Rumor Has It...

A curious graduate takes it upon herself to investigate four tales that have become part of campus lore -- and determine what\u27s fact and what\u27s fiction

Arkansas Agricultural Chemical Ground-Water Management Plan

The Arkansas Agricultural Chemical Ground-Water Management Plan (SMP) is based on the Draft State Pesticide Ground- Water Management Plan Guidance and The Pesticides and Ground-Water Protection Strategy prepared by the U.S. Environmental Protection Agency (EPA). The need for a plan to protect ground water from contamination by agricultural chemicals and agents arises from evidence nationwide that using these chemicals can, in some instances, lead to contamination. In February 1988, EPA proposed a strategy to regulate certain pesticides by prohibiting their use in areas vulnerable to leaching unless a state develops and implements an acceptable management plan. The advantage of a state plan as opposed to a federal plan is that a state plan can provide protection for ground-water resources without unnecessarily restricting pesticide use. State plans can be more sensitive to local conditions such as soil types, farming practices and hydrogeological considerations

eXframe: reusable framework for storage, analysis and visualization of genomics experiments

<p>Abstract</p> <p>Background</p> <p>Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types.</p> <p>Results</p> <p>We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients.</p> <p>Conclusion</p> <p>The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.</p

Colon and rectal cancer incidence and water trihalomethane concentrations in New South Wales, Australia

BACKGROUND There is evidence, although inconsistent, that long term exposure to disinfection by products (DBPs) increases the risk of bowel cancer. No study has been conducted in Australia to examine this association and due to difference in the methods of disinfection the risk can vary across geographical regions and. This study was conducted to analyse the association of trihalomethanes (THMs) in water with colon and rectal cancer in NSW Australia. METHODS Average yearly concentrations of total and individual species of THMs were obtained for 50 local government areas (LGAs). Indirectly-standardized incidence rates of colon and rectal cancers in LGAs for the period 1995 to 2001 were regressed against mean THM concentrations lagged five years, adjusting for socioeconomic status, high risk drinking, smoking status, usual source of water and year of diagnosis, including local and global random effects within a Bayesian framework. The incidence rate ratios (IRRs) for an interquartile range (IQR) increase in THMs were estimated. RESULTS Using five year lag of exposure there was a positive association between bromoform concentration and CRC in men (IRR = 1.025, 95% CI 1.010, 1.040) but not in women (IRR = 1.003, 95% CI 0.987, 1.018). The association in men was mainly found in colon cancer with bromoform (IRR = 1.035, 95% CI 1.017, 1.053). There was no appreciable association of colorectal cancer with other species of THMs. Sensitivity analyses did not materially change the associations observed. CONCLUSION A positive association was observed between colon cancer and water bromoform concentrations in men. Given the potential population impact of such an association, further research into the relationship between THMs, particularly brominated species, and colorectal cancer is warranted.This study was conducted as part of a PhD thesis. The PhD was funded by the Endeavor International Postgraduate Research Scholarship program of the Australian Government and the University of Sydney’s international postgraduate award program and Sydney School of Public Health. The expenditure for data collection was borne by the Sydney School of Public Health, the University of Sydney. The case data were provided by the NSW central cancer registry. The exposure data were provided by the Sydney Water Corporation and the Hunter Water Corporation in NSW, Australia