The Kumaraswamy Weibull distribution with application to failure data

For the first time, we introduce and study some mathematical properties of the Kumaraswamy Weibull distribution that is a quite flexible model in analyzing positive data. It contains as special sub-models the exponentiated Weibull, exponentiated Rayleigh, exponentiated exponential, Weibull and also the new Kumaraswamy exponential distribution. We provide explicit expressions for the moments and moment generating function. We examine the asymptotic distributions of the extreme values. Explicit expressions are derived for the mean deviations, Bonferroni and Lorenz curves, reliability and Renyi entropy. The moments of the order statistics are calculated. We also discuss the estimation of the parameters by maximum likelihood. We obtain the expected information matrix. We provide applications involving two real data sets on failure times. Finally, some multivariate generalizations of the Kumaraswamy Weibull distribution are discussed. (C) 2010 The Franklin Institute. Published by Elsevier Ltd. All rights reserved.

Using a New Criterion to Identify Sites for Mean Soil Water Storage Evaluation

Establishing a few sites in which measurements of soil water storage (SWS) are time stable significantly reduces the efforts involved in determining average values of SWS. This study aimed to apply a new criterion the mean absolute bias error (MABE)-to identify temporally stable sites for mean SWS evaluation. The performance of MABE was compared with that of the commonly used criterion, the standard deviation of relative difference (SDRD). From October 2004 to October 2008, SWS of four soil layers (0-1.0, 1.0-2.0,2.0-3.0, and 3.0-4.0 m) was measured, using a neutron probe, at 28 sites on a hillslope of the Loess Plateau, China. A total of 37 SWS data sets taken over time were divided into two subsets, the first consisting of 22 dates collected during the calibration period from October 2004 to September 2006, and the second with 15 dates collected during the validation period from October 2006 to October 2008. The results showed that if a critical value of 5% for MABE was defined, more than half the sites were temporally stable for both periods, and the number of temporally stable sires generally increased with soil depth. Compared with SDRD, MABE was more suitable for the identification of time-stable sites for mean SS prediction. Since the absolute prediction error of drier sites is more sensitive to changes in relative difference in terms of mean SWS prediction, the sites of wet sectors should be preferable for mean SWS prediction for the same changes in relative difference.

Formulating Mixed Models for Experiments, Including Longitudinal Experiments

Mixed models have become important in analyzing the results of experiments, particularly those that require more complicated models (e.g., those that involve longitudinal data). This article describes a method for deriving the terms in a mixed model. Our approach extends an earlier method by Brien and Bailey to explicitly identify terms for which autocorrelation and smooth trend arising from longitudinal observations need to be incorporated in the model. At the same time we retain the principle that the model used should include, at least, all the terms that are justified by the randomization. This is done by dividing the factors into sets, called tiers, based on the randomization and determining the crossing and nesting relationships between factors. The method is applied to formulate mixed models for a wide range of examples. We also describe the mixed model analysis of data from a three-phase experiment to investigate the effect of time of refinement on Eucalyptus pulp from four different sources. Cubic smoothing splines are used to describe differences in the trend over time and unstructured covariance matrices between times are found to be necessary.

Spatio-temporal variability behavior of land surface soil water content in shrub- and grass-land

The knowledge of the relationship between spatial variability of the surface soil water content (theta) and its mean across a spatial domain (theta(m)) is crucial for hydrological modeling and understanding soil water dynamics at different scales. With the aim to compare the soil moisture dynamics and variability between the two land uses and to explore the relationship between the spatial variability of theta and theta(m), this study analyzed sets of surface theta measurements performed with an impedance soil moisture probe, collected 136 times during a period of one year in two transects covering different land uses, i.e., korshinsk peashrub transect (KPT) and bunge needlegrass transect (BNT), in a watershed of the Loess Plateau, China. Results showed that the temporal pattern of theta behaved similarly for the two land uses, with both relative wetter soils during wet period and relative drier soils during dry period recognized in BNT. Soil moisture tended to be temporally stable among different dates, and more stable patterns could be observed for dates with more similar soil water conditions. The magnitude of the spatial variation of theta in KPT was greater than that in ENT. For both land uses, the standard deviation (SD) of theta in general increased as theta(m) increased, a behavior that could be well described with a natural logarithmic function. Convex relationship of CV and theta(m) and the maximum CV for both land uses (43.5% in KPT and 41.0% in BNT) can, therefore, be ascertained. Geostatistical analysis showed that the range in KPT (9.1 m) was shorter than that in BNT (15.1 m). The nugget effects, the structured variability, hence the total variability increased as theta(m) increased. For both land uses, the spatial dependency in general increased with increasing theta(m). 2011 Elsevier B.V. All rights reserved.

