Validating protein structure using kernel density estimates

Measuring the quality of determined protein structures is a very important problem in bioinformatics. Kernel density estimation is a well-known nonparametric method which is often used for exploratory data analysis. Recent advances, which have extended previous linear methods to multi-dimensional circular data, give a sound basis for the analysis of conformational angles of protein backbones, which lie on the torus. By using an energy test, which is based on interpoint distances, we initially investigate the dependence of the angles on the amino acid type. Then, by computing tail probabilities which are based on amino-acid conditional density estimates, a method is proposed which permits inference on a test set of data. This can be used, for example, to validate protein structures, choose between possible protein predictions and highlight unusual residue angles.     

The effects of food stamp receipt on weight gained by expectant mothers

With over 66% of Americans overweight, expectant mothers are unusual because they are encouraged to gain weight while pregnant. Food stamp receipt (FSR) may facilitate recommended weight gain by providing resources for food and nutrition. I examine the effects of FSR on the amount of weight gained by low-income expectant mothers using NLSY79 data. Results indicate FSR decreases the probability gaining insufficient weight but does not exacerbate the probability of gaining too much weight. Examining the effects of FSR on pregnancy weight gain is important because low birth weight is more likely when expectant mothers gain insufficient weight.     

The Stability of Same‐Sex Cohabitation,Different‐Sex Cohabitation,and Marriage

This study contributes to the emerging demographic literature on same‐sex couples by comparing the level and correlates of union stability among 4 types of couples: (a) male same‐sex cohabitation, (b) female same‐sex cohabitation, (c) different‐sex cohabitation, and (d) different‐sex marriage. The author analyzed data from 2 British birth cohort studies: the National Child Development Study (N = 11,469) and the 1970 British Cohort Study (N = 11,924). These data contain retrospective histories of same‐sex and different‐sex unions throughout young adulthood (age 16–34) from 1974 through 2004. Event‐history analyses showed that same‐sex cohabitations have higher rates of dissolution than do different‐sex cohabiting and marital unions. Among same‐sex couples, male couples had slightly higher dissolution rates than did female couples. In addition, same‐sex couples from the 1958 and 1970 birth cohorts had similar levels of union stability. The demographic correlates of union stability are generally similar for same‐sex and different‐sex unions.     

Comparison of Type I error rates and statistical power of different propensity score methods

Propensity score analysis (PSA) is a technique to correct for potential confounding in observational studies. Covariate adjustment, matching, stratification, and inverse weighting are the four most commonly used methods involving propensity scores. The main goal of this research is to determine which PSA method performs the best in terms of protecting against spurious association detection, as measured by Type I error rate, while maintaining sufficient power to detect a true association, if one exists. An examination of these PSA methods along with ordinary least squares regression was conducted under two cases: correct PSA model specification and incorrect PSA model specification. PSA covariate adjustment and PSA matching maintain the nominal Type I error rate, when the PSA model is correctly specified, but only PSA covariate adjustment achieves adequate power levels. Other methods produced conservative Type I Errors in some scenarios, while liberal Type I error rates were observed in other scenarios.     

The Analysis of Methadone Clinic Data Using Marginal and Conditional Logistic Models with Mixture or Random Effects

The paper develops methods for the statistical analysis of outcomes of methadone maintenance treatment (MMT). Subjects for this study were a cohort of patients entering MMT in Sydney in 1986. Urine drug tests on these subjects were performed weekly during MMT, and were reported as either positive or negative for morphine, the marker of recent heroin use. To allow correlation between the repeated binary measurements, a marginal logistic model was fitted using the generalized estimating equation (GEE) approach and the alternating logistic regression approach. Conditional logistic models are also considered. Results of separate fitting to each patient and score tests suggest that there is substantial between-patient variation in response to MMT. To account for the population heterogeneity and to facilitate subject-specific inference, the conditional logistic model is extended by introducing random intercepts. The two, three and four group mixture models are also investigated. The model of best fit is a three group mixture model, in which about a quarter of the subjects have a poor response to MMT, with continued heroin use independent of daily dose of methadone; about a quarter of the subjects have a very good response, with little or no heroin use, again independent of dose; and about half the subjects responded in a dose-dependent fashion, with reduced heroin use while receiving higher doses of methadone. These findings are consistent with clinical experience. There is also an association between reduced drug use and increased duration in treatment. The mixture model is recommended since it is quite tractable in terms of estimation and model selection as well as being supported by clinical experience.     

Male‐male sexual contact in the U.S.A.: Findings from five sample surveys, 1970–1990

Estimates of the prevalence of male‐male sexual contact are derived using data from five probability surveys conducted between 1970 and 1990. Estimated minimums of 5 to 7 percent of U.S. men report some same‐gender sexual contact during adulthood. Because of the likelihood of underreporting, these estimates might be considered lower bounds on the actual prevalence of such contact. Estimates show relatively little variation across social and demographic subgroups with the major exception that higher prevalence is reported among never‐married men, particularly those 35 and older. Some lesser variations are also found by service in the military, current residence, and current religious affiliation. Fragmentary evidence from these surveys suggests that some men may have episodic male‐male contact in adulthood while other men may have a relatively consistent and exclusive pattern of same‐gender contacts. Only one‐quarter to one‐half of the U.S. men who report male‐male contacts in adulthood also report having had such contacts during the preceding 12 months. In addition, the majority of men reporting same‐gender contacts in adulthood also report some male‐female contacts. Among men reporting same‐gender contacts in the preceding 12 months, however, the majority report exclusively male sexual contacts throughout adulthood. Potential implications of these findings for HIV prevention and research are discussed.     

A content analysis of sexually explicit magazines sold in an adult bookstore

The development of a survey instrument for measuring the cognitive association of sex, love, and marriage (SLM) is reported. The SLM scale was tested in two phases with two distinct data sets. The first data set comprised the responses of 321 undergraduates at a New England state university. In this first phase, the specific item composition of the scale was determined, and initial reliability and internal consistency were established. The second data set included the responses of 835 undergraduates from three U.S. universities: a Northeastern state university, a Southwestern state university, and a Northwestern state university. In this second phase, additional reliability information was obtained, and the issue of construct validity was explored. By analysis, we judged that the SLM scale is, as expected, significantly related to extramarital sexual attitudes, premarital sexual attitudes, premarital sexual behavior, religiosity, and current relationship involvement. The theoretical significance of SLM association and the possible uses of the SLM scale as a research tool are discussed.     

Inclusion of Don't Know Respondents,Reliability of Indexes and Representativeness in Survey Research

Abstract

Data from the General Social Survey, 1972–1996 were examined to see whether index reliability changes when the don't know respondents are included. On the abortion and civil liberty attitude indexes, reliability remained the same regardless of whether the don't knows were included or excluded. Reliability actually increased somewhat when the don't know respondents were included on two cognitive indexes measuring vocabulary knowledge and reasoning performance. When don't knows are excluded by list-wise deletion, attrition occurs very disproportionately among the least educated and oldest groups. Since there is no trade-off of increased reliability for decreased representativeness, list-wise deletion of cases is hard to justify.