Spatio-temporal modeling of agricultural yield data with an application to pricing crop insurance contracts

This article presents a statistical model of agricultural yield data based on a set of hierarchical Bayesian models that allows joint modeling of temporal and spatial autocorrelation. This method captures a comprehensive range of the various uncertainties involved in predicting crop insurance premium rates as opposed to the more traditional ad hoc, two-stage methods that are typically based on independent estimation and prediction. A panel data set of county-average yield data was analyzed for 290 counties in the State of Parana (Brazil) for the period of 1990 through 2002. Posterior predictive criteria are used to evaluate different model specifications. This article provides substantial improvements in the statistical and actuarial methods often applied to the calculation of insurance premium rates. These improvements are especially relevant to situations where data are limited.

Dosage-dependent shift in the spore community of arbuscular mycorrhizal fungi following application of tannery sludge

The controlled disposal of tannery sludge in agricultural soils is a viable alternative for recycling such waste; however, the impact of this practice on the arbuscular mycorrhizal fungi (AMF) communities is not well understood. We studied the effects of low-chromium tannery sludge amendment in soils on AMF spore density, species richness and diversity, and root colonization levels. Sludge was applied at four doses to an agricultural field in Rolandia, Parana state, Brazil. The sludge was left undisturbed on the soil surface and then the area was harrowed and planted with corn. The soil was sampled at four intervals and corn roots once within a year (2007/2008). AMF spore density was low (1 to 49 spores per 50 cm(3) of soil) and decreased as doses of tannery sludge increased. AMF root colonization was high (64%) and unaffected by tannery sludge. Eighteen AMF species belonging to six genera (Acaulospora, Glomus, Gigaspora, Scutellospora, Paraglomus, and Ambispora) were recorded. At the sludge doses of 9.0 and 22.6 Mg ha(-1), we observed a decrease in AMF species richness and diversity, and changes in their relative frequencies. Hierarchical grouping analysis showed that adding tannery waste to the soil altered AMF spore community in relation to the control, modifying the mycorrhizal status of soil and selectively favoring the sporulation of certain species.

Assessing the association between phenolic compounds and the antioxidant activity of Brazilian red wines using chemometrics

The objective of this study was to evaluate the association among chemical parameters, the commercial value, and the antioxidant activity of Brazilian red wines using chemometric techniques. Twenty-nine samples from five different varieties were assessed. Samples were separated into three groups using hierarchical cluster analysis: cluster 1 presented the highest antioxidant activity towards DPPH (68.51% of inhibition) and ORAC (30,918.64 mu mol Trolox Equivalents/L), followed by cluster 3 (DPPH = 59.36% of inhibition: ORAC = 25,255.02 mu mol Trolox Equivalents/L) and then cluster 2 (DPPH = 46.67% of inhibition; ORAC = 19,395.74 gmol Trolox Equivalents/L). Although the correlation between the commercial value and the antioxidant activity on DPPH and ORAC was not statistically significant (P = 0.13 and P = 0.06, respectively), cluster 1 grouped the samples with higher commercial values. Cluster analysis applied to the variables suggested that non-anthocyanin flavonoids were the main phenolic class exerting antioxidant activity on Brazilian red wines. (C) 2010 Elsevier Ltd. All rights reserved.

Novel benzofuroxan derivatives against multidrug-resistant Staphylococcus aureus strains: Design using Topliss` decision tree, synthesis and biological assay

The aim of this study was the design of a set of benzofuroxan derivatives as antimicrobial agents exploring the physicochemical properties of the related substituents. Topliss` decision tree approach was applied to select the substituent groups. Hierarchical cluster analysis was also performed to emphasize natural clusters and patterns. The compounds were obtained using two synthetic approaches for reducing the synthetic steps as well as improving the yield. The minimal inhibitory concentration method was employed to evaluate the activity against multidrug-resistant Staphylococcus aureus strains. The most active compound was 4-nitro-3-(trifluoromethyl)[N`-(benzofuroxan-5-yl) methylene] benzhydrazide (MIC range 12.7-11.4 mu g/mL), pointing out that the antimicrobial activity was indeed influenced by the hydrophobic and electron-withdrawing property of the substituent groups 3-CF(3) and 4-NO(2), respectively. (C) 2011 Elsevier Ltd. All rights reserved.

