Calibration of a Species-Specific Spectral Vegetation Index for Leaf Area Index (LAI) Monitoring: Example with MODIS Reflectance Time-Series on Eucalyptus Plantations

The leaf area index (LAI) is a key characteristic of forest ecosystems. Estimations of LAI from satellite images generally rely on spectral vegetation indices (SVIs) or radiative transfer model (RTM) inversions. We have developed a new and precise method suitable for practical application, consisting of building a species-specific SVI that is best-suited to both sensor and vegetation characteristics. Such an SVI requires calibration on a large number of representative vegetation conditions. We developed a two-step approach: (1) estimation of LAI on a subset of satellite data through RTM inversion; and (2) the calibration of a vegetation index on these estimated LAI. We applied this methodology to Eucalyptus plantations which have highly variable LAI in time and space. Previous results showed that an RTM inversion of Moderate Resolution Imaging Spectroradiometer (MODIS) near-infrared and red reflectance allowed good retrieval performance (R-2 = 0.80, RMSE = 0.41), but was computationally difficult. Here, the RTM results were used to calibrate a dedicated vegetation index (called "EucVI") which gave similar LAI retrieval results but in a simpler way. The R-2 of the regression between measured and EucVI-simulated LAI values on a validation dataset was 0.68, and the RMSE was 0.49. The additional use of stand age and day of year in the SVI equation slightly increased the performance of the index (R-2 = 0.77 and RMSE = 0.41). This simple index opens the way to an easily applicable retrieval of Eucalyptus LAI from MODIS data, which could be used in an operational way.

Application of the log-conformation tensor to three-dimensional time-dependent free surface flows

The numerical simulation of flows of highly elastic fluids has been the subject of intense research over the past decades with important industrial applications. Therefore, many efforts have been made to improve the convergence capabilities of the numerical methods employed to simulate viscoelastic fluid flows. An important contribution for the solution of the High-Weissenberg Number Problem has been presented by Fattal and Kupferman [J. Non-Newton. Fluid. Mech. 123 (2004) 281-285] who developed the matrix-logarithm of the conformation tensor technique, henceforth called log-conformation tensor. Its advantage is a better approximation of the large growth of the stress tensor that occur in some regions of the flow and it is doubly beneficial in that it ensures physically correct stress fields, allowing converged computations at high Weissenberg number flows. In this work we investigate the application of the log-conformation tensor to three-dimensional unsteady free surface flows. The log-conformation tensor formulation was applied to solve the Upper-Convected Maxwell (UCM) constitutive equation while the momentum equation was solved using a finite difference Marker-and-Cell type method. The resulting developed code is validated by comparing the log-conformation results with the analytic solution for fully developed pipe flows. To illustrate the stability of the log-conformation tensor approach in solving three-dimensional free surface flows, results from the simulation of the extrudate swell and jet buckling phenomena of UCM fluids at high Weissenberg numbers are presented. (C) 2012 Elsevier B.V. All rights reserved.

A marker-and-cell approach to free surface 2-D multiphase flows

This work describes a methodology to simulate free surface incompressible multiphase flows. This novel methodology allows the simulation of multiphase flows with an arbitrary number of phases, each of them having different densities and viscosities. Surface and interfacial tension effects are also included. The numerical technique is based on the GENSMAC front-tracking method. The velocity field is computed using a finite-difference discretization of a modification of the NavierStokes equations. These equations together with the continuity equation are solved for the two-dimensional multiphase flows, with different densities and viscosities in the different phases. The governing equations are solved on a regular Eulerian grid, and a Lagrangian mesh is employed to track free surfaces and interfaces. The method is validated by comparing numerical with analytic results for a number of simple problems; it was also employed to simulate complex problems for which no analytic solutions are available. The method presented in this paper has been shown to be robust and computationally efficient. Copyright (c) 2012 John Wiley & Sons, Ltd.

