The impact of measurement errors in the identification of regulatory networks

Background: There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise. Results: This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data. Conclusions: Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.

Heterogeneous modeling of an anaerobic sequencing batch biofilm reactor (ASBBR)

The objective of this study was to estimate the first-order intrinsic kinetic constant (k(1)) and the liquid-phase mass transfer coefficient (k(c)) in a bench-scale anaerobic sequencing batch biofilm reactor (ASBBR) fed with glucose. A dynamic heterogeneous mathematical model, considering two phases (liquid and solid), was developed through mass balances in the liquid and solid phases. The model was adjusted to experimental data obtained from the ASBBR applied for the treatment of glucose-based synthetic wastewater with approximately 500 mg L-1 of glucose, operating in 8 h batch cycles, at 30 degrees C and 300 rpm. The values of the parameters obtained were 0.8911 min(-1) for k(1) and 0.7644 cm min(-1) for kc. The model was validated utilizing the estimated parameters with data obtained from the ASBBR operating in 3 h batch cycles, with a good representation of the experimental behavior. The solid-phase mass transfer flux was found to be the limiting step of the overall glucose conversion rate.

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.

Growth parameters and mortality rate of the Scomber japonicus peruanus (Jordán & Hubb, 1925) along the Peruvian coast, South Pacific

The growth parameters and the mortality rates of the Scomber japonicus peruanus (Chub mackerel) were studied based on monthly data of frequency of fork length classes obtained from commercial landings off the Peruvian coast from 1996 to 1998. The asymptotic body length and growth rate values obtained by the ELEFAN I (Electronic Length Frequency Analysis) ranged from 40.20 cm to 42.20 cm and from 0.38 to 0.39, respectively. The oscillation amplitude was 0.60; the Winter point values varied from 0.50 to 0.60 and the performance index from 2.79 to 2.84. The total mortality rate of the Chub mackerel obtained by the linearized catch curve oscillated between 1.68 and 3.35. The rate of fishing mortality varied from 1.16 to 2.78 and the exploitation rate from 0.68 to 0.84. The annual rate of natural mortality estimated by the Pauly's method ranged from 0.52 to 0.53. The results obtained allow us to conclude that the longevity of the Chub mackerel was slightly over seven years.

Genetic parameters for pre-weaning traits in Braunvieh cattle

The objective of this study was to estimate genetic parameters for pre-weaning traits of Braunvieh cattle raised under tropical conditions in Brazil. The weight and weight gain parameters were birth weight (BW, N = 9955), weight at 120 days of age (W120, N = 5901), weaning weight at 205 days (WW, N = 6970), weight gain from birth to 205 days (GAIN205, N = 6013), weight gain from birth to 120 days (GAIN120, N = 5135), and weight gain from 120 to 205 days (GAIN85, N = 4482). Variance components were estimated using the animal model with the MTDFREML software. The relationship matrix included 35,188 animals; phenotypic measures were available for 18,688. Direct and maternal heritability increased from birth to weaning, with estimates of 0.23 +/- 0.037, 0.25 +/- 0.050, 0.41 +/- 0.059 for direct heritability for BW, W120 and WW, respectively, 0.08 +/- 0.012, 0.15 +/- 0.032, 0.22 +/- 0.036 for maternal genetic effects, and 0.18, 0.14 and 0.16 for total heritability estimates. For pre-weaning gains, estimates of heritability were 0.36 +/- 0.059, 0.30 +/- 0.059, 0.12 +/- 0.035 for direct genetic effects of the traits GAIN205, GAIN120 and GAIN85, respectively, 0.23 +/- 0.038, 0.17 +/- 0.037, 0.03 +/- 0.029 for estimates of maternal heritability, and 0.12, 0.13, 0.16 for total heritability, respectively. Genetic correlations between weights were greater between measures taken at shorter intervals. This information can be used to optimize the design of programs for genetic improvement of Braunvieh cattle raised under tropical conditions.

Genetic parameters for productive life traits and reproductive efficiency traits at 6 years in Nellore cattle

The objective of the present study was to estimate (co)variance components for length of productive life (LPL) and some alternative reproductive traits of 6-year-old Nellore cattle. The data set contained 57,410 records for age at first calving from Nellore females and was edited to remove animal records with uncertain paternity and cows with just one piece of calving information. Only animals with age at first calving ranging from 23 to 48 months and calving intervals between 11 and 24 months were kept for analysis. LPL and life production ( LP) were used to describe productive life. LPL was defined as the number of months a cow was kept in the herd until she was 6 years old, given that she was alive at first calving and LP was defined as total number of calves in that time. Four traits were used to describe reproductive traits: two breeding efficiencies on original scale were estimated using Wilcox and Tomar functions (BEW and BET, respectively), and two breeding efficiencies transformed (ASBEW and ASBET, respectively), using the function [arcsine (square root (BEi/100))]. Estimates of heritability for measures of LPL and LP were low and ranged from 0.04 to 0.05. Estimates of heritability for breeding efficiencies on original and transformed scales oscillated from 0.18 to 0.32. Estimates of genetic correlations ranged from -0.57 to 0.79 for LPL and other traits and from 0.28 to 0.63 for LP and other traits.

Zero-phonon emission and magnetic polaron parameters in EuTe

A phonon structure in the photoluminescence of EuTe was discovered, with a well-defined zero-phonon emission line (ZPL). The ZPL redshifts linearly with the intensity of applied magnetic field, indicating spin relaxation of the photoexcited electron, and saturates at a lower magnetic field than the optical absorption bandgap, which is attributed to formation of magnetic polarons. From the difference in these saturation fields, the zero-field polaron binding energy and radius are estimated to be 43 meV and 3.2 (in units of the EuTe lattice parameter), respectively. (C) 2011 American Institute of Physics. [doi:10.1063/1.3634030]

Experimental and numerical investigation of dynamic heat transfer parameters in packed bed

Dynamic experiments in a nonadiabatic packed bed were carried out to evaluate the response to disturbances in wall temperature and inlet airflow rate and temperature. A two-dimensional, pseudo-homogeneous, axially dispersed plug-flow model was numerically solved and used to interpret the results. The model parameters were fitted in distinct stages: effective radial thermal conductivity (K (r)) and wall heat transfer coefficient (h (w)) were estimated from steady-state data and the characteristic packed bed time constant (tau) from transient data. A new correlation for the K (r) in packed beds of cylindrical particles was proposed. It was experimentally proved that temperature measurements using radially inserted thermocouples and a ring-shaped sensor were not distorted by heat conduction across the thermocouple or by the thermal inertia effect of the temperature sensors.

An estimate of biometric parameters in eucalyptus clone plantations in Southern Bahia: an application of the airborne laser scanning (ALS) technology

The application of airborne laser scanning (ALS) technologies in forest inventories has shown great potential to improve the efficiency of forest planning activities. Precise estimates, fast assessment and relatively low complexity can explain the good results in terms of efficiency. The evolution of GPS and inertial measurement technologies, as well as the observed lower assessment costs when these technologies are applied to large scale studies, can explain the increasing dissemination of ALS technologies. The observed good quality of results can be expressed by estimates of volumes and basal area with estimated error below the level of 8.4%, depending on the size of sampled area, the quantity of laser pulses per square meter and the number of control plots. This paper analyzes the potential of an ALS assessment to produce certain forest inventory statistics in plantations of cloned Eucalyptus spp with precision equal of superior to conventional methods. The statistics of interest in this case were: volume, basal area, mean height and dominant trees mean height. The ALS flight for data assessment covered two strips of approximately 2 by 20 Km, in which clouds of points were sampled in circular plots with a radius of 13 m. Plots were sampled in different parts of the strips to cover different stand ages. The clouds of points generated by the ALS assessment: overall height mean, standard error, five percentiles (height under which we can find 10%, 30%, 50%,70% and 90% of the ALS points above ground level in the cloud), and density of points above ground level in each percentile were calculated. The ALS statistics were used in regression models to estimate mean diameter, mean height, mean height of dominant trees, basal area and volume. Conventional forest inventory sample plots provided real data. For volume, an exploratory assessment involving different combinations of ALS statistics allowed for the definition of the most promising relationships and fitting tests based on well known forest biometric models. The models based on ALS statistics that produced the best results involved: the 30% percentile to estimate mean diameter (R(2)=0,88 and MQE%=0,0004); the 10% and 90% percentiles to estimate mean height (R(2)=0,94 and MQE%=0,0003); the 90% percentile to estimate dominant height (R(2)=0,96 and MQE%=0,0003); the 10% percentile and mean height of ALS points to estimate basal area (R(2)=0,92 and MQE%=0,0016); and, to estimate volume, age and the 30% and 90% percentiles (R(2)=0,95 MQE%=0,002). Among the tested forest biometric models, the best fits were provided by the modified Schumacher using age and the 90% percentile, modified Clutter using age, mean height of ALS points and the 70% percentile, and modified Buckman using age, mean height of ALS points and the 10% percentile.

