Biomedical subjects

Rick Stevens

Publications and source records attributed to Rick Stevens.

7 recordsLinked to original sources

PubMed2006

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of approximately 50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development.

Bacteria↗

PubMed2006

Pharmaceuticals and personal care products in biosolids/sewage sludge: the interface between analytical chemistry and regulation.

Modern sanitary practices result in large volumes of human waste, as well as domestic and industrial sewage, being collected and treated at common collection points, wastewater treatment plants (WWTPs). In recognition of the growing use of sewage sludge as fertilizers and soil amendments, and the scarcity of current data regarding the chemical constituents in sewage sludge, the US National Research Council (NRC) in 2002 produced a report on sewage sludge. Among the NRC's recommendations was the need for investigating the occurrence of pharmaceuticals and personal care products (PPCPs) in sewage sludge. PPCPs are a diverse array of non-regulated contaminants that had not been studied in previous sewage sludge surveys but which are likely to be present. The focus of this paper will be to review the current analytical methodologies available for investigating whether pharmaceuticals are present in WWTP-produced sewage sludge, to summarize current regulatory practices regarding sewage sludge, and to report on the presence of pharmaceuticals in sewage sludge.

Agriculture↗

PubMed2006

Essential genes on metabolic maps.

Within the past five years genome-scale gene essentiality data sets have been published for ten diverse bacterial species. These data are a rich source of information about cellular networks that we are only beginning to explore. The analysis of these data, very heterogeneous in nature, is a challenging task. Even the definition of 'essential genes' in various genome-scale studies varies from genes 'absolutely required for survival' to those 'strongly contributing to fitness' and robust competitive growth. A comparative analysis of gene essentiality across multiple organisms based on projection of experimentally observed essential genes to functional roles in a collection of metabolic pathways and subsystems is emerging as a powerful tool of systems biology.

Computational Biology↗

PubMed2005

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

Acyl Coenzyme A↗

PubMed2005

Distributed collaborative radiological visualization using access grid.

This paper describes early technical success toward enabling high quality distributed shared volumetric visualization of radiological data in concert with multipoint video collaboration using Grid infrastructures. Key principles are the use of commodity off-the-shelf hardware for client machines and open source software to permit deployment of over a large and diverse group of sites. Key software used includes the Access Grid Toolkit, the Visualization Toolkit, and Chromium.

Diagnostic Imaging↗

PubMed2005

Developing a distributed collaborative radiological visualization application.

Leveraging the advances of today's commodity graphics hardware, adoption of community proven collaboration technology, and the use of standard Web and Grid technologies a flexible system is designed to enable the construction of a distributed collaborative radiological visualization application. The system builds from a prototype application as well as requirements gathered from users. Finally constraints on the system are evaluated to complete the design process.

Artificial Intelligence↗

PubMedDate not supplied

Color nonuniformity in projection-based displays: analysis and solutions.

Large-area displays made up of several projectors show significant variation in color. In this paper, we identify different projector parameters that cause the color variation and study their effects on the luminance and chrominance characteristics of the display. This work leads to the realization that luminance varies significantly within and across projectors, while chrominance variation is relatively small, especially across projectors of same model. To address this situation, we present a method to achieve luminance matching across all pixels of a multiprojector display that results in photometrically uniform displays. We use a camera as a measurement device for this purpose. Our method comprises a one-time calibration step that generates a per channel per projector luminance attenuation map (LAM), which is then used to correct any image projected on the display at interactive rates on commodity graphics hardware. To the best of our knowledge, this is the first effort to match luminance across all the pixels of a multiprojector display.

Algorithms↗