An application of the GLUE methodology for estimating the parameters of the INCA-N model

The conceptual and parameter uncertainty of the semi-distributed INCA-N (Integrated Nutrients in Catchments-Nitrogen) model was studied using the GLUE (Generalized Likelihood Uncertainty Estimation) methodology combined with quantitative experimental knowledge, the concept known as 'soft data'. Cumulative inorganic N leaching, annual plant N uptake and annual mineralization proved to be useful soft data to constrain the parameter space. The INCA-N model was able to simulate the seasonal and inter-annual variations in the stream-water nitrate concentrations, although the lowest concentrations during the growing season were not reproduced. This suggested that there were some retention processes or losses either in peatland/wetland areas or in the river which were not included in the INCA-N model. The results of the study suggested that soft data was a way to reduce parameter equifinality, and that the calibration and testing of distributed hydrological and nutrient leaching models should be based both on runoff and/or nutrient concentration data and the qualitative knowledge of experimentalist. (c) 2006 Elsevier B.V. All rights reserved.

Quantitative pulsed phase thermography applied to steel plates

Pulsed Phase Thermography (PPT) has been proven effective on depth retrieval of flat-bottomed holes in different materials such as plastics and aluminum. In PPT, amplitude and phase delay signatures are available following data acquisition (carried out in a similar way as in classical Pulsed Thermography), by applying a transformation algorithm such as the Fourier Transform (FT) on thermal profiles. The authors have recently presented an extended review on PPT theory, including a new inversion technique for depth retrieval by correlating the depth with the blind frequency fb (frequency at which a defect produce enough phase contrast to be detected). An automatic defect depth retrieval algorithm had also been proposed, evidencing PPT capabilities as a practical inversion technique. In addition, the use of normalized parameters to account for defect size variation as well as depth retrieval from complex shape composites (GFRP and CFRP) are currently under investigation. In this paper, steel plates containing flat-bottomed holes at different depths (from 1 to 4.5 mm) are tested by quantitative PPT. Least squares regression results show excellent agreement between depth and the inverse square root blind frequency, which can be used for depth inversion. Experimental results on steel plates with simulated corrosion are presented as well. It is worth noting that results are improved by performing PPT on reconstructed (synthetic) rather than on raw thermal data.

Compression of polymer brushes: quantitative comparison of self-consistent field theory with experiment

The self-consistent field theory (SCFT) prediction for the compression force between two semi-dilute polymer brushes is compared to the benchmark experiments of Taunton et al. [Nature, 1988, 332, 712]. The comparison is done with previously established parameters, and without any fitting parameters whatsoever. The SCFT provides a significant quantitative improvement over the classical strong-stretching theory (SST), yielding excellent quantitative agreement with the experiment. Contrary to earlier suggestions, chain fluctuations cannot be ignored for normal experimental conditions. Although the analytical expressions of SST provide invaluable aids to understanding the qualitative behavior of polymeric brushes, the numerical SCFT is necessary in order to provide quantitatively accurate predictions.

Computer generation and quantitative morphometric analysis of virtual neurons

An important goal in computational neuroanatomy is the complete and accurate simulation of neuronal morphology. We are developing computational tools to model three-dimensional dendritic structures based on sets of stochastic rules. This paper reports an extensive, quantitative anatomical characterization of simulated motoneurons and Purkinje cells. We used several local and global algorithms implemented in the L-Neuron and ArborVitae programs to generate sets of virtual neurons. Parameters statistics for all algorithms were measured from experimental data, thus providing a compact and consistent description of these morphological classes. We compared the emergent anatomical features of each group of virtual neurons with those of the experimental database in order to gain insights on the plausibility of the model assumptions, potential improvements to the algorithms, and non-trivial relations among morphological parameters. Algorithms mainly based on local constraints (e.g., branch diameter) were successful in reproducing many morphological properties of both motoneurons and Purkinje cells (e.g. total length, asymmetry, number of bifurcations). The addition of global constraints (e.g., trophic factors) improved the angle-dependent emergent characteristics (average Euclidean distance from the soma to the dendritic terminations, dendritic spread). Virtual neurons systematically displayed greater anatomical variability than real cells, suggesting the need for additional constraints in the models. For several emergent anatomical properties, a specific algorithm reproduced the experimental statistics better than the others did. However, relative performances were often reversed for different anatomical properties and/or morphological classes. Thus, combining the strengths of alternative generative models could lead to comprehensive algorithms for the complete and accurate simulation of dendritic morphology.

