (data previously published). The EK method consisted of chromosomal DNA separation by pulsed-field gel electrophoresis using a CHEF system. The microsatellite markers were investigated by PCR using three polymorphic loci: EF3, CDC3, and HIS3. Dendrograms were generated by the SAHN method and UPGMA algorithm based on similarity matrices (S(SM)). The discriminatory power of the three methods was over 95%, however a paired analysis among them showed a parity of 19.7-22.4% in the identification of strains. Weak correlation was also observed among the genetic similarity matrices (S(SM)(MLEE) x S(SM)(EK) x S(SM)(SSRs)). Clustering analyses showed a mean of 9 +/- 12.4 isolates per cluster (3.8 +/- 8 isolates/taxon) for MLEE, 6.2 +/- 4.9 isolates per cluster (4 +/- 4.5 isolates/taxon) for SSRs, and 4.1 +/- 2.3 isolates per cluster (2.6 +/- 2.3 isolates/taxon) for EK. A total of 45 (13%), 39(11.2%), 5 (1.4%) and 3 (0.9%) clusters pairs from 347 showed similarity (Si) of 0.1-10%, 10.1-20%, 20.1-30% and 30.1-40%, respectively. Clinical and molecular epidemiological correlation involving the opportunistic pathogen C. albicans may be attributed dependently of each method of genotyping (i.e., MLEE, EK, and SSRs) supplemented with similarity and grouping analysis. Therefore, the use of genotyping systems that give results which offer minimum disparity, or the combination of the results of these systems, can provide greater security and consistency in the determination of strains and their genetic relationships. (C) 2010 Elsevier B.V. All rights reserved.

Analysis of rain quality data from the South African interior

Rain acidity may be ascribed to emissions from power station stacks, as well as emissions from other industry, biomass burning, maritime influences, agricultural influences, etc. Rain quality data are available for 30 sites in the South African interior, some from as early as 1985 for up to 14 rainfall seasons, while others only have relatively short records. The article examines trends over time in the raw and volume weighted concentrations of the parameters measured, separately for each of the sites for which sufficient data are available. The main thrust, however, is to examine the inter-relationship structure between the concentrations within each rain event (unweighted data), separately for each site, and to examine whether these inter-relationships have changed over time. The rain events at individual sites can be characterized by approximately eight combinations of rainfall parameters (or rain composition signatures), and these are common to all sites. Some sites will have more events from one signature than another, but there appear to be no signatures unique to a single site. Analysis via factor and cluster analysis, with a correspondence analysis of the results, also aid interpretation of the patterns. This spatio-temporal analysis, performed by pooling all rain event data, irrespective of site or time period, results in nine combinations of rainfall parameters being sufficient to characterize the rain events. The sites and rainfall seasons show patterns in these combinations of parameters, with some combinations appearing more frequently during certain rainfall seasons. In particular, the presence of the combination of low acetate and formate with high magnesium appears to be increasing in the later rainfall seasons, as does this combination together with calcium, sodium, chloride, potassium and fluoride. As expected, sites close together exhibit similar signatures. Copyright © 2002 John Wiley & Sons, Ltd.

Analysis of the distances covered by first division Brazilian soccer players obtained with an automatic tracking method

Methods based on visual estimation still is the most widely used analysis of the distances that is covered by soccer players during matches, and most description available in the literature were obtained using such an approach. Recently, systems based on computer vision techniques have appeared and the very first results are available for comparisons. The aim of the present study was to analyse the distances covered by Brazilian soccer players and compare the results to the European players', both data measured by automatic tracking system. Four regular Brazilian First Division Championship matches between different teams were filmed. Applying a previously developed automatic tracking system (DVideo, Campinas, Brazil), the results of 55 outline players participated in the whole game (n = 55) are presented. The results of mean distances covered, standard deviations (s) and coefficient of variation (cv) after 90 minutes were 10,012 m, s = 1,024 m and cv = 10.2%, respectively. The results of three-way ANOVA according to playing positions, showed that the distances covered by external defender (10642 ± 663 m), central midfielders (10476 ± 702 m) and external midfielders (10598 ± 890 m) were greater than forwards (9612 ± 772 m) and forwards covered greater distances than central defenders (9029 ± 860 m). The greater distances were covered in standing, walking, or jogging, 5537 ± 263 m, followed by moderate-speed running, 1731 ± 399 m; low speed running, 1615 ± 351 m; high-speed running, 691 ± 190 m and sprinting, 437 ± 171 m. Mean distance covered in the first half was 5,173 m (s = 394 m, cv = 7.6%) highly significant greater (p < 0.001) than the mean value 4,808 m (s = 375 m, cv = 7.8%) in the second half. A minute-by-minute analysis revealed that after eight minutes of the second half, player performance has already decreased and this reduction is maintained throughout the second half. ©Journal of Sports Science and Medicine (2007).

Autoregressive decomposition and pole tracking applied to vocal fold nodule signals

This letter describes a novel algorithm that is based on autoregressive decomposition and pole tracking used to recognize two patterns of speech data: normal voice and disphonic voice caused by nodules. The presented method relates the poles and the peaks of the signal spectrum which represent the periodic components of the voice. The results show that the perturbation contained in the signal is clearly depicted by pole's positions. Their variability is related to jitter and shimmer. The pole dispersion for pathological voices is about 20% higher than for normal voices, therefore, the proposed approach is a more trustworthy measure than the classical ones. © 2007.

