Adverse moisture events predict seasonal abundance of Lyme disease vector ticks (Ixodes scapularis).

BACKGROUND: Lyme borreliosis (LB) is the most commonly reported vector-borne disease in north temperate regions worldwide, affecting an estimated 300,000 people annually in the United States alone. The incidence of LB is correlated with human exposure to its vector, the blacklegged tick (Ixodes scapularis). To date, attempts to model tick encounter risk based on environmental parameters have been equivocal. Previous studies have not considered (1) the differences between relative humidity (RH) in leaf litter and at weather stations, (2) the RH threshold that affects nymphal blacklegged tick survival, and (3) the time required below the threshold to induce mortality. We clarify the association between environmental moisture and tick survival by presenting a significant relationship between the total number of tick adverse moisture events (TAMEs - calculated as microclimatic periods below a RH threshold) and tick abundance each year. METHODS: We used a 14-year continuous statewide tick surveillance database and corresponding weather data from Rhode Island (RI), USA, to assess the effects of TAMEs on nymphal populations of I. scapularis. These TAMEs were defined as extended periods of time (>8 h below 82% RH in leaf litter). We fit a sigmoid curve comparing weather station data to those collected by loggers placed in tick habitats to estimate RH experienced by nymphal ticks, and compiled the number of historical TAMEs during the 14-year record. RESULTS: The total number of TAMEs in June of each year was negatively related to total seasonal nymphal tick densities, suggesting that sub-threshold humidity episodes >8 h in duration naturally lowered nymphal blacklegged tick abundance. Furthermore, TAMEs were positively related to the ratio of tick abundance early in the season when compared to late season, suggesting that lower than average tick abundance for a given year resulted from tick mortality and not from other factors. CONCLUSIONS: Our results clarify the mechanism by which environmental moisture affects blacklegged tick populations, and offers the possibility to more accurately predict tick abundance and human LB incidence. We describe a method to forecast LB risk in endemic regions and identify the predictive role of microclimatic moisture conditions on tick encounter risk.

Sensitivity of Raman spectra to chemical functional groups.

Spectral features in Raman spectra of organic molecules can be attributed to certain functional groups. A library of 1222 Raman spectra was used to train an artificial neural network (ANN) for predicting the presence of 13 functional groups. Sensitivity analysis was applied to the ANN models to determine a sensitivity factor or feature spectrum for each functional group. The feature spectra could then be used to predict the presence of specific groups based on Bayes' theorem. Once a model is constructed for each functional group, it can be applied directly to measured spectra of structurally unknown molecules and provide real-time predictions. Prediction accuracies of greater than 90% were obtained for aromatic, alkene, aldehyde, ketone, ester, nitro, and nitrile linkages. Accuracies for alcohols and amines were in the 80% range.

Sensitivity of infrared spectra to chemical functional groups.

Spectral features from specific regions in infrared spectra of organic molecules can consistently be attributed to certain functional groups. Artificial neural networks were employed as a pattern recognition tool to elucidate the relationships between functional groups and spectral features. The ability of these network models to predict the presence and absence of a variety of functional groups was evaluated. The sensitivity of the artificial neural network over the entire infrared spectral region was used to generate a spectral factor representation of the major information associated with each functional group. The resulting sensitivity factors were utilized in a much simpler model for functional group prediction. Ultimately, the presence of a functional group was predicted based on the dot product of an unknown spectrum with the corresponding sensitivity factor. A probability based on Bayes' theorem was assigned to each of the predictions. The prediction accuracies were greater than 90% for all 13 functional groups considered in the investigation.

PentaPlot: a software tool for the illustration of genome mosaicism.

BACKGROUND: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. RESULTS: The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. CONCLUSION: PentaPlot is being made publicly available as an open source project at http://pentaplot.sourceforge.net.

Visualization of the phylogenetic content of five genomes using dekapentagonal maps.

The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.