Determination of tube theory parameters using a simple grid model as an example

Although the tube theory is successful in describing entangled polymers qualitatively, a more quantitative description requires precise and consistent definitions of its parameters. Here we investigate the simplest model of entangled polymers, namely a single Rouse chain in a cubic lattice of line obstacles, and illustrate the typical problems and uncertainties of the tube theory. In particular we show that in general one needs 3 entanglement related parameters, but only 2 combinations of them are relevant for the long-time dynamics. Conversely, the plateau modulus can not be determined from these two parameters and requires a more detailed model of entanglements with explicit entanglement forces, such as the slipsprings model. It is shown that for the grid model the Rouse time within the tube is larger than the Rouse time of the free chain, in contrast to what the standard tube theory assumes.

Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers

We report on the assembly of tumor necrosis factor receptor 1 (TNF-R1) prior to ligand activation and its ligand-induced reorganization at the cell membrane. We apply single-molecule localization microscopy to obtain quantitative information on receptor cluster sizes and copy numbers. Our data suggest a dimeric pre-assembly of TNF-R1, as well as receptor reorganization toward higher oligomeric states with stable populations comprising three to six TNF-R1. Our experimental results directly serve as input parameters for computational modeling of the ligand-receptor interaction. Simulations corroborate the experimental finding of higher-order oligomeric states. This work is a first demonstration how quantitative, super-resolution and advanced microscopy can be used for systems biology approaches at the single-molecule and single-cell level.

Sovereign debt with adverse selection : a quantitative approach

We construct a dynamic equilibrium model to quantitatively study sovereign debt with contingent services and country risk spreads such that the benefits of defaulting are tempered by higher interest rates in the future. For a wide range of parameters, the only equilibrium of the model is one in which the sovereign defaults in all states, unless defaulting incurs additional costs. Due to the adverse selection problem, some countries choose to delay default in order to reduce reputation loss. Although equilibria with no default imply in greater welfare levels, they are not sustainable in the highly indebted and volatile countries.

A quantitative nature of somatic embryogenesis in soybean

The objectives of this research were to investigate the genetic parameters associated with the in vitro formation of somatic embryos in soybean and to determine the effect of light intensity on the embryogenic capability of F-1, F-2, and backcross (RC1P1 and RC1P2) progenies derived from crosses between embryogenic (IAS-5 and Embrapa-1) and nonembryogenic (Parana) cultivars. Immature cotyledons (4-6 mm in length) derived from the parental lines, F-1, F-2, RC1P1, and RC1P2 were grown for 90 d on the inductive N10 medium, after which the number of somatic embryos was recorded. Chi-square tests for goodness of fit showed that the genetic component of the somatic embryogenesis trait is controlled in a quantitative manner by approximately 10 genes. A normal distribution for somatic embryo formation in the F-2 generations was observed reinforcing the quantitative nature of the trait. Variation in light intensity (8-12 and 27-33 mu mol m(-2) s(-1)) had no effect on somatic embryo formation in the parental material tested.

Analytical Validation of Quantitative High-Performance Liquid Chromatographic Methods in Pharmaceutical Analysis: A Practical Approach

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Quantitative microscopy characterization of hydrous niobium phosphate into bleached cellulose

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Quantitative variation in the tropical maize population, ESALQ-PB1

A boa produtividade e os valores intermediários para altura da planta e altura da espiga caracterizam a população de milho ESALQ-PB1 como agronomicamente promissora. São relatadas estimativas de parâmetros para 13 caracteres: altura da planta (PH), altura da espiga (EH), posição relativa da espiga (EP), comprimento do pendão (TL), peso do pendão (TW), número de ramificações do pendão (TB), peso de espigas (EW), peso de grãos (GW), comprimento da espiga (EL), diâmetro da espiga (ED), número de fileiras de grãos (RN), número de grãos por fileira (KR) e prolificidade (PR). Os resultados se referem a um único ambiente (um local e um ano). Foi detectada variação genética para todos os caracteres, e são apresentadas estimativas da variância genética aditiva. Os coeficientes de herdabilidade (indivíduos) variaram de 0,14 a 0,72 e foram considerados altos para PH, EH e TB; intermediários para EP, TL, TW, EL e ED, e baixos para EW, GW, KR e PR. O coeficiente de herdabilidade para médias de progênies mostrou aproximadamente a mesma tendência, variando de 0,40 a 0,75. O maior ganho esperado por seleção foi para TB (27% por ciclo) sob seleção massal e para TW (16,4%) por seleção entre progênies; o menor ganho esperado foi para ED, tanto por seleção massal (1,9%) como por seleção entre progênies (2,9%). Coeficientes de correlação aditiva (rA) 0.5

Strong and fast phase modulation for quantitative analysis of photorefractive gratings

A new approach for studying photorefractive gratings in two-wave mixing experiments by a phase modulation technique is presented. The introduction of a large-amplitude, high-frequency sinusoidal phase modulation in one of the input beams blurs the interference pattern and provides powerful harmonic signals for accurate measurements of the grating diffraction efficiency eta and the output phase shift rho between the transmitted and diffracted waves. The blurring of the light fringes can be used to suppress the higher spatial harmonics of the grating, allowing a space-charge field with sinusoidal profile to be recorded. Although the presence of such a strong phase modulation affects the beam coupling in a rather complicated way, it is shown that for the special case of equal intensity input beams, the effect of the phase modulation on eta and rho is reduced to a weakening of the coupling strength. The potentialities of the technique are illustrated in a study of refractive-index waves excited by running interference patterns in a Bi12TiO20 crystal. Expressions for the diffraction efficiency and the output phase shift are derived and used to match numerically calculated curves to the experimental data. The theoretical model is supported by the very good data fitting and allows the computation of important material parameters.