Evaluation of tropospheric and ionospheric effects on the geographic localization of data collection platforms

The Brazilian National Institute for Space Research (INPE) is operating the Brazilian Environmental Data Collection System that currently amounts to a user community of around 100 organizations and more than 700 data collection platforms installed in Brazil. This system uses the SCD-1, SCD-2, and CBERS-2 low Earth orbit satellites to accomplish the data collection services. The main system applications are hydrology, meteorology, oceanography, water quality, and others. One of the functionalities offered by this system is the geographic localization of the data collection platforms by using Doppler shifts and a batch estimator based on least-squares technique. There is a growing demand to improve the quality of the geographical location of data collection platforms for animal tracking. This work presents an evaluation of the ionospheric and tropospheric effects on the Brazilian Environmental Data Collection System transmitter geographic location. Some models of the ionosphere and troposphere are presented to simulate their impacts and to evaluate performance of the platform location algorithm. The results of the Doppler shift measurements, using the SCD-2 satellite and the data collection platform (DCP) located in Cuiabá town, are presented and discussed.

Tracking the fin trade: Genetic stock identification in western Atlantic scalloped hammerhead sharks Sphyrna lewini

Location or stock-specific landing data are necessary to improve management of shark stocks, especially those imperiled by overexploitation as a result of the international shark fin trade. In the current absence of catch monitoring directly at extraction sites, genetic stock identification of fins collected from major market supply chain endpoints offers an overlooked but potentially useful approach for tracing the fins back to their geographical, or stock of, origin. To demonstrate the feasibility of this approach, we used mitochondrial control region (mtCR) sequences to trace the broad geographical origin of 62 Hong Kong market-derived Sphyrna lewini fins. Of these fins 21% were derived from the western Atlantic, where this species is listed as 'Endangered' by the International Union for the Conservation of Nature (IUCN). We also show that S. lewini mtCR sequences are geographically segregated in the western Atlantic (overall ΦST = 0.74, n = 177 sharks), indicating that breeding females either remain close to, or home back to, their natal region for parturition. Mixed stock analysis simulations showed that it is possible to estimate the relative contributions of these mitochondrial stocks to fin mixtures in globally sourced trade hubs. These findings underscore the feasibility of using genetic stock identification to source market-derived shark fins to obtain essential and otherwise unavailable data on exploitation levels, and thus to productively inform stock assessment and management of S. lewini and potentially also of other fished shark species. © Inter-Research 2009.

Remote Sensing Detection of atmospheric pollutants using Lidar, Sodar and correlation with air quality data in an industrial area

Optical remote sensing techniques have obvious advantages for monitoring gas and aerosol emissions, since they enable the operation over large distances, far from hostile environments, and fast processing of the measured signal. In this study two remote sensing devices, namely a Lidar (Light Detection and Ranging) for monitoring the vertical profile of backscattered light intensity, and a Sodar (Acoustic Radar, Sound Detection and Ranging) for monitoring the vertical profile of the wind vector were operated during specific periods. The acquired data were processed and compared with data of air quality obtained from ground level monitoring stations, in order to verify the possibility of using the remote sensing techniques to monitor industrial emissions. The campaigns were carried out in the area of the Environmental Research Center (Cepema) of the University of São Paulo, in the city of Cubatão, Brazil, a large industrial site, where numerous different industries are located, including an oil refinery, a steel plant, as well as fertilizer, cement and chemical/petrochemical plants. The local environmental problems caused by the industrial activities are aggravated by the climate and topography of the site, unfavorable to pollutant dispersion. Results of a campaign are presented for a 24- hour period, showing data of a Lidar, an air quality monitoring station and a Sodar. © 2011 SPIE.

Systematic review of the effects of fatigue on spatiotemporal gait parameters

PURPOSE: This systematic review aimed to assess changes on spatiotemporal gait parameters due to fatigue. MATERIAL AND METHOD: A search was carried out in literature published from 1950 to December 2010 and retrieved 771 articles using terms referring to walking and fatigue in the title, abstract or keywords. Two researchers assessed the selection and quality of each article independently. RESULTS: Seven studies were selected for this systematic review, two of which reported on the same data set. Several spatiotemporal parameters were reported to change with fatigue, but the few variables studied in multiple studies, gait speed and stride or step length and stride time, were affected only in single studies. Fatigue appears to modulate spatiotemporal gait parameters, but the effects of fatigue appear to be dependent on the muscles that were fatigued, and age that appears to be a moderator of the effects of fatigue on gait. © 2013 - IOS Press and the authors. All rights reserved.

Tracking the evolution of sex chromosome systems in Melanoplinae grasshoppers through chromosomal mapping of repetitive DNA sequences

Background: The accumulation of repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X 1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X 2X2♀ sex chromosome systems. Results: Our data indicate a non-spreading of heterochromatic blocks and pool of repetitive DNAs (C 0 t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. Conclusions: These results suggest a common origin and subsequent differential accumulation of repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for repetitive DNAs in the diversification of sex chromosome systems in grasshoppers. © 2013Palacios-Gimenez et al.; licensee BioMed Central Ltd.

Análise das ações técnicas de jogadores e das estratégias de finalizações no futebol, a partir do tracking computacional

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)