Use of DHPLC for rapid screening of recombinant clones.

n/

Data preparation and interannotator agreement: BioCreAtIvE Task 1B

<p>Abstract</p> <p>Background</p> <p>We prepared and evaluated training and test materials for an assessment of text mining methods in molecular biology. The goal of the assessment was to evaluate the ability of automated systems to generate a list of unique gene identifiers from PubMed abstracts for the three model organisms Fly, Mouse, and Yeast. This paper describes the preparation and evaluation of answer keys for training and testing. These consisted of lists of normalized gene names found in the abstracts, generated by adapting the gene list for the full journal articles found in the model organism databases. For the training dataset, the gene list was pruned automatically to remove gene names not found in the abstract; for the testing dataset, it was further refined by manual annotation by annotators provided with guidelines. A critical step in interpreting the results of an assessment is to evaluate the quality of the data preparation. We did this by careful assessment of interannotator agreement and the use of answer pooling of participant results to improve the quality of the final testing dataset.</p> <p>Results</p> <p>Interannotator analysis on a small dataset showed that our gene lists for Fly and Yeast were good (87% and 91% three-way agreement) but the Mouse gene list had many conflicts (mostly omissions), which resulted in errors (69% interannotator agreement). By comparing and pooling answers from the participant systems, we were able to add an additional check on the test data; this allowed us to find additional errors, especially in Mouse. This led to 1% change in the Yeast and Fly "gold standard" answer keys, but to an 8% change in the mouse answer key.</p> <p>Conclusion</p> <p>We found that clear annotation guidelines are important, along with careful interannotator experiments, to validate the generated gene lists. Also, abstracts alone are a poor resource for identifying genes in paper, containing only a fraction of genes mentioned in the full text (25% for Fly, 36% for Mouse). We found that there are intrinsic differences between the model organism databases related to the number of synonymous terms and also to curation criteria. Finally, we found that answer pooling was much faster and allowed us to identify more conflicting genes than interannotator analysis.</p

Breastfeeding and obesity in Brazilian children

The association between breastfeeding and obesity is inconsistent by the literature. This study aims to assess whether obesity is associated to occurrence of breastfeeding and to duration of total and exclusive breastfeeding in Brazilian children. A cross-sectional study was conducted with 764 children enrolled in public and private schools from Viçosa, Minas Gerais, Brazil. Obesity (outcome variable) was defined as body mass index above the +2 standard deviations score using sex and age specific standards of World Health Organization. Exposure was the occurrence and duration of breastfeeding. Potential confounders were controlled by multiple logistic regression analysis and were divided in two groups: children (gender, age, birth weight, gestational age, order of birth, number of siblings, number of persons in the residence, type of school, physical activity patterns and time watching television) and mothers (age, nutritional status, level of education, weight gain during pregnancy, smokes currently and during the pregnancy). Prevalence of obesity was 10.7%; 6.8% of the children were not breastfed and 59.0% did not receive exclusive breastfeeding. After adjustment for confounding variables by logistic regression analysis, no statistically significant association was observed between obesity and the occurrence and/or duration of total and exclusive breastfeeding. There was no dose-response effect of duration of breastfeeding on prevalence of obesity. Our results do not support the hypothesis that breastfeeding promotion would reduce obesity in this population. Controversial findings regarding this association by literature indicate a need for further investigations

From Profile to Surface Monitoring: SPC for Cylindrical Surfaces Via Gaussian Processes

Quality of machined products is often related to the shapes of surfaces that are constrained by geometric tolerances. In this case, statistical quality monitoring should be used to quickly detect unwanted deviations from the nominal pattern. The majority of the literature has focused on statistical profile monitoring, while there is little research on surface monitoring. This paper faces the challenging task of moving from profile to surface monitoring. To this aim, different parametric approaches and control-charting procedures are presented and compared with reference to a real case study dealing with cylindrical surfaces obtained by lathe turning. In particular, a novel method presented in this paper consists of modeling the manufactured surface via Gaussian processes models and monitoring the deviations of the actual surface from the target pattern estimated in phase I. Regardless of the specific case study in this paper, the proposed approach is general and can be extended to deal with different kinds of surfaces or profiles

a transverse and longitudinal mr imaging voxel based morphometry study in patients with primary cervical dystonia

BACKGROUND AND PURPOSE: Findings of standard MR imaging examinations are usually normal in primary CD. These findings are now increasingly challenged by studies using advanced neuroimaging techniques detecting abnormalities in brain areas that may be functionally involved in the pathophysiology of CD. Our purpose was to evaluate GM volumes in patients with CD at baseline and 5 years later. MATERIALS AND METHODS: We enrolled 19 patients (F/M = 15:4, mean age = 53.2 + 11.2 years), 12 of whom were studied at baseline and again approximately 5 years later. Twenty-eight healthy volunteers acted as controls (F/M = 17:11, mean age = 47.5 + 15.6 years). The subjects were imaged with a 1.5T scanner by using a 3D T1-weighted sequence on 150 contiguous axial 1-mm-thick sections to apply VBM. RESULTS: At entry, VBM analysis disclosed significantly lower GM volumes in the left caudate head and putamen and in the premotor and primary sensorimotor cortices bilaterally in patients than in controls. No correlation was found between decreased GM volumes and patient age, severity of dystonia, or disease duration. At the 5-year follow-up, GM volumes in the left primary sensorimotor cortex in patients had decreased significantly from baseline. CONCLUSIONS: The findings obtained at entry and after a 5-year follow-up consistently showed decreased caudate, putamen, and sensorimotor cortex GM volumes in patients with CD, and they probably play a pathophysiologic role in CD