Assessing Significance of Peptide Spectrum Matches in Proteomics: A Multiple Testing Approach

In the analysis of data from proteomic mass spectrometry experiments, an important issue is determining which of the observed peptide spectrum matches (PSMs) represent true positives. We view this problem through a multiple testing framework and develop procedures for deciding true PSMs. A key feature that makes the problem relative unique to the differential expression problem in microarray analysis is that the null distribution can potentially be estimated from the data. However, this renders much of the asymptotic results from the statistical literature to be invalid. We prove some new key results for this problem using empirical process theory. We also develop a new multiple testing procedure that employs multivariate information from the peptide sequence searches. The proposed methods are studied using a real data set as well as simulated data.     

History and Future of Introduction of Exotic Arthropod Biological Control Agents in Spain: A Dilemma?

The first documented introduction of an exotic invertebrate biological control agent (IBCA) in Spain occurred in 1908. Sixty-four additional species have been introduced since then. Information, both previously recorded and original data, on the species introduced for pest control is summarized. Most of the introduced IBCAs focused on citrus pests and homopterans clearly predominate among target phytophagous species. Success has been more frequent for IBCAs used in seasonal inoculative strategies (50.0% of cases) than in classical biological control programs (17.1% of cases). Concerns about potential non-target effects of such species are increasing, but post-release evaluation has often been insufficient to draw any conclusions about them. Most of the beneficial species introduced in Spain were parasitoids (n = 53), and the remaining species were predators (n = 12). Only four parasitoids are considered specialized monophagous natural enemies. The mean number of host species parasitized by parasitoids is 15.2, whereas the mean number of prey species attacked by predators is 21.2. Therefore, polyphagy appears to be quite common among the IBCAs that have been introduced in Spain. The rationale guiding many of these introductions in the past would not be acceptable nowadays. Since classical biological control is such a valuable strategy for pest control, straightforward protocols to evaluate exotic candidate species are urgently needed.     

Contributions to the mathematical theory of epidemics—II. The problem of endemicity

(1) A mathematical investigation has been made of the prevalence of a disease in a population from which certain individuals are being removed as the result of the disease, whilst fresh individuals are being introduced as the result of birth or immigration. Allowance is made for the effects of the immunity produced as the result of an attack of the disease, but the effect of deaths from other causes is not taken into account, and the action of the disease is supposed to be independent of the age of the individual. (2) As a special case of the above, results have been obtained for a closed population in which no deaths occur and to which no fresh individuals are added, but in which the individuals after being infected acquire immunity, and then may be again infected. A threshold density of population exists analogous to that described in the previous paper, which is such that no disease can exist in a population, the density of which is below the threshold. (3) In other special cases investigated when either immigration or birth is operative in the supply of fresh individuals, as well as in the general case, only one steady state of disease is possible. To reach this state the population must be of a certain density which will be determined by the functions characterizing the infectivity, morbidity, etc., of the disease. (4) Increase of the immigration rate or of the birth-rate results in an increase in the rate of infection of the healthy individuals and also in the percentage rate of infection, the percentage of sick, and in the percentage of mortality from the disease. This result is, of course, a necessary consequence of our assumption that the disease is the only cause of death. (5) More particular results have been obtained by substituting constants in the place of the undetermined functions assumed in the general theory. Further, under these conditions the nature of the steady states has been more fully investigated and it has been shown that in all cases, except one, the steady states are stable ones. In the exception, a disturbance would result in purely periodic oscillations about the steady state.