Definition of priority areas for forest conservation through the ordered weighted averaging method

The general objective of this study was to evaluate the ordered weighted averaging (OWA) method, integrated to a geographic information systems (GIS), in the definition of priority areas for forest conservation in a Brazilian river basin, aiming at to increase the regional biodiversity. We demonstrated how one could obtain a range of alternatives by applying OWA, including the one obtained by the weighted linear combination method and, also the use of the analytic hierarchy process (AHP) to structure the decision problem and to assign the importance to each criterion. The criteria considered important to this study were: proximity to forest patches; proximity among forest patches with larger core area; proximity to surface water; distance from roads: distance from urban areas; and vulnerability to erosion. OWA requires two sets of criteria weights: the weights of relative criterion importance and the order weights. Thus, Participatory Technique was used to define the criteria set and the criterion importance (based in AHP). In order to obtain the second set of weights we considered the influence of each criterion, as well as the importance of each one, on this decision-making process. The sensitivity analysis indicated coherence among the criterion importance weights, the order weights, and the solution. According to this analysis, only the proximity to surface water criterion is not important to identify priority areas for forest conservation. Finally, we can highlight that the OWA method is flexible, easy to be implemented and, mainly, it facilitates a better understanding of the alternative land-use suitability patterns. (C) 2008 Elsevier B.V. All rights reserved.

Macroscopic root water uptake distribution using a matric flux potential approach

Hydrological models featuring root water uptake usually do not include compensation mechanisms such that reductions in uptake from dry layers are compensated by an increase in uptake from wetter layers. We developed a physically based root water uptake model with an implicit compensation mechanism. Based on an expression for the matric flux potential (M) as a function of the distance to the root, and assuming a depth-independent value of M at the root surface, uptake per layer is shown to be a function of layer bulk M, root surface M, and a weighting factor that depends on root length density and root radius. Actual transpiration can be calculated from the sum of layer uptake rates. The proposed reduction function (PRF) was built into the SWAP model, and predictions were compared to those made with the Feddes reduction function (FRF). Simulation results were tested against data from Canada (continuous spring wheat [(Triticum aestivum L.]) and Germany (spring wheat, winter barley [Hordeum vulgare L.], sugarbeet [Beta vulgaris L.], winter wheat rotation). For the Canadian data, the root mean square error of prediction (RMSEP) for water content in the upper soil layers was very similar for FRF and PRF; for the deeper layers, RMSEP was smaller for PRF. For the German data, RMSEP was lower for PRF in the upper layers and was similar for both models in the deeper layers. In conclusion, but dependent on the properties of the data sets available for testing,the incorporation of the new reduction function into SWAP was successful, providing new capabilities for simulating compensated root water uptake without increasing the number of input parameters or degrading model performance.

Colletotrichum gloeosporioides, a new causal agent of citrus post-bloom fruit drop

Citrus post-bloom fruit drop (caused by Colletotrichum acutatum) frequently occurs in the southwestern region of So Paulo State, Brazil. A survey of Colletotrichum isolates associated with symptoms of post-bloom fruit drop in So Paulo State showed C. gloeosporioides in addition to C. acutatum. The objectives of this study were to confirm the identification of C. gloeosporioides isolated from symptomatic citrus flowers, to test the pathogenicity of C. gloeosporioides isolates, to compare the development of disease caused by C. gloeosporioides and C. acutatum, and to determine the frequency of C. gloeosporioides in a sample of isolates obtained from symptomatic flowers in different regions of So Paulo State. Through the use of species-specific primers by PCR, 17.3% of 139 isolates were C. gloeosporioides, and the remaining 82.7% were C. acutatum. The pathogenicity tests, carried out in 3-year old potted plants of sweet oranges indicated that both species caused typical symptoms of the disease including blossom blight and persistent calyces. Incubation periods (3.5 and 3.9 days, respectively, for C. acutatum and C. gloeosporioides) and fruit sets (6.7 and 8.5%, respectively for C. acutatum and C. gloeosporioides) were similar for both species. The incidences of blossom blight and persistent calyces were higher on plants inoculated with C. acutatum than in those inoculated with C. gloeosporioides. Conidial germination was similar for both species under different temperatures and wetness periods. Under optimal conditions, appressorium formation and melanisation were higher for C. gloeosporioides than for C. acutatum. These results indicated that Colletotrichum gloeosporioides is a new causal agent of post-bloom fruit drop.

Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that. has been used for estimating the average degree of dominance of quantitative trait 106 (QTL) and also for studying heterosis. In this study, we first develop a multiple-interval mapping (MIM) model for design III that provides a platform to estimate the number, genomic positions, augmented additive and dominance effects, and epistatic interactions of QTL. The model can be used for parents with any generation of selling. We apply the method to two data sets, one for maize and one for rice. Our results show that heterosis in maize is mainly due to dominant gene action, although overdominance of individual QTL could not completely be ruled out due to the mapping resolution and limitations of NC design III. For rice, the estimated QTL dominant effects could not explain the observed heterosis. There is evidence that additive X additive epistatic effects of QTL could be the main cause for the heterosis in rice. The difference in the genetic basis of heterosis seems to be related to open or self pollination of the two species. The MIM model for NC design III is implemented in Windows QTL Cartographer, a freely distributed software.

Genetic structure and mating system of Euterpe edulis Mart. populations: A comparative analysis using microsatellite and allozyme markers

A comparative study between microsatellite and allozyme markers was conducted on the genetic structure and mating system in natural populations of Euterpe edulis Mart. Three cohorts, including seedlings, saplings, and adults, were examined in 4 populations using 10 allozyme loci and 10 microsatellite loci. As expected, microsatellite markers had a much higher degree of polymorphism than allozymes, but estimates of multilocus outcrossing rate ((t) over cap (m) = 1.00), as well as estimates of genetic structure (F(IS), G(ST)), were similar for the 2 sets of markers. Estimates of R(ST), for microsatellites, were higher than those of GST, but results of both statistics revealed a close agreement for the genetic structure of the species. This study provides support for the important conclusion that allozymes are still useful and reliable markers to estimate population genetic parameters. Effects of sample size on estimates from hypervariable loci are also discussed in this paper.

Canonical discriminant analysis applied to broiler chicken performance

The mechanisms involved in the control of growth in chickens are too complex to be explained only under univariate analysis because all related traits are biologically correlated. Therefore, we evaluated broiler chicken performance under a multivariate approach, using the canonical discriminant analysis. A total of 1920 chicks from eight treatments, defined as the combination of four broiler chicken strains (Arbor Acres, AgRoss 308, Cobb 500 and RX) from both sexes, were housed in 48 pens. Average feed intake, average live weight, feed conversion and carcass, breast and leg weights were obtained for days 1 to 42. Canonical discriminant analysis was implemented by SAS((R)) CANDISC procedure and differences between treatments were obtained by the F-test (P < 0.05) over the squared Mahalanobis` distances. Multivariate performance from all treatments could be easily visualised because one graph was obtained from two first canonical variables, which explained 96.49% of total variation, using a SAS((R)) CONELIP macro. A clear distinction between sexes was found, where males were better than females. Also between strains, Arbor Acres, AgRoss 308 and Cobb 500 (commercial) were better than RX (experimental), Evaluation of broiler chicken performance was facilitated by the fact that the six original traits were reduced to only two canonical variables. Average live weight and carcass weight (first canonical variable) were the most important traits to discriminate treatments. The contrast between average feed intake and average live weight plus feed conversion (second canonical variable) were used to classify them. We suggest analysing performance data sets using canonical discriminant analysis.

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.

Using Imaging Spectroscopy to study soil properties

Imaging Spectroscopy (IS) is a promising tool for studying soil properties in large spatial domains. Going from point to image spectrometry is not only a journey from micro to macro scales, but also a long stage where problems such as dealing with data having a low signal-to-noise level, contamination of the atmosphere, large data sets, the BRDF effect and more are often encountered. In this paper we provide an up-to-date overview of some of the case studies that have used IS technology for soil science applications. Besides a brief discussion on the advantages and disadvantages of IS for studying soils, the following cases are comprehensively discussed: soil degradation (salinity, erosion, and deposition), soil mapping and classification, soil genesis and formation, soil contamination, soil water content, and soil swelling. We review these case studies and suggest that the 15 data be provided to the end-users as real reflectance and not as raw data and with better signal-to-noise ratios than presently exist. This is because converting the raw data into reflectance is a complicated stage that requires experience, knowledge, and specific infrastructures not available to many users, whereas quantitative spectral models require good quality data. These limitations serve as a barrier that impedes potential end-users, inhibiting researchers from trying this technique for their needs. The paper ends with a general call to the soil science audience to extend the utilization of the IS technique, and it provides some ideas on how to propel this technology forward to enable its widespread adoption in order to achieve a breakthrough in the field of soil science and remote sensing. (C) 2009 Elsevier Inc. All rights reserved.

