A generalized modified Weibull distribution for lifetime modeling

A four parameter generalization of the Weibull distribution capable of modeling a bathtub-shaped hazard rate function is defined and studied. The beauty and importance of this distribution lies in its ability to model monotone as well as non-monotone failure rates, which are quite common in lifetime problems and reliability. The new distribution has a number of well-known lifetime special sub-models, such as the Weibull, extreme value, exponentiated Weibull, generalized Rayleigh and modified Weibull distributions, among others. We derive two infinite sum representations for its moments. The density of the order statistics is obtained. The method of maximum likelihood is used for estimating the model parameters. Also, the observed information matrix is obtained. Two applications are presented to illustrate the proposed distribution. (C) 2008 Elsevier B.V. All rights reserved.

Parametric and nonparametric statistical modelling of crop yield: implications for pricing crop insurance contracts

This article considers alternative methods to calculate the fair premium rate of crop insurance contracts based on county yields. The premium rate was calculated using parametric and nonparametric approaches to estimate the conditional agricultural yield density. These methods were applied to a data set of county yield provided by the Statistical and Geography Brazilian Institute (IBGE), for the period of 1990 through 2002, for soybean, corn and wheat, in the State of Paran. In this article, we propose methodological alternatives to pricing crop insurance contracts resulting in more accurate premium rates in a situation of limited data.

Genetic Diversity and a PCR-Based Method for Xanthomonas axonopodis Detection in Passion Fruit

Xanthomonas axonopodis pv. passiflorae causes bacterial spot in passion fruit. It attacks the purple and yellow passion fruit as well as the sweet passion fruit. The diversity of 87 isolates of pv. passiflorae collected from across 22 fruit orchards in Brazil was evaluated using molecular profiles and statistical procedures, including an unweighted pair-group method with arithmetical averages-based dendrogram, analysis of molecular variance (AMOVA), and an assigning test that provides information on genetic structure at the population level. Isolates from another eight pathovars were included in the molecular analyses and all were shown to have a distinct repetitive sequence-based polymerase chain reaction profile. Amplified fragment length polymorphism technique revealed considerable diversity among isolates of pv. passiflorae, and AMOVA showed that most of the variance (49.4%) was due to differences between localities. Cluster analysis revealed that most genotypic clusters were homogeneous and that variance was associated primarily with geographic origin. The disease adversely affects fruit production and may kill infected plants. A method for rapid diagnosis of the pathogen, even before the disease symptoms become evident, has value for producers. Here, a set of primers (Xapas) was designed by exploiting a single-nucleotide polymorphism between the sequences of the intergenic 16S-23S rRNA spacer region of the pathovars. Xapas was shown to effectively detect all pv. passiflorae isolates and is recommended for disease diagnosis in passion fruit orchards.

Modeling of transpiration reduction in van Genuchten-Mualem type soils

We derive an analytic expression for the matric flux potential (M) for van Genuchten-Mualem (VGM) type soils which can also be written in terms of a converging infinite series. Considering the first four terms of this series, the accuracy of the approximation was verified by comparing it to values of M estimated by numerical finite difference integration. Using values of the parameters for three soils from different texture classes, the proposed four-term approximation showed an almost perfect match with the numerical solution, except for effective saturations higher than 0.9. Including more terms reduced the discrepancy but also increased the complexity of the equation. The four-term equation can be used for most applications. Cases with special interest in nearly saturated soils should include more terms from the infinite series. A transpiration reduction function for use with the VGM equations is derived by combining the derived expression for M with a root water extraction model. The shape of the resulting reduction function and its dependency on the derivative of the soil hydraulic diffusivity D with respect to the soil water content theta is discussed. Positive and negative values of dD/d theta yield concave and convex or S-shaped reduction functions, respectively. On the basis of three data sets, the hydraulic properties of virtually all soils yield concave reduction curves. Such curves based solely on soil hydraulic properties do not account for the complex interactions between shoot growth, root growth, and water availability.

