Quality Control Analysis in Real-time (QC-ART) : A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data

Liquid chromatography-mass spectrometry (LC-MS)-based proteomics studies of large sample cohorts can easily require from months to years to complete. Acquiring consistent, high-quality data in such large-scale studies is challenging because of normal variations in instrumentation performance over time, as well as artifacts introduced by the samples themselves, such as those because of collection, storage and processing. Existing quality control methods for proteomics data primarily focus on post-hoc analysis to remove low-quality data that would degrade downstream statistics; they are not designed to evaluate the data in near real-time, which would allow for interventions as soon as deviations in data quality are detected. In addition to flagging analyses that demonstrate outlier behavior, evaluating how the data structure changes over time can aide in understanding typical instrument performance or identify issues such as a degradation in data quality because of the need for instrument cleaning and/or re-calibration. To address this gap for proteomics, we developed Quality Control Analysis in Real-Time (QC-ART), a tool for evaluating data as they are acquired to dynamically flag potential issues with instrument performance or sample quality. QC-ART has similar accuracy as standard post-hoc analysis methods with the additional benefit of real-time analysis. We demonstrate the utility and performance of QC-ART in identifying deviations in data quality because of both instrument and sample issues in near real-time for LC-MS-based plasma proteomics analyses of a sample subset of The Environmental Determinants of Diabetes in the Young cohort. We also present a case where QC-ART facilitated the identification of oxidative modifications, which are often underappreciated in proteomic experiments.Peer reviewe

Determinants of Salivary Cotinine among Smokeless Tobacco Users : A Cross-Sectional Survey in Bangladesh

INTRODUCTION: More than 80% of all smokeless tobacco (ST) products in the world are consumed in South Asia; yet little is known about their consumption behaviour, addictiveness, and toxic properties. This paper, for the first time, describes associations between salivary cotinine concentrations among ST users in Bangladesh and their socio-demographic characteristics and tobacco use behaviours. METHODS: In a survey of ST users in Dhaka, Bangladesh, we purposively recruited 200 adults who were non-smokers but consumed ST on a regular basis. In-person interviews were conducted to obtain information about socio-demographic and ST use behaviours, and saliva samples were collected to measure cotinine concentration. Simple and multiple linear regression analyses were conducted to test associations between the log transformed salivary cotinine concentration and other study variables. RESULTS: The geometric mean of cotinine concentration among ST users was 380ng/ml (GSD:2). Total duration of daily ST use in months had a statistically significant association with cotinine concentration. Other ST use characteristics including type and quantity of ST use, swallowing of tobacco juice, urges and strength of urges and attempts to cut down on tobacco use were not found to be associated with cotinine concentration in a multivariable model. CONCLUSION: This is the first report from Bangladesh studying cotinine concentration among ST users and it points towards high levels of addiction. This warrants effective tobacco control policies to help ST cessation and prevention

Parallel computing in information retrieval - An updated review

The progress of parallel computing in Information Retrieval (IR) is reviewed. In particular we stress the importance of the motivation in using parallel computing for Text Retrieval. We analyse parallel IR systems using a classification due to Rasmussen [1] and describe some parallel IR systems. We give a description of the retrieval models used in parallel Information Processing.. We describe areas of research which we believe are needed

Is There Any Association between Use of Smokeless Tobacco Products and Coronary Heart Disease in Bangladesh?

BACKGROUND: Most epidemiological studies exploring the association between smokeless tobacco (SLT) use and coronary heart disease (CHD) have been in Western populations, and have focused on SLT products used in those countries. Few studies come from South Asian countries. Our objective was to determine the association between SLT use and CHD among non-smoking adults in Bangladesh. METHODS: A matched case-control study of non-smoking Bangladeshi adults aged 40–75 years was conducted in 2010. Incident cases of CHD were selected from two cardiac hospitals. Community controls, matched to CHD cases, were selected from neighbourhoods, and hospital controls were selected from outpatient departments of the same hospitals. The Rose Angina Questionnaire (RAQ) was also used to re-classify cases and controls. RESULTS: The study enrolled 302 cases, 1,208 community controls and 302 hospital controls. Current use was higher among community controls (38%) compared to cases (33%) and hospital controls (32%). Current use of SLT was not significantly associated with an increased risk of CHD when community controls were used (adjusted OR 0.87, 95% CI 0.63–1.19), or when hospital controls were used (adjusted OR 1.00, 95% CI 0.63–1.60), or when both control groups were combined (adjusted OR 1.00, 95% CI 0.74–1.34). Risk of CHD did not increase with use of individual types except gul, frequency, duration, past use of SLT products, or using the RAQ to re-classify cases and controls. There was a significant association between gul use and CHD when both controls were combined (adjusted OR 2.93, 95% CI 1.28–6.70). CONCLUSIONS: There was no statistically significant association between SLT use in general and CHD among non-smoking adults in Bangladesh. Further research on the association between gul use and CHD in Bangladesh along with SLT use and CHD in other parts of the subcontinent will guide public health policy and interventions that focus on SLT-related diseases.Muhammad Azia Rahman, Nicola Spurrier, Mohammad Afzal Mahmood, Mahmudur Rahman, Soehl Reza Choudhury and Stephen Leede