Health Services Research in The Privacy Age

BACKGROUND: Strengthened regulations concerning privacy of health information are affecting large-scale health outcomes research. OBJECTIVE: To create a data collection system that would facilitate outcomes research, avoid selection bias, and fulfill obligations to protect privacy. DESIGN: We created a web-based system that uses touch-screen computer technology for longitudinal collection of data. The system provides access to information in deidentified form, enables it to be linked to health services and outcomes data, and allows patients to join a research registry project (RRP) and be placed on a prospective subject list (PSL). PARTICIPANTS, MEASUREMENTS, AND RESULTS: Pilot testing in 86 consecutive patients who were seen at a large, urban, university-based general medicine practice and had a mean age of 50 years showed that 81 patients had no difficulty, 5 had some difficulty, and none had considerable difficulty using the computer technology to complete a health survey. No patients refused to complete the survey and all patients completed the entire survey. Forty-seven (55%) joined the RRP and 42 of these 47 (89%) joined the PSL. RRP participants were less likely than RRP nonparticipants to be divorced or widowed (P=.03) and less likely to have hypertension (P=.03) but had no other significant differences in sociodemographic or clinical characteristics. PSL participants did not differ from PSL nonparticipants. CONCLUSIONS: The new system ensures privacy and appears to facilitate research recruitment and avoid selection bias

Systems biology of the structural proteome

Background: The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology. Results: Here, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository (https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/). Conclusions: Translating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM-PRO offers insight into the physical embodiment of an organism’s genotype, and its use in this comparative framework enables exploration of adaptive strategies for these organisms, opening the door to many new lines of research. With these provided tools, tutorials, and background, the reader will be in a position to run GEM-PRO for their own purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0271-6) contains supplementary material, which is available to authorized users