Calcaneal apophysitis: a quantitative radiographic evaluation of the secondary ossification center

Background: Calcaneal apophysitis in children is a self-limited condition that may interfere with walking and physical performance in sports, thus causing concern to the patient and parents. There is still controversy about the significance of the radiographic changes in children with heel pain, since the report of Sever in 1912. One of the reasons is that normal children may display a considerable variation in the radiographic aspects of the secondary ossification center of the calcaneus at different ages. Methods: In this investigation, the developmental aspects of primary and secondary ossification centers of the calcaneus were studied in radiographs obtained from healthy boys and from boys with calcaneal apophysitis. The normal population comprised 392 children and adolescents ranging in age from 6 to 15 years. There were 69 individuals with calcaneal apophysitis ranging in age from 8 to 14 years. Lateral standard radiographs were obtained of both heels, and a copper step wedge was used as a calibration to determine bone density. The following parameters were analyzed on the plain films: time of appearance, fusion and number of fragments of the secondary nucleus, area and bone densitometry of the primary and secondary ossification centers of the calcaneus. Results: In the normal population, the ossification of the secondary nucleus began at 7 years of age, and at 15 years of age, the nucleus was fused in all individuals. In the apophysitis group, the secondary ossification center was present and not fused in all individuals. Both secondary nuclei increased in size with age with no difference between the two groups. Regarding bone density, both the primary and secondary nuclei were less dense in the apophysitis group than their counterparts in the normal population. The most significant difference between the two populations referred to the degree of fragmentation, which was greater in the apophysitis group. Conclusion: Our data showed that the sclerotic aspect of the secondary nucleus of the calcaneus is a normal feature and, therefore, should not be used to establish the diagnosis of Sever's disease. The most consistent difference between the normal and apophysitis group was related to the more fragmented aspect of the secondary nucleus in the latter individuals, which may suggest a mechanical etiology for that condition.

Dielectric thermal analysis as a tool for quantitative-evaluation of the viscosity and the kinetics of epoxy resin cure

Dielectric thermal analysis has been proved as a valuable tool for monitoring the epoxy curing process and the related rheological properties in the fabrication of polymer-matrix composite materials. This technique also has the potential to be applied in the monitoring of magnet impregnation processes as well as in quality control. In this work we present the quantitative evaluation of the viscosity changing and the curing kinetics for a commercial Stycast epoxy resin system at different temperatures through the impedance analysis. The results showed correlation between the real component of the complex impedance and the isothermal reaction extent. Comparing the dielectric analysis result with the viscosity measured by rotational rheometer we observed a similar behavior reported for dynamic mechanic analysis. The results comparison have shown that the kinetics parameters obtained from DSC and DETA analysis showed different sensitivities related to the characteristics of curing stages. We concluded that the dielectric thermal analysis should be applied in quantitative evaluation of cure kinetics.

Genetic parameters by Bayesian inference for dual purpose Jaffarabadi buffaloes

Knowledge of genetic parameters is essential for improved reproductive management and increased yield. Quantitative analysis of genetic parameters is lacking for many breeds of buffaloes. This article provides the first estimate of genetic parameters for dual purpose (meat and milk) Brazilian Jaffarabadi buffaloes, using Bayesian inference. Data on milk yield (MY), lactation length (LL), weight at 205 days (W205) and 365 (W365) days of age, and average daily gain (ADG) from 205 to 365 days of age were collected in two herds. Bivariate analyses (using the program MTGSAM) were performed with the Gibbs sampler to obtain estimates of variance and covariance. Average lactation milk yield and lactation length were 1 620.2 +/- 450.9 kg and 257.6 +/- 46.8 days, respectively, and the mean values for weight traits (kg) were 181.6 +/- 63.3 (W205), 298.04 +/- 116.1 (W365), and 0.73 +/- 0.35 (ADG). Heritability estimates (modes) were 0.16 for MY, 0.10 for LL, 0.43 for W205, 0.48 for W365 and 0.32 for ADG. There was a high genetic correlation (0.96) between milk yield and lactation length and very high genetic correlations (0.99) between the three growth traits. Our data suggest that both milk production and growth traits have clear potential for yield improvement through direct selection in this dual purpose breed. The selection for weight at an early age would be successful and selection for MY can be performed in the first lactation.