A General Framework for Formal Tests of Interaction after Exhaustive Search Methods with Applications to MDR and MDR-PDT

The initial presentation of multifactor dimensionality reduction (MDR) featured cross-validation to mitigate over-fitting, computationally efficient searches of the epistatic model space, and variable construction with constructive induction to alleviate the curse of dimensionality. However, the method was unable to differentiate association signals arising from true interactions from those due to independent main effects at individual loci. This issue leads to problems in inference and interpretability for the results from MDR and the family-based compliment the MDR-pedigree disequilibrium test (PDT). A suggestion from previous work was to fit regression models post hoc to specifically evaluate the null hypothesis of no interaction for MDR or MDR-PDT models. We demonstrate with simulation that fitting a regression model on the same data as that analyzed by MDR or MDR-PDT is not a valid test of interaction. This is likely to be true for any other procedure that searches for models, and then performs an uncorrected test for interaction. We also show with simulation that when strong main effects are present and the null hypothesis of no interaction is true, that MDR and MDR-PDT reject at far greater than the nominal rate. We also provide a valid regression-based permutation test procedure that specifically tests the null hypothesis of no interaction, and does not reject the null when only main effects are present. The regression-based permutation test implemented here conducts a valid test of interaction after a search for multilocus models, and can be applied to any method that conducts a search to find a multilocus model representing an interaction

The hand of Homo naledi

A nearly complete right hand of an adult hominin was recovered from the Rising Star cave system, South Africa. Based on associated hominin material, the bones of this hand are attributed to Homo naledi. This hand reveals a long, robust thumb and derived wrist morphology that is shared with Neandertals and modern humans, and considered adaptive for intensified manual manipulation. However, the finger bones are longer and more curved than in most australopiths, indicating frequent use of the hand during life for strong grasping during locomotor climbing and suspension. These markedly curved digits in combination with an otherwise human-like wrist and palm indicate a significant degree of climbing, despite the derived nature of many aspects of the hand and other regions of the postcranial skeleton in H. naledi

Processing of inconsistent emotional information: an fMRI study

Previous studies investigating the anterior cingulate cortex (ACC) have relied on a number of tasks which involved cognitive control and attentional demands. In this fMRI study, we tested the model that ACC functions as an attentional network in the processing of language. We employed a paradigm that requires the processing of concurrent linguistic information predicting that the cognitive costs imposed by competing trials would engender the activation of ACC. Subjects were confronted with sentences where the semantic content conflicted with the prosodic intonation (CONF condition) randomly interspaced with sentences which conveyed coherent discourse components (NOCONF condition). We observed the activation of the rostral ACC and the middle frontal gyrus when the NOCONF condition was subtracted from the CONF condition. Our findings provide evidence for the involvement of the rostral ACC in the processing of complex competing linguistic stimuli, supporting theories that claim its relevance as a part of the cortical attentional circuit. The processing of emotional prosody involved a bilateral network encompassing the superior and medial temporal cortices. This evidence confirms previous research investigating the neuronal network that supports the processing of emotional information

Patterns of Tobacco-Use Behavior Among Chinese Smokers with Medical Conditions

Understanding the characteristics of Chinese American smokers with medical conditions and factors associated with their tobacco-use behaviors will guide effective cessation programs. In 2008, the authors described socio-demographic profiles of Chinese smokers with medical conditions treated during the period 2002–2006, documented their tobacco-use behaviors (i.e., average daily cigarette use, nicotine dependence, and number of past-year quit attempts), and drew comparisons between subjects recruited from hospitals (IP) and ambulatory settings (OP). Compared to OP, IP were significantly older, less educated, less acculturated, and more likely to be retired. Of the two groups, IP had poorer disease profiles, smoked less (4.4 vs. 11.9 cigarettes per day), and had lower nicotine-addiction scores (5.5 vs. 6.7). There was no difference between groups in past-year quit attempts. After adjustments, the data revealed that being employed and OP was associated with higher average daily cigarette use; IP were less nicotine dependent than OP; and for both groups, years of smoking was negatively associated with past-year quit attempts. Our study suggests that, more than acculturation level, health status influences the Chinese smoker’s level of cigarette use and nicotine addiction. Given the severity of their disease profiles, IP should be aggressively targeted for intervention, as they are more likely to be light smokers and to be less nicotine dependent than OP. Future tobacco treatment studies should pay attention to health status among smokers in health-care settings in order to provide a more accurate assessment of treatment needs and of barriers to successful smoking cessation