Spatial Modeling of a Soil Fertility Index using Visible-Near-Infrared Spectra and Terrain Attributes

Our objective was to develop a methodology to predict soil fertility using visible near-infrared (vis-NIR) diffuse reflectance spectra and terrain attributes derived from a digital elevation model (DEM). Specifically, our aims were to: (i) assemble a minimum data set to develop a soil fertility index for sugarcane (Sarcharum officinarum L.) (SFI-SC) for biofuel production in tropical soils; (ii) construct a model to predict the SFI-SC using soil vis-NIR spectra and terrain attributes; and (iii) produce a soil fertility map for our study area and assess it by comparing it with a green vegetation index (GVI). The study area was 185 ha located in sao Paulo State, Brazil. In total, 184 soil samples were collected and analyzed for a range of soil chemical and physical properties. Their vis-NIR spectra were collected from 400 to 2500 nm. The Shuttle Radar Topographic Mission 3-arcsec (90-m resolution) DEM of the area was used to derive 17 terrain attributes. A minimum data set of soil properties was selected to develop the SFI-SC. The SFI-SC consisted of three classes: Class 1, the highly fertile soils; Class 2, the fertile soils; and Class 3, the least fertile soils. It was derived heuristically with conditionals and using expert knowledge. The index was modeled with the spectra and terrain data using cross-validated decision trees. The cross-validation of the model correctly predicted Class 1 in 75% of cases, Class 2 in 61%, and Class 3 in 65%. A fertility map was derived for the study area and compared with a map of the GVI. Our approach offers a methodology that incorporates expert knowledge to derive the SFI-SC and uses a versatile spectro-spatial methodology that may be implemented for rapid and accurate determination of soil fertility and better exploration of areas suitable for production.

Modeling soil organic carbon dynamics in Oxisols of Ibiruba (Brazil) with the Century Model

introduction of conservation practices in degraded agricultural land will generally recuperate soil quality, especially by increasing soil organic matter. This aspect of soil organic C (SOC) dynamics under distinct cropping and management systems can be conveniently analyzed with ecosystem models such as the Century Model. In this study, Century was used to simulate SOC stocks in farm fields of the Ibiruba region of north central Rio Grande do Sul state in Southern Brazil. The region, where soils are predominantly Oxisols, was originally covered with subtropical woodlands and grasslands. SOC dynamics was simulated with a general scenario developed with historical data on soil management and cropping systems beginning with the onset of agriculture in 1900. From 1993 to 2050, two contrasting scenarios based on no-tillage soil management were established: the status quo scenario, with crops and agricultural inputs as currently practiced in the region and the high biomass scenario with increased frequency of corn in the cropping system, resulting in about 80% higher biomass addition to soils. Century simulations were in close agreement with SOC stocks measured in 2005 in the Oxisols with finer texture surface horizon originally under woodlands. However, simulations in the Oxisols with loamy surface horizon under woodlands and in the grassland soils were not as accurate. SOC stock decreased from 44% to 50% in fields originally under woodland and from 20% to 27% in fields under grasslands with the introduction of intensive annual grain crops with intensive tillage and harrowing operations. The adoption of conservation practices in the 1980s led to a stabilization of SOC stocks followed by a partial recovery of native stocks. Simulations to 2050 indicate that maintaining status quo would allow SOC stocks to recover from 81% to 86% of the native stocks under woodland and from 80% to 91 % of the native stocks under grasslands. Adoption of a high biomass scenario would result in stocks from 75% to 95% of the original stocks under woodlands and from 89% to 102% in the grasslands by 2050. These simulations outcomes underline the importance of cropping system yielding higher biomass to further increase SOC content in these Oxisols. This application of the Century Model could reproduce general trends of SOC loss and recovery in the Oxisols of the Ibiruba region. Additional calibration and validation should be conducted before extensive usage of Century as a support tool for soil carbon sequestration projects in this and other regions can be recommended. (C) 2009 Elsevier B.V. All rights reserved.

Parameterization and Evaluation of Predictions of DSSAT/CANEGRO for Brazilian Sugarcane

The DSSAT/CANEGRO model was parameterized and its predictions evaluated using data from five sugarcane (Sacchetrum spp.) experiments conducted in southern Brazil. The data used are from two of the most important Brazilian cultivars. Some parameters whose values were either directly measured or considered to be well known were not adjusted. Ten of the 20 parameters were optimized using a Generalized Likelihood Uncertainty Estimation (GLUE) algorithm using the leave-one-out cross-validation technique. Model predictions were evaluated using measured data of leaf area index (LA!), stalk and aerial dry mass, sucrose content, and soil water content, using bias, root mean squared error (RMSE), modeling efficiency (Eff), correlation coefficient, and agreement index. The Decision Support System for Agrotechnology Transfer (DSSAT)/CANEGRO model simulated the sugarcane crop in southern Brazil well, using the parameterization reported here. The soil water content predictions were better for rainfed (mean RMSE = 0.122mm) than for irrigated treatment (mean RMSE = 0.214mm). Predictions were best for aerial dry mass (Eff = 0.850), followed by stalk dry mass (Eff = 0.765) and then sucrose mass (Eff = 0.170). Number of green leaves showed the worst fit (Eff = -2.300). The cross-validation technique permits using multiple datasets that would have limited use if used independently because of the heterogeneity of measures and measurement strategies.

