TESTING STATISTICAL HYPOTHESIS ON RANDOM TREES AND APPLICATIONS TO THE PROTEIN CLASSIFICATION PROBLEM

Efficient automatic protein classification is of central importance in genomic annotation. As an independent way to check the reliability of the classification, we propose a statistical approach to test if two sets of protein domain sequences coming from two families of the Pfam database are significantly different. We model protein sequences as realizations of Variable Length Markov Chains (VLMC) and we use the context trees as a signature of each protein family. Our approach is based on a Kolmogorov-Smirnov-type goodness-of-fit test proposed by Balding et at. [Limit theorems for sequences of random trees (2008), DOI: 10.1007/s11749-008-0092-z]. The test statistic is a supremum over the space of trees of a function of the two samples; its computation grows, in principle, exponentially fast with the maximal number of nodes of the potential trees. We show how to transform this problem into a max-flow over a related graph which can be solved using a Ford-Fulkerson algorithm in polynomial time on that number. We apply the test to 10 randomly chosen protein domain families from the seed of Pfam-A database (high quality, manually curated families). The test shows that the distributions of context trees coming from different families are significantly different. We emphasize that this is a novel mathematical approach to validate the automatic clustering of sequences in any context. We also study the performance of the test via simulations on Galton-Watson related processes.

Functional specialization of Eucalyptus fine roots: contrasting potential uptake rates for nitrogen, potassium and calcium tracers at varying soil depths

1. Little is known about the role of deep roots in the nutrition of forest trees and their ability to provide a safety-net service taking up nutrients leached from the topsoil. 2. To address this issue, we studied the potential uptake of N, K and Ca by Eucalyptus grandis trees (6 years of age - 25 m mean height), in Brazil, as a function of soil depth, texture and water content. We injected NO(3)(-)- (15)N, Rb(+) (analogue of K(+)) and Sr(2+) (analogue of Ca(2+)) tracers simultaneously in a solution through plastic tubes at 10, 50, 150 and 300 cm in depth in a sandy and a clayey Ferralsol soil. A complete randomized design was set up with three replicates of paired trees per injection depth and soil type. Recently expanded leaves were sampled at various times after tracer injection in the summer, and the experiment was repeated in the winter. Soil water contents were continuously monitored at the different depths in the two soils. 3. Determination of foliar Rb and Sr concentrations and (15)N atom % made it possible to estimate the relative uptake potential (RUP) of tracer injections from the four soil depths and the specific RUP (SRUP), defined as RUP, per unit of fine root length density in the corresponding soil layer. 4. The highest tracer uptake rates were found in the topsoil, but contrasting RUP distributions were observed for the three tracers. Whilst the RUP was higher for NO(3)(-)- (15)N than for Rb(+) and Sr(2+) in the upper 50 cm of soil, the highest SRUP values for Sr(2+) and Rb(+) were found at a depth of 300 cm in the sandy soil, as well as in the clayey soil when gravitational solutions reached that depth. 5. Our results suggest that the fine roots of E. grandis trees exhibit contrasting potential uptake rates with depth depending on the nutrient. This functional specialization of roots might contribute to the high growth rates of E. grandis trees, efficiently providing the large amounts of nutrients required throughout the development of these fast-growing plantations.

THREE-DIMENSIONAL PHOTOIONIZATION STRUCTURE AND DISTANCES OF PLANETARY NEBULAE. IV. NGC 40

Continuing our series of papers on the three-dimensional (3D) structure and accurate distances of planetary nebulae (PNe), we present here the results obtained for PN NGC 40. Using data from different sources and wavelengths, we construct 3D photoionization models and derive the physical quantities of the ionizing source and nebular gas. The procedure, discussed in detail in the previous papers, consists of the use of 3D photoionization codes constrained by observational data to derive the 3D nebular structure, physical and chemical characteristics, and ionizing star parameters of the objects by simultaneously fitting the integrated line intensities, the density map, the temperature map, and the observed morphologies in different emission lines. For this particular case we combined hydrodynamical simulations with the photoionization scheme in order to obtain self-consistent distributions of density and velocity of the nebular material. Combining the velocity field with the emission-line cubes we also obtained the synthetic position-velocity plots that are compared to the observations. Finally, using theoretical evolutionary tracks of intermediate-and low-mass stars, we derive the mass and age of the central star of NGC 40 as (0.567 +/- 0.06) M(circle dot) and (5810 +/- 600) yr, respectively. The distance obtained from the fitting procedure was (1150 +/- 120) pc.

