Nancy McMillan

Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUSand BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

ANALYSIS OF PROTEIN ACTIVITY DATA BY GAUSSIAN STOCHASTIC PROCESS MODELS

The effects of certain chemical additives at maintaining a high level of activity in protein constructs during storage is investigated. We use a semiparametric regression technique to model the effects of the additives on protein activity. The model is extended to handle categorical explanatory variables. On the basis of the available data, the important factors are estimated to be buffer, detergent, protein concentration, and storage temperature. The relationships among protein activity and these factors appear to be moderately nonlinear with strong interaction effects. These features are revealed in a data-adaptive way by the semi parametric model, without explicit modeling of the nonlinearities or interactions. We use cross-validation to assess the fit of our model. The protein activity response appears to be extremely erratic. We recommend several sets of storage conditions and that further design points be chosen in regions around these estimated optima.

Benefits and Costs of Four Approaches to Improving Rollover Stability of Cargo Tank Motor Vehicles

Four broad approaches to decreasing the number of cargo tank rollovers were evaluated: driver training, electronic stability aids, improvements in design of the vehicle itself, and highway design. A study of rollover crash statistics confirmed many expectations, but a few of the factors were not as strong as might have been expected. The portion of rollovers that occur on freeways is 15% to 20%. A driver error of one kind or another (e.g., decision or performance error) figures in about three-fourths of cargo tank rollovers. Inattention and distraction account for about 15%. Evasive maneuvers were a factor in 5% to 10% of rollovers. Drivers must be trained to appreciate the diverse causes for rollovers and to anticipate the situations that lead to them. Adherence to viable work and rest schedules is crucial. Electronic stability aids automatically slow the truck when it rounds a curve too fast. They can be remarkably effective in preventing this scenario. However, crash statistics and anecdotal accounts consistently show many other factors that can lead to rollovers. Significant reductions in rollover rates can be achieved with modest changes in vehicle stability. Cargo tank trailers of improved stability are currently available for some cargoes. When mountainous terrain or other factors dictate highway designs that can contribute to rollovers, drivers need to be made aware through signage or dispatch instructions. A comprehensive benefit–cost analysis, conducted from a societal point of view during a 20-year window, projected that the improvements will be cost beneficial.