A phylogenetic study of canine parvovirus type 2c in midwestern Brazil

Since the late 1970s, canine parvovirus type 2 (CPV-2) has emerged as a causative agent of fatal severe acute hemorrhagic enteritis in dogs. To date, three antigenic types of CPV-2 were described worldwide (CPV-2a/b/c). This study was conducted to determine the variants of CPV-2 circulating in dogs from the Cuiabá Municipality in Midwestern Brazil. Out of 50 fecal samples, collected between 2009 and 2011, 27 tested positive for CPV-2. A 583 bp fragment of the VP2 gene was amplified by PCR, 13 representative samples were analyzed further by DNA sequencing. All strains were characterized as CPV-2c, displayed a low genetic variability although observed several amino acid substitution. These findings indicated that CPV-2c has been circulating in dogs from the Cuiabá Municipality in Midwestern Brazil.

Parasites of the freshwater fish trade in Brazil: science metric study

This paper presents a science metric study of parasites of fish farming in Brazil, including a significant review of the literature. The methodology used was based on researching articles in three different databases, carried out ​on May 2012: ISI (Institute for Scientific Information), SciELO (Scientific Electronic Library Online), and Google Academic. The number of articles on fish parasites is mounting (currently over 110), having much increased since 1995. However, the quantity is still low compared with the amount of papers on parasites of fish from natural environments. In Brazil, the farmed fish that have been studied the most are pacu, tilapia and tambaqui. Monogeneans represent the most prevalent group, followed by protozoa and crustaceans. The regions most researched were the southeast and south, making up 84% of the total literature. The main issue addressed in articles was pathology, followed by treatment and record. In conclusion, the treatment of parasitic diseases of farmed fish in Brazil is still incipient, highlighting the importance and usefulness of management practices to prevent the occurrence of health problems.

Enterohemorrhagic Escherichia coli O157: H7 from healthy dairy cattle in Mid-West Brazil: occurrence and molecular characterization

Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 represents the major Shiga toxin-producing E. coli (STEC) strain related to large outbreaks and severe diseases such as hemorrhagic colitis (HC) and the potentially lethal hemolytic uremic syndrome (HUS). The aim of this study was to report the occurrence and molecular characterization of O157:H7 isolates obtained by rectal swab from 52 healthy dairy cattle belonging to 21 farms in Mid-West of Brazil. Detection of 16SrRNA, stx1, stx2, rfbO157, fliCh7, eae, ehxA, saa, cnf1, chuA, yjaA and TSPE4.C2 genes was performed by PCR. The isolates were further characterized by serotyping. Two hundred and sixty E. coli isolates were obtained, of which 126 were characterized as STEC. Two isolates from the same cow were identified as serotype O157:H7. Both isolates presented the stx2, eae, ehxA, saa and cnf1 virulence factor genes and the chuA gene in the phylogenetic classification (virulent group D), suggesting that they were clones. The prevalence of O157:H7 was found to be 1.92% (1/52 animals), demonstrating that healthy dairy cattle from farms in the Mid-West of Brazil are an important reservoir for highly pathogenic E. coli O157:H7.

Patterns of parasitism by Amblyomma rotundatum (Ixodidae) on Rhinella schneideri (Bufonidae) in islands of São Francisco River, Minas Gerais, Brazil

Abstract: We sampled ticks from specimens of the rococo toad Rhinella schneideriby flannel dragging on two Islands located in the São Francisco River near the Três Marias hydroelectric dam, southeastern Brazil. A total of 120 toads was examined, of which 63 (52.5%) were parasitized only by Amblyomma rotundatumtotaling 96 larvae, 163 nymphs and 134 females. The burden of parasitism ranged from one to 43 ticks, with a mean intensity of infestation of 6.2±5.5 ticks per host. The tick A. rotundatumexhibited highly aggregated distribution. Peak abundance of larvae and nymphs occurred in the dry season (May to September), whereas peak abundance of females occurred in the wet season (October to April). We collected most ticks near the head and hind limbs of R. schneideri. The finding of two engorged A. rotundatumnymphs in the same resting places of two toads and the absence of this species in the dragged areas suggest a nidicolous behavior at the studied site.

The survival and establishment potential of spores of Cyathea delgadii Sternb. in soils from Itirapina and Moji Guaçu (SP), Brazil

Germination of spores of Cyathea delgadii was carried out in soils collected in March 1997 (rainy season) at three depths (0-5, 5-10 and 10-15 cm) from the cerrado, open-cerrado, gallery forest and marsh at Moji Guaçu and cerradão, cerrado and gallery forest at Pedregulho, in Itirapina, both in the state of São Paulo, Brazil. Viability of spores mixed with soil and buried in the cerrado at the Reserva in Moji Guaçu were conducted for up to 10 months. The spores germinated in all soils. Germination in the soils was significantly lower than in distilled water. Germination was higher in soils from the gallery forest and cerrado than from open cerrado, cerradão and marsh. The germination was the same in the soil samples from the three depths of gallery forest, cerrado and cerradão. Spores of C. delgadii maintained viability longer when buried in cerrado soil than when dry stored at 4°C. After 10 months germination was 50.5% in buried spores against 3.8% in spores of the same age and harvest, stored at 4°C.

Temporal dynamics of two species of Chaetophoraceae (Chlorophyta) in tropical streams of São Paulo State, Southeastern Brazil

Temporal dynamics of the chaetophoracean green algae Chaetophora elegans (Roth) C.A. Agardh and Stigeoclonium amoenum Kützing populations was investigated biweekly during late autumn trhough early spring (April to October) in two tropical streams from northwestern São Paulo State, southeastern Brazil. Abundances of one population of each species was evaluated by the quadrat technique in terms of percent cover and frequency. The fluctuations were related to the following stream variables: temperature, turbidity, specific conductance, pH, oxygen saturation, depth, substratum type, current velocity, irradiance and nutrients. Percent cover and frequency of C. elegans had lower values throughout the study period and was positively correlated to rainfall. Other correlations (i.e. positive of percent cover with depth and current velocity and negative with irradiance) were consistently found, reinforcing the strong influence of rainfall. On the other hand, percent cover and frequency of S. amoenum had higher values, with maximum growth from June to September. Percent cover was negatively correlated to rainfall. Results suggest the precipitation regime as the most important driving force to temporal changes in both populations, but playing different roles in each one. The gelatinous thallus of C. elegans seem to be favored by the increment of current velocity, since higher flows can improve the nutrient uptake by means of reduction in diffusion shell without promoting excessive drag force. In contrast, tufts of S. amoenum are, presumably, more exposed to drag force, and, consequently, more susceptible to mechanical damage effects due to higher current velocities.

Molecular systematics of Thorea (Rhodophyta, Thoreales) species in Brazil

This study aimed to evaluate species level taxonomy and phylogenetic relationship among Thorea species in Brazil and other regions of the world using two molecular markers - RUBISCO large subunit plastid gene (rbcL) and nuclear small-subunit ribosomal DNA (SSU rDNA). Three samples of Thorea from Brazil (states of Mato Grosso do Sul and São Paulo) and one sample from Dominican Republic (DR) were sequenced. Analyses based on partial sequences of rbcL (1,282 bp) and complete sequences of SSU (1,752 bp) were essentially congruent and revealed that Thoreales formed a distinct monophyletic clade, which had two major branches with high support, representing the genera Thorea and Nemalionopsis. Thorea clade had four main branches with high support for all analyses, each one representing the species: 1) T. gaudichaudii C. Agardh from Asia (Japan and Philippines) - this clade occurred only in the rbcL analyses; 2) T. violacea Bory from Asia (Japan) and North America (U.S.A. and DR); 3) T. hispida (Thore) Desvaux from Europe (England) and Asia (Japan); 4) a distinct group with the three Brazilian samples (sequence identity: rbcL 97.2%, 1,246 bp; SSU 96.0-98.1%, 1,699-1,720 bp). The Brazilian samples clearly formed a monophyletic clade based on both molecular markers and was interpreted as a separate species, for which we resurrected the name T. bachmannii Pujals. Morphological and molecular evidences indicate that the Thoreales is well-resolved at ordinal and generic levels. In contrast, Thorea species recognized by molecular data require additional characters (e.g. reproductive and chromosome numbers) to allow consistent and reliable taxonomic circumscription aiming at a world revision based on molecular and morphological evidences.