Serologic and molecular diagnostic and bioassay in mice for detection of Toxoplasma gondii in free ranges chickens from Pantanal of Mato Grosso do Sul

Holsback L., Pena H.F.J., Ragozo A., Lopes E. G., Gennari S. M. & Soares R. M. 2012. Serologic and molecular diagnostic and bioassay in mice for detection of Toxoplasma gondii in free range chickens from Pantanal of Mato Grosso do Sul. Pesquisa Veterinaria Brasileira 32(8): 721-726. Setor de Veterinaria e Producao Animal, Universidade Estadual do Norte do Parana, Campus Luiz Meneghel, Rodovia BR 369 Km 54, Bandeirantes, PR 86360-000, Brazil. E-mail: lhsfertonani@uenp.edu.br The aim of this study was to investigate the occurrence of Toxoplasma gondii and compare the results obtained in the Modified Agglutination Test (MAT), Polimerase Chain Reaction (PCR) and bioassay in mice. In order to accomplish this, 40 free-range chickens from eight farms in neighboring areas to the Pantanal in Nhecolandia, Mato Grosso do Sul, were euthanized and blood samples, brain and heart were collected. The occurrence of anti-T. gondii antibodies found in chickens was 67.5% (27 samples), considering as a cutoff point the dilution 1:5. Among the samples analyzed, 7 (25.9%) were positive in the dilution 1: 5, 3 (11.1%) in 1: 10, 2 (7.4%) in 1: 20, 3 (11.1%) in 1: 320, 1 (3.7%) in 1: 640, 3 (11.1%) in 1: 1280, 2 (7.4%) in 1: 2560, 4 (14.8%) in 1: 5120 and 2 (7.4%) in 1: 10.240. From the mixture of tissue samples (brain and heart) from the chickens analyzed, 16 (40%) presented electrophoretic bands compatible with T. gondii by PCR (gene B1). In the comparison of techniques, 59.26% positivity in PCR was revealed among animals that were seropositive in MAT (cutoff 1: 5). From 141 inoculated mice, six (4.44%) died of acute toxoplasmosis between 15 and 23 days after inoculation. Surviving mice were sacrificed at 74 days after inoculation, and a total of 28 cysts were found in the brains of 10 distinct groups. From the seropositive hens, 27 bioassays were performed and 11 (40.7%) isolates were obtained. A greater number of isolations happened in mice that were inoculated with tissues from chickens that had high titers for anti-T. gondii antibodies. Chronic infection in mice was observed in nine groups (33.3%) from five different properties. Among the surviving mice, 25.6% were positive for T. gondii in MAT (1: 25). From mice positive in PCR, 87.5% were also positive in MAT. Among the PCR-negative mice, 5.2% were positive for T. gondii in MAT. It can be concluded through this study that the occurrence of infecton by T. gondii in the rural properties studied was high, that PCR directed to gene B1 does not confirm the viability of the parasite, but it can be used as a screening method for the selection of chickens infected by T. gondii, that the animals with titer greater than 10 must be prioritized for the selection of animals for bioassay, since for them, the chances of isolating the parasite are greater and that seroconversion in experimentally infected mice is not a good indicator for isolating the agent.

Augmented Lagrangian method with nonmonotone penalty parameters for constrained optimization

At each outer iteration of standard Augmented Lagrangian methods one tries to solve a box-constrained optimization problem with some prescribed tolerance. In the continuous world, using exact arithmetic, this subproblem is always solvable. Therefore, the possibility of finishing the subproblem resolution without satisfying the theoretical stopping conditions is not contemplated in usual convergence theories. However, in practice, one might not be able to solve the subproblem up to the required precision. This may be due to different reasons. One of them is that the presence of an excessively large penalty parameter could impair the performance of the box-constraint optimization solver. In this paper a practical strategy for decreasing the penalty parameter in situations like the one mentioned above is proposed. More generally, the different decisions that may be taken when, in practice, one is not able to solve the Augmented Lagrangian subproblem will be discussed. As a result, an improved Augmented Lagrangian method is presented, which takes into account numerical difficulties in a satisfactory way, preserving suitable convergence theory. Numerical experiments are presented involving all the CUTEr collection test problems.

