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At least 127 records · Page 7Linked to original sources
PubMed1998

Genome projects and gene pools: new germplasm for plant breeding?

Crop gene pools have adapted to and sustained the demands of agricultural systems for thousands of years. Yet, very little is known about their content, distribution, architecture, or circuitry. The presumably shallow elite gene pools often continue to yield genetic gains while the exotic pools remain mostly untapped, uncharacterized, and underutilized. The concept and content of a crop's gene pools are being changed by advancements in plant science and technology. In the first generation of plant genomics, DNA markers have refined some perceptions of genetic variation by providing a glimpse of a primary source, DNA polymorphism. The markers have provided new and more powerful ways of assessing genetic relationships, diversity, and merit by infusing genetic information for the first time in many scenarios or in a more comprehensive manner for others. As a result, crop gene pools may be supplemented through more rapid and directed methods from a greater variety of sources. Previously limited by the barriers of sexual reproduction, the native gene pools will soon be complemented by another gene pool (transgenes) and perhaps by other native exotic gene pools through comparative analyses of plants' biological repertoire. Plant genomics will be an important force of change for crop improvement. The plant science community and crop gene pools may be united and enriched as never before. Also, the genomes and gene pools, the products of evolution and crop domestication, will be reduced and subjected to the vagaries and potential divisiveness of intellectual property considerations. Let the gains begin.

Journal Article↗
PubMed1999

Models for stochastic climate prediction.

There has been a recent burst of activity in the atmosphere/ocean sciences community in utilizing stable linear Langevin stochastic models for the unresolved degree of freedom in stochastic climate prediction. Here several idealized models for stochastic climate modeling are introduced and analyzed through unambiguous mathematical theory. This analysis demonstrates the potential need for more sophisticated models beyond stable linear Langevin equations. The new phenomena include the emergence of both unstable linear Langevin stochastic models for the climate mean and the need to incorporate both suitable nonlinear effects and multiplicative noise in stochastic models under appropriate circumstances. The strategy for stochastic climate modeling that emerges from this analysis is illustrated on an idealized example involving truncated barotropic flow on a beta-plane with topography and a mean flow. In this example, the effect of the original 57 degrees of freedom is well represented by a theoretically predicted stochastic model with only 3 degrees of freedom.

Journal Article↗
PubMed2006

Agility literature review: classifications, training and testing.

At present, no agreement on a precise definition of agility within the sports science community exists. The term is applied to a broad range of sport contexts, but with such great inconsistency, it further complicates our understanding of what trainable components may enhance agility. A new definition of agility is proposed: "a rapid whole-body movement with change of velocity or direction in response to a stimulus". Agility has relationships with trainable physical qualities such as strength, power and technique, as well as cognitive components such as visual-scanning techniques, visual-scanning speed and anticipation. Agility testing is generally confined to tests of physical components such as change of direction speed, or cognitive components such as anticipation and pattern recognition. New tests of agility that combine physical and cognitive measures are encouraged.

Acceleration↗
PubMedDate not supplied

Peer Review as a QA Tool in Environmental Applications.

Peer Review is commonly applied during the final stage of a project and is used in the science community to determine the soundness of a conclusion and if the quality of information meets the standards of the scientific and technical community. Quality Assurance and Quality Control procedures are most effective when applied to planning, then during the process stage of a project, and during the review of a product. The gold standard for validating the quality of a study's results is comparison with a referenced data set, model, or result (Azouzi, 1999). However, costs can severely limits this approach for many applications. This article proposes an additional means for quality assessment using peer review as a quality assessment tool during the planning, process, and review of a project.

Journal Article↗
PubMed1996

Washington politics and genetic engineering research: when worlds collide.

In earlier research, I developed a notion of "biopolitics" to help explain, first, the recombinant DNA debate of the 1970-1980s, and, second, the human gene transfer-therapy debate of the 1980-1990s. Drawing upon results gleaned from two recent meetings of high moment in the nation's capital, I expand upon the theoretical and empirical parameters of the biopolitical argument to elucidate the clash of policy preferences arising from two new areas of genetic experimentation: (i) human embryo research and (ii) the creation of commercially viable therapeutics to combat disease. I show the manner in which members of the biological science community and their policy allies are forced to cope with the realities of the "Washington political game," and why it is necessary for them to develop a sophisticated sense of what that "game" is.

