Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in Sao Paulo, Brazil

The dengue virus has a single-stranded positive-sense RNA genome of similar to 10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1-4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in Sao Jose do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000-2001. Sixty DENV-3 from Sao Jose do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.

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.

Tracking 10-year competitive winning performance of judo athletes across age groups

Little information is available concerning early specialization and competitive success in judo across the early training years. Thus, the present objective was to verify the stability of individual competitive performance of a state-level championship for judo athletes who had been previously successful. For this, 406 athletes from six age groups (9 to 20+ years old) of each sex were followed for 10 years. Using recorded data from the Sao Paulo State Judo Federation beginning in 1999, the scores and standings for these judo players were analyzed. The proportion of medal winners during this period was not constant, differing from the grand mean in all groups of both 204 males and 202 females. At the end of this period, only 7% of the male and 5% of the female athletes had maintained their competitive levels. Successful competitive performance in early judo competition was not associated with success later in adulthood.

Stable MPC for tracking with maximal domain of attraction

In this work, a stable MPC that maximizes the domain of attraction of the closed-loop system is proposed. The proposed approach is suitable to real applications in the sense that it accounts for the case of output tracking, it is offset free if the output target is reachable and minimizes the offset if some of the constraints are active at steady state. The new approach is based on the definition of a Minkowski functional related to the input and terminal constraints of the stable infinite horizon MPC. It is also shown that the domain of attraction is defined by the system model and the constraints, and it does not depend on the controller tuning parameters. The proposed controller is illustrated with small order examples of the control literature. (C) 2011 Elsevier Ltd. All rights reserved.

Robust model predictive controller with output feedback and target tracking

A model predictive controller (MPC) is proposed, which is robustly stable for some classes of model uncertainty and to unknown disturbances. It is considered as the case of open-loop stable systems, where only the inputs and controlled outputs are measured. It is assumed that the controller will work in a scenario where target tracking is also required. Here, it is extended to the nominal infinite horizon MPC with output feedback. The method considers an extended cost function that can be made globally convergent for any finite input horizon considered for the uncertain system. The method is based on the explicit inclusion of cost contracting constraints in the control problem. The controller considers the output feedback case through a non-minimal state-space model that is built using past output measurements and past input increments. The application of the robust output feedback MPC is illustrated through the simulation of a low-order multivariable system.

MPC for tracking zone regions

This paper deals with the problem of tracking target sets using a model predictive control (MPC) law. Some MPC applications require a control strategy in which some system outputs are controlled within specified ranges or zones (zone control), while some other variables - possibly including input variables - are steered to fixed target or set-point. In real applications, this problem is often overcome by including and excluding an appropriate penalization for the output errors in the control cost function. In this way, throughout the continuous operation of the process, the control system keeps switching from one controller to another, and even if a stabilizing control law is developed for each of the control configurations, switching among stable controllers not necessarily produces a stable closed loop system. From a theoretical point of view, the control objective of this kind of problem can be seen as a target set (in the output space) instead of a target point, since inside the zones there are no preferences between one point or another. In this work, a stable MPC formulation for constrained linear systems, with several practical properties is developed for this scenario. The concept of distance from a point to a set is exploited to propose an additional cost term, which ensures both, recursive feasibility and local optimality. The performance of the proposed strategy is illustrated by simulation of an ill-conditioned distillation column. (C) 2010 Elsevier Ltd. All rights reserved.

Adaptive Carrier Tracking for Mars to Earth Communications During Entry, Descent, and Landing

We propose a robust and low complexity scheme to estimate and track carrier frequency from signals traveling under low signal-to-noise ratio (SNR) conditions in highly nonstationary channels. These scenarios arise in planetary exploration missions subject to high dynamics, such as the Mars exploration rover missions. The method comprises a bank of adaptive linear predictors (ALP) supervised by a convex combiner that dynamically aggregates the individual predictors. The adaptive combination is able to outperform the best individual estimator in the set, which leads to a universal scheme for frequency estimation and tracking. A simple technique for bias compensation considerably improves the ALP performance. It is also shown that retrieval of frequency content by a fast Fourier transform (FFT)-search method, instead of only inspecting the angle of a particular root of the error predictor filter, enhances performance, particularly at very low SNR levels. Simple techniques that enforce frequency continuity improve further the overall performance. In summary we illustrate by extensive simulations that adaptive linear prediction methods render a robust and competitive frequency tracking technique.

