Making Common Fund data more findable: catalyzing a data ecosystem.

The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs' Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.

Sources and composition of natural and anthropogenic hydrocarbons in sediments from an impacted estuary.

Hydrocarbons in estuarine sediments provide information on sources of sedimentary organic matter (OM), and they are thus useful for tracing natural and anthropogenic OM inputs to the estuary. Here, we assessed the amounts, compositions and sources of natural and anthropogenic hydrocarbons from the sediments of a large, ecologically important estuary, Mobile Bay in Southeast USA. TOC/TN ratios and δ13C of organic carbon suggest that the bulk natural OM was sourced from marine phytoplankton and bacteria mixed with marsh and terrigenous C3 plants. Normal alkanes show high proportions of long-chain compounds with a high Carbon Preference Index, indicating the importance of C3 plants-derived OM in Mobile Bay. High concentrations of biogenic hopanes and perylene indicate microbial sources and degradation played an important role in shaping OM compositions. Anthropogenic hydrocarbons, αß-hopanes and polycyclic aromatic hydrocarbons (PAHs), were widely detected in Mobile Bay sediments. The source diagnostic ratios of hopanes and steranes suggest they were sourced from coal and diesel combustions. The source diagnostic ratios of PAHs, together with a positive correlation between PAHs and total mercury, suggests that PAHs originated primarily from coal combustion. We proposed two ratios, αß-hopanes/(ßß-hopanes+hopenes) and 16 PAHs/perylene, to evaluate anthropogenic versus natural contributions of hydrocarbons. These ratios were higher in the western estuary than in the eastern estuary, suggesting elevated anthropogenic hydrocarbon inputs to the western estuary. Correspondingly, the toxic equivalent quantity (TEQBaQ) of PAHs showed a higher ecological risk for the western estuary. This spatially uneven distribution of hydrocarbon pollutants can be attributed to more concentrated urban and industrial areas on the western shore, suggesting the importance of adjacent pollution sources. Collectively, our results provide new insights into the origins and dynamics of natural and anthropogenic OM and highlight the significance of coal combustion in contributing hydrocarbon pollutants in Mobile Bay sediments.

Neoadjuvant chemoradiotherapy for esophageal cancer using weekly Paclitaxel and Carboplatin plus infusional 5-Fluorouracil.

PURPOSE: To evaluate neoadjuvant therapy with weekly paclitaxel/carboplatin plus 5-fluorouracil (5-FU) with conformal radiotherapy in a phase II trial in resectable esophageal carcinoma. METHODS: Twenty-four patients with T2-4N0-1M0-1a esophageal carcinoma were treated with paclitaxel 45 mg/m(2) intravenously over 1 hour and carboplatin at an area under the concentration-time curve (AUC) of 2 intravenously over 30 minutes on days 1, 8, 15, 22, and 29. 5-Fluorouracil 225 mg/m(2) was delivered as a continuous infusion on days 1-33. Concurrent conformal radiation was delivered to a dose of 45 Gy. Responders underwent surgical resection within 8 weeks of completing chemoradiotherapy. Kaplan-Meier survival analysis and log-rank test of survival dependent on pathologic response were performed. RESULTS: Progressive disease was discovered at surgery in three patients. Of the remaining 21 patients, pathologic complete response (pCR) was demonstrated in 12 (pCR rate of 57%) and partial response (PR) occurred in 9, including 4 with near complete response. Median follow-up in all patients was 23 months. Overall survival among all 24 patients was 48% at 3 years, with a median of 31 months. Disease-free survival was 57% at 3 years, with a median of 38 months. Differences in survival time based on pCR vs. PR showed a trend favoring pCR for disease-free survival (P = .12) but not overall survival (P > .20). Grade 3/4 toxicities included esophagitis in 33% of patients, hypotension in 29%, stomatitis in 25%, neutropenia in 13%, and anemia in 8%. CONCLUSION: This study demonstrates the activity of neoadjuvant paclitaxel, carboplatin, 5-FU, and conformal radiotherapy in the treatment of localized esophageal cancer. Evaluation with a larger number of patients and longer follow-up will be required to definitively assess the long-term efficacy of this regimen.