Financial distress, financial constraint and investment decision: Evidence from Brazil

This paper analyses the presence of financial constraint in the investment decisions of 367 Brazilian firms from 1997 to 2004, using a Bayesian econometric model with group-varying parameters. The motivation for this paper is the use of clustering techniques to group firms in a totally endogenous form. In order to classify the firms we used a hybrid clustering method, that is, hierarchical and non-hierarchical clustering techniques jointly. To estimate the parameters a Bayesian approach was considered. Prior distributions were assumed for the parameters, classifying the model in random or fixed effects. Ordinate predictive density criterion was used to select the model providing a better prediction. We tested thirty models and the better prediction considers the presence of 2 groups in the sample, assuming the fixed effect model with a Student t distribution with 20 degrees of freedom for the error. The results indicate robustness in the identification of financial constraint when the firms are classified by the clustering techniques. (C) 2010 Elsevier B.V. All rights reserved.

Evaluation of Adaptive Genetic Algorithm to Environmental Modeling of Peponapis and Cucurbita

This paper presents a free software tool that supports the next-generation Mobile Communications, through the automatic generation of models of components and electronic devices based on neural networks. This tool enables the creation, training, validation and simulation of the model directly from measurements made on devices of interest, using an interface totally oriented to non-experts in neural models. The resulting model can be exported automatically to a traditional circuit simulator to test different scenarios.

Exploring the random genesis of co-occurrence networks

Using the network random generation models from Gustedt (2009)[23], we simulate and analyze several characteristics (such as the number of components, the degree distribution and the clustering coefficient) of the generated networks. This is done for a variety of distributions (fixed value, Bernoulli, Poisson, binomial) that are used to control the parameters of the generation process. These parameters are in particular the size of newly appearing sets of objects, the number of contexts in which new elements appear initially, the number of objects that are shared with `parent` contexts, and, the time period inside which a context may serve as a parent context (aging). The results show that these models allow to fine-tune the generation process such that the graphs adopt properties as can be found in real world graphs. (C) 2011 Elsevier B.V. All rights reserved.

Experimental and theoretical study of transport properties in uniaxially pressed (Bi, Pb)(2)Sr(2)Ca(2)Cu(3)O(10+delta) ceramic samples

Experimental and theoretical studies on the magnetic field dependence of the electrical resistance R(B(a)) and the transport noise (TN) in polycrystalline high-T(c) superconductors subjected to different uniaxial compacting pressures were conducted. X-ray diffraction rocking curves were performed in different surfaces of the samples in order to investigated the degree of texture The results indicated an improvement of the degree of texture with increasing the uniaxial compacting pressure In theoretical simulations of the data, the polycrystalline superconductors were described as a series-parallel array of Josephson devices The intergranular magnetic field is described within the framework of the intragranular flux-trapping model and the distribution of the grain-boundary angles is assumed to follow the Rayleigh statistical function The proposed model describes well the experimental magnetoresistance R(B(a)) data We have found that the behavior of the R(B(a)) curves changes appreciably when different uniaxially compacting pressures are applied to the sample and such a changes are reproduced by the model when different grain-boundary angles distributions are used In addition, changes in the R(B(a)) dependence have their counterparts in the experimental transport noise signals (C) 2009 Elsevier B.V. All rights reserved

Three-Dimensional Stress Distribution in the Human Periodontal Ligament in Masticatory, Parafunctional, and Trauma Loads: Finite Element Analysis

Background: The presence of the periodontal ligament (PDL) makes it possible to absorb and distribute loads produced during masticatory function and other tooth contacts into the alveolar process via the alveolar bone proper. However, several factors affect the integrity of periodontal structures causing the destruction of the connective matrix and cells, the loss of fibrous attachment, and the resorption of alveolar bone. Methods: The purpose of this study was to evaluate the stress distribution by finite element analysis in a PDL in three-dimensional models of the upper central incisor under three different load conditions: 100 N occlusal loading at 45 degrees (model 1: masticatory load); 500 N at the incisal edge at 45 degrees (model 2: parafunctional habit); and 800 N at the buccal surface at 90 degrees (model 3: trauma case). The models were built from computed tomography scans. Results: The stress distribution was quite different among the models. The most significant values (harmful) of tensile and compressive stresses were observed in models 2 and 3, with similarly distinct patterns of stress distributions along the PDL. Tensile stresses were observed along the internal and external aspects of the PDL, mostly at the cervical and middle thirds. Conclusions: The stress generation in these models may affect the integrity of periodontal structures. A better understanding of the biomechanical behavior of the PDL under physiologic and traumatic loading conditions might enhance the understanding of the biologic reaction of the PDL in health and disease. J Periodontol 2009;80:1859-1867.