Planktonic diatoms in lotic and lentic environments in the Lago dos Tigres hydrologic system (Britânia, Goiás, Brazil): Coscinodiscophyceae and Fragilariophyceae

A floristic study of Coscinodiscophyceae and Fragilariophyceae in the Lago dos Tigres hydrologic system is presented. Phytoplankton samples were collected with a plankton net (25 µm mesh) at 11 sampling stations, three in lotic areas and eight in lacustrine zones. Eleven species of Coscinodiscophyceae and eight of Fragilariophyceae were identified; descriptions, comments, their geographic distributions for the midwestern region of Brazil, type of environment (lentic/lotic), and illustrations are provided. Among the taxa found, 13 were recorded for the first time in midwestern Brazil: Aulacoseira alpigena, A. distans, A. granulata var. angustissima, A. granulata var. valida, A. muzzanensis, Discostella stelligera var. stelligera, Fragilaria capucina var. fragilarioides, F. delicatissima var. delicatissima, F. javanica, Pleurosira laevis, Staurosira acutirostrata, Staurosirella crassa, and Ulnaria ulna.

Occurrence of Akodon cursor (Rodentia, Cricetidae) with 14, 15 and 16 chromosome cytotypes in the same geographic area in Southern Brazil

The karyotype of Akodon cursor (initially identified as A. arviculoides) had been reported with chromosomal numbers 14 and 15 in the South and Southeast and 16 in Northeastern Brazil. We found the three cytotypes in a region of Southern Brazil. The G-band patterns of these specimens were the same as those from southeastern and northeastern regions. Seventeen different combinations of chromosomes due to a complex rearrangement in pair 1 and pericentric inversions in pairs 2 and 3 were identified. Seven of these combinations are new to in the literature.

Distribution of HCV genotypes among different exposure categories in Brazil

Hepatitis C virus (HCV) infection is widespread and responsible for more than 60% of chronic hepatitis cases. HCV presents a genetic variability which has led to viral classification into at least 6 genotypes and a series of subtypes. These variants present characteristic geographical distribution, but their association with different responses to treatment with interferon and severity of disease still remains controversial. The aim of this study was to investigate the patterns of distribution of HCV genotypes among different exposure categories in Brazil. Two hundred and fifty anti-HCV positive samples were submitted to HCV-RNA detection by RT-PCR and their genotype was determined by restriction fragment length polymorphism (RFLP) analysis. In addition, the genotype/subtype of 60 samples was also determined by a reverse hybridization assay. HCV 1 was the most prevalent (72.0%), followed by type 3 (25.3%), HCV 2 (2.0%) and HCV 4 (0.7%). The HCV genotype distribution varied among the different exposure categories, with HCV 1 being more frequent among blood donors, hemophiliacs and hemodialysis patients. A high frequency of HCV 3 was observed in cirrhotic patients, blood donors from the South of Brazil and injecting drug users (IDUs). The general distribution of the HCV genotype in Brazil is similar to that in other regions of the world.

