Using data from web-server logs to develop a concept-based browse set for water quality and agriculture

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Increasing consistency of disease biomarker prediction across datasets

Microarray studies with human subjects often have limited sample sizes which hampers the ability to detect reliable biomarkers associated with disease and motivates the need to aggregate data across studies. However, human gene expression measurements may be influenced by many non-random factors such as genetics, sample preparations, and tissue heterogeneity. These factors can contribute to a lack of agreement among related studies, limiting the utility of their aggregation. We show that it is feasible to carry out an automatic correction of individual datasets to reduce the effect of such 'latent variables' (without prior knowledge of the variables) in such a way that datasets addressing the same condition show better agreement once each is corrected. We build our approach on the method of surrogate variable analysis but we demonstrate that the original algorithm is unsuitable for the analysis of human tissue samples that are mixtures of different cell types. We propose a modification to SVA that is crucial to obtaining the improvement in agreement that we observe. We develop our method on a compendium of multiple sclerosis data and verify it on an independent compendium of Parkinson's disease datasets. In both cases, we show that our method is able to improve agreement across varying study designs, platforms, and tissues. This approach has the potential for wide applicability to any field where lack of inter-study agreement has been a concern. © 2014 Chikina, Sealfon

3,5-Dimethylisoxazoles Act As Acetyl-lysine-mimetic Bromodomain Ligands

Histone-lysine acetylation is a vital chromatin post-translational modification involved in the epigenetic regulation of gene transcription. Bromodomains bind acetylated lysines, acting as readers of the histone-acetylation code. Competitive inhibitors of this interaction have antiproliferative and anti-inflammatory properties. With 57 distinct bromodomains known, the discovery of subtype-selective inhibitors of the histone-bromodomain interaction is of great importance. We have identified the 3,5 dimethylisoxazole moiety as a novel acetyl-lysine bioisostere, which displaces acetylated histone-mimicking peptides from bromodomains. Using X-ray crystallographic analysis, we have determined the interactions responsible for the activity and selectivity of 4-substituted 3,5-dimethylisoxazoles against a selection of phylogenetically diverse bromodomains. By exploiting these interactions, we have developed compound 4d, which has IC50 values of <5 μM for the bromodomain-containing proteins BRD2(1) and BRD4(1). These compounds are promising leads for the further development of selective probes for the bromodomain and extra C-terminal domain (BET) family and CREBBP bromodomains

Effects of Agricultural Conservation Practices on Fish and Wildlife Volume 2

This bibliography, in two volumes, is part of a multi-volume set developed by the Water Quality Information Center at the National Agricultural Library in support of the United States Department of Agriculture’s Conservation Effects Assessment Project (CEAP). The bibliography is a guide to recent scientific literature covering effects of agricultural conservation practices on fish and wildlife. The citations listed here provide information on how conservation programs and practices designed to improve fish and wildlife habitat, as well as those intended for other purposes, e.g., water quality improvement, affect various aquatic and terrestrial fauna

Effects of Agricultural Conservation Practices on Fish and Wildlife

This bibliography, in two volumes, is part of a multi-volume set developed by the Water Quality Information Center at the National Agricultural Library in support of the U.S. Department of Agriculture’s Conservation Effects Assessment Project (CEAP). The bibliography is a guide to recent scientific literature covering effects of agricultural conservation practices on fish and wildlife. The citations listed here provide information on how conservation programs and practices designed to improve fish and wildlife habitat, as well as those intended for other purposes, e.g., water quality improvement, affect various aquatic and terrestrial fauna

Abstract The National Agricultural Library’s Database of Online Documents Covering Water and Agriculture

Agricultural operations can have a negative effect on water quality. The National Water Quality Inventory, 1998 Report to Congress (the most recent biennial report in this series) indicates that agriculture is a major source of water quality impairment of assessed rivers and lakes in the United States. Information is a key ingredient of problem solving. With the emergence of the World Wide Web, many documents produced by state and federal agencies, extension services and other organizations involved with water issues are being published and freely distributed online. While water quality information may be available electronically, the information is scattered across many Web sites. In addition, the organization and access mechanisms among sites is not consistent. These characteristics make it difficult to rapidly locate and access a comprehensive collection of documents related to a particular water issue associated with agriculture, for example, the relationship between nutrient management practices and nitrate movement into groundwater. Internet search engines are not precise enough to easily locate specific documents. To improve access to electronic documents covering water and agriculture, the Water Quality Information Center at the National Agricultural Library has developed a prototype database (located a

Use of Industrial Byproducts in Agriculture

Massive quantities of industrial byproducts are produced every day. Governments and private industries throughout the world are researching ways to divert the byproducts from landfills and use them in beneficial ways. This bibliography is a guide to recent scientific literature regarding the use of industrial byproducts in agriculture. The byproducts featured in this guide originate from coal combustion, construction and demolition activity, paper manufacturing, iron and steel making, tire use, and wood products manufacturing and use

Implementing Agricultural Conservation Practices: Barriers and Incentives: A Conservation Effects Assessment Bibliography

This bibliography is one in a multi-volume set developed by the Water Quality Information Center at the National Agricultural Library in support of the U.S. Department of Agriculture’s Conservation Effects Assessment Project (CEAP). The bibliography is a guide to recent literature examining agricultural producers’ views of conservation programs and practices. It provides people working in the area of agriculture and the environment with a guide to information resources that focus on the psychological and socioeconomic factors that influence agricultural producers’ behavior with regard to environmental issues

Data and Modeling for Environmental Credit Trading: A Conservation Effects Assessment Bibliography

This bibliography is one in a multi-volume set developed by the Water Quality Information Center at the National Agricultural Library in support of the U.S. Department of Agriculture’s Conservation Effects Assessment Project (CEAP). The bibliography is a guide to literature on the data and modeling requirements for environmental credit trading. It provides people interested in environmental credit trading and agriculture with information about the current state of data acquisition and use of simulation models in this emerging field