University of Virginia

About: University of Virginia is a education organization based out in Charlottesville, Virginia, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 52543 authors who have published 113268 publications receiving 5220506 citations. The organization is also known as: U of V & UVa.

GenProg: A Generic Method for Automatic Software Repair

Abstract: This paper describes GenProg, an automated method for repairing defects in off-the-shelf, legacy programs without formal specifications, program annotations, or special coding practices. GenProg uses an extended form of genetic programming to evolve a program variant that retains required functionality but is not susceptible to a given defect, using existing test suites to encode both the defect and required functionality. Structural differencing algorithms and delta debugging reduce the difference between this variant and the original program to a minimal repair. We describe the algorithm and report experimental results of its success on 16 programs totaling 1.25 M lines of C code and 120K lines of module code, spanning eight classes of defects, in 357 seconds, on average. We analyze the generated repairs qualitatively and quantitatively to demonstrate that the process efficiently produces evolved programs that repair the defect, are not fragile input memorizations, and do not lead to serious degradation in functionality.

Virtual reality on a WIM: interactive worlds in miniature

Abstract: This paper explores a user interface technique which augments an immersive head tracked display with a hand-held miniature copy of the virtual environment We call this interface technique the Worlds in Miniature (WIM) metaphor By establishing a direct relationship between life-size objects in the virtual world and miniature objects in the WIM, we can use the WIM as a tool for manipulating objects in the virtual environment In addition to describing object manipulation, this paper explores ways in which Worlds in Miniature can act as a single unifying metaphor for such application independent interaction techniques as object selection, navigation, path planning, and visualization The WIM metaphor naturally offers multiple points of view and multiple scales at which the user can operate, all without requiring explicit modes or commands Informal user observation indicates that users adapt to the Worlds in Miniature metaphor quickly and that physical props are helpful in manipulating the WIM and other objects in the environment

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Abstract: Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. © 2009 Macmillan Publishers Limited. All rights reserved.

Randomized controlled trial of intraputamenal glial cell line-derived neurotrophic factor infusion in Parkinson disease.

Abstract: Objective Glial cell line–derived neurotrophic factor (GDNF) exerts potent trophic influence on midbrain dopaminergic neurons. This randomized controlled clinical trial was designed to confirm initial clinical benefits observed in a small, open-label trial using intraputamenal (Ipu) infusion of recombinant human GDNF (liatermin). Methods Thirty-four PD patients were randomized 1 to 1 to receive bilateral continuous Ipu infusion of liatermin 15μg/putamen/day or placebo. The primary end point was the change in Unified Parkinson Disease Rating Scale (UPDRS) motor score in the practically defined off condition at 6 months. Secondary end points included other UPDRS scores, motor tests, dyskinesia ratings, patient diaries, and 18F-dopa uptake. Results At 6 months, mean percentage changes in “off” UPDRS motor score were −10.0% and −4.5% in the liatermin and placebo groups, respectively. This treatment difference was not significant (95% confidence interval, −23.0 to 12.0, p = 0.53). Secondary end point results were similar between the groups. A 32.5% treatment difference favoring liatermin in mean 18F-dopa influx constant (p = 0.019) was observed. Serious, device-related adverse events required surgical repositioning of catheters in two patients and removal of devices in another. Neutralizing antiliatermin antibodies were detected in three patients (one on-study and two in the open-label extension). Interpretation Liatermin did not confer the predetermined level of clinical benefit to patients with PD despite increased 18F-dopa uptake. It is uncertain whether technical differences between this trial and positive open-label studies contributed in any way this negative outcome. Ann Neurol 2006