Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD).

Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of morbidity and mortality in the United States and cigarette smoking is a primary determinant of the disease. COPD is characterized by chronic airflow limitation as measured by the forced expiratory volume in one second (FEV(1)). In this study, the plasma proteomes of 38 middle-aged or older adult smokers with mild to moderate COPD, with FEV(1) decline characterized as either rapid (RPD, n = 20) or slow or absent (SLW, n = 18), were interrogated using a comprehensive high-throughput proteomic approach, the accurate mass and time (AMT) tag technology. This technology is based upon a putative mass and time tag database (PMT), high-resolution LC separations and high mass accuracy measurements using FT-ICR MS with a 9.4-T magnetic field. The peptide and protein data were analyzed using three statistical approaches to address ambiguities related to the high proportion of missing data inherent to proteomic analysis. The RPD and SLW groups were differentiated by 55 peptides which mapped to 33 unique proteins. Twelve of the proteins have known roles in the complement or coagulation cascade and, despite an inability to adjust for some factors known to affect lung function decline, suggest potential mechanistic biomarkers associated with the rate of lung function decline in COPD. Whether these proteins are the cause or result of accelerated decline will require further research.

H2/CO/air premixed and partially premixed flame structure at different pressures based on reaction limit analysis.

Premixed and partially premixed flames (PPFs) of H2/CO/air syngas are studied numerically to investigate the effect of pressure on syngas PPF structure. Chemical characteristics of the syngas flame at different pressures are investigated based on reaction limit analysis using a one-dimensional configuration. The results show that CO affects the syngas reaction limits through both physical effects that consist mainly in dilution and chemical effects that are related to both R23 (CO + OH = CO2 + H) and HCO pathway. In particular, the HCO pathway weakens the flame at low pressures due to the chain-terminating effect of R25 (HCO + O2 = CO + HO2) and R26 (HCO + H = CO + H2), and enhances the flame at high pressures because of the contribution of R25 to the HO2 chain-branching process. These CO chemical characteristics are also observed in the premixed zone of 50% H2 + 50% CO syngas PPFs whereas only R23 is important in the non-premixed zone.

GeneCite: a stand-alone open source tool for high-throughput literature and pathway mining.

Systematic extraction of relevant biological facts from available massive scientific knowledge source is emerging as a significant task for the science community. Its success depends on several key factors, including the precision of a given search, the time of its accomplishment, and the communicative prowess of the mined information to the users. GeneCite - a stand-alone Java-based high-throughput data mining tool - is designed to carry out these tasks for several important knowledge sources simultaneously, allowing the users to integrate the results and interpret biological significance in a time-efficient manner. GeneCite provides an integrated high-throughput search platform serving as an information retrieval (IR) tool for probing online literature database (PubMed) and the sequence-tagged sites' database (UniSTS), respectively. It also operates as a data retrieval (DR) tool to mine an archive of biological pathways integrated into the software itself. Furthermore, GeneCite supports a retrieved data management system (DMS) showcasing the final output in a spread-sheet format. Each cell of the output file holds a real-time connection (hyperlink) to the given online archive reachable at the users' convenience. The software is free and currently available online www.bioinformatics.org; www.wrair.army.mil/Resources.