A split-pot experiment with sorghum to test a root water uptake partitioning model

Correct modeling of root water uptake partitioning over depth is an important issue in hydrological and crop growth models. Recently a physically based model to describe root water uptake was developed at single root scale and upscaled to the root system scale considering a homogeneous distribution of roots per soil layer. Root water uptake partitioning is calculated over soil layers or compartments as a function of respective soil hydraulic conditions, specifically the soil matric flux potential, root characteristics and a root system efficiency factor to compensate for within-layer root system heterogeneities. The performance of this model was tested in an experiment performed in two-compartment split-pot lysimeters with sorghum plants. The compartments were submitted to different irrigation cycles resulting in contrasting water contents over time. The root system efficiency factor was determined to be about 0.05. Release of water from roots to soil was predicted and observed on several occasions during the experiment; however, model predictions suggested root water release to occur more often and at a higher rate than observed. This may be due to not considering internal root system resistances, thus overestimating the ease with which roots can act as conductors of water. Excluding these erroneous predictions from the dataset, statistical indices show model performance to be of good quality.

Carotenoids production from a newly isolated Sporidiobolus pararoseus strain by submerged fermentation

This work aimed at evaluating the total carotenoids production by a newly isolated Sporidiobolus pararoseus. Bioproduction was carried out in an orbital shaker, using 10% (w/v) of inoculum (25 A degrees C, 180 rpm for 35 h), incubated for 120 h in a dark room. Liquid N(2) and dimethylsulphoxide (DMSO) were used for cell rupture, and carotenoids were extracted with a solution of acetone/methanol (7:3, v/v). Optimization of carotenoids bioproduction was achieved by experimental design technique. Initially, a Plackett-Burman design was used for the screening of the most important factors, after the statistical analysis, a complete second-order design was carried out to optimize the concentration of total carotenoids in a conventional medium. Maximum concentration of 856 mu g/L of total carotenoids was obtained in a medium containing 60 g/L of glucose, 15 g/L of peptone, and 15 g/L of malt extract, 25 A degrees C, initial pH 4.0 and 180 rpm. Fermentation kinetics showed that the maximum concentration of total carotenoids was reached after 102 h of fermentation and that carotenoids bioproduction was associated with cell growth.

Cu and Fe metallic ions-mediated oxidation of low-density lipoproteins studied by NMR, TEM and Z-scan technique

In this work we report on a study of the morphological changes of LDL induced in vitro by metallic ions (Cu(2+) and Fe(3+)). These modifications were characterized by transmission electron microscopy, nuclear magnetic resonance and the Z-scan technique. The degree of oxidative modification of LDL was determined by the TBARS and lipid hydroperoxides assays. It is shown that distinct pathways for modifying lipoproteins lead to different morphological transformations of the particles characterized by changes in size and/or shape of the resulting particles, and by the tendency to induce aggregation of the particles. There were no evidence of melting of particles promoted by oxidative processes with Cu and Fe. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Molecular Modeling Suggests Cruzain Specificity for Peptide Primaquine Prodrugs

Chagas` disease, infection caused by the protozoan Trypanosoma cruzi, is an important, social and medical ailment in the Latin America. This disease is endemic in 21 countries, mostly Latin America countries, with more than 300,000 new cases every year and about 16-18 million infected people. Current therapy is not effective in the chronic phase of the disease. Thus, new and better drugs are urgently needed. In this sense, the in vitro activity of primaquine (PQ) was reported. Based on this, peptide prodrugs of primaquine containing dipeptides - lysine-arginine (LysArg), phenylalanine-alanine (PheAla) and phenylalanine-arginine (PheArg) -- as carriers, were designed to be selectively cleaved by cruzain, a specific cysteine protease of T. cruzi. The prodrugs have shown to be active against tripomastigote forms according to this order: LysArg-PQ> PheAla-PQ> PheArg-PQ. The molecular mechanism of action considered a probable nucleophilic attack of the catalytic residue of cruzain (Cys25) on the respective prodrug amide carbonyl carbon, releasing PQ. In order to test this hypothesis, molecular modeling studies were performed, physicochemical parameters and stereoelectronic features calculated by using the AM1 semi-empirical method suggest that the amide carbonyl carbon is favorable for cleavage, where the LysArg showed the most electronic reactive and sterically disposable, leading to the prodrug release and action. In addition, the docking study indicates the occurrence of specific interactions between prodrugs and the pockets S1 and S2 of cruzain through the dipeptides carriers, being the distance between cruzain Cys25 and the amide carbonyl group related to the biological activity of the prodrugs.