Increase of mild disability in Japanese elders: A seven year follow-up cohort study

BACKGROUND: Japan has the highest life expectancy in the world. In a 2002 census government report, 18.5% of Japanese were 65 years old and over and 7.9% were over 75 years old. In this ageing population, the increase in the number of dependent older persons, especially those with mild levels of disability, has had a significant impact on the insurance budget. This study examines the increase of mild disability and its related factors. METHODS: All community-dwelling residents aged 65 and over and without functional decline (n = 1560), of Omishima town, Japan, were assessed in 1996 using a simple illustrative measure, "the Typology of the Aged with Illustrations" to establish a baseline level of function and were followed annually until 2002. The prevalence and incidence of low to severe disability, and their association with chronic conditions present at the commencement of the study, was analyzed. A polychotomous logistic regression model was constructed to estimate the association of each chronic condition with two levels of disability. RESULTS: An increase in mild functional decline was more prevalent than severe functional decline. The accumulation of mild disability was more prominent in women. The major chronic conditions associated with mild disability were chronic arthritis and diabetes in women, and cerebrovascular accident and malignancy in men. CONCLUSION: This study showed a tendency for mild disability prevalence to increase in Japanese elders, and some risk factors were identified. As mild disability increasingly prevalent, these findings will help determine priorities for its prevention in Japanese elders

LD-Spline: Mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium

<p>Abstract</p> <p>Background</p> <p>Gene-centric analysis tools for genome-wide association study data are being developed both to annotate single locus statistics and to prioritize or group single nucleotide polymorphisms (SNPs) prior to analysis. These approaches require knowledge about the relationships between SNPs on a genotyping platform and genes in the human genome. SNPs in the genome can represent broader genomic regions via linkage disequilibrium (LD), and population-specific patterns of LD can be exploited to generate a data-driven map of SNPs to genes.</p> <p>Methods</p> <p>In this study, we implemented LD-Spline, a database routine that defines the genomic boundaries a particular SNP represents using linkage disequilibrium statistics from the International HapMap Project. We compared the LD-Spline haplotype block partitioning approach to that of the four gamete rule and the Gabriel et al. approach using simulated data; in addition, we processed two commonly used genome-wide association study platforms.</p> <p>Results</p> <p>We illustrate that LD-Spline performs comparably to the four-gamete rule and the Gabriel et al. approach; however as a SNP-centric approach LD-Spline has the added benefit of systematically identifying a genomic boundary for each SNP, where the global block partitioning approaches may falter due to sampling variation in LD statistics.</p> <p>Conclusion</p> <p>LD-Spline is an integrated database routine that quickly and effectively defines the genomic region marked by a SNP using linkage disequilibrium, with a SNP-centric block definition algorithm.</p

Albiglutide, a Long Lasting Glucagon-Like Peptide-1 Analog, Protects the Rat Heart against Ischemia/Reperfusion Injury: Evidence for Improving Cardiac Metabolic Efficiency

BACKGROUND: The cardioprotective effects of glucagon-like peptide-1 (GLP-1) and analogs have been previously reported. We tested the hypothesis that albiglutide, a novel long half-life analog of GLP-1, may protect the heart against I/R injury by increasing carbohydrate utilization and improving cardiac energetic efficiency. METHODS/PRINCIPAL FINDINGS: Sprague-Dawley rats were treated with albiglutide and subjected to 30 min myocardial ischemia followed by 24 h reperfusion. Left ventricle infarct size, hemodynamics, function and energetics were determined. In addition, cardiac glucose disposal, carbohydrate metabolism and metabolic gene expression were assessed. Albiglutide significantly reduced infarct size and concomitantly improved post-ischemic hemodynamics, cardiac function and energetic parameters. Albiglutide markedly increased both in vivo and ex vivo cardiac glucose uptake while reducing lactate efflux. Analysis of metabolic substrate utilization directly in the heart showed that albiglutide increased the relative carbohydrate versus fat oxidation which in part was due to an increase in both glucose and lactate oxidation. Metabolic gene expression analysis indicated upregulation of key glucose metabolism genes in the non-ischemic myocardium by albiglutide. CONCLUSION/SIGNIFICANCE: Albiglutide reduced myocardial infarct size and improved cardiac function and energetics following myocardial I/R injury. The observed benefits were associated with enhanced myocardial glucose uptake and a shift toward a more energetically favorable substrate metabolism by increasing both glucose and lactate oxidation. These findings suggest that albiglutide may have direct therapeutic potential for improving cardiac energetics and function

