Multiple Imputation in Three or More Stages.

Missing values present challenges in the analysis of data across many areas of research. Handling incomplete data incorrectly can lead to bias, over-confident intervals, and inaccurate inferences. One principled method of handling incomplete data is multiple imputation. This article considers incomplete data in which values are missing for three or more qualitatively different reasons and applies a modified multiple imputation framework in the analysis of that data. Included are a proof of the methodology used for three-stage multiple imputation with its limiting distribution, an extension to more than three types of missing values, an extension to the ignorability assumption with proof, and simulations demonstrating that the estimator is unbiased and efficient under the ignorability assumption.

Education, cognitive function, and severity of neuropathology in Alzheimer disease.

BACKGROUND: Education may modulate the degree to which the neuropathology of Alzheimer disease (AD) is expressed as impaired cognitive performance. METHODS: We studied 2,051 participants age 65+ years at 27 AD Centers who died and underwent autopsy. All took the Mini-Mental State Examination (MMSE) within 2 years before death. Braak & Braak stage, neuritic plaque density, and Consortium to Establish a Registry for Alzheimer's Disease and National Institute on Aging (NIA)/Reagan diagnostic classifications quantified AD neuropathologic severity. Multivariate analyses modeled MMSE in relation to education and neuropathologic severity, adjusting for age at death, Lewy body pathology, and vascular dementia. RESULTS: Higher education was associated with higher MMSE scores when AD neuropathology was absent or mild. But with more advanced neuropathology, differences in MMSE scores among education levels were attenuated. For example, among patients without AD by NIA/Reagan criteria, fitted MMSE scores ranged from 19.6 for patients with less than high school education to 25.9 with education beyond high school. But among patients with neuropathologically advanced AD, the range of scores by education was only 7.1 to 8.6. CONCLUSIONS: We found no evidence of larger education-related differences in cognitive function when Alzheimer disease (AD) neuropathology was more advanced. Higher Mini-Mental State Examination scores among more educated persons with mild or no AD may reflect better test-taking skills or cognitive reserve, but these advantages may ultimately be overwhelmed by AD neuropathology.

A prospective study of calf factors affecting age, body size, and body condition score at first calving of holstein dairy heifers.

Data were collected prospectively on parameters related to first calving on 18 farms located in Northeastern Pennsylvania. This project was designed to study possible residual effects of calf management practices and events occurring during the first 16 wk of life on age, BW, skeletal growth, and body condition score at first calving. Multiple imputation method for handling missing data was incorporated in these analyses. This method has the advantage over ad hoc single imputations because the appropriate error structure is maintained. Much similarity was found between the multiple imputation method and a traditional mixed model analysis, except that some estimates from the multiple imputation method seemed more logical in their effects on the parameter measured. Factors related to increased age at first calving were increased difficulty of delivery, antibiotic treatment of sick calves, increased amount of milk or milk replacer fed before weaning, reduced quality of forage fed to weaned calves, maximum humidity, mean daily temperature, and maximum ammonia levels in calf housing areas. Body weight at calving tended to increase with parity of the dam, increased amount of grain fed to calves, increased ammonia levels, and increased mean temperature of the calf housing area. Body condition score at calving tended to be positively influenced by delivery score at first calving, dam parity, and milk or milk replacer dry matter intake. Withers height at calving was positively affected by treatment of animals with antibiotics and increased mean temperature in the calf area. This study demonstrated that nutrition, housing, and management factors that affect health and growth of calves have long-term effects on the animal at least through first calving.

Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae Yap1p transcription factor is required for the H2O2-dependent activation of many antioxidant genes including the TRX2 gene encoding thioredoxin 2. To identify factors that regulate Yap1p activity, we carried out a genetic screen for mutants that show elevated expression of a TRX2-HIS3 fusion in the absence of H2O2. Two independent mutants isolated in this screen carried mutations in the TRR1 gene encoding thioredoxin reductase. Northern blot and whole-genome expression analysis revealed that the basal expression of most Yap1p targets and many other H2O2-inducible genes is elevated in Deltatrr1 mutants in the absence of external stress. In Deltatrr1 mutants treated with H2O2, the Yap1p targets, as well as genes comprising a general environmental stress response and genes encoding protein-folding chaperones, are hyperinduced. However, despite the elevated expression of genes encoding antioxidant enzymes, Deltatrr1 mutants are extremely sensitive to H2O2. The results suggest that cells lacking thioredoxin reductase have diminished capacity to detoxify oxidants and/or to repair oxidative stress-induced damage and that the thioredoxin system is involved in the redox regulation of Yap1p transcriptional activity.

Genomic expression programs in the response of yeast cells to environmental changes.

We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (approximately 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.

Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and saccharomyces cerevisiae responses to oxidative stress.

