Argudas: arguing with gene expression information

In situ hybridization gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information are often both incomplete and inconsistent. This presentation examines a system, Argudas, designed to help tackle these issues. Argudas is an evolution of an existing system, and so that system is reviewed as a means of both explaining and justifying the behavior of Argudas. Throughout the discussion of Argudas a number of issues will be raised including the appropriateness of argumentation in biology and the challenges faced when integrating apparently similar online biological databases

Argumentation in biology : exploration and analysis through a gene expression use case

Argumentation theory conceptualises the human practice of debating. Implemented as computational argumentation it enables a computer to perform a virtual debate. Using existing knowledge from research into argumentation theory, this thesis investigates the potential of computational argumentation within biology. As a form of non-monotonic reasoning, argumentation can be used to tackle inconsistent and incomplete information - two common problems for the users of biological data. Exploration of argumentation shall be conducted by examining these issues within one biological subdomain: in situ gene expression information for the developmental mouse. Due to the complex and often contradictory nature of biology, occasionally it is not apparent whether or not a particular gene is involved in the development of a particular tissue. Expert biological knowledge is recorded, and used to generate arguments relating to this matter. These arguments are presented to the user in order to help him/her decide whether or not the gene is expressed. In order to do this, the notion of argumentation schemes has been borrowed from philosophy, and combined with ideas and technologies from arti cial intelligence. The resulting conceptualisation is implemented and evaluated in order to understand the issues related to applying computational argumentation within biology. Ultimately, this work concludes with a discussion of Argudas - a real world tool developed for the biological community, and based on the knowledge gained during this work

A conceptual approach to gene expression analysis enhanced by visual analytics

The analysis of gene expression data is a complex task for biologists wishing to understand the role of genes in the formation of diseases such as cancer. Biologists need greater support when trying to discover, and comprehend, new relationships within their data. In this paper, we describe an approach to the analysis of gene expression data where overlapping groupings are generated by Formal Concept Analysis and interactively analyzed in a tool called CUBIST. The CUBIST workflow involves querying a semantic database and converting the result into a formal context, which can be simplified to make it manageable, before it is visualized as a concept lattice and associated charts

Restoration Methods for Deepwater Swamps

Planting in deepwater swamp areas is difficult and time consuming, and nursery-grown seedlings are often not suited for such conditions. Baldcypress [Taxodium distichum (L.) Rich.], water tupelo (Nyssa aquatica L.), swamp blackgum [N. sylvatica var. biflora (Walt.) Sarg.], and green ash (Fraxinus pennsylvanica Marsh.) have been planted at various flooded sites in South Carolina and Louisiana. One of the most effective means of planting these species in flooded situations was to heavily prune the lateral roots, grasp the seedling at the root collar, and push it into the soil. Excellent results have been obtained with baldcypress, whereas green ash was most sensitive to root pruning and water depth. Water tupelo and swamp blackgum were intermediate in response. Tree shelters are commonly used to reduce herbivory problems, and height growth inside the shelters is increased. Additional research is needed to compare operational performance of various techniques under conditions of interacting stresses such as herbivory and flooding

The Athletic Training Practice-Based Research Network: A National Model for Point-of-Care Sports Injury and Outcomes Documentation to Improve Athlete Health and Wellness

There is mounting evidence to suggest that sport-related injuries can negatively impact an individual’s well-being and quality of life on a long-term basis. As a result, there has been increased interest in the medical community to gain a better understanding of effective treatment interventions to ensure optimal short- and long-term health. Despite the growing problem of sport-related injuries and the need to identify effective treatment interventions, there is surprisingly little data to describe the types of treatments provided for common sport-related injuries at the point-of-care and how those treatments can potentially impact short- and long-term patient outcomes. In this paper, we aim to (1) introduce the Athletic Training Practice-Based Research Network (AT-PBRN) as an infrastructure for collecting the requisite data to address current gaps in sports medicine literature, (2) summarize findings from the AT-PBRN, and (3) describe future directions of the AT-PBRN