Improving the tracking capability of adaptive filters via convex combination

As is well known, Hessian-based adaptive filters (such as the recursive-least squares algorithm (RLS) for supervised adaptive filtering, or the Shalvi-Weinstein algorithm (SWA) for blind equalization) converge much faster than gradient-based algorithms [such as the least-mean-squares algorithm (LMS) or the constant-modulus algorithm (CMA)]. However, when the problem is tracking a time-variant filter, the issue is not so clear-cut: there are environments for which each family presents better performance. Given this, we propose the use of a convex combination of algorithms of different families to obtain an algorithm with superior tracking capability. We show the potential of this combination and provide a unified theoretical model for the steady-state excess mean-square error for convex combinations of gradient- and Hessian-based algorithms, assuming a random-walk model for the parameter variations. The proposed model is valid for algorithms of the same or different families, and for supervised (LMS and RLS) or blind (CMA and SWA) algorithms.

Sequence analysis, chromosomal distribution and long-range organization show that rapid turnover of new and old pBuM satellite DNA repeats leads to different patterns of variation in seven species of the Drosophila buzzatii cluster

We aimed to study patterns of variation and factors influencing the evolutionary dynamics of a satellite DNA, pBuM, in all seven Drosophila species from the buzzatii cluster (repleta group). We analyzed 117 alpha pBuM-1 (monomer length 190 bp) and 119 composite alpha/beta (370 bp) pBuM-2 repeats and determined the chromosome location and long-range organization on DNA fibers of major sequence variants. Such combined methodologies in the study of satDNAs have been used in very few organisms. In most species, concerted evolution is linked to high copy number of pBuM repeats. Species presenting low-abundance and scattered distributed pBuM repeats did not undergo concerted evolution and maintained part of the ancestral inter-repeat variability. The alpha and alpha/beta repeats colocalized in heterochromatic regions and were distributed on multiple chromosomes, with notable differences between species. High-resolution FISH revealed array sizes of a few kilobases to over 0.7 Mb and mutual arrangements of alpha and alpha/beta repeats along the same DNA fibers, but with considerable changes in the amount of each variant across species. From sequence, chromosomal and phylogenetic data, we could infer that homogenization and amplification events involved both new and ancestral pBuM variants. Altogether, the data on the structure and organization of the pBuM satDNA give insights into genome evolution including mechanisms that contribute to concerted evolution and diversification.

Low Satellite DNA Variability in Natural Populations of Drosophila antonietae Involved in Different Evolutionary Events

Drosophila antonietae is a cactophilic species that is found in the mesophilic forest of the Parana`-Paraguay river basin and in the dunes of the South Atlantic coast of Brazil. Although the genetic structure of the Parana`-Paraguay river basin populations has already been established, the relationship between these populations and those on the Atlantic coast is controversial. In this study, we compared 33 repetitive units of pBuM-2 satellite DNA isolated from individuals from 8 populations of D. antonietae in these geographic regions, including some populations found within a contact zone with the closely related D. serido. The pBuM-2 sequences showed low interpopulational variability. This result was interpreted as a consequence of both gene flow among the populations and unequal crossing over promoting homogenization of the tandem arrays. The results presented here, together with those of previous studies, highlight the use of pBuM-2 for solving taxonomic conflicts within the D. buzzatii species cluster.

