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1.  Temporal patterns in daily measurements of inorganic and organic speciated PM2.5 in Denver 
Airborne particulate matter less than 2.5 μm in aerodynamic diameter (PM2.5) has been linked to a wide range of adverse health effects and as a result is currently regulated by the U.S. Environmental Protection Agency. PM2.5 originates from a multitude of sources and has heterogeneous physical and chemical characteristics. These features complicate the link between PM2.5 emission sources, ambient concentrations and health effects. The goal of the Denver Aerosol Sources and Health (DASH) study is to investigate associations between sources and health using daily measurements of speciated PM2.5 in Denver.
The datxa set being collected for the DASH study will be the longest daily speciated PM2.5 data set of its kind covering 5.5 years of daily inorganic and organic speciated measurements. As of 2008, 4.5 years of bulk measurements (mass, inorganic ions and total carbon) and 1.5 years of organic molecular marker measurements have been completed. Several techniques were used to reveal long-term and short-term temporal patterns in the bulk species and the organic molecular marker species. All species showed a strong annual periodicity, but their monthly and seasonal behavior varied substantially. Weekly periodicities appear in many compound classes with the most significant weekday/weekend effect observed for elemental carbon, cholestanes, hopanes, select polycyclic aromatic hydrocarbons (PAHs), heavy n-alkanoic acids and methoxyphenols. Many of the observed patterns can be explained by meteorology or anthropogenic activity patterns while others do not appear to have such obvious explanations. Similarities and differences in these findings compared to those reported from other cities are highlighted.
PMCID: PMC3593308  PMID: 23486844
Particulate matter; PM2.5; Chemical speciation; Organic molecular markers; Weekday/weekend
2.  An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis 
BMC Bioinformatics  2008;9:4.
In spite of two-dimensional gel electrophoresis (2-DE) being an effective and widely used method to screen the proteome, its data standardization has still not matured to the level of microarray genomics data or mass spectrometry approaches. The trend toward identifying encompassing data standards has been expanding from genomics to transcriptomics, and more recently to proteomics. The relative success of genomic and transcriptomic data standardization has enabled the development of central repositories such as GenBank and Gene Expression Omnibus. An equivalent 2-DE-centric data structure would similarly have to include a balance among raw data, basic feature detection results, sufficiency in the description of the experimental context and methods, and an overall structure that facilitates a diversity of usages, from central reposition to local data representation in LIMs systems.
Results & Conclusion
Achieving such a balance can only be accomplished through several iterations involving bioinformaticians, bench molecular biologists, and the manufacturers of the equipment and commercial software from which the data is primarily generated. Such an encompassing data structure is described here, developed as the mature successor to the well established and broadly used earlier version. A public repository, AGML Central, is configured with a suite of tools for the conversion from a variety of popular formats, web-based visualization, and interoperation with other tools and repositories, and is particularly mass-spectrometry oriented with I/O for annotation and data analysis.
PMCID: PMC2231339  PMID: 18179696

Results 1-2 (2)