New measurement of the B-11(p,alpha(0))Be-8 bare-nucleus S(E) factor via the Trojan horse method

A new measurement of the B-11(p,alpha(0))Be-8 has been performed applying the Trojan horse method (THM) to the H-2(B-11,alpha Be-8(0))n quasi-free reaction induced at a laboratory energy of 27 MeV. The astrophysical S(E) factor has been extracted from similar to 600 keV down to zero energy by means of an improved data analysis technique and it has been compared with direct data available in the literature. The range investigated here overlaps with the energy region of the light element LiBeB stellar burning and with that of future aneutronic fusion power plants using the B-11+p fuel cycle. The new investigation described here confirms the preliminary results obtained in the recent TH works. The origin of the discrepancy between the direct estimate of the B-11(p,alpha(0))Be-8 S(E)-factor at zero energy and that from a previous THM investigation is quantitatively corroborated. The results obtained here support, within the experimental uncertainties, the low-energy S(E)-factor extrapolation and the value of the electron screening potential deduced from direct measurements.

Bioelectrical impedance with different equations versus deuterium oxide dilution method for the inference of body composition in healthy older persons

There is no consensus regarding the accuracy of bioimpedance for the determination of body composition in older persons. This study aimed to compare the assessment of lean body mass of healthy older volunteers obtained by the deuterium dilution method (reference) with those obtained by two frequently used bioelectrical impedance formulas and one formula specifically developed for a Latin-American population. A cross-sectional study. Twenty one volunteers were studied, 12 women, with mean age 72 +/- 6.7 years. Urban community, Ribeiro Preto, Brazil. Fat free mass was determined, simultaneously, by the deuterium dilution method and bioelectrical impedance; results were compared. In bioelectrical impedance, body composition was calculated by the formulas of Deuremberg, Lukaski and Bolonchuck and Valencia et al. Lean body mass of the studied volunteers, as determined by bioelectrical impedance was 37.8 +/- 9.2 kg by the application of the Lukaski e Bolonchuk formula, 37.4 +/- 9.3 kg (Deuremberg) and 43.2 +/- 8.9 kg (Valencia et. al.). The results were significantly correlated to those obtained by the deuterium dilution method (41.6 +/- 9.3 Kg), with r=0.963, 0.932 and 0.971, respectively. Lean body mass obtained by the Valencia formula was the most accurate. In this study, lean body mass of older persons obtained by the bioelectrical impedance method showed good correlation with the values obtained by the deuterium dilution method. The formula of Valencia et al., developed for a Latin-American population, showed the best accuracy.

The boundedness of penalty parameters in an augmented Lagrangian method with constrained subproblems

Augmented Lagrangian methods are effective tools for solving large-scale nonlinear programming problems. At each outer iteration, a minimization subproblem with simple constraints, whose objective function depends on updated Lagrange multipliers and penalty parameters, is approximately solved. When the penalty parameter becomes very large, solving the subproblem becomes difficult; therefore, the effectiveness of this approach is associated with the boundedness of the penalty parameters. In this paper, it is proved that under more natural assumptions than the ones employed until now, penalty parameters are bounded. For proving the new boundedness result, the original algorithm has been slightly modified. Numerical consequences of the modifications are discussed and computational experiments are presented.

Processing of high resolution magic angle spinning spectra of breast cancer cells by the filter diagonalization method

Proton nuclear magnetic resonance (H-1 NMR) spectroscopy for detection of biochemical changes in biological samples is a successful technique. However, the achieved NMR resolution is not sufficiently high when the analysis is performed with intact cells. To improve spectral resolution, high resolution magic angle spinning (HR-MAS) is used and the broad signals are separated by a T-2 filter based on the CPMG pulse sequence. Additionally, HR-MAS experiments with a T-2 filter are preceded by a water suppression procedure. The goal of this work is to demonstrate that the experimental procedures of water suppression and T-2 or diffusing filters are unnecessary steps when the filter diagonalization method (FDM) is used to process the time domain HR-MAS signals. Manipulation of the FDM results, represented as a tabular list of peak positions, widths, amplitudes and phases, allows the removal of water signals without the disturbing overlapping or nearby signals. Additionally, the FDM can also be used for phase correction and noise suppression, and to discriminate between sharp and broad lines. Results demonstrate the applicability of the FDM post-acquisition processing to obtain high quality HR-MAS spectra of heterogeneous biological materials.

