Reliability and validity of a short form household food security scale in a Caribbean community

BACKGROUND: We evaluated the reliability and validity of the short form household food security scale in a different setting from the one in which it was developed. METHODS: The scale was interview administered to 531 subjects from 286 households in north central Trinidad in Trinidad and Tobago, West Indies. We evaluated the six items by fitting item response theory models to estimate item thresholds, estimating agreement among respondents in the same households and estimating the slope index of income-related inequality (SII) after adjusting for age, sex and ethnicity. RESULTS: Item-score correlations ranged from 0.52 to 0.79 and Cronbach's alpha was 0.87. Item responses gave within-household correlation coefficients ranging from 0.70 to 0.78. Estimated item thresholds (standard errors) from the Rasch model ranged from -2.027 (0.063) for the 'balanced meal' item to 2.251 (0.116) for the 'hungry' item. The 'balanced meal' item had the lowest threshold in each ethnic group even though there was evidence of differential functioning for this item by ethnicity. Relative thresholds of other items were generally consistent with US data. Estimation of the SII, comparing those at the bottom with those at the top of the income scale, gave relative odds for an affirmative response of 3.77 (95% confidence interval 1.40 to 10.2) for the lowest severity item, and 20.8 (2.67 to 162.5) for highest severity item. Food insecurity was associated with reduced consumption of green vegetables after additionally adjusting for income and education (0.52, 0.28 to 0.96). CONCLUSIONS: The household food security scale gives reliable and valid responses in this setting. Differing relative item thresholds compared with US data do not require alteration to the cut-points for classification of 'food insecurity without hunger' or 'food insecurity with hunger'. The data provide further evidence that re-evaluation of the 'balanced meal' item is required

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

We describe a statistical framework for QTL mapping using bulk segregant analysis (BSA) based on high throughput, short-read sequencing. Our proposed approach is based on a smoothed version of the standard statistic, and takes into account variation in allele frequency estimates due to sampling of segregants to form bulks as well as variation introduced during the sequencing of bulks. Using simulation, we explore the impact of key experimental variables such as bulk size and sequencing coverage on the ability to detect QTLs. Counterintuitively, we find that relatively large bulks maximize the power to detect QTLs even though this implies weaker selection and less extreme allele frequency differences. Our simulation studies suggest that with large bulks and sufficient sequencing depth, the methods we propose can be used to detect even weak effect QTLs and we demonstrate the utility of this framework by application to a BSA experiment in the budding yeast Saccharomyces cerevisiae

The intergenerational association between parents' problem gambling and impulsivity-hyperactivity/inattention behaviors in children

Despite the well-established association between problem gambling and ADHD core categories of impulsivity-hyperactivity and inattention, the link between parents’ problem gambling and impulsivity-hyperactivity/inattention (IH/I) behaviors in children has not been investigated. This study investigated the association between parents’ problem gambling and children’s IH/I behaviors while controlling for potential confounding variables. A population-based prospective cohort followed-up from kindergarten to age 30, the Quebec Longitudinal Study of Kindergarten Children (QLSKC), provided data over three generations. Among 1358 participants at age 30, parents with a child aged 1 year or older (N=468; Mean age=4.65 years; SD=2.70) were selected. Generalized Linear Models included measures of grandparents’ and parents’ problem gambling, parents’ IH/I behaviors in childhood, and a host of risk factors and comorbidities to predict IH/I in children. Intergenerational bivariate associations were observed between grandparents’ problem gambling, parents’ IH/I in childhood and problem gambling at age 30, and between parents’ IH/I, problem gambling, and children’s IH/I behaviors. Parents’ problem gambling predicted children’s IH/I behaviors above and beyond the effects of covariates such as family and socioeconomic characteristics, alcohol and drug use, depression symptoms and parents’ gambling involvement. Parents’ IH/I behaviors in childhood also predicted children’s IH/I and had a moderating, enhancing effect on parents’ problem gambling association with their offspring’s IH/I behaviors. Problem gambling is a characteristic of parents’ mental health that is distinctively associated with children’s IH/I behaviors, above and beyond parents’ own history of IH/I and of typically related addictive, psychopathological or socioeconomic risk factors and comorbidities

Evidence from Individual Inference for High-Dimensional Coexistence: Long-Term Experiments on Recruitment Response

Background: For competing species to coexist, individuals must compete more with others of the same species than with those of other species. Ecologists search for tradeoffs in how species might partition the environment. The negative correlations among competing species that would be indicative of tradeoffs are rarely observed. A recent analysis showed that evidence for partitioning the environment is available when responses are disaggregated to the individual scale, in terms of the covariance structure of responses to environmental variation. That study did not relate that variation to the variables to which individuals were responding. To understand how this pattern of variation is related to niche variables, we analyