A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies

Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.     

RBR: library-less repeat detection for ESTs

MOTIVATION: Repeat sequences in ESTs are a source of problems, in particular for clustering. ESTs are therefore commonly masked against a library of known repeats. High quality repeat libraries are available for the widely studied organisms, but for most other organisms the lack of such libraries is likely to compromise the quality of EST analysis. RESULTS: We present a fast, flexible and library-less method for masking repeats in EST sequences, based on match statistics within the EST collection. The method is not linked to a particular clustering algorithm. Extensive testing on datasets using different clustering methods and a genomic mapping as reference shows that this method gives results that are better than or as good as those obtained using RepeatMasker with a repeat library. AVAILABILITY: The implementation of RBR is available under the terms of the GPL from http://www.ii.uib.no/~ketil/bioinformatics CONTACT: ketil.malde@bccs.uib.no SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Physical Activity versus Sedentary Behavior: Associations with Lipoprotein Particle Subclass Concentrations in Healthy Adults

Background

Physical activity (PA) and sedentary behavior (SED) may have independent effects on health and disease. This might be due to PA and SED having distinct effects on lipoprotein metabolism. The aim of this study was to determine associations between lipoprotein subclass particle concentrations (-P) and accelerometer-measured SED and moderate-to-vigorous PA (MVPA) in a sample of healthy adult subjects.

Methods

Lipoprotein subclass particle concentrations were determined by proton nuclear magnetic resonance spectroscopy, whereas SED and MVPA were measured using Agtigraph GT1M and GT3X+ accelerometers. We obtained valid data in 73 subjects (30 men and 43 women, age 40.5 ± 10.6 years; body mass index 24.0 ± 2.8). Multiple regression analysis was used to determine associations (partial correlations) with lipoproteins.

Results

Positive associations were detected between SED and small VLDL-P, large LDL-P and TG (partial r = 0.24 to 0.25, p < .047). Corresponding associations were non-significant for MVPA (partial r = -0.12 to 0.04, p > .355). On the contrary, MVPA was positively associated with large HDL-P, average HDL size, Apo A1 and HDL-cholesterol (partial r = 0.28 to 0.50, p < .027), whereas SED was not (partial r = -0.06 to 0.07, p > .607).

Conclusion

There might be a specific effect of SED versus MVPA on lipoprotein metabolism. However, our results must be interpreted carefully due to possible effect-modification by gender and a low sample size. Thus, our findings should be viewed as preliminary.     

Tailored Implementation of Evidence-Based Practice for Patients with Chronic Diseases

Background

When designing interventions and policies to implement evidence based healthcare, tailoring strategies to the targeted individuals and organizations has been recommended. We aimed to gather insights into the ideas of a variety of people for implementing evidence-based practice for patients with chronic diseases, which were generated in five European countries.

Methods

A qualitative study in five countries (Germany, Netherlands, Norway, Poland, United Kingdom) was done, involving overall 115 individuals. A purposeful sample of four categories of stakeholders (healthcare professionals, quality improvement officers, healthcare purchasers and authorities, and health researchers) was involved in group interviews in each of the countries to generate items for improving healthcare in different chronic conditions per country: chronic obstructive pulmonary disease, cardiovascular disease, depression in elderly people, multi-morbidity, obesity. A disease-specific standardized list of determinants of practice in these conditions provided the starting point for these groups. The content of the suggested items was categorized in a pre-defined framework of 7 domains and specific themes in the items were identified within each domain.

Results

The 115 individuals involved in the study generated 812 items, of which 586 addressed determinants of practice. These largely mapped onto three domains: individual health professional factors, patient factors, and professional interactions. Few items addressed guideline factors, incentives and resources, capacity of organizational change, or social, political and legal factors. The relative numbers of items in the different domains were largely similar across stakeholder categories within each of the countries. The analysis identified 29 specific themes in the suggested items across countries.

Conclusion

The type of suggestions for improving healthcare practice was largely similar across different stakeholder groups, mainly addressing healthcare professionals, patient factors and professional interactions. As this study is one of the first of its kind, it is important that more research is done on tailored implementation strategies.     

The Andersen Aerobic Fitness Test: Reliability and Validity in 10-Year-Old Children

Background

High aerobic fitness is consistently associated with a favorable metabolic risk profile in children. Direct measurement of peak oxygen consumption (VO_2peak) is often not feasible, thus indirect tests such as the Andersen test are required in many settings. The present study seeks to determine the reliability and validity of the Andersen test in 10-year-old children.

Methods

A total of 118 10-year-old children (67 boys and 51 girls) were recruited from one school and performed four VO_2peak tests over three weeks: three Andersen tests (indirect) and one continuous progressive treadmill test (direct). Of these, 104 children provided valid data on all Andersen tests and 103 children also provided valid data on the direct treadmill test. Reliability and validity were assessed using Bland Altman plots and linear regression analysis.

Results

Bias (mean change) and random error (limits of agreement) were 26.7±125.2 m for test 2 vs. test 1 (p<.001 for mean difference) and 3.9±88.8 m for test 3 vs. test 2 (p = .514 for mean difference). The equation to estimate VO_2peak suggested by Andersen et al. (2008) showed a poor fit in the present sample; thus, we suggest a new equation: VO_2peak = 23.262+0.050*Andersen distance –3.858*gender –0.376*body weight (R² = 0.61, standard error of the estimate = 5.69, p<.001, boys = 0, girls = 1).

Conclusions

The Andersen test provided reliable and valid data on a group level. However, a substantial degree of individual variability was found for estimates of VO_2peak. Researchers should be aware of the amount of noise in indirect tests that estimate aerobic fitness.