Monitoring the authenticity of Brazilian UHT milk: A chemometric approach

In this work, chemometric methods are reported as potential tools for monitoring the authenticity of Brazilian ultra-high temperature (UHT) milk processed in industrial plants located in different regions of the country. A total of 100 samples were submitted to the qualitative analysis of adulterants such as starch, chlorine, formal. hydrogen peroxide and urine. Except for starch, all the samples reported, at least, the presence of one adulterant. The use of chemometric methodologies such as the Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) enabled the verification of the occurrence of certain adulterations in specific regions. The proposed multivariate approaches may allow the sanitary agency authorities to optimise materials, human and financial resources, as they associate the occurrence of adulterations to the geographical location of the industrial plants. (c) 2010 Elsevier Ltd. All rights reserved.

A chemometric study on the analgesic activity of cannabinoid compounds using SDA, KNN and SIMCA methods

The supervised pattern recognition methods K-Nearest Neighbors (KNN), stepwise discriminant analysis (SDA), and soft independent modelling of class analogy (SIMCA) were employed in this work with the aim to investigate the relationship between the molecular structure of 27 cannabinoid compounds and their analgesic activity. Previous analyses using two unsupervised pattern recognition methods (PCA-principal component analysis and HCA-hierarchical cluster analysis) were performed and five descriptors were selected as the most relevants for the analgesic activity of the compounds studied: R (3) (charge density on substituent at position C(3)), Q (1) (charge on atom C(1)), A (surface area), log P (logarithm of the partition coefficient) and MR (molecular refractivity). The supervised pattern recognition methods (SDA, KNN, and SIMCA) were employed in order to construct a reliable model that can be able to predict the analgesic activity of new cannabinoid compounds and to validate our previous study. The results obtained using the SDA, KNN, and SIMCA methods agree perfectly with our previous model. Comparing the SDA, KNN, and SIMCA results with the PCA and HCA ones we could notice that all multivariate statistical methods classified the cannabinoid compounds studied in three groups exactly in the same way: active, moderately active, and inactive.

The phylogeography of African Brazilians

Background/Aims: Approximately four million Africans were taken as slaves to Brazil, where they interbred extensively with Amerindians and Europeans. We have previously shown that while most White Brazilians carry Y chromosomes of European origin, they display high proportions of African and Amerindian mtDNA lineages, because of sex-biased genetic admixture. Methods: We studied the Y chromosome and mtDNA haplogroup structure of 120 Black males from Sao Paulo, Brazil. Results: Only 48% of the Y chromosomes, but 85% of the mtDNA haplogroups were characteristic of sub-Saharan Africa, confirming our previous observation of sexually biased mating. We mined literature data for mtDNA and Y chromosome haplogroup frequencies for African native populations from regions involved in Atlantic Slave Trade. Principal Components Analysis and Bayesian analysis of population structure revealed no genetic differentiation of Y chromosome marker frequencies between the African regions. However, mtDNA examination unraveled considerable genetic structure, with three clusters at Central-West Africa, West Africa and Southeast Africa. A hypothesis is proposed to explain this structure. Conclusion: Using these mtDNA data we could obtain for the first time an estimate of the relative ancestral contribution of Central-West (0.445), West (0.431) and Southeast Africa (0.123) to African Brazilians from Sao Paulo. These estimates are consistent with historical information. Copyright (c) 2008 S. Karger AG, Basel.

Molecular Characterization, Distribution, and Dynamics of Hepatitis C Virus Genotypes in Blood Donors in Colombia

Hepatitis C virus (HCV) is a frequent cause of acute and chronic hepatitis and a leading cause for cirrhosis of the liver and hepatocellular carcinoma. HCV is classified in six major genotypes and more than 70 subtypes. In Colombian blood banks, serum samples were tested for anti-HCV antibodies using a third-generation ELISA. The aim of this study was to characterize the viral sequences in plasma of 184 volunteer blood donors who attended the ""Banco Nacional de Sangre de la Cruz Roja Colombiana,`` Bogota, Colombia. Three different HCV genomic regions were amplified by nested PCR. The first of these was a segment of 180 bp of the 5`UTR region to confirm the previous diagnosis by ELISA. From those that were positive to the 5`UTR region, two further segments were amplified for genotyping and subtyping by phylogenetic analysis: a segment of 380 bp from the NS5B region; and a segment of 391 bp from the E1 region. The distribution of HCV subtypes was: 1b (82.8%), 1a (5.7%), 2a (5.7%), 2b (2.8%), and 3a (2.8%). By applying Bayesian Markov chain Monte Carlo simulation, it was estimated that HCV-1b was introduced into Bogota around 1950. Also, this subtype spread at an exponential rate between about 1970 to about 1990, after which transmission of HCV was reduced by anti-HCV testing of this population. Among Colombian blood donors, HCV genotype 1b is the most frequent genotype, especially in large urban conglomerates such as Bogota, as is the case in other South American countries. J. Med. Virol. 82: 1889-1898, 2010. (C) 2010 Wiley-Liss, Inc.

Bronchoscopic lung-volume reduction with Exhale airway stents for emphysema (EASE trial): randomised, sham-controlled, multicentre trial

Background Airway bypass is a bronchoscopic lung-volume reduction procedure for emphysema whereby transbronchial passages into the lung are created to release trapped air, supported with paclitaxel-coated stents to ease the mechanics of breathing. The aim of the EASE (Exhale airway stents for emphysema) trial was to evaluate safety and efficacy of airway bypass in people with severe homogeneous emphysema. Methods We undertook a randomised, double-blind, sham-controlled study in 38 specialist respiratory centres worldwide. We recruited 315 patients who had severe hyperinflation (ratio of residual volume [RV] to total lung capacity of >= 0.65). By computer using a random number generator, we randomly allocated participants (in a 2:1 ratio) to either airway bypass (n=208) or sham control (107). We divided investigators into team A (masked), who completed pre-procedure and post-procedure assessments, and team B (unmasked), who only did bronchoscopies without further interaction with patients. Participants were followed up for 12 months. The 6-month co-primary efficacy endpoint required 12% or greater improvement in forced vital capacity (FVC) and 1 point or greater decrease in the modified Medical Research Council dyspnoea score from baseline. The composite primary safety endpoint incorporated five severe adverse events. We did Bayesian analysis to show the posterior probability that airway bypass was superior to sham control (success threshold, 0.965). Analysis was by intention to treat. This study is registered with ClinicalTrials.gov, number NCT00391612. Findings All recruited patients were included in the analysis. At 6 months, no difference between treatment arms was noted with respect to the co-primary efficacy endpoint (30 of 208 for airway bypass vs 12 of 107 for sham control; posterior probability 0.749, below the Bayesian success threshold of 0.965). The 6-month composite primary safety endpoint was 14.4% (30 of 208) for airway bypass versus 11.2% (12 of 107) for sham control (judged non-inferior, with a posterior probability of 1.00 [Bayesian success threshold >0.95]). Interpretation Although our findings showed safety and transient improvements, no sustainable benefit was recorded with airway bypass in patients with severe homogeneous emphysema.

Hepatitis Delta virus genotype 8 infection in Northeast Brazil: Inheritance from African slaves?

Hepatitis Delta virus (HDV) is endemic worldwide, but its prevalence varies in different geographical areas. While in the Brazilian Amazon, HDV is known to be endemic and to represent a significant public health problem, few studies have assessed its prevalence in other regions in the country. This study evaluated the seroprevalence of HDV among HBsAg chronic carriers from Maranhao state, a region located in the Northeast of Brazil. Among 133 patients, 5 had anti-HD, of whom 3 had HDV RNA. HDV genotypes were characterized by Bayesian phylogenetic analysis of nucleotide sequences from the HDAg coding region. HDV-3 was identified in one patient who lives in Maranhao, but was born in Amazonas state (Western Amazon basin). Phylogenetic analysis shows that this HDV-3 sequence grouped with other HDV-3 sequences isolated in this state, which suggests that the patient probably contracted HDV infection there. Surprisingly, the other two patients were infected with HDV-8, an African genotype. These patients were born and have always lived in Urbano Santos, a rural county of Maranhao state, moreover they had never been to Africa and denied any contact with people from that continent. This is the first description of the HDV-8 in non-native African populations. This genotype may have been introduced to Brazil through the slaves brought to the country from the West Africa regions during the 16-18th centuries. Our results indicate that the need of clinical and epidemiological studies to investigate the presence of this infection in other areas in Brazil. (C) 2011 Elsevier B.V. All rights reserved.

A multilevel model for the study of breastfeeding determinants in Brazil

The benefits of breastfeeding for the children`s health have been highlighted in many studies. The innovative aspect of the present study lies in its use of a multilevel model, a technique that has rarely been applied to studies on breastfeeding. The data reported were collected from a larger study, the Family Budget Survey-Pesquisa de Orcamentos Familiares, carried out between 2002 and 2003 in Brazil that involved a sample of 48 470 households. A representative national sample of 1477 infants aged 0-6 months was used. The statistical analysis was performed using a multilevel model, with two levels grouped by region. In Brazil, breastfeeding prevalence was 58%. The factors that bore a negative influence on breastfeeding were over four residents living in the same household [odds ratio (OR) = 0.68, 90% confidence interval (CI) = 0.51-0.89] and mothers aged 30 years or more (OR = 0.68, 90% CI = 0.53-0.89). The factors that positively influenced breastfeeding were the following: higher socio-economic levels (OR = 1.37, 90% CI = 1.01-1.88), families with over two infants under 5 years (OR = 1.25, 90% CI = 1.00-1.58) and being a resident in rural areas (OR = 1.25, 90% CI = 1.00-1.58). Although majority of the mothers was aware of the value of maternal milk and breastfed their babies, the prevalence of breastfeeding remains lower than the rate advised by the World Health Organization, and the number of residents living in the same household along with mothers aged 30 years or older were both factors associated with early cessation of infant breastfeeding before 6 months.