Study of surface free energy on a lattice-gas model applied to Liquid bridge

The pulmonary crackling and the formation of liquid bridges are problems that for centuries have been attracting the attention of scientists. In order to study these phenomena, it was developed a canonical cubic lattice-gas­ like model to explain the rupture of liquid bridges in lung airways [A. Alencar et al., 2006, PRE]. Here, we further develop this model and add entropy analysis to study thermodynamic properties, such as free energy and force. The simulations were performed using the Monte Carlo method with Metropolis algorithm. The exchange between gas and liquid particles were performed randomly according to the Kawasaki dynamics and weighted by the Boltzmann factor. Each particle, which can be solid (s), liquid (l) or gas (g), has 26 neighbors: 6 + 12 + 8, with distances 1, √2 and √3, respectively. The energy of a lattice's site m is calculated by the following expression: Em = ∑k=126 Ji(m)j(k) in witch (i, j) = g, l or s. Specifically, it was studied the surface free energy of the liquid bridge, trapped between two planes, when its height is changed. For that, was considered two methods. First, just the internal energy was calculated. Then was considered the entropy. It was fond no difference in the surface free energy between this two methods. We calculate the liquid bridge force between the two planes using the numerical surface free energy. This force is strong for small height, and decreases as the distance between the two planes, height, is increased. The liquid-gas system was also characterized studying the variation of internal energy and heat capacity with the temperature. For that, was performed simulation with the same proportion of liquid and gas particle, but different lattice size. The scale of the liquid-gas system was also studied, for low temperature, using different values to the interaction Jij.

Computational simulation of the flow-induced vibration of a circular cylinder subjected to wake interference

In this work, we considered the flow around two circular cylinders of equal diameter placed in tandem with respect to the incident uniform flow. The upstream cylinder was fixed and the downstream cylinder was completely free to move in the cross-stream direction, with no spring or damper attached to it. The centre-to-centre distance between the cylinders was four diameters, and the Reynolds number was varied from 100 to 645. We performed two- and three-dimensional simulations of this flow using a Spectral/hp element method to discretise the flow equations, coupled to a simple Newmark integration routine that solves the equation of the dynamics of the cylinder. The differences of the behaviours observed in the two- and three-dimensional simulations are highlighted and the data is analysed under the light of previously published experimental results obtained for higher Reynolds numbers.

New Improved Version of J 1 ...J 4 Interferometry Method and its Application to Nanometric Vibration Measurements

Piezoelectric ceramics, such as PZT, can generate subnanometric displacements, bu t in order to generate multi- micrometric displacements, they should be either driven by high electric voltages (hundreds of volts ), or operate at a mechanical resonant frequency (in narrow band), or have large dimensions (tens of centimeters). A piezoelectric flextensional actuator (PFA) is a device with small dimensions that can be driven by reduced voltages and can operate in the nano- and micro scales. Interferometric techniques are very adequate for the characterization of these devices, because there is no mechanical contact in the measurement process, and it has high sensitivity, bandwidth and dynamic range. A low cost open-loop homodyne Michelson interferometer is utilized in this work to experimentally detect the nanovi brations of PFAs, based on the spectral analysis of the interfero metric signal. By employing the well known J 1 ...J 4 phase demodulation method, a new and improved version is proposed, which presents the following characteristics: is direct, self-consistent, is immune to fading, and does not present phase ambiguity problems. The proposed method has resolution that is similar to the modified J 1 ...J 4 method (0.18 rad); however, differently from the former, its dynamic range is 20% larger, does not demand Bessel functions algebraic sign correction algorithms and there are no singularities when the static phase shift between the interferometer arms is equal to an integer multiple of  /2 rad. Electronic noise and random phase drifts due to ambient perturbations are taken into account in the analysis of the method. The PFA nanopositioner characterization was based on the analysis of linearity betw een the applied voltage and the resulting displacement, on the displacement frequency response and determination of main resonance frequencies.