Carbide lime and industrial hydrated lime characterization

This paper focuses on the characterization of carbide lime (CL) - a by-product of acetylene production, composed mainly of calcium hydroxide with minor parts of carbonate - and compares its features to those of ""dry"" hydrated lime (HL) commonly used as a building material. Chemical, thermogravimetric and X-ray diffraction analyses indicated that the limes are similar in chemical and mineralogical compositions. except for the presence of carbon in the waste. Morphological and elemental chemical analyses by SEM and EDS revealed that CL particles differ from HL ones in their morphology and by the presence of carbon formations, Physical characterization included density and BET surface area of the materials. as well as, their particle size distributions in deionized water at diverse time periods. CL underwent agglomeration after approximately 60 min in water, whereas HL progressively became finer with time as determined by laser diffraction. In addition, water retention and squeeze flow tests were used to assess the pastes` fresh properties. (c) 2009 Elsevier B.V. All rights reserved.

What loggers leave behind: Impacts on big-leaf mahogany (Swietenia macrophylla) commercial populations and potential for post-logging recovery in the Brazilian Amazon

The sustainability of current harvest practices for high-value Meliaceae can be assessed by quantifying logging intensity and projecting growth and survival by post-logging populations over anticipated intervals between harvests. From 100%-area inventories of big-leaf mahogany (Swietenia macrophylla) covering 204 ha or more at eight logged and unlogged forest sites across southern Brazilian Amazonia, we report generally higher landscape-scale densities and smaller population-level mean diameters in eastern forests compared to western forests, where most commercial stocks survive. Density of trees >= 20 cm diameter varied by two orders of magnitude and peaked at 1.17 ha(-1). Size class frequency distributions appeared unimodal at two high-density sites, but were essentially arnodal or flat elsewhere; diameter increment patterns indicate that populations were multi- or all-aged. At two high-density sites, conventional logging removed 93-95% of commercial trees (>= 45 cm diameter at the time of logging), illegally eliminated 31-47% of sub-merchantable trees, and targeted trees as small as 20 cm diameter. Projected recovery by commercial stems during 30 years after conventional logging represented 9.9-37.5% of initial densities and was highly dependent on initial logging intensity and size class frequency distributions of commercial trees. We simulated post-logging recovery over the same period at all sites according to the 2003 regulatory framework for mahogany in Brazil, which raised the minimum diameter cutting limit to 60 cm and requires retention during the first harvest of 20% of commercial-sized trees. Recovery during 30 years ranged from approximately 0 to 31% over 20% retention densities at seven of eight sites. At only one site where sub-merchantable trees dominated the population did the simulated density of harvestable stems after 30 years exceed initial commercial densities. These results indicate that 80% harvest intensity will not be sustainable over multiple cutting cycles for most populations without silvicultural interventions ensuring establishment and long-term growth of artificial regeneration to augment depleted natural stocks, including repeated tending of outplanted seedlings. Without improved harvest protocols for mahogany in Brazil as explored in this paper, future commercial supplies of this species as well as other high-value tropical timbers are endangered. Rapid changes in the timber industry and land-use in the Amazon are also significant challenges to sustainable management of mahogany. (C) 2007 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.