Adaptive Markov chain Monte Carlo and Bayesian filtering for state space models

This thesis is concerned with the state and parameter estimation in state space models. The estimation of states and parameters is an important task when mathematical modeling is applied to many different application areas such as the global positioning systems, target tracking, navigation, brain imaging, spread of infectious diseases, biological processes, telecommunications, audio signal processing, stochastic optimal control, machine learning, and physical systems. In Bayesian settings, the estimation of states or parameters amounts to computation of the posterior probability density function. Except for a very restricted number of models, it is impossible to compute this density function in a closed form. Hence, we need approximation methods. A state estimation problem involves estimating the states (latent variables) that are not directly observed in the output of the system. In this thesis, we use the Kalman filter, extended Kalman filter, Gauss–Hermite filters, and particle filters to estimate the states based on available measurements. Among these filters, particle filters are numerical methods for approximating the filtering distributions of non-linear non-Gaussian state space models via Monte Carlo. The performance of a particle filter heavily depends on the chosen importance distribution. For instance, inappropriate choice of the importance distribution can lead to the failure of convergence of the particle filter algorithm. In this thesis, we analyze the theoretical Lᵖ particle filter convergence with general importance distributions, where p ≥2 is an integer. A parameter estimation problem is considered with inferring the model parameters from measurements. For high-dimensional complex models, estimation of parameters can be done by Markov chain Monte Carlo (MCMC) methods. In its operation, the MCMC method requires the unnormalized posterior distribution of the parameters and a proposal distribution. In this thesis, we show how the posterior density function of the parameters of a state space model can be computed by filtering based methods, where the states are integrated out. This type of computation is then applied to estimate parameters of stochastic differential equations. Furthermore, we compute the partial derivatives of the log-posterior density function and use the hybrid Monte Carlo and scaled conjugate gradient methods to infer the parameters of stochastic differential equations. The computational efficiency of MCMC methods is highly depend on the chosen proposal distribution. A commonly used proposal distribution is Gaussian. In this kind of proposal, the covariance matrix must be well tuned. To tune it, adaptive MCMC methods can be used. In this thesis, we propose a new way of updating the covariance matrix using the variational Bayesian adaptive Kalman filter algorithm.

Prevalence of hepatitis C virus (HCV) infection and HCV genotypes of hemodialysis patients in Salvador, Northeastern Brazil

Hepatitis C virus (HCV) infection has been identified as the major cause of chronic liver disease among patients on chronic hemodialysis (HD), despite the important reduction in risks obtained by testing candidate blood donors for anti-HCV antibodies and the use of recombinant erythropoietin to treat anemia. A cross-sectional study was performed to estimate the prevalence of HCV infection and genotypes among HD patients in Salvador, Northeastern Brazil. Anti-HCV seroprevalence was determined by ELISA in 1243 HD patients from all ten different dialysis centers of the city. HCV infection was confirmed by RT-PCR and genotyping was performed by restriction fragment length polymorphism. Anti-HCV seroprevalence among HD patients was 10.5% (95% CI: 8.8-12.3) (Murex anti-HCV, Abbott Murex, Chicago, IL, USA). Blood samples for qualitative HCV detection and genotyping were collected from 125/130 seropositive HD patients (96.2%). HCV-RNA was detected in 92/125 (73.6%) of the anti-HCV-positive patients. HCV genotype 1 (77.9%) was the most prevalent, followed by genotype 3 (10.5%) and genotype 2 (4.6%). Mixed infections of genotypes 1 and 3 were found in 7.0% of the total number of patients. The present results indicate a significant decrease in anti-HCV prevalence from 23.8% detected in a study carried out in 1994 to 10.5% in the present study. The HCV genotype distribution was closely similar to that observed in other hemodialysis populations in Brazil, in local candidate blood donors and in other groups at risk of transfusion-transmitted infection.

