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.     

Composition-consistent tournament solutions and social choice functions

This paper introduces a new axiom for choice in preference profiles and tournaments, called composition-consistency. A social choice function is composition-consistent if it is non-sensitive to the cloning of one or several outcomes. The key feature of the composition consistency property is an operation concept called multiple composition product of profiles. The paper provides a brief overview of some social choice functions studied in the literature. Concerning the tournament solutions, it is proved that the Top Cycle, the Slater and the Copeland solutions are not composition-consistent, whereas the Banks, Uncovered Set, TEQ, Minimal Covering Set are composition-consistent. Moreover, we define the composition-consistent hull of a solution as the smallest composition-consistent solution containing . The composition-consistent hulls of the Top cycle and Copeland solutions are specified, and we give some hints about the location of the hull of the Slater set. Concerning social choice functions, it is shown that Kemeny, Borda and Minimax social choice functions are not composition-consistent, whereas the Paretian one is composition-consistent. Moreover, we prove that the latter is the composition-consistent hull of the Borda and Minimax functions.     

Income Diversity,Technology Choice and Agricultural Research Policy in Sub‐Saharan Africa

This article makes an initial analysis of the implications of income diversification for technical change and agricultural research policy in Africa, leading to two insights. First, that the dilution effect of income diversification means that, as the proportion of non‐farm income increases, so must the expected gains from adopting a new agricultural technology. Second, that diversified producers will face disproportionately large transactions costs associated with information acquisition to inform technology choice decisions. Two hypotheses about how diversified producers are likely to react are then explored. Both point to the conclusion that income diversification among the poor is likely to constrain significantly the direct poverty impacts of agricultural research. The policy implications of these findings are then considered.     

Perceived social standing among Asian immigrants in the US: Do reasons for immigration matter?

We investigate the association between a subjective measure of social status and the reasons for immigration among Asian immigrants in the US. We use data from the National Latino and Asian American Study to test several hypotheses about this association. Our analyses show the positive effect on perceived social standing of migrating for better education, the negative effect of migrating to seek employment, and the negative impact of refugee status. Migrating for family reunification can be associated with various circumstances, which lead to differing outcomes. The results suggest that the notion that immigrants arrive in the US with limited resources and few skills and move slowly up the socioeconomic ladder must be reassessed in light of the complex social context and factors such as ethnicity, gender, divergent immigration paths, and a range of associated circumstances.     

Joint modeling of longitudinal and survival data with the Cox model and two-phase sampling

A common objective of cohort studies and clinical trials is to assess time-varying longitudinal continuous biomarkers as correlates of the instantaneous hazard of a study endpoint. We consider the setting where the biomarkers are measured in a designed sub-sample (i.e., case-cohort or two-phase sampling design), as is normative for prevention trials. We address this problem via joint models, with underlying biomarker trajectories characterized by a random effects model and their relationship with instantaneous risk characterized by a Cox model. For estimation and inference we extend the conditional score method of Tsiatis and Davidian (Biometrika 88(2):447–458, 2001) to accommodate the two-phase biomarker sampling design using augmented inverse probability weighting with nonparametric kernel regression. We present theoretical properties of the proposed estimators and finite-sample properties derived through simulations, and illustrate the methods with application to the AIDS Clinical Trials Group 175 antiretroviral therapy trial. We discuss how the methods are useful for evaluating a Prentice surrogate endpoint, mediation, and for generating hypotheses about biological mechanisms of treatment efficacy.     

Evaluation of a Training to Reduce Provider Bias Toward Pregnant Patients With Substance Abuse

The objective of this article is not to present a scientific or systematic study, but to provide an initial framework for designing a training workshop to enhance health practitioners’ (nurses, social workers, physicians, etc.) knowledge regarding substance abuse treatment and to decrease their bias toward substance-abusing women, particularly pregnant women in rural communities. We incorporated the 4 Transdisciplinary Foundations from the Substance Abuse and Mental Health Services Administration Competencies Model, with specific competencies targeted that related to provider bias. After the conference, 52 of the 70 participants completed a questionnaire to self-assess knowledge level and confidence in skill related to substance abuse management. Participant mean scores were statistically significantly higher following the conference than 1 week prior (p < .001) in the area of “gender difference with substance abuse,” moving from an average of 2.6 to 4.5 on a 5-point Likert scale. Our conference was successful in increasing attendees’ knowledge about gender difference and substance abuse among pregnant patients.