Improved maximum likelihood estimators in a heteroskedastic errors-in-variables model

This paper develops a bias correction scheme for a multivariate heteroskedastic errors-in-variables model. The applicability of this model is justified in areas such as astrophysics, epidemiology and analytical chemistry, where the variables are subject to measurement errors and the variances vary with the observations. We conduct Monte Carlo simulations to investigate the performance of the corrected estimators. The numerical results show that the bias correction scheme yields nearly unbiased estimates. We also give an application to a real data set.

Birnbaum-Saunders nonlinear regression models

We introduce, for the first time, a new class of Birnbaum-Saunders nonlinear regression models potentially useful in lifetime data analysis. The class generalizes the regression model described by Rieck and Nedelman [Rieck, J.R., Nedelman, J.R., 1991. A log-linear model for the Birnbaum-Saunders distribution. Technometrics 33, 51-60]. We discuss maximum-likelihood estimation for the parameters of the model, and derive closed-form expressions for the second-order biases of these estimates. Our formulae are easily computed as ordinary linear regressions and are then used to define bias corrected maximum-likelihood estimates. Some simulation results show that the bias correction scheme yields nearly unbiased estimates without increasing the mean squared errors. Two empirical applications are analysed and discussed. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification

Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.

Per capita versus adult-equivalent estimates of calorie availability in household budget surveys

This study aims to estimate an adult-equivalent scale for calorie requirements and to determine the differences between adult-equivalent and per capita measurements of calorie availability in the Brazilian population. The study used data from the 2002-2003 Brazilian Household Budget Survey. The calorie requirement for a reference adult individual was based on the mean requirements for adult males and females (2,550kcal/day). The conversion factors were defined as the ratios between the calorie requirements for each age group and gender and that of the reference adult. The adult-equivalent calorie availability levels were higher than the per capita levels, with the largest differences in rural and low-income households. Differences in household calorie availability varied from 22kcal/day (households with adults and an adolescent) to 428kcal/day (households with elderly individuals), thus showing that per capital measurements can underestimate the real calorie availability, since they overlook differences in household composition.

Genetic trend estimates of meat quality traits in a male broiler line

The present research was conducted to estimate the genetic trends for meat quality traits in a male broiler line. The traits analyzed were initial pH, pH at 6 h after slaughter, final pH, initial range of falling pH, final range of falling pH, lightness, redness, yellowness, weep loss, drip loss, shrink loss, and shear force. The number of observations varied between 618 and 2125 for each trait. Genetic values were obtained by restricted maximum likelihood, and the numerator relationship matrix had 107,154 animals. The genetic trends were estimated by regression of the broiler average genetic values with respect to unit of time (generations), and the average genetic trend was estimated by regression coefficients. Generally, for the traits analyzed, small genetic trends were obtained, except for drip loss and shear force, which were higher. The small magnitude of the trends found could be a consequence of the absence of selection for meat quality traits in the line analyzed. The estimates of genetic trends obtained were an indication of an improvement in the meat quality traits in the line analyzed, except for drip loss.

Multi-trait and random regression mature weight heritability and breeding value estimates in Nelore cattle

Mature weight breeding values were estimated using a multi-trait animal model (MM) and a random regression animal model (RRM). Data consisted of 82 064 weight records from 8 145 animals, recorded from birth to eight years of age. Weights at standard ages were considered in the MM. All models included contemporary groups as fixed effects, and age of dam (linear and quadratic effects) and animal age as covariates. In the RRM, mean trends were modelled through a cubic regression on orthogonal polynomials of animal age and genetic maternal and direct and maternal permanent environmental effects were also included as random. Legendre polynomials of orders 4, 3, 6 and 3 were used for animal and maternal genetic and permanent environmental effects, respectively, considering five classes of residual variances. Mature weight (five years) direct heritability estimates were 0.35 (MM) and 0.38 (RRM). Rank correlation between sires' breeding values estimated by MM and RRM was 0.82. However, selecting the top 2% (12) or 10% (62) of the young sires based on the MM predicted breeding values, respectively 71% and 80% of the same sires would be selected if RRM estimates were used instead. The RRM modelled the changes in the (co) variances with age adequately and larger breeding value accuracies can be expected using this model.

Estimates of genetic trend for carcass traits in a commercial broiler line

Data from the slaughter of 24,001 chickens that were part of a selection program for the production of commercial broilers were used to estimate genetic trend for absolute carcass (CW), breast meat (BRW), and leg (LW) weights, and relative carcass (CY), breast meat (BRY), and leg (LY) weights. The components of (co) variance and breeding values of individuals were obtained by the restricted maximum likelihood method applied to animal models. The relationship matrix was composed of 132,442 birds. The models included as random effects, maternal additive genetic and permanent environmental for CW, BRW, LW, CY, and BRY, and only maternal permanent environmental for LY, besides the direct additive genetic and residual effects, and as fixed effects, hatch week, parents' mating group and sex. The estimates of genetic trend were obtained by average regression of breeding value on generation, and the average genetic trend was estimated by regression coefficients. The genetic trends for CW (+ 6.0336 g/generation), BRW (+ 3.6723 g/generation), LW (+ 1.5846 g/generation), CY (+ 0.1195%/generation), and BRY (+ 0.1388%/generation) were positive, and they were in accordance with the objectives of the selection program for these traits. The genetic trend for LY(-0.0019%/generation) was negative, possibly due to the strong emphasis on selection for BRY and the negative correlations between these two traits.

[O/Fe] ESTIMATES FOR CARBON-ENHANCED METAL-POOR STARS FROM NEAR-INFRARED SPECTROSCOPY

We report on oxygen abundances determined from medium-resolution near-infrared spectroscopy for a sample of 57 carbon-enhanced metal-poor (CEMP) stars selected from the Hamburg/ESO Survey. The majority of our program stars exhibit oxygen-to-iron ratios in the range +0.5 < [O/Fe]< + 2.0. The [O/Fe] values for this sample are statistically compared to available high-resolution estimates for known CEMP stars as well as to high-resolution estimates for a set of carbon-normal metal-poor stars. Carbon, nitrogen, and oxygen abundance patterns for a sub-sample of these stars are compared to yield predictions for very metal-poor asymptotic giant branch (AGB) abundances in the recent literature. We find that the majority of our sample exhibit patterns that are consistent with previously studied CEMP stars having s-process-element enhancements and thus have very likely been polluted by carbon- and oxygen-enhanced material transferred from a metal-poor AGB companion.

Dynamical estimates of chaotic systems from Poincare recurrences

We show a function that fits well the probability density of return times between two consecutive visits of a chaotic trajectory to finite size regions in phase space. It deviates from the exponential statistics by a small power-law term, a term that represents the deterministic manifestation of the dynamics. We also show how one can quickly and easily estimate the Kolmogorov-Sinai entropy and the short-term correlation function by realizing observations of high probable returns. Our analyses are performed numerically in the Henon map and experimentally in a Chua's circuit. Finally, we discuss how our approach can be used to treat the data coming from experimental complex systems and for technological applications. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3263943]

How Much Older Do You Get When a Wrinkle Appears on Your Face? Modifying Age Estimates by Number of Wrinkles

The present study investigated the influence of wrinkles on facial age judgments. In Experiment 1, preadolescents, young adults, and middle-aged adults made categorical age judgments for male and female faces. The qualitative (type of wrinkle) and quantitative (density of wrinkles and depth of furrows) contributions of wrinkles were analyzed. Results indicated that the greater the number of wrinkles and the depth of furrows, the older a face was rated. The roles of the gender of the face and the age of the participants were discussed. In Experiment 2, participants performed relative age judgments by comparing pairs of faces. Results revealed that the number of wrinkles had more influence on the perceived facial age than the type of wrinkle. A MDS analysis showed the main dimensions on which participants based their judgments, namely, the number of wrinkles and the depth of furrows. We conclude that the quantitative component is more likely to increase perceived facial age. Nevertheless, other variables, such as the gender of the face and the age of the participants, also seem to be involved in the age estimation process.

Risk Estimates of Dengue in Travelers to Dengue Endemic Areas Using Mathematical Models

Dengue has emerged as a frequent problem in international travelers. The risk depends on destination, duration, and season of travel. However, data to quantify the true risk for travelers to acquire dengue are lacking. We used mathematical models to estimate the risk of nonimmune persons to acquire dengue when traveling to Singapore. From the force of infection, we calculated the risk of dengue dependent on duration of stay and season of arrival. Our data highlight that the risk for nonimmune travelers to acquire dengue in Singapore is substantial but varies greatly with seasons and epidemic cycles. For instance, for a traveler who stays in Singapore for 1 week during the high dengue season in 2005, the risk of acquiring dengue was 0.17%, but it was only 0.00423% during the low season in a nonepidemic year such as 2002. Risk estimates based on mathematical modeling will help the travel medicine provider give better evidence-based advice for travelers to dengue endemic countries.

The Relationship between Intraocular Pressure Reduction and Rates of Progressive Visual Field Loss in Eyes with Optic Disc Hemorrhage

Purpose: To evaluate rates of visual field progression in eyes with optic disc hemorrhages and the effect of intraocular pressure (IOP) reduction on these rates. Design: Observational cohort study. Participants: The study included 510 eyes of 348 patients with glaucoma who were recruited from the Diagnostic Innovations in Glaucoma Study (DIGS) and followed for an average of 8.2 years. Methods: Eyes were followed annually with clinical examination, standard automated perimetry visual fields, and optic disc stereophotographs. The presence of optic disc hemorrhages was determined on the basis of masked evaluation of optic disc stereophotographs. Evaluation of rates of visual field change during follow-up was performed using the visual field index (VFI). Main Outcome Measures: The evaluation of the effect of optic disc hemorrhages on rates of visual field progression was performed using random coefficient models. Estimates of rates of change for individual eyes were obtained by best linear unbiased prediction (BLUP). Results: During follow-up, 97 (19%) of the eyes had at least 1 episode of disc hemorrhage. The overall rate of VFI change in eyes with hemorrhages was significantly faster than in eyes without hemorrhages (-0.88%/year vs. -0.38%/year, respectively, P < 0.001). The difference in rates of visual field loss pre- and post-hemorrhage was significantly related to the reduction of IOP in the post-hemorrhage period compared with the pre-hemorrhage period (r = -0.61; P < 0.001). Each 1 mmHg of IOP reduction was associated with a difference of 0.31%/year in the rate of VFI change. Conclusions: There was a beneficial effect of treatment in slowing rates of progressive visual field loss in eyes with optic disc hemorrhage. Further research should elucidate the reasons why some patients with hemorrhages respond well to IOP reduction and others seem to continue to progress despite a significant reduction in IOP levels. Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references. Ophthalmology 2010; 117: 2061-2066 (C) 2010 by the American Academy of Ophthalmology.

Estimates of Interethnic Admixture in the Brazilian Population Using a Panel of 24 X-Linked Insertion/Deletion Markers

Objectives. In this study, we aimed to identify ancestry informative haplotypes and make interethnic admixture estimates using X-chromosome markers. Methods. A significant sample (461 individuals) of European, African, and Native American populations was analyzed, and four linkage groups were identified. The data obtained were used to describe the ancestral contribution of populations from four different geographical regions of Brazil (745 individuals). Results. The global interethnic admixture estimates of the four mixed populations under investigation were calculated applying all the 24 insertion/deletion (INDEL) markers. In the North region, a larger Native Americans ancestry was observed (42%). The Northeast and Southeast regions had smaller Native American contribution (27% in both of them). In the South region, there was a large European contribution (46%). Conclusions. The estimates obtained are compatible with expectations for a colonization model with biased admixture between European men (one X chromosome) and Native American and African women (two X chromosomes), so the 24 X-INDEL panel described here can be a useful to make admixture interethnic estimates in Brazilian populations. Am. J. Hum. Biol. 22:849-852,2010. (C) 2010 Wiley-Liss, Inc.

Use of a predictive model for food insecurity estimates in Brazil

In 2004 the National Household Survey (Pesquisa Nacional par Amostras de Domicilios - PNAD) estimated the prevalence of food and nutrition insecurity in Brazil. However, PNAD data cannot be disaggregated at the municipal level. The objective of this study was to build a statistical model to predict severe food insecurity for Brazilian municipalities based on the PNAD dataset. Exclusion criteria were: incomplete food security data (19.30%); informants younger than 18 years old (0.07%); collective households (0.05%); households headed by indigenous persons (0.19%). The modeling was carried out in three stages, beginning with the selection of variables related to food insecurity using univariate logistic regression. The variables chosen to construct the municipal estimates were selected from those included in PNAD as well as the 2000 Census. Multivariate logistic regression was then initiated, removing the non-significant variables with odds ratios adjusted by multiple logistic regression. The Wald Test was applied to check the significance of the coefficients in the logistic equation. The final model included the variables: per capita income; years of schooling; race and gender of the household head; urban or rural residence; access to public water supply; presence of children; total number of household inhabitants and state of residence. The adequacy of the model was tested using the Hosmer-Lemeshow test (p=0.561) and ROC curve (area=0.823). Tests indicated that the model has strong predictive power and can be used to determine household food insecurity in Brazilian municipalities, suggesting that similar predictive models may be useful tools in other Latin American countries.

Extended time weather forecasts contributes to agricultural productivity estimates

Weather conditions in critical periods of the vegetative crop development influence crop productivity, thus being a basic parameter for crop forecast. Reliable extended period weather forecasts may contribute to improve the estimation of agricultural productivity. The production of soybean plays an important role in the Brazilian economy, because this country is ranked among the largest producers of soybeans in the world. This culture can be significantly affected by water conditions, depending on the intensity of water deficit. This work explores the role of extended period weather forecasts for estimating soybean productivity in the southern part of Brazil, Passo Fundo, and Londrina (State of Rio Grande do Sul and Parana, respectively) in the 2005/2006 harvest. The goal was to investigate the possible contribution of precipitation forecasts as a substitute for the use of climatological data on crop forecasts. The results suggest that the use of meteorological forecasts generate more reliable productivity estimates during the growth period than those generated only through climatological information.