Plasma amino acids in pregnancy, placental intervillous space and preterm newborn infants

Plasma amino acid levels have never been studied in the placental intervillous space of preterm gestations. Our objective was to determine the possible relationship between plasma amino acids of maternal venous blood (M), of the placental intervillous space (PIVS) and of the umbilical vein (UV) of preterm newborn infants. Plasma amino acid levels were analyzed by ion-exchange chromatography in M from 14 parturients and in the PIVS and UV of their preterm newborn infants. Mean gestational age was 34 ± 2 weeks, weight = 1827 ± 510 g, and all newborns were considered adequate for gestational age. The mean Apgar score was 8 and 9 at the first and fifth minutes. Plasma amino acid values were significantly lower in M than in PIVS (166%), except for aminobutyric acid. On average, plasma amino acid levels were significantly higher in UV than in M (107%) and were closer to PIVS than to M values, except for cystine and aminobutyric acid (P < 0.05). Comparison of the mean plasma amino acid concentrations in the UV of preterm to those of term newborn infants previously studied by our group showed no significant difference, except for proline (P < 0.05), preterm > term. These data suggest that the mechanisms of active amino acid transport are centralized in the syncytiotrophoblast, with their passage to the fetus being an active bidirectional process with asymmetric efflux. PIVS could be a reserve amino acid space for the protection of the fetal compartment from inadequate maternal amino acid variations.

Use of alcohol among the inhabitants of the 107 largest cities in Brazil - 2001

Alcohol is part of the history of humanity, seemingly as a result of countless factors including the easy production of alcoholic beverages in practically all regions of the world. The authors studied aspects of the use of and the dependence on alcohol in Brazil, through a household survey conducted by Centro Brasileiro de Informações sobre Drogas Psicotrópicas (CEBRID). A total of 8,589 interviews were held in 107 of the largest cities in Brazil, all of them with more than 200 thousand inhabitants. The study was planned to gather information within the household environment about a stratified probabilistic sample obtained in three selection phases: 1) the censitaire sectors for each municipality, 2) a systematic randomized sampling, and 3) drafting a respondent by lot in each household to provide information. Approximately 11.2% of the subjects were concerned with their own consumption of alcohol. The signs/symptoms of the syndrome of dependence evident in a greater percentage were the desire to stop or reduce the use of alcohol and to stop or reduce resorting to alcoholic beverages more often than desired, as reported by 14.5 and 9.4% of the respondents, respectively. The regions in Brazil with the highest percentage of dependents were the North (16.3%) and the Northeast (19.9%). According to the estimates obtained in the survey, 5.2% of the teenagers were concerned about the use of alcohol. The estimates obtained in this survey reveal a need to implant specific preventive programs for the problem of alcohol, especially for the very young.

Correlates of C-reactive protein levels in young adults: a population-based cohort study of 3827 subjects in Brazil

The socio-demographic, behavioral and anthropometric correlates of C-reactive protein levels were examined in a representative young adult Brazilian population. The 1982 Pelotas Birth Cohort Study (Brazil) recruited over 99% of births in the city of Pelotas that year (N = 5914). Individuals belonging to the cohort have been prospectively followed up. In 2004-2005, 77.4% of the cohort was traced, members were interviewed and 3827 individuals donated blood. Analyses of the outcome were based on a conceptual model that differentiated confounders from potential mediators. The following independent variables were studied in relation to levels of C-reactive protein in sex-stratified analyses: skin color, age, family income, education, parity, body mass index, waist circumference, smoking, fat/fiber/alcohol intake, physical activity, and minor psychiatric disorder. Geometric mean (95% confidence interval) C-reactive protein levels for the 1919 males and 1908 females were 0.89 (0.84-0.94) and 1.96 mg/L (1.85-2.09), respectively. Pregnant women and those using oral contraceptive therapies presented the highest C-reactive protein levels and all sub-groups of women had higher levels than men (P < 0.001). Significant associations between C-reactive protein levels were observed with age, socioeconomic indicators, obesity status, smoking, fat and alcohol intake, and minor psychiatric disorder. Associations were stronger at higher levels of C-reactive protein and some associations were sex-specific. We conclude that both distal (socio-demographic) and proximal (anthropometric and behavioral) factors exert strong effects on C-reactive protein levels and that the former are mediated to some degree by the latter.