QSAR Modeling of a Set of Pyrazinoate Esters as Antituberculosis Prodrugs

Tuberculosis is an infection caused mainly by Mycobacterium tuberculosis. A first-line antimycobacterial drug is pyrazinamide (PZA), which acts partially as a prodrug activated by a pyrazinamidase releasing the active agent, pyrazinoic acid (POA). As pyrazinoic acid presents some difficulty to cross the mycobacterial cell wall, and also the pyrazinamide-resistant strains do not express the pyrazinamidase, a set of pyrazinoic acid esters have been evaluated as antimycobacterial agents. In this work, a QSAR approach was applied to a set of forty-three pyrazinoates against M. tuberculosis ATCC 27294, using genetic algorithm function and partial least squares regression (WOLF 5.5 program). The independent variables selected were the Balaban index (I), calculated n-octanol/water partition coefficient (ClogP), van-der-Waals surface area, dipole moment, and stretching-energy contribution. The final QSAR model (N = 32, r(2) = 0.68, q(2) = 0.59, LOF = 0.25, and LSE = 0.19) was fully validated employing leave-N-out cross-validation and y-scrambling techniques. The test set (N = 11) presented an external prediction power of 73%. In conclusion, the QSAR model generated can be used as a valuable tool to optimize the activity of future pyrazinoic acid esters in the designing of new antituberculosis agents.

Molecular modeling as a promising tool to study dendrimer prodrugs delivery

Molecular modeling methodologies were applied to perform preliminary studies concerning the release of active agents from potentially antichagasic and antileishmanial dendrimer prodrugs. The dendrimer was designed having myo-inositol as a core, L-malic acid as a spacer group, and hydroxymethylnitrofurazone (NFOH), 3-hydroxyflavone or quercetin, as active compounds. Each dendrimer presented a particular behavior concerning to the following investigated properties: spatial hindrance, map of electrostatic potential (MEP), and the lowest unoccupied molecular orbital energy (E(LUMO)). Additionally, the findings suggested that the carbonyl group next to the active agent seems to be the most promising ester breaking point. (C) 2009 Elsevier B.V. All rights reserved.

Host-guest complexation of a nitroheterocyclic compound with cyclodextrins: a spectrofluorimetric and molecular modeling study

Nitroheterocyclic compounds (NC) were candidate drugs proposed for Chagas disease chemotherapy. In this study, we investigated the complexation of hydroxymethylnitrofurazone (NFOH), a potential antichagasic compound, with alpha-cyclodextrin (alpha-CD), beta-cyclodextrin (beta-CD), Hydroxypropyl-beta-cyclodextrin (HP-beta-CD), Dimethyl-beta-cyclodextrin (DM-beta-CD) and gamma-cyclodextrin (gamma-CD) by fluorescence spectroscopy and molecular modeling studies. Hildebrand-Benesi equation was used to calculate the formation constants of NFOH with cyclodextrins based on the fluorescence differences in the CDs solution. The complexing capacity of NFOH with different CDs was compared through the results of association constant according to the following order: DM-beta-CD > beta-CD > alpha-CD > HP-beta-CD > gamma-CD. Molecular modeling studies give support for the experimental assignments, in favor of the formation of an inclusion complex between cyclodextrins with NFOH. This is an important study to investigate the effects of different kinds of cyclodextrins on the inclusion complex formation with NFOH and to better characterize a potential formulations to be used as therapeutic options for the oral treatment of Chagas disease.

Design, synthesis, antimicrobial activity and molecular modeling studies of novel benzofuroxan derivatives against Staphylococcus aureus

Molecular modi. cation is a quite promising strategy in the design and development of drug analogs with better bioavailability, higher intrinsic activity and less toxicity. In the search of new leads with potential antimicrobial activity, a new series of 14 4-substituted [N`-(benzofuroxan-5-yl) methylene] benzohydrazides, nifuroxazide derivatives, were synthesized and tested against standard and multidrug-resistant Staphylococcus aureus strains. The selection of the substituent groups was based on physicochemical properties, such as hydrophobicity and electronic effect. These properties were also evaluated through the lipophilic and electrostatic potential maps, respectively, considering the compounds with better biological pro. le. Twelve compounds exhibited similar bacteriostatic activity against standard and multidrug-resistant strains. The most active compound was the 4-CF(3) substituted derivative, which presented a minimum inhibitory concentration (MIC) value of 14.6-13.1 mu g/mL, and a ClogP value of 1.87. The results highlight the benzofuroxan derivatives as potential leads for designing new future antimicrobial drug candidates. (C) 2009 Elsevier Ltd. All rights reserved.