Advisory Committees↗
PubMed2004

Taverna: a tool for the composition and enactment of bioinformatics workflows.

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.

Computational Biology↗
PubMed2005

Rethinking gender differences in health: why we need to integrate social and biological perspectives.

The complexity of gender differences in health (i.e., men's lower life expectancy and women's greater morbidity) extends beyond notions of either social or biological disadvantage. Gaps remain in understanding the antecedents of such differences and the issues this paradox raises regarding the connections between social and biological processes. Our goals in this analytic essay are to make the case that gender differences in health matter and that understanding these differences requires an explanation of why rational people are not effective in making health a priority in their everyday lives. We describe some salient gender health differences in cardiovascular disease, immune function and disorders, and depression and indicate why neither social nor biological perspectives alone are sufficient to account for them. We consider the limitations of current models of socioeconomic and racial/ethnic health disparities to explain the puzzling gender differences in health. Finally, we discuss constrained choice, a key issue that is missing in the current understanding of these gender differences, and call on the social science community to work with biomedical researchers on the interdisciplinary work required to address the paradoxical differences in men's and women's health.

Cardiovascular Diseases↗
PubMed2004

ProteinDBS: a real-time retrieval system for protein structure comparison.

We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time. This system applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. When meaningful contents, represented in a multi-dimensional feature space, have been extracted from distance matrices, an advanced indexing structure, Entropy Balanced Statistical (EBS) k-d tree, is utilized to index the data. Our system is able to return search results in ranked order from a database with 46 075 chains in seconds, exhibiting a reasonably high degree of precision. To our knowledge, this is the first real-time search engine for protein structure comparison. ProteinDBS provides two types of query method: query by Protein Data Bank protein chain ID and by new structures uploaded by users. The system is hosted at http://ProteinDBS.rnet.missouri.edu.

Computer Graphics↗
PubMed2004

ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval.

We have developed a web server for the life sciences community to use to search for short repeats of DNA sequence of length between 3 and 10,000 bases within multiple species. This search employs a unique and fast hash function approach. Our system also applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. Furthermore, we have incorporated a part of the Gene Ontology database into our information retrieval algorithms to broaden the coverage of the search. Our web server and tutorial can be found at http://acmes.rnet.missouri.edu.

Algorithms↗
PubMed2002

Protein design is NP-hard.

Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design.

Algorithms↗
PubMed2005

Research strategies for safety evaluation of nanomaterials, Part III: nanoscale technologies for assessing risk and improving public health.

Risk assessment in the environmental health sciences focuses on understanding the nature of environmental exposures and the potential harm posed by those exposures which in turn is determined by the perturbation of biological pathways and the individual's susceptibility to damage. While there are extensive research efforts ongoing in these areas, progress in each is currently slowed by technological limitations including comprehensive assessment of multiple exposures in real time and dynamic assessment of biological response with high temporal and quantitative resolution. This Forum article discusses recent technological innovations capitalizing on the emergent properties of nanoscale materials and their potential adaptation to improving individual exposure assessment, determination of biological response, and environmental remediation. The ultimate goal is to raise the environmental health science community's awareness of these possibilities and encourage the development of improved strategies for assessing risk and improving public health.

Biomedical Research↗
PubMed1998

"Patient informatics": creating new partnerships in medical decision making.

The amassing of health information on the Internet and World Wide Web continues unabated. Patients anxious to participate in decisions about their own treatment have turned to the Internet to confirm diagnoses, validate physician-recommended treatment, or seek alternative therapies. While increased information for patients has been linked to improved outcomes, there are inherent dangers associated with the kind of unauthenticated information available on the Web. The authors discuss the nature of these dangers as well as review the advantages for patients of "information therapy" (improved access to health information). They also examine how the Internet has begun to affect the physician-patient relationship, and describe how the Internet and information technology can be effectively used by physicians in patient care. They recommend that the academic health sciences community seize the opportunity to take the lead in ensuring that patients have access to reliable health information, and suggest that "patient informatics" be integrated by academic physicians and educators into the teaching of clinical skills.

Academic Medical Centers↗
PubMed2005

Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.

The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.

Algorithms↗
PubMed2004

Chromatin techniques for plant cells.