Activated satellite cells in medial rectus muscles of patients with strabismus

PURPOSE. The goal of this study was to determine whether the medial rectus muscles of patients with a history of medial rectus underaction or overaction show alterations in the process of satellite cell activation when compared with normal age-matched control muscles. METHODS. Medial rectus muscles were obtained with consent from adult patients undergoing surgical resection due to medial rectus underaction or overaction and were prepared for histologic examination by fixation and paraffin embedding. Control muscles were obtained from cornea donor eyes of adults who had no history of strabismus or neuromuscular disease. Cross sections were obtained and stained immunohistochemically for the presence of activated satellite cells, as identified by MyoD immunoreactivity, and the presence of the total satellite cell population, as identified by Pax7 immunoreactivity. The percentages of MyoD- and Pax7-positive satellite cells per 100 myofibers in cross section were calculated. RESULTS. As predicted from results in the literature, MyoD-positive satellite cells, indicative of activation, were present in both the control and resected muscles. In the underacting medial rectus muscles, the percentages of MyoD- and Pax7-positive satellite cells, based on the number of myofibers, were approximately twofold higher than the percentages in the control muscles. In the overacting medial rectus muscles, the percentage of MyoD- positive satellite cells was twofold less than in the control muscles, whereas the percentage of Pax7-positive satellite cells significantly increased compared with that in the control specimens. CONCLUSIONS. The presence of an increased number of activated satellite cells in the resected underacting medial rectus muscles and the decreased numbers of activated satellite cells in the overacting muscles was unexpected. The upregulation in the number of MyoD- positive satellite cells in underacting muscles suggests that there is potential for successful upregulation of size in these muscles, as the cellular machinery for muscle repair and regeneration, the satellite cells, is retained and active in patients with medial rectus underaction. The decreased number of activated satellite cells in overacting MR muscle suggests that factors as yet unknown in these overacting muscles are able to affect the number of satellite cells and/or their responsiveness compared with normal age-matched control muscles. These hypotheses are currently being tested.

Tracking the Ovarian Cycle in Black-and-Gold Howlers (Alouatta caraya) by Measuring Fecal Steroids and Observing Vaginal Bleeding

A better understanding of a species` reproductive physiology can help conservation programs to manage primates in the wild and develop assisted reproductive technologies in captivity. We investigated whether measurements of fecal progestin and estrogen metabolites obtained by a radioimmunoassay could be used to monitor the ovarian cycle of Alouatta caraya. We also compared the occurrence of vaginal bleeding with the hormone profiles. We collected fecal samples from 3 adult and 1 subadult captive female over 5 mo and performed vaginal cytology for the adults. The interval between fecal progestin surges in the adult females was 19.11 +/- 2.14 d (n = 18 cycles). Fecal progestin concentrations remained at basal values for 9.83 +/- 2.21 d (n = 18) and rose to elevated values for 9.47 +/- 0.72 d (n = 19). The subadult female showed basal levels of fecal estrogen and progestin concentrations throughout the study, suggesting that our hormone measurements are valid to monitor the ovarian cycle. Bleeding periods coincided with basal levels of fecal estrogens and progestin at intervals of 19.8 +/- 0.9 d and lasted for 4.1 +/- 1.0 d. Although we obtained these data from only 3 individuals, the results indicate that this species likely has a menstrual-type ovarian cycle. These data provide the first endocrine profile for the Alouatta caraya ovarian cycle and are similar to results obtained for other howler species. This similarity is important for comparative studies of howlers, allowing for a better understanding of their reproductive physiology and contributing to a critical information base for managing Alouatta species.

Comparing detection and location performance of perpendicular and parallel broadside GPR antenna orientations

GPR (Ground Penetrating Radar) results are shown for perpendicular broadside and parallel broadside antenna orientations. Performance in detection and localization of concrete tubes and steel tanks is compared as a function of acquisition configuration. The comparison is done using 100 MHz and 200 MHz center frequency antennas. All tubes and tanks are buried at the geophysical test site of IAG/USP in Sao Paulo city, Brazil. The results show that the long steel pipe with a 38-mm diameter was well detected with the perpendicular broadside configuration. The concrete tubes were better detected with the parallel broadside configuration, clearly showing hyperbolic diffraction events from all targets up to 2-m depth. Steel tanks were detected with the two configurations. However, the parallel broadside configuration was generated to a much lesser extent an apparent hyperbolic reflection corresponding to constructive interference of diffraction hyperbolas of adjacent targets placed at the same depth. Vertical concrete tubes and steel tanks were better contained with parallel broadside antennas, where the apexes of the diffraction hyperbolas better corresponded to the horizontal location of the buried target disposition. The two configurations provide details about buried targets emphasizing how GPR multi-component configurations have the potential to improve the subsurface image quality as well as to discriminate different buried targets. It is judged that they hold some applicability in geotechnical and geoscientific studies. (C) 2009 Elsevier B.V. All rights reserved.

Satellite Rainfall Estimates Over South America - Possible Applicability to the Water Management of Large Watersheds1

This work analyzes high-resolution precipitation data from satellite-derived rainfall estimates over South America, especially over the Amazon Basin. The goal is to examine whether satellite-derived precipitation estimates can be used in hydrology and in the management of larger watersheds of South America. High spatial-temporal resolution precipitation estimates obtained with the CMORPH method serve this purpose while providing an additional hydrometeorological perspective on the convective regime over South America and its predictability. CMORPH rainfall estimates at 8-km spatial resolution for 2003 and 2004 were compared with available rain gauge measurements at daily, monthly, and yearly accumulation time scales. The results show the correlation between satellite-derived and gauge-measured precipitation increases with accumulation period from daily to monthly, especially during the rainy season. Time-longitude diagrams of CMORPH hourly rainfall show the genesis, strength, longevity, and phase speed of convective systems. Hourly rainfall analyses indicate that convection over the Amazon region is often more organized than previously thought, thus inferring that basin scale predictions of rainfall for hydrological and water management purposes have the potential to become more skillful. Flow estimates based on CMORPH and the rain gauge network are compared to long-term observed average flow. The results suggest this satellite-based rainfall estimation technique has considerable utility. Other statistics for monthly accumulations also suggest CMORPH can be an important source of rainfall information at smaller spatial scales where in situ observations are lacking.

Chromosome polymorphism in Astyanax fasciatus (Teleostei, Characidae). 2-Chromosomal location of a satellite DNA

Studies about composition of repetitive sequences and their chromosomal location have been helpful to evolutionary studies in many distinct organisms. In order to keep on assessing the possible relationships among different cytotypes of Astyanax fasciatus (Teleostei, Characiformes) in the Mogi-Guacu River (Sao Paulo State, Brazil), C-banding, chromomycin A 3 staining, and fluorescent in situ hybridization with a repetitive DNA sequence (As51) isolated from Astyanax scabripinnis were performed in the present work. The constitutive heterochromatin was distributed in terminal regions on long arms of submetacentric, subtelocentric, and acrocentric chromosomes and in the terminal region on short arms of a pair of submetacentric chromosomes in both standard cytotypes. This latter heterochromatic site was also GC-rich, as revealed by chromomycin A(3) staining, corresponding to the nucleolar organizer region (NOR), as shown by previous studies. The sites of the satellite As51 DNA were located in terminal regions on long arms of several chromosomes. Some variant karyotypic forms, which diverge from the two standard cytotypes, also presented distinctive chromosomes carrying As51 satellite DNA. It is possible that the standard 2n = 46 cytotype represents an invader population in the Mogi-Guacu River able to interbreed with the resident standard 2n = 48 cytotype. Therefore, the variant karyotypes would be related to a possible viable offspring, where complementary chromosomal rearrangements could favor new locations of the satellite DNA analyzed. Copyright (C) 2008 S. Karger AG, Basel