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iii Abstract In early 2010, the Long-Baseline Neutrino Experiment (LBNE) science collaboration initiated a study to investigate the physics potential of the experiment with a broad set of different beam, near-and far-detector configurations. Nine initial topics were identified as scientific areas that motivate construction of a long-baseline neutrino(More)
UNLABELLED Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present(More)
Ecosystem recovery following disturbance requires the reestablishment of key soil biogeochemical processes. This long-term 7 year study describes effects of organic material, moisture, and vegetation on soil microbial community development in the Athabasca Oil Sands Region of Western Canada. Phospholipid fatty acid analysis was used to characterize and(More)
SUMMARY Treatment with fixed orthodontic appliances can cause enamel demineralization by increased biofilm adhesion. The purpose of the present study was to investigate whether a polytetrafluoroethylene (PTFE) coating reduces biofilm formation on orthodontic brackets. One PTFE-coated bracket and one uncoated stainless steel bracket were bonded symmetrically(More)
A fundamental step in the analysis of environmental sequence information is the prediction of potential genes or open reading frames (ORFs) encoding the metabolic potential of individual cells and entire microbial communities. FragGeneScan, a software designed to predict intact and incomplete ORFs on short sequencing reads combines codon usage bias,(More)
Accurate description of the microbial communities driving matter and energy transformations in complex ecosystems such as soils cannot yet be effectively accomplished using assembly-based approaches despite the rise of next generation sequencing technologies. Here we present SOFA, an open source pipeline enabling comparative functional annotation of(More)
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between(More)
FAST is a multi-threaded, I/O optimized Seed-and-Extend alignment program. FAST is extensible to nucleotide sequences making it comparable to both BLASTn and BLASTp, and also features several new usage flags reporting only HSPs meeting user defined e-value cut-offs. FASTs threaded database construction allows fast, low memory database construction e.g.,(More)