A large number of recent studies have demonstrated that many important aspects of plant development are regulated by heritable changes in gene expression that do not involve changes in DNA sequence. Rather, these regulatory mechanisms involve modifications of chromatin structure that affect the accessibility of target genes to regulatory factors that can control their expression. The central component of chromatin is the nucleosome, containing the highly conserved histone proteins that are known to be subject to a wide range of post-translational modifications, which act as recognition codes for the binding of chromatin-associated factors. In addition to these histone modifications, DNA methylation can also have a dramatic influence on gene expression. To accommodate the burgeoning interest of the plant science community in the epigenetic control of plant development, a series of methods used routinely in our laboratories have been compiled that can facilitate the characterization of putative chromatin-binding factors at the biochemical, molecular and cellular levels.

Chromatin↗
PubMed2005

Matching and reconstruction of brachytherapy seeds using the Hungarian algorithm (MARSHAL).

Intraoperative dosimetric quality assurance in prostate brachytherapy critically depends on discerning the three-dimensional (3D) locations of implanted seeds. The ability to reconstruct the implanted seeds intraoperatively will allow us to make immediate provisions for dosimetric deviations from the optimal implant plan. A method for seed reconstruction from segmented C-arm fluoroscopy images is proposed. The 3D coordinates of the implanted seeds can be calculated upon resolving the correspondence of seeds in multiple x-ray images. We formalize seed-matching as a combinatorial optimization problem, which has salient features: (a) extensively studied solutions by the computer science community; (b) proof for the nonexistence of any polynomial time exact algorithm; and (c) a practical pseudo-polynomial algorithm that mostly runs in O(N3) time using any number of images. We prove that two images are insufficient to correctly match the seeds, while a third image renders the matching problem to be of nonpolynomial complexity. We utilize the special structure of the problem and propose a pseudopolynomial time algorithm. Using three presegmented images, matching and reconstruction of brachytherapy seeds using the Hungarian algorithm achieved complete matching in simulation experiments; and 98.5% in phantom experiments. 3D reconstruction error for correctly matched seeds has a mean of 0.63 mm, and 0.9 mm for incorrectly matched seeds. The maximum seed reconstruction error in each implant was typically around 1.32 mm. Both on synthetic data and in phantom experiments, matching rate and reconstruction error achieved using presegmented images was found to be sufficient for prostate brachytherapy. The algorithm is extendable to deal with arbitrary number of images without any loss in speed or accuracy. The algorithm is sufficiently generic to provide a practical solution to any correspondence problem, across different imaging modalities and features.

Algorithms↗
PubMed2002

Complex sampling designs and statistical issues in secondary analysis.

Conducting secondary analysis using large national survey data sets to answer pressing research questions is gaining acceptance in the nursing science community. There are, however, challenges confronted by researchers who wish to apply secondary analysis to large data sets due to the incorporation of complex sampling designs. This article presents sampling design issues inherent in many large national surveys and explains the rationale for applying sample and variance estimation weights when conducting statistical analyses. In addition, the rationale for using statistical software packages capable of analyzing data derived from complex sampling designs is described. Examples of differences in statistical outcomes with and without weights using Stata and SPSS are provided using data from the Medical Expenditure Panel Survey (MEPS). Based on the example analyses, the implications of the statistical outcome differences for study findings are discussed.

Data Collection↗
PubMed2005

A human corneal equivalent constructed from SV40-immortalised corneal cell lines.

Within the last decade, extensive research in the field of tissue and organ engineering has focused on the development of in vitro models of the cornea. The use of organotypic, three-dimensional corneal equivalents has several advantages over simple monolayer cultures. The aim of this study was to develop a corneal equivalent model composed of the same cell types as in the natural human tissue, but by using immortalised cell lines to ensure reproducibility and to minimise product variation. We report our success in the establishment of an SV40-immortalised human corneal keratocyte cell line (designated HCK). A collagen matrix, built up with these cells, displayed the morphological characteristics of the human stromal tissue and served as a biomatrix for the immortalised human corneal epithelial and endothelial cells. Histological cross-sections of the whole-cornea equivalents resemble human corneas in tissue structure. This organotypic in vitro model may serve as a research tool for the ophthalmic science community, as well as a model system for testing for eye irritancy and drug efficacy.

Actins↗