Sex differences in risk factors for coronary heart disease: a study in a Brazilian population

BACKGROUND: In Brazil coronary heart disease (CHD) constitutes the most important cause of death in both sexes in all the regions of the country and interestingly, the difference between the sexes in the CHD mortality rates is one of the smallest in the world because of high rates among women. Since a question has been raised about whether or how the incidence of several CHD risk factors differs between the sexes in Brazil the prevalence of various risk factors for CHD such as high blood cholesterol, diabetes mellitus, hypertension, obesity, sedentary lifestyle and cigarette smoking was compared between the sexes in a Brazilian population; also the relationships between blood cholesterol and the other risk factors were evaluated. RESULTS: The population presented high frequencies of all the risk factors evaluated. High blood cholesterol (CHOL) and hypertension were more prevalent among women as compared to men. Hypertension, diabetes and smoking showed equal or higher prevalence in women in pre-menopausal ages as compared to men. Obesity and physical inactivity were equally prevalent in both sexes respectively in the postmenopausal age group and at all ages. CHOL was associated with BMI, sex, age, hypertension and physical inactivity. CONCLUSIONS: In this population the high prevalence of the CHD risk factors indicated that there is an urgent need for its control; the higher or equal prevalences of several risk factors in women could in part explain the high rates of mortality from CHD in females as compared to males

Predicting Impaired Extinction of Traumatic Memory and Elevated Startle

Emotionally traumatic experiences can lead to debilitating anxiety disorders, such as phobias and Post-Traumatic Stress Disorder (PTSD). Exposure to such experiences, however, is not sufficient to induce pathology, as only up to one quarter of people exposed to such events develop PTSD. These statistics, combined with findings that smaller hippocampal size prior to the trauma is associated with higher risk of developing PTSD, suggest that there are pre-disposing factors for such pathology. Because prospective studies in humans are limited and costly, investigating such pre-dispositions, and thus advancing understanding of the genesis of such pathologies, requires the use of animal models where predispositions are identified before the emotional trauma. Most existing animal models are retrospective: they classify subjects as those with or without a PTSD-like phenotype long after experiencing a traumatic event. Attempts to create prospective animal models have been largely unsuccessful.Here we report that individual predispositions to a PTSD-like phenotype, consisting of impaired rate and magnitude of extinction of an emotionally traumatic event coupled with long-lasting elevation of acoustic startle responses, can be revealed following exposure to a mild stressor, but before experiencing emotional trauma. We compare, in rats, the utility of several classification criteria and report that a combination of criteria based on acoustic startle responses and behavior in an anxiogenic environment is a reliable predictor of a PTSD-like phenotype.There are individual predispositions to developing impaired extinction and elevated acoustic startle that can be identified after exposure to a mildly stressful event, which by itself does not induce such a behavioral phenotype. The model presented here is a valuable tool for studying the etiology and pathophysiology of anxiety disorders and provides a platform for testing behavioral and pharmacological interventions that can reduce the probability of developing pathologic behaviors associated with such disorders

Food Composition of the Diet in Relation to Changes in Waist Circumference Adjusted for Body Mass Index

Dietary factors such as low energy density and low glycemic index were associated with a lower gain in abdominal adiposity. A better understanding of which food groups/items contribute to these associations is necessary.To ascertain the association of food groups/items consumption on prospective annual changes in "waist circumference for a given BMI" (WC(BMI)), a proxy for abdominal adiposity.We analyzed data from 48,631 men and women from 5 countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Anthropometric measurements were obtained at baseline and after a median follow-up time of 5.5 years. WC(BMI) was defined as the residuals of waist circumference regressed on BMI, and annual change in WC(BMI) (ΔWC(BMI), cm/y) was defined as the difference between residuals at follow-up and baseline, divided by follow-up time. The association between food groups/items and ΔWC(BMI) was modelled using centre-specific adjusted linear regression, and random-effects meta-analyses to obtain pooled estimates.Higher fruit and dairy products consumption was associated with a lower gain in WC(BMI) whereas the consumption of white bread, processed meat, margarine, and soft drinks was positively associated with ΔWC(BMI). When these six food groups/items were analyzed in combination using a summary score, those in the highest quartile of the score--indicating a more favourable dietary pattern--showed a ΔWC(BMI) of -0.11 (95% CI -0.09 to -0.14) cm/y compared to those in the lowest quartile.A dietary pattern high in fruit and dairy and low in white bread, processed meat, margarine, and soft drinks may help to prevent abdominal fat accumulation