The glutathione- and thioredoxin-dependent reduction systems are responsible for maintaining the reduced environment of the Escherichia coli and Saccharomyces cerevisiae cytosol. Here we examine the roles of these two cellular reduction systems in the bacterial and yeast defenses against oxidative stress. The transcription of a subset of the genes encoding glutathione biosynthetic enzymes, glutathione reductases, glutaredoxins, thioredoxins, and thioredoxin reductases, as well as glutathione- and thioredoxin-dependent peroxidases is clearly induced by oxidative stress in both organisms. However, only some strains carrying mutations in single genes are hypersensitive to oxidants. This is due, in part, to the redundant effects of the gene products and the overlap between the two reduction systems. The construction of strains carrying mutations in multiple genes is helping to elucidate the different roles of glutathione and thioredoxin, and studies with such strains have recently revealed that these two reduction systems modulate the activities of the E. coli OxyR and SoxR and the S. cerevisiae Yap1p transcriptional regulators of the adaptive responses to oxidative stress.

The molecular mechanism of regulation of the NhaA Na+/H+ antiporter of Escherichia coli, a key transporter in the adaptation to Na+ and H+.

The NhaA Na+/H+ antiporter is the main system responsible for adaptation to Na+ and alkaline pH (in the presence of Na+) in Escherichia coli and many other enteric bacteria. It is under intricate control. At the protein level it is regulated directly by pH, one of its regulatory signals. A pH shift from 7 to 8.5 activates the antiporter and, in a fashion correlated with the activity change, confers a conformation change that, in isolated membrane vesicles, is reflected in the exposure of trypsin-cleavable sites. H225 and G338 are essential for the pH response of NhaA. nhaA transcription is dependent on NhaR, a positive regulator of the LysR family, and is regulated by Na+, the other environmental signal. Na+ affects the NhaR/nhaA interaction directly by changing the footprint of NhaR on nhaA in a pH-dependent fashion. The expression of nhaA is also under global regulation of H-NS. We suggest that the pattern of regulation of nhaA found in E. coli is a paradigm for the response of proteins and genes to H+ and Na+, the most common ions that challenge every cell.

A functional homolog of Escherichia coli NhaR in Vibrio cholerae.

Escherichia coli NhaR controls expression of a sodium/proton (Na+/H+) antiporter, NhaA. The Vibrio cholerae NhaR protein shows over 60% identity to those of Escherichia coli and Salmonella enteritidis. V. cholerae NhaR complements an E. coli nhaR mutant for growth in 100 mM LiCl-33 mM NaCl, pH 7.6, and enhances the Na+-dependent induction of an E. coli chromosomal nhaA::lacZ fusion. These findings indicate functional homology to E. coli NhaR. Two V. cholerae nhaR mutants were constructed by using kanamycin resistance cartridge insertion at different sites to disrupt the gene. Both mutants showed sensitivity to growth in 120 mM LiCl, pH 9.2, compared with the wild-type strain and could be complemented by the introduction of V. cholerae nhaR on a low-copy-number plasmid. An nhaR mutation had no detectable effect on the virulence of the V. cholerae strain in the infant mouse model, suggesting that the antiporter system involved is not required in vivo, at least in this animal model.

Utilizing gravity in the removal of a large intraocular foreign body.

This article describes an unconventional technique for the removal of a nonmagnetic intraocular foreign body that is too large or too smooth to be grasped by intraocular forceps and does not float on perfluorocarbon liquids. By flipping the patient to a face-down position and allowing the gravitational forces to help remove the object, one can hope to avoid further ocular damage. This approach should be considered in similar cases of very large and smooth intravitreal foreign bodies to avoid severe and irreversible damage to the retina.

Patterns of discipline enforcement and the perception of justice in two educational frameworks in Israel.

The purpose of the present study was to examine the types of discipline enforcement measures employed in the Israeli elementary and junior high schools, and their fairness as viewed by students. The central hypothesis was that patterns of discipline enforcement vary considerably depending on school characteristics. These patterns, in turn, together with students' sex, socioeconomic and ethnic background, and academic status within the school, determine students' perceptions of justice concerning misbehavior management. It was found that junior high school teachers rely more on problem-centered, and elementary school teachers rely more on relationship-centered techniques of discipline enforcement. However, in spite of these differences and the report of about half of the students that they personally had been unfairly treated, the majority of the respondents reported that the punishments employed in their school were generally fair, and that the severity of punishments was in the right proportion to the severity of the misconduct. Students' traits have accounted for only a small percentage of the variance of the various dimensions of justice that were examined. It has been suggested that students' perceptions of justice are related to an overall tendency to perceive schools' authority as legitimate rather than to schools' structural characteristics, misbehavior management techniques, and students' traits. Several possible bases of schools' legitimation are discussed.