Spatial heterogeneity of leaf wetness duration in apple trees and its influence on performance of a warning system for sooty blotch and flyspeck

To determine the effect of sensor placement on the performance of a disease-warning system for sooty blotch and flyspeck (SBFS), we measured leaf wetness duration (LWD) at 12 canopy positions in apple trees, then simulated operation of the disease-warning system using LWD measurements from different parts of the canopy. LWD sensors were placed in four trees within one Iowa orchard during two growing seasons, and in one tree in each of four orchards during a single growing season. The LWD measurements revealed substantial heterogeneity among sensor locations. In all data sets, the upper, eastern portion of the canopy had the longest mean daily LWD, and was the first site to form dew and the last to dry. The lower, western portion of the canopy averaged about 3 It less LWD per day than the top of the canopy, and was the last zone where dew formed and the first to dry off. On about 25% of nights when dew occurred in the top of the canopy, no dew formed in the lower, western canopy. Intracanopy variability of LWD was more pronounced when dew was the sole source of wetness than on days when rainfall occurred. Daily LWD in the upper, eastern portion of the canopy was slightly less than reference measurements made at a 0.7-m height over turfgrass located near the orchard. When LWD measurements from several canopy positions were input to the SBFS warning system, timing of occurrence of a fungicide-spray threshold varied by as much as 30 days among canopy positions. Under Iowa conditions, placement of an LWD sensor at an unobstructed site over turfgrass was a fairly accurate surrogate for the wettest part of the canopy. Therefore, such an extra-canopy LWD sensor might be substituted for a within-canopy sensor to enhance operational reliability of the SBFS warning system.

Transcriptional responses of host peripheral blood cells to tuberculosis infection

Host responses following exposure to Mycobacterium tuberculosis (TB) are complex and can significantly affect clinical outcome. These responses, which are largely mediated by complex immune mechanisms involving peripheral blood cells (PBCs) such as T-lymphocytes, NK cells and monocyte-derived macrophages, have not been fully characterized. We hypothesize that different clinical outcome following TB exposure will be uniquely reflected in host gene expression profiles, and expression profiling of PBCs can be used to discriminate between different TB infectious outcomes. In this study, microarray analysis was performed on PBCs from three TB groups (BCG-vaccinated, latent TB infection, and active TB infection) and a control healthy group. Supervised learning algorithms were used to identify signature genomic responses that differentiate among group samples. Gene Set Enrichment Analysis was used to determine sets of genes that were co-regulated. Multivariate permutation analysis (p < 0.01) gave 645 genes differentially expressed among the four groups, with both distinct and common patterns of gene expression observed for each group. A 127-probeset, representing 77 known genes, capable of accurately classifying samples into their respective groups was identified. In addition, 13 insulin-sensitive genes were found to be differentially regulated in all three TB infected groups, underscoring the functional association between insulin signaling pathway and TB infection. Published by Elsevier Ltd.

Production of a collagenase from Candida albicans URM3622

Culture conditions (pH, time, temperature, inoculum size, orbital agitation speed and substrate concentration) for an extracellular collagenase produced by Candida albicans URM3622 were studied using three experimental designs (one 2(6-2) fractionary factorial and two 2(3) full factorial). The analysis of the 2(6-2) fractionary design data indicated that agitation speed and substrate concentration had the most significant effect on collagenase production. Based on these results, two successive 2(3) full factorial design experiments were run in which the effects of substrate concentration, orbital agitation speed and pH were further studied. These two sets of experiments showed that all variables chosen were significant for the enzyme production, with the maximum collagenolytic activity of 6.8 +/- 0.4 U achieved at pH 7.0 with an orbital agitation speed of 160 rpm and 2% substrate concentration. Maximum collagenolytic activity was observed at pH 8.2 and 45 degrees C. The collagenase was stable within a pH range of 7.2-8.2 and over a temperature range of 28-45 degrees C. These results clearly indicate that C. albicans URM3622 is a potential resource for collagenase production and could be of interest for pharmaceutical, cosmetic and food industry. Crown Copyright (C) 2008 Published by Elsevier B.V. All rights reserved.