Spatial pattern of black spot incidence within citrus trees related to disease severity and pathogen dispersal

Guignardia citricarpa, the causal agent of citrus black spot, forms airborne ascospores on decomposing citrus leaves and water-spread conidia on fruits, leaves and twigs. The spatial pattern of diseased fruit in citrus tree canopies was used to assess the importance of ascospores and conidia in citrus black spot epidemics in Sao Paulo State, Brazil. The aggregation of diseased fruit in the citrus tree canopy was quantified by the binomial dispersion index (D) and the binary form of Taylor`s Power Law for 303 trees in six groves. D was significantly greater than 1 in 251 trees. The intercept of the regression line of Taylor`s Power Law was significantly greater than 0 and the slope was not different from 1, implying that diseased fruit was aggregated in the canopy independent of disease incidence. Disease incidence (p) and severity (S) were assessed in 2875 citrus trees. The incidence-severity relationship was described (R-2 = 88.7%) by the model ln(S) = ln(a) + bCLL(p) where CLL = complementary log-log transformation. The high severity at low incidence observed in many cases is also indicative of low distance spread of G. citricarpa spores. For the same level of disease incidence, some trees had most of the diseased fruit with many lesions and high disease severity, whereas other trees had most of the fruit with few lesions and low disease severity. Aggregation of diseased fruit in the trees suggests that splash-dispersed conidia have an important role in increasing the disease in citrus trees in Brazil.

Discriminant analysis of trace elements in normal, benign and malignant breast tissues measured by total reflection X-ray fluorescence

In this work total reflection X-ray fluorescence spectrometry has been employed to determine trace element concentrations in different human breast tissues (normal, normal adjacent, benign and malignant). A multivariate discriminant analysis of observed levels was performed in order to build a predictive model and perform tissue-type classifications. A total of 83 breast tissue samples were studied. Results showed the presence of Ca, Ti, Fe, Cu and Zn in all analyzed samples. All trace elements, except Ti, were found in higher concentrations in both malignant and benign tissues, when compared to normal tissues and normal adjacent tissues. In addition, the concentration of Fe was higher in malignant tissues than in benign neoplastic tissues. An opposite behavior was observed for Ca, Cu and Zn. Results have shown that discriminant analysis was able to successfully identify differences between trace element distributions from normal and malignant tissues with an overall accuracy of 80% and 65% for independent and paired breast samples respectively, and of 87% for benign and malignant tissues. (C) 2009 Elsevier B.V. All rights reserved.

Multicollinearity and financial constraint in investment decisions: a Bayesian generalized ridge regression

This paper addresses the investment decisions considering the presence of financial constraints of 373 large Brazilian firms from 1997 to 2004, using panel data. A Bayesian econometric model was used considering ridge regression for multicollinearity problems among the variables in the model. Prior distributions are assumed for the parameters, classifying the model into random or fixed effects. We used a Bayesian approach to estimate the parameters, considering normal and Student t distributions for the error and assumed that the initial values for the lagged dependent variable are not fixed, but generated by a random process. The recursive predictive density criterion was used for model comparisons. Twenty models were tested and the results indicated that multicollinearity does influence the value of the estimated parameters. Controlling for capital intensity, financial constraints are found to be more important for capital-intensive firms, probably due to their lower profitability indexes, higher fixed costs and higher degree of property diversification.

Phylogeography of the cactophilic species Drosophila gouveai: demographic events and divergence timing in dry vegetation enclaves in eastern Brazil

Aim The aim of this study was to assess the causal mechanisms underlying populational subdivision in Drosophila gouveai, a cactophilic species associated with xeric vegetation enclaves in eastern Brazil. A secondary aim was to investigate the genetic effects of Pleistocene climatic fluctuations on these environments. Location Dry vegetation enclaves within the limits of the Cerrado domain in eastern Brazil. Methods We determined the mitochondrial DNA haplotypes of 55 individuals (representing 12 populations) based on sequence data of a 483-bp fragment from the cytochrome c oxidase subunit II (COII) gene. Phylogenetic and coalescent analyses were used to test for the occurrence of demographic events and to infer the time of divergence amongst genetically independent groups. Results Our analyses revealed the existence of two divergent subclades (G1 and G2) plus an introgressed clade restricted to the southernmost range of D. gouveai. Subclades G1 and G2 displayed genetic footprints of range expansion and segregated geographical distributions in south-eastern and some central highland regions, east and west of the Parana River valley. Molecular dating indicated that the main demographic and diversification events occurred in the late to middle Pleistocene. Main conclusions The phylogeographical and genetic patterns observed for D. gouveai in this study are consistent with changes in the distribution of dry vegetation in eastern Brazil. All of the estimates obtained by molecular dating indicate that range expansion and isolation pre-dated the Last Glacial Maximum, occurring during the late to middle Pleistocene, and were probably triggered by climatic changes during the Pleistocene. The current patchy geographical distribution and population subdivision in D. gouveai is apparently closely linked to these past events.