Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis

BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108

Socioeconomic Inequalities in Mortality Rates in Old Age in the World Health Organization Europe Region

Socioeconomic adversity is among the foremost fundamental causes of human suffering, and this is no less true in old age. Recent reports on socioeconomic inequalities in mortality rate in old age suggest that a low socioeconomic position continues to increase the risk of death even among the oldest old. We aimed to examine the evidence for socioeconomic mortality rate inequalities in old age, including information about associations with various indicators of socioeconomic position and for various geographic locations within the World Health Organization Region for Europe. The articles included in this review leave no doubt that inequalities in mortality rate by socioeconomic position persist into the oldest ages for both men and women in all countries for which information is available, although the relative risk measures observed were rarely higher than 2.00. Still, the available evidence base is heavily biased geographically, inasmuch as it is based largely on national studies from Nordic and Western European countries and local studies from urban areas in Southern Europe. This bias will hamper the design of European-wide policies to reduce inequalities in mortality rate. We call for a continuous update of the empiric evidence on socioeconomic inequalities in mortality rate

Colorectal Cancer Screening in Switzerland: Cross-Sectional Trends (2007-2012) in Socioeconomic Disparities.

BACKGROUND: Despite universal health care coverage, disparities in colorectal cancer (CRC) screening by income in Switzerland have been reported. However, it is not known if these disparities have changed over time. This study examines the association between socioeconomic position and CRC screening in Switzerland between 2007 and 2012. METHODS: Data from the 2007 (n = 5,946) and 2012 (n = 7,224) population-based Swiss Health Interview Survey data (SHIS) were used to evaluate the association between monthly household income, education, and employment with CRC screening, defined as endoscopy in the past 10 years or fecal occult blood test (FOBT) in the past 2 years. Multivariable Poisson regression was used to estimate prevalence ratios (PR) and 95% Confidence Intervals (CI) adjusting for demographics, health status, and health utilization. RESULTS: CRC screening increased from 18.9% in 2007 to 22.2% in 2012 (padjusted: = 0.036). During the corresponding time period, endoscopy increased (8.2% vs. 15.0%, padjusted:<0.001) and FOBT decreased (13.0% vs. 9.8%, padjusted:0.002). CRC screening prevalence was greater in the highest income (>$6,000) vs. lowest income (≤$2,000) group in 2007 (24.5% vs. 10.5%, PR:1.37, 95%CI: 0.96-1.96) and in 2012 (28.6% vs. 16.0%, PR:1.45, 95%CI: 1.09-1.92); this disparity did not significantly change over time. CONCLUSIONS: While CRC screening prevalence in Switzerland increased from 2007 to 2012, CRC screening coverage remains low and disparities in CRC screening by income persisted over time. These findings highlight the need for increased access to CRC screening as well as enhanced awareness of the benefits of CRC screening in the Swiss population, particularly among low-income residents

Complexity-Based Measures Inform Tai Chi\u27s Impact on Standing Postural Control in Older Adults with Peripheral Neuropathy

Background: Tai Chi training enhances physical function and may reduce falls in older adults with and without balance disorders, yet its effect on postural control as quantified by the magnitude or speed of center-of-pressure (COP) excursions beneath the feet is less clear. We hypothesized that COP metrics derived from complex systems theory may better capture the multi-component stimulus that Tai Chi has on the postural control system, as compared with traditional COP measures. Methods: We performed a secondary analysis of a pilot, non-controlled intervention study that examined the effects of Tai Chi on standing COP dynamics, plantar sensation, and physical function in 25 older adults with peripheral neuropathy. Tai Chi training was based on the Yang style and consisted of three, one-hour group sessions per week for 24 weeks. Standing postural control was assessed with a force platform at baseline, 6, 12, 18, and 24 weeks. The degree of COP complexity, as defined by the presence of fluctuations existing over multiple timescales, was calculated using multiscale entropy analysis. Traditional measures of COP speed and area were also calculated. Foot sole sensation, six-minute walk (6MW) and timed up-and-go (TUG) were also measured at each assessment. Results: Traditional measures of postural control did not change from baseline. The COP complexity index (mean±SD) increased from baseline (4.1±0.5) to week 6 (4.5±0.4), and from week 6 to week 24 (4.7±0.4) (p=0.02). Increases in COP complexity—from baseline to week 24—correlated with improvements in foot sole sensation (p=0.01), the 6MW (p=0.001) and TUG (p=0.01). Conclusions: Subjects of the Tai Chi program exhibited increased complexity of standing COP dynamics. These increases were associated with improved plantar sensation and physical function. Although more research is needed, results of this non-controlled pilot study suggest that complexity-based COP measures may inform the study of complex mind-body interventions, like Tai Chi, on postural control in those with peripheral neuropathy or other age-related balance disorders

Do good health and material circumstances protect older people from the increased risk of death after bereavement?

This is an open access Article. Copyright @ 2012 The AuthorsAn increased risk of death in persons who have suffered spousal bereavement has been described in many populations. The impact of modifying factors, such as chronic disease and material circumstances, is less well understood. The authors followed 171,120 couples 60 years of age or older in a United Kingdom primary care database between 2005 and 2010 for an average of 4 years. A total of 26,646 (15.5%) couples experienced bereavement, with mean follow up after bereavement of 2 years. In a model adjusted for age, sex, comorbid conditions at baseline, material deprivation based on area of residence, season, and smoking status, the hazard ratio for mortality in the first year after bereavement was 1.25 (95% confidence interval: 1.18, 1.33). Further adjustment for changes in comorbid conditions throughout follow up did not alter the hazard ratio for bereavement (hazard ratio = 1.27, 95% confidence interval: 1.19, 1.35). The association was strongest in individuals with no significant chronic comorbid conditions throughout follow up (hazard ratio = 1.50, 95% confidence interval: 1.28, 1.77) and in more affluent couples (P = 0.035). In the first year after bereavement, the association between bereavement and death is not primarily mediated through worsening or new onset of chronic disease. Good health and material circumstances do not protect individuals from increased mortality rates after bereavement.This study was funded by a grant from the Dunhill Medical Trust