A modified false discovery rate multiple-comparisons procedure for discrete data, applied to human immunodeficiency virus genetics

Summary.  To help to design vaccines for acquired immune deficiency syndrome that protect broadly against many genetic variants of the human immunodeficiency virus, the mutation rates at 118 positions in HIV amino-acid sequences of subtype C versus those of subtype B were compared. The false discovery rate (FDR) multiple-comparisons procedure can be used to determine statistical significance. When the test statistics have discrete distributions, the FDR procedure can be made more powerful by a simple modification. The paper develops a modified FDR procedure for discrete data and applies it to the human immunodeficiency virus data. The new procedure detects 15 positions with significantly different mutation rates compared with 11 that are detected by the original FDR method. Simulations delineate conditions under which the modified FDR procedure confers large gains in power over the original technique. In general FDR adjustment methods can be improved for discrete data by incorporating the modification proposed.     

Mapping water quality by local scoring

The mean density of bacteria in a water body is commonly monitored using quantal assay. This paper describes the use of local scoring in estimating the spatial distribution of mean density from quantal assay results at a set of point locations. An application to estimating the mean density of fecal conform bacteria in a coastal pond is presented. Model diagnostics based on a parametric bootstrap are also presented.     

Employment growth in high-tech new ventures

We specify and estimate a model of the early employment growth of technology-driven new ventures. Our estimated model is derived from labor demand theory. A data set of 100 German firms is used to conduct this analysis. The study’s findings support the relevance of the theory as applied to these nascent firms. Employment growth is significantly enhanced in ventures exhibiting high profits, experienced founders, formal information processes, and outsourced product distribution. Our findings also confirm aspects of Penrose’s theory of firm growth suggesting that transactions costs associated with larger founder teams may inhibit employment growth.     

Analytical approximations for iterated bootstrap confidence intervals

Standard algorithms for the construction of iterated bootstrap confidence intervals are computationally very demanding, requiring nested levels of bootstrap resampling. We propose an alternative approach to constructing double bootstrap confidence intervals that involves replacing the inner level of resampling by an analytical approximation. This approximation is based on saddlepoint methods and a tail probability approximation of DiCiccio and Martin (1991). Our technique significantly reduces the computational expense of iterated bootstrap calculations. A formal algorithm for the construction of our approximate iterated bootstrap confidence intervals is presented, and some crucial practical issues arising in its implementation are discussed. Our procedure is illustrated in the case of constructing confidence intervals for ratios of means using both real and simulated data. We repeat an experiment of Schenker (1985) involving the construction of bootstrap confidence intervals for a variance and demonstrate that our technique makes feasible the construction of accurate bootstrap confidence intervals in that context. Finally, we investigate the use of our technique in a more complex setting, that of constructing confidence intervals for a correlation coefficient.     

Psychosocial adaption to pregnancy in prison.

1. Childbearing for incarcerated women is complicated by characteristics of special needs associated with psychosocial adaptation to increased stress, a restrictive physical environment, alteration of social support systems, and the displacement of the maternal role functions after birth. 2. Psychiatric nurses are in a unique position to affect the health care provided for pregnant inmates by virtue of their knowledge and expertise in assessing and treating problems in psychosocial adaptation. 3. Assessment of pregnant inmates is based on identification of the presence and magnitude of dimensions of stress, environmental restrictiveness, social support systems, and maternal role displacement.     

A subjectivist approach to consecutive conflict

An easily applied approach is developed to provide one participant in a sequence of conflicts with an optimal strategy. A goal of this article is to demonstrate that it is mathematically feasible to incorporate a decision maker's subjective distributions over the effects his actions will have on the outcomes of future conflicts. Unlike many other approaches, the model of this article does not restrict the beliefs that the participant is allowed to express. The participant, not the decision theorist, decides on what is relevent. Model assumptions required for updating rules, such as Bayesian updating, are not required unless they really are appropriate for the situation.Thanks are due to J. B. Kadane for suggesting the problem and for many helpful discussions.