DENSITY PROFILE, VELOCITY ANISOTROPY, AND LINE-OF-SIGHT EXTERNAL CONVERGENCE OF SLACS GRAVITATIONAL LENSES

Data from 58 strong-lensing events surveyed by the Sloan Lens ACS Survey are used to estimate the projected galaxy mass inside their Einstein radii by two independent methods: stellar dynamics and strong gravitational lensing. We perform a joint analysis of these two estimates inside models with up to three degrees of freedom with respect to the lens density profile, stellar velocity anisotropy, and line-of-sight (LOS) external convergence, which incorporates the effect of the large-scale structure on strong lensing. A Bayesian analysis is employed to estimate the model parameters, evaluate their significance, and compare models. We find that the data favor Jaffe`s light profile over Hernquist`s, but that any particular choice between these two does not change the qualitative conclusions with respect to the features of the system that we investigate. The density profile is compatible with an isothermal, being sightly steeper and having an uncertainty in the logarithmic slope of the order of 5% in models that take into account a prior ignorance on anisotropy and external convergence. We identify a considerable degeneracy between the density profile slope and the anisotropy parameter, which largely increases the uncertainties in the estimates of these parameters, but we encounter no evidence in favor of an anisotropic velocity distribution on average for the whole sample. An LOS external convergence following a prior probability distribution given by cosmology has a small effect on the estimation of the lens density profile, but can increase the dispersion of its value by nearly 40%.

Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal

In many mammals social organization promotes genetic structuring, which can be influenced by the dispersal pattern of the species. We analyzed the population genetic structure and dispersal of white-lipped peccaries (Tayassu pecan) from the Pantanal, Brazil. We genotyped 100 individuals at 7 microsatellite loci from 2 adjacent locations with no obvious geographic barrier between them. We found a significant but low F(ST) value, and the Bayesian analysis indicated a unique cluster. No significant differences were observed between mean assignment indices of resident males and females from both locations, and the probability of being born at the location sampled of > 30% of the individuals analyzed was lower than average. Mean relatedness between resident female, male, and opposite-sex pairs was not statistically different in both locations. These results suggest a low degree of genetic differentiation between the locations analyzed, and dispersal by both sexes (contrary to the predicted male-biased dispersal of most mammalian species).

Independent fusions and recent origins of sex chromosomes in the evolution and diversification of glass knife fishes (Eigenmannia)

The genus Eigenmannia comprises several species groups that display a surprising variety of diploid chromosome numbers and sex-determining systems. In this study, hypotheses regarding phylogenetic relationships and karyotype evolution were investigated using a combination of molecular and cytogenetic methods. Phylogenetic relationships were analyzed for 11 cytotypes based on sequences from five mitochondrial DNA regions. Parsimony-based character mapping of sex chromosomes confirms previous suggestions of multiple origins of sex chromosomes. Molecular cytogenetic analyses involved chromosome painting using probes derived from whole sex chromosomes from two taxa that were hybridized to metaphases of their respective sister cytotypes. These analyses showed that a multiple XY system evolved recently (<7 mya) by fusion. Furthermore, one of the chromosomes that fused to form the neo-Y chromosome is fused independently to another chromosome in the sister cytotype. This may constitute an efficient post-mating barrier and might imply a direct function of sex chromosomes in the speciation processes in Eigenmannia. The other chromosomal sex-determination system investigated is shown to have differentiated by an accumulation of heterochromatin on the X chromosome. This has occurred in the past 0.6 my, and is the most recent chromosomal sex-determining system described to date. These results show that the evolution of sex-determining systems can proceed very rapidly. Heredity (2011) 106, 391-400; doi:10.1038/hdy.2010.82; published online 23 June 2010

The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless, our results argue against the indiscriminate use of molecular clock rates in evolutionary research and advocate the verification of the appropriateness of the traditional clock rate by means of independent calibrations in individual studies. (C) 2009 Elsevier Inc. All rights reserved.