Evaluation of the sensitivity of a medical data-mining application to the number of elements in small databases

Data-mining methods can be used to generate rules, or identify patterns, from medical data to assist clinical diagnosis and decision-making. However, in the initial stages of a clinical study on a new diagnostic approach, there could be a limited medical dataset available; or the medical characteristics could mean that the number of patients involved in the study will never be large. Diagnoses made using the rules discovered from such small medical databases should be considered suspect unless a confidence range for a particular diagnosis can be established. A method to evaluate the sensitivity and reliability of data-mining with small databases is presented in this paper. Efron's bootstrap method for statistical testing was used to assess the accuracy of the rules produced during the training step of the data-mining algorithm. The case study for validating this new approach was based on a limited-sized mammographic database previously used to discover associations between the diagnostic features of breast masses in mammograms and the biopsy-based classification of the masses. Using the new approach, it was possible to distinguish between the association rules that were sensitive to the size of the training datasets from those that were not. The methods proposed should lead to an efficient way for validating the patterns discovered in medical data-mining applications using small datasets.     

Phylogenetic overview of Erysiphaceae based on nrDNA and MCM7 sequences

The classification system and evolutionary history of Erysiphaceae have been studied based on the results of molecular phylogenetic analyses. However, the sequence data used for these phylogenetic estimations have been limited to the nrDNA of ca., 50 taxa, and the relationships among higher taxonomic groups are not well understood. To provide a phylogenetic overview of Erysiphaceae, we performed phylogenetic estimations based on nrDNA and MCM7 sequences obtained from ca., 270 taxa. The phylogenetic tree showed a similar topology to the trees obtained in previous studies, although the branching order between Golovinomyceteae and Phyllactinieae was different and Phyllactinieae was not monophyletic. Phyllactinieae and Erysipheae were estimated to diversify after the divergence of Golovinomyceteae, suggesting an evolutionary trend in which non-catenate conidia + endoparasitic or non-catenate conidia + ectoparasitic lineages were derived from catenate conidia + ectoparasitic lineages. Phyllactinieae was divided into a clade of Phyllactinia + Leveillula and other clade(s) consisting of Pleochaeta and Queirozia. The phylogenetic hypothesis of Erysiphaceae was updated based on the largest dataset to date, but the higher-level phylogenetic relationships remain unclear. For a more robust phylogenetic hypothesis of Erysiphaceae, further sequence data, including protein coding regions, should be added to the dataset of nrDNA sequences.     

Blind Count Surveys of White-Tailed Deer and Population Estimates Using Bowden's Estimators

Abstract: Conducting surveys from blinds when supplemental feed (bait) has been provided has not been evaluated for estimating parameters of ungulate populations. We conducted blind count surveys of white-tailed deer (Odocoileus virginianus) in a 214-ha enclosure in central Texas, USA, in 2007 and 2008 to address 2 main objectives: 1) to evaluate a blind count survey protocol developed for use on small parcels of land, and 2) to use data collected from blind count surveys to conduct simulations to evaluate the reliability of abundance and sex ratio estimates obtained from Bowden's estimator. In each year population abundance (2007: 60; 2008: 48) and sex ratio (M:F, 2007: 0.58; 2008: 0.71) were known as were sighting frequencies of every animal. The enclosure had 5 blinds and we baited each blind with corn. We encountered many deer during surveys because there were only 2 deer in 2007 and 1 deer in 2008 that we did not view from blinds ≥1 time. To evaluate bias and precision of abundance and sex ratio estimates we conducted 10,000 bootstrap simulations. We evaluated both parameters in relation to the percentage of each population marked, number of surveys conducted from blinds, and whether surveys were conducted in the morning, evening, or both morning and evening. Also, we evaluated abundance in relation to whether we identified animals with unique marks to individual, and we evaluated sex ratio in relation to intersexual distribution of marks. Abundance estimates were less biased and more precise when we uniquely identified all marked animals and 40–70% of the population was marked. Sex ratio estimates were less biased when 40–70% of the population was marked and surveys were conducted in the morning and evening. Sex ratio estimates, however, were less precise than abundance estimates. Unbiased estimates of white-tailed deer population parameters can be obtained from blind count surveys conducted on small parcels of enclosed land and when animals are baited.     

The geometry of natural selection in cave and spring populations of the amphipod Gammarus minus Say (Crustacea: Amphipoda)

The shape of the fitness function was investigated in a spring population (Davis Spring) and a cave population (Organ Cave) of the amphipod Gammarus minus in southern West Virginia. The first three principal components of a series of size, antennal and eye measurements and two fitness components (amplexus and number of eggs) were investigated. Smoothing splines using generalized cross-validation scores were found as were least-squares quadratic regression equations. Confidence intervals on shape, as determined by a smoothing parameter, were calculated using a bootstrap approach. Out of 18 cases, there were six cases of no selection, six cases of directional (monotonic) selection, one case of stabilizing selection, one case of disruptive selection, and four cases of selection with multiple internal maxima and minima. Selection on the cave population was frequently directional (5), resulting from strong directional selection for increased size, larger antennae, and smaller eyes. Selection on the spring population, the ancestral habitat for the species, was frequently non-monotonic (five cases) and rarely directional (one case). In both populations, stabilizing selection was rare and no more common than disruptive selection.     

PHYLOGENETIC PLACEMENT OF AN UNUSUAL CORAL MUSHROOM CHALLENGES THE CLASSIC HYPOTHESIS OF STRICT COEVOLUTION IN THE APTEROSTIGMA PILOSUM GROUP ANT–FUNGUS MUTUALISM

The ∼50 million-year-old fungus-farming ant mutualism is a classic example of coevolution , involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma -cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution.