Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART.

MOTIVATION: Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC SDTM clinical data standard into the tranSMART i2b2 via a guiding master ontology tree positively impacts and supports the efficacy of data sharing, visualization and exploration across datasets. RESULTS: We present here a schema for the organization of SDTM variables into the tranSMART i2b2 tree along with a script and test dataset to exemplify the mapping strategy. The eTRIKS master tree concept is demonstrated by making use of fictitious data generated for four patients, including 16 SDTM clinical domains. We describe how the usage of correct visit names and data labels can help to integrate multiple readouts per patient and avoid ETL crashes when running a tranSMART loading routine. AVAILABILITY AND IMPLEMENTATION: The eTRIKS Master Tree package and test datasets are publicly available at https://doi.org/10.5281/zenodo.1009098 and a functional demo installation at https://public.etriks.org/transmart/datasetExplorer/ under eTRIKS-Master Tree branch, where the discussed examples can be visualized.

Translation strategy for the qualification of drug-induced vascular injury biomarkers.

Drug-induced vascular injury (DIVI) is a common preclinical toxicity usually characterized by hemorrhage, vascular endothelial and smooth muscle damage, and inflammation. DIVI findings can cause delays or termination of drug candidates due to low safety margins. The situation is complicated by the absence of sensitive, noninvasive biomarkers for monitoring vascular injury and the uncertain relevance to humans. The Safer And Faster Evidence-based Translation (SAFE-T) consortium is a public-private partnership funded within the European Commission's Innovative Medicines Initiative (IMI) aiming to accelerate drug development by qualifying biomarkers for drug-induced organ injuries, including DIVI. The group is using patients with vascular diseases that have key histomorphologic features (endothelial damage, smooth muscle damage, and inflammation) in common with those observed in DIVI, and has selected candidate biomarkers associated with these features. Studied populations include healthy volunteers, patients with spontaneous vasculitides and other vascular disorders. Initial results from studies with healthy volunteers and patients with vasculitides show that a panel of biomarkers can successfully discriminate the population groups. The SAFE-T group plans to seek endorsement from health authorities (European Medicines Agency and Food and Drug Administration) to qualify the biomarkers for use in regulatory decision-making processes.

The assessment of high sensitivity C-reactive protein as a systemic marker in moderate asthma patients and changing levels by inhaled corticosteroids.

OBJECTIVES: To see if high-sensitivity C-reactive protein levels increase even in the early stages of asthma, and to evaluate if corticosteroid therapy affects the levels in asthma patients. METHODS: The case-control pilot study was conducted at Yedikule Chest Disease and Surgery Education and Research Hospital, Turkey, from February to April 2011. Patients newly diagnosed with asthma who reported symptoms that occurred six months before diagnosis were included in the study.The protein levels were measured pre-treatment and one month post-treatment. In addition, pulmonary function test and total Immunoglobulin-E measurements were taken and the prick test was performed. Statistical analysis was done using SPSS 15. RESULTS: There were 15 cases; 8 (53%) females and 7 (47%) males. Besides, there were 19 Controls; 9 (47%) females and 10 (53%) males. The mean age of the Cases was 29.13+/-10.30 years, while for the Controls it was 28.9+/-5.35 years. The difference was not statistically significant (p<0.54). The difference in protein levels pre and post-treatment was not significant. However, a higher level in the pre-treatment period was found compared to the Controls. Posttreatment levels in the Cases were not significantly different than the Controls. CONCLUSION: Elevated high-sensitivity C-reactive protein levels in asthmatic patients may indicate an increased risk for cardiovascular disease. Future studies in asthma patients should focus on this relationship.