On estimation and influence diagnostics for zero-inflated negative binomial regression models

The zero-inflated negative binomial model is used to account for overdispersion detected in data that are initially analyzed under the zero-Inflated Poisson model A frequentist analysis a jackknife estimator and a non-parametric bootstrap for parameter estimation of zero-inflated negative binomial regression models are considered In addition an EM-type algorithm is developed for performing maximum likelihood estimation Then the appropriate matrices for assessing local influence on the parameter estimates under different perturbation schemes and some ways to perform global influence analysis are derived In order to study departures from the error assumption as well as the presence of outliers residual analysis based on the standardized Pearson residuals is discussed The relevance of the approach is illustrated with a real data set where It is shown that zero-inflated negative binomial regression models seems to fit the data better than the Poisson counterpart (C) 2010 Elsevier B V All rights reserved

Fluctuating abundance of humpback whales (Megaptera novaeangliae) in a calving ground off coastal Brazil

The humpback whale (Megaptera novaeangliae) population that uses Abrolhos Bank, off the east coast of Brazil as a breeding ground is increasing. To describe temporal changes in the relative abundance of humpback whales around Abrolhos, seven years (1998-2004) of whale count data were collected during July through to November. During one-hour-scans, observers determined group size within 9.3 km (5 n.m.) of a land-based observing station. A total Of 930 scans, comprising 7996 sightings of adults and 2044 calves were analysed using generalized linear models that included variables for time of day, day of the season, years and two-way interactions as possible predictors. The pattern observed was the gradual build-up and decline in whale counts within seasons. Patterns and peaks of adult and calf counts varied among years. Although fluctuation was observed, there was generally an increasing trend in adult counts among years. Calf counts increased only in 2004. These fluctuations may have been caused by some environmental conditions in humpback whales` summering grounds and also by changes in spatial-temporal concentrations in Abrolhos Bank. The general pattern observed within the study area mirrored what was observed in the whole Abrolhos Bank. Knowledge of the consistency with which humpback whales use this important nursing area should prove beneficial for designing future monitoring programmes especially related to whale watching activities around Abrolhos Archipelago.

Power series generalized nonlinear models

We introduce in this paper a new class of discrete generalized nonlinear models to extend the binomial, Poisson and negative binomial models to cope with count data. This class of models includes some important models such as log-nonlinear models, logit, probit and negative binomial nonlinear models, generalized Poisson and generalized negative binomial regression models, among other models, which enables the fitting of a wide range of models to count data. We derive an iterative process for fitting these models by maximum likelihood and discuss inference on the parameters. The usefulness of the new class of models is illustrated with an application to a real data set. (C) 2008 Elsevier B.V. All rights reserved.

An empirical evaluation of imputation accuracy for association statistics reveals increased type-I error rates in genome-wide associations

Background: Genome wide association studies (GWAS) are becoming the approach of choice to identify genetic determinants of complex phenotypes and common diseases. The astonishing amount of generated data and the use of distinct genotyping platforms with variable genomic coverage are still analytical challenges. Imputation algorithms combine directly genotyped markers information with haplotypic structure for the population of interest for the inference of a badly genotyped or missing marker and are considered a near zero cost approach to allow the comparison and combination of data generated in different studies. Several reports stated that imputed markers have an overall acceptable accuracy but no published report has performed a pair wise comparison of imputed and empiric association statistics of a complete set of GWAS markers. Results: In this report we identified a total of 73 imputed markers that yielded a nominally statistically significant association at P < 10(-5) for type 2 Diabetes Mellitus and compared them with results obtained based on empirical allelic frequencies. Interestingly, despite their overall high correlation, association statistics based on imputed frequencies were discordant in 35 of the 73 (47%) associated markers, considerably inflating the type I error rate of imputed markers. We comprehensively tested several quality thresholds, the haplotypic structure underlying imputed markers and the use of flanking markers as predictors of inaccurate association statistics derived from imputed markers. Conclusions: Our results suggest that association statistics from imputed markers showing specific MAF (Minor Allele Frequencies) range, located in weak linkage disequilibrium blocks or strongly deviating from local patterns of association are prone to have inflated false positive association signals. The present study highlights the potential of imputation procedures and proposes simple procedures for selecting the best imputed markers for follow-up genotyping studies.

Universal zero-bias conductance through a quantum wire side-coupled to a quantum dot

A numerical renormalization-group study of the conductance through a quantum wire containing noninteracting electrons side-coupled to a quantum dot is reported. The temperature and the dot-energy dependence of the conductance are examined in the light of a recently derived linear mapping between the temperature-dependent conductance and the universal function describing the conductance for the symmetric Anderson model of a quantum wire with an embedded quantum dot. Two conduction paths, one traversing the wire, the other a bypass through the quantum dot, are identified. A gate potential applied to the quantum wire is shown to control the current through the bypass. When the potential favors transport through the wire, the conductance in the Kondo regime rises from nearly zero at low temperatures to nearly ballistic at high temperatures. When it favors the dot, the pattern is reversed: the conductance decays from nearly ballistic to nearly zero. When comparable currents flow through the two channels, the conductance is nearly temperature independent in the Kondo regime, and Fano antiresonances in the fixed-temperature plots of the conductance as a function of the dot-energy signal interference between them. Throughout the Kondo regime and, at low temperatures, even in the mixed-valence regime, the numerical data are in excellent agreement with the universal mapping.

Double generalized linear model for tissue culture proportion data: a Bayesian perspective

Joint generalized linear models and double generalized linear models (DGLMs) were designed to model outcomes for which the variability can be explained using factors and/or covariates. When such factors operate, the usual normal regression models, which inherently exhibit constant variance, will under-represent variation in the data and hence may lead to erroneous inferences. For count and proportion data, such noise factors can generate a so-called overdispersion effect, and the use of binomial and Poisson models underestimates the variability and, consequently, incorrectly indicate significant effects. In this manuscript, we propose a DGLM from a Bayesian perspective, focusing on the case of proportion data, where the overdispersion can be modeled using a random effect that depends on some noise factors. The posterior joint density function was sampled using Monte Carlo Markov Chain algorithms, allowing inferences over the model parameters. An application to a data set on apple tissue culture is presented, for which it is shown that the Bayesian approach is quite feasible, even when limited prior information is available, thereby generating valuable insight for the researcher about its experimental results.

Surgical Treatment of Myelomeningocele Carried Out at `Time Zero` Immediately after Birth

Background/Aims: To present a protocol of immediate surgical repair of myelomeningocele (MMC) after birth (`time zero`) and compare this surgical outcome with the surgery performed after the newborn`s admission to the nursery before the operation. Methods: Data from the medical files of 31 patients with MMC that underwent surgery after birth and after admission at the nursery ( group I) were compared with a group of 23 patients with MMC admitted and prospectively followed, who underwent surgery immediately after birth - `at time zero` ( group II). Results: The preoperative rupture of the MMC occurred more frequently in group I (67 vs. 39%, p < 0.05). The need for ventriculoperitoneal shunt was 84% in group I and 65% in group II and 4 of them were performed during the same anesthetic time as the immediate MMC repair, with no statistically significant difference. Group I had a higher incidence of small dehiscences when compared to group II ( 29 vs. 13%, p < 0.05); however, there was no statistically significant difference regarding infections. After 1 year of follow-up, 61% of group I showed neurodevelopmental delay, whereas only 35% of group II showed it. Conclusions: The surgical intervention carried out immediately after the birth showed benefits regarding a lower incidence of preoperative rupture of the MMC, postoperative dehiscences and lower incidence of neurodevelopmental delay 1 year after birth. Copyright (C) 2009 S. Karger AG, Basel

Thermal dependence of the zero-bias conductance through a nanostructure

We show that the conductance of a quantum wire side-coupled to a quantum dot, with a gate potential favoring the formation of a dot magnetic moment, is a universal function of the temperature. Universality prevails even if the currents through the dot and the wire interfere. We apply this result to the experimental data of Sato et al. (Phys. Rev. Lett., 95 (2005) 066801). Copyright (C) EPLA, 2009

Inflated beta distributions

This paper considers the issue of modeling fractional data observed on [0,1), (0,1] or [0,1]. Mixed continuous-discrete distributions are proposed. The beta distribution is used to describe the continuous component of the model since its density can have quite different shapes depending on the values of the two parameters that index the distribution. Properties of the proposed distributions are examined. Also, estimation based on maximum likelihood and conditional moments is discussed. Finally, practical applications that employ real data are presented.

Inflammation markers in healthy and periodontitis patients: a preliminary data screening

Advances in diagnostic research are moving towards methods whereby the periodontal risk can be identified and quantified by objective measures using biomarkers. Patients with periodontitis may have elevated circulating levels of specific inflammatory markers that can be correlated to the severity of the disease. The purpose of this study was to evaluate whether differences in the serum levels of inflammatory biomarkers are differentially expressed in healthy and periodontitis patients. Twenty-five patients (8 healthy patients and 17 chronic periodontitis patients) were enrolled in the study. A 15 mL blood sample was used for identification of the inflammatory markers, with a human inflammatory flow cytometry multiplex assay. Among 24 assessed cytokines, only 3 (RANTES, MIG and Eotaxin) were statistically different between groups (p<0.05). In conclusion, some of the selected markers of inflammation are differentially expressed in healthy and periodontitis patients. Cytokine profile analysis may be further explored to distinguish the periodontitis patients from the ones free of disease and also to be used as a measure of risk. The present data, however, are limited and larger sample size studies are required to validate the findings of the specific biomarkers.

Effectiveness of a new toothbrush design versus a conventional tongue scraper in improving breath odor and reducing tongue microbiota

For centuries, specific instruments or regular toothbrushes have routinely been used to remove tongue biofilm and improve breath odor. Toothbrushes with a tongue scraper on the back of their head have recently been introduced to the market. The present study compared the effectiveness of a manual toothbrush with this new design, i.e., possessing a tongue scraper, and a commercial tongue scraper in improving breath odor and reducing the aerobic and anaerobic microbiota of tongue surface. The evaluations occurred at 4 moments, when the participants (n=30) had their halitosis quantified with a halimeter and scored according to a 4-point scoring system corresponding to different levels of intensity. Saliva was collected for counts of aerobic and anaerobic microorganisms. Data were analyzed statistically by Friedman's test (p<0.05). When differences were detected, the Wilcoxon test adjusted for Bonferroni correction was used for multiple comparisons (group to group). The results confirmed the importance of mechanical cleaning of the tongue, since this procedure provided an improvement in halitosis and reduction of aerobe and anaerobe counts. Regarding the evaluated methods, the toothbrush's tongue scraper and conventional tongue scraper had a similar performance in terms of breath improvement and reduction of tongue microbiota, and may be indicated as effective methods for tongue cleaning.

Histologic grading and nucleolar organizer regions in oral squamous cell carcinomas

OBJECTIVE: The purposes of this study were to histologically assess different types of oral squamous cell carcinoma and the silver-binding nucleolar organizer region (AgNOR) morphology in neoplastic cells, as well as to quantify the number of AgNORs in each type of carcinoma in order to relate AgNOR count and histologic grading. MATERIAL AND METHODS: Twenty-eight cases of oral squamous cell carcinoma were divided into 4 groups, namely well-differentiated, moderately differentiated, poorly differentiated, and undifferentiated. For NOR study, 3-µm-thick sections were stained with 50% aqueous silver nitrate solution. The predominant microscopic pattern of NORs was determined. Quantitative analyses of NORs were obtained of all cells present on each histological field using a 0.025 mm² eyepiece graticule. Different histological fields were analyzed until the total number of NORs was 120 cells for each tumor. Kruskall-Wallis test was applied to compare the groups of sample data at a significance level of p=0.05. RESULTS: The mean number of AgNORs per nucleus was 3.20 for the well-differentiated group, 5.33 for the moderately differentiated one, 8.27 for the poorly differentiated one, and 10.08 for the undifferentiated one. AgNOR count was significantly different (p<0.05) among all of the studied groups. CONCLUSION: AgNOR staining technique seems to be a useful diagnostic tool since differences in AgNOR numeric values can be identified in the different types of oral squamous cell carcinoma. This technique is easy to handle and inexpensive, thus justifying its large use in histopathology.

O extrato de maracujá sobre a morfometria de hepatócitos da tilápia do Nilo

Avaliaram-se os efeitos do extrato de maracujá veiculado na dieta (0, 50, 100 e 200mg kg-1) sobre o consumo de alimento, o ganho em peso e os níveis de glicose e cortisol plasmático de juvenis de tilápias do Nilo (87,0±6,6g). Ao final do experimento (28 dias), os peixes foram eutanasiados para remoção do fígado, visando à avaliação da área citoplasmática, contagem de células e verificação dos estoques de glicogênio hepático. Os dados foram submetidos à ANOVA unidirecional, comparando-se as médias pelo Teste de Tukey (P<0,05), com posterior estudo de regressão, buscando estabelecer as curvas das áreas citoplasmáticas, em função das diferentes doses do extrato. A inclusão do extrato na dieta não afetou o consumo de alimento e o crescimento e todos os peixes apresentaram aumento da glicose e redução do cortisol plasmático, porém sem diferenças entre os tratamentos. As curvas de regressão indicaram aumento quadrático da área citoplasmática com a elevação da doses do extrato, principalmente para 100mg kg-1, resultando em uma curva dose-resposta em forma de "U" invertido. O aumento da área do citoplasma decorreu de um acúmulo de glicogênio hepático, conforme comprovado pela prova da amilase salivar. Concluiu-se que o extrato de maracujá pode ser fornecido na dieta de juvenis de tilápia, sem prejudicar o consumo alimentar e o crescimento dos animais e que o produto altera a morfometria dos hepatócitos, sugerindo a atividade de flavonóides sobre o metabolismo de carboidratos.

Efeitos da administração de monensina por meio de cápsulas de liberação controlada no desempenho de vacas Holandesas no início da lactação

Com o objetivo de estudar o efeito da monensina sobre a produção e composição de leite, a contagem de células somáticas, a condição corporal e os parâmetros sangüíneos e reprodutivos de vacas da raça Holandesa de alta produção no início de lactação, foram utilizadas 44 vacas com produção diária de 33,44 ± 4,93 litros de leite, em delineamento inteiramente casualizado, com dois tratamentos: um controle (C) e outro com cápsulas de liberação controlada de monensina com eficácia de 100 dias (300 mg/vaca/dia). A administração individual de monensina foi realizada 30 dias antes da data provável do parto. A monensina não alterou a produção, a composição do leite e a contagem de células somáticas do leite nem a condição corporal e a concentração de glicose e BHBA (beta-hidroxibutirato) no soro das vacas, no entanto, diminuiu a concentração de AGNE (ácidos graxos não-esterificados) no soro das vacas com 60 dias de lactação. O período de serviço e o número de serviços por concepção não diferiram entre os tratamentos, porém, a administração de monensina diminuiu o número de animais que apresentaram retenção de placenta e laminite. A administração de monensina para vacas Holandesas de alta produção no início de lactação não modifica a produção e a composição do leite, contudo, diminui a concentração de AGNE 60 dias após o parto e a incidência de laminite e retenção de placenta nas vacas no pós-parto.

Calagem e adubação boratada na produção de feijoeiro

Objetivou-se avaliar os efeitos da aplicação de calcário e boro nos atributos químicos de um Latossolo, estado nutricional e produtividade da cultura do feijoeiro. As doses de calcário empregadas foram crescentes, considerando-se a saturação por bases igual a 70%, correspondendo às doses: zero; 0,6; 1,2 (v = 70%); 1,8 e 2,4 t ha-1. O calcário utilizado apresentava poder relativo de neutralização total (PRNT), poder de neutralização (PN) e reatividade (RE) de 131; 137 e 95%, respectivamente. As doses de boro estudadas foram iguais a 0 (zero); 0,6; 1,2; 1,8; e 2,4 mg dm-3 de B, sendo a referência para definição das mesmas a de 1,2 mg dm-3 de B (ou 1,2 kg ha-1 de B). Utilizou-se como fonte o ácido bórico (H3BO3) p.a. (17% B). Na época do florescimento foi avaliado o estado nutricional das plantas e, aos 90 dias foram avaliadas a fertilidade do solo e a produção de grãos. No solo houve melhoria dos atributos pH, SB, V e na concentração de Ca e Mg, e do B com o emprego da adubação boratada. A interação da calagem com a adubação boratada promoveu maior acúmulo de Ca, Mg e B nas plantas. Os dados apresentados demonstram que o feijoeiro foi responsivo à calagem e à adubação boratada, tendo atingido bons índices de produção com a utilização de 1,8 kg ha-1 de B com doses crescentes de calcário.