Random regression models to estimate test-day milk yield genetic parameters Holstein cows in Southeastern Brazil

A total of 152,145 weekly test-day milk yield records from 7317 first lactations of Holstein cows distributed in 93 herds in southeastern Brazil were analyzed. Test-day milk yields were classified into 44 weekly classes of DIM. The contemporary groups were defined as herd-year-week of test-day. The model included direct additive genetic, permanent environmental and residual effects as random and fixed effects of contemporary group and age of cow at calving as covariable, linear and quadratic effects. Mean trends were modeled by a cubic regression on orthogonal polynomials of DIM. Additive genetic and permanent environmental random effects were estimated by random regression on orthogonal Legendre polynomials. Residual variances were modeled using third to seventh-order variance functions or a step function with 1, 6,13,17 and 44 variance classes. Results from Akaike`s and Schwarz`s Bayesian information criterion suggested that a model considering a 7th-order Legendre polynomial for additive effect, a 12th-order polynomial for permanent environment effect and a step function with 6 classes for residual variances, fitted best. However, a parsimonious model, with a 6th-order Legendre polynomial for additive effects and a 7th-order polynomial for permanent environmental effects, yielded very similar genetic parameter estimates. (C) 2008 Elsevier B.V. All rights reserved.

Influence of Urea, Isopropanol, and Propylene Glycol on Rutin In Vitro Release from Cosmetic Semisolid Systems Estimated by Factorial Design

Rutin, one of the major flavonoids found in an assortment of plants, was reported to act as a sun protection factor booster with high anti-UVA defense, antioxidant, antiaging, and anticellulite, by improvement of the cutaneous microcirculation. This research work aimed at evaluating the rutin in vitro release from semisolid systems, in vertical diffusion cells, containing urea, isopropanol and propylene glycol, associated or not, according to the factorial design with two levels with center point. Urea (alone and in association with isopropanol and propylene glycol) and isopropanol (alone and in association with propylene glycol) influenced significant and negatively rutin liberation in diverse parameters: flux (g/cm2.h); apparent permeability coefficient (cm/h); rutin amount released (g/cm2); and liberation enhancement factor. In accordance with the results, the presence of propylene glycol 5.0% (wt/wt) presented statistically favorable to promote rutin release from this semisolid system with flux = 105.12 8.59 g/cm2.h; apparent permeability coefficient = 7.01 0.572 cm/h; rutin amount released = 648.80 53.01 g/cm2; and liberation enhancement factor = 1.21 0.07.

Bioavailability of dietary sodium copper chlorophyllin and its effect on antioxidant defence parameters of Wistar rats

BACKGROUND: There has been growing interest in sodium copper chlorophyllin (Cu-Chl) as a food colourant and supplement owing to its beneficial biological activities. Studies have revealed that this green pigment inhibits experimental carcinogenesis and interacts with proteins and genotoxic agents. Health-related activities have also been associated with the prevention of lipid peroxidation. However, intestinal absorption of this pigment has been considered insignificant, raising questions of whether eventual biological properties are related to pre- or post-absorptive actions. In this study, intestinal absorption of Cu-Chl and its appearance in serum and organs were estimated by high-performance liquid chromatography analysis in rat feeding experiments. The effect of ingested Cu-Chl on lipid peroxidation was analysed by measuring thiobarbituric acid-reactive substances and antioxidant enzyme activities in hepatic and brain tissues of oxidative stress-induced rats. RESULTS: The two main components of commercial Cu-Chl, namely Cu-chlorin e(6) and Cu-chlorin e(4), showed different digestive behaviours, and only Cu-chlorin e4 was found in serum, liver and kidneys. Antioxidant activity in vivo could be observed in brain and seemed to be related to in situ protection but not to antioxidant enzyme modulation. CONCLUSION: As at least one of the major components of Cu-Chl is effectively absorbed, further pharmacolkinetic studies are encouraged to access absorption rates and the role of ingested copper chlorophyllins in mammals. (C) 2009 Society of Chemical Industry

Influence of ventilatory settings on static and functional haemodynamic parameters during experimental hypovolaemia

Background and objective The influence of ventilatory settings on static and functional haemodynamic parameters during mechanical ventilation is not completely known. The purpose of this study was to evaluate the effect of positive end-expiratory pressure, tidal volume and inspiratory to expiratory time ratio variations on haemodynamic parameters during haemorrhage and after transfusion of shed blood. Methods Ten anaesthetized pigs were instrumented and mechanically ventilated with a tidal volume of 8 ml kg(-1), a positive end-expiratory pressure of 5 cmH(2)O and an inspiratory to expiratory ratio of 1 : 2. Then, they were submitted in a random order to different ventilatory settings (tidal volume 16 ml kg(-1), positive end-expiratory pressure 15 cmH(2)O or inspiratory to expiratory time ratio 2: 1). Functional and static haemodynamic parameters (central venous pressure, pulmonary artery occlusion pressure, right ventricular end-diastolic volume and pulse pressure variation) were evaluated at baseline, during hypovolaemia (withdrawal of 20% of estimated blood volume) and after an infusion of withdrawn blood (posttransfusion). Results During baseline, a positive end-expiratory pressure of 15cmH(2)O significantly increased pulmonary artery occlusion pressure from 14.6 +/- 1.6 mmHg to 17.4 +/- 1.7 mmHg (P<0.001) and pulse pressure variation from 15.8 +/- 8.5% to 25.3 +/- 9.5% (P<0.001). High tidal volume increased pulse pressure variation from 15.8 8.5% to 31.6 +/- 10.4% (P<0.001), and an inspiratory to expiratory time ratio of 2: 1 significantly increased only central venous pressure. During hypovolaemia, high positive end-expiratory pressure influenced all studied variables, and high tidal volume strongly increased pulse pressure variation (40.5 +/- 12.4% pre vs. 84.2 +/- 19.1 % post, P<0.001). The inversion of the inspiratory to expiratory time ratio only slightly increased filling pressures during hypovolaemia, without without affecting pulse pressure variation or right ventricle end-diastolic volume. Conclusion We concluded that pulse pressure variation measurement is influenced by cyclic variations in intrathoracic pressure, such as those caused by augmentations in tidal volume. The increase in mean airway pressure caused by positive end-expiratory pressure affects cardiac filling pressures and also pulse pressure variation, although to a lesser extent. Inversion of the inspiratory to expiratory time ratio does not induce significant changes in static and functional haemodynamic parameters. Eur J Anaesthesiol 26:66-72 (c) 2009 European Society of Anaesthesiology.

Bayesian estimation of regression parameters in elliptical measurement error models

The main object of this paper is to discuss the Bayes estimation of the regression coefficients in the elliptically distributed simple regression model with measurement errors. The posterior distribution for the line parameters is obtained in a closed form, considering the following: the ratio of the error variances is known, informative prior distribution for the error variance, and non-informative prior distributions for the regression coefficients and for the incidental parameters. We proved that the posterior distribution of the regression coefficients has at most two real modes. Situations with a single mode are more likely than those with two modes, especially in large samples. The precision of the modal estimators is studied by deriving the Hessian matrix, which although complicated can be computed numerically. The posterior mean is estimated by using the Gibbs sampling algorithm and approximations by normal distributions. The results are applied to a real data set and connections with results in the literature are reported. (C) 2011 Elsevier B.V. All rights reserved.

Metal transport parameters of a gneiss saprolitic silty soil for liner design

Diffusion coefficients and retardation factors of two metal cations (Cd2+ and Pb2+) were measured for a compacted Brazilian saprolitic soil derived from gneiss, aiming to assess its geoenvironmental performance as a liner for waste disposal sites. This soil occurs extensively all over the country in very thick layers, but has not been used in liners because of its hydraulic conductivity, higher than 10(-9) m/s when compacted at optimum water content of standard Proctor energy, but which can be reduced by means of appropriate compaction techniques or additives. Batch, column, and diffusion tests were carried out with monospecies synthetic solutions at pH 1, 3, and 5.5. Measured diffusion coefficients varied between 0.5 and 4 X 10(-10) m(2)/s. Retardation factors show that cadmium, a very mobile cation, is not adsorbed at pH I but is significantly retained at pH 3 and pH 5.5, whereas lead is retained at all tested pH values though slightly at pH 1. Estimated retardation factors from batch tests were 1.3-2.3 times those resulting from column tests and at its highest when obtained by diffusion tests; whereas batch tests allow a more complete exposure of the soil grains to the solution, time-dependent nonspecific adsorption may take longer to occur. The importance of contact time was observed and should be considered in further investigations. Its significant retention of metals suggests a promising utilization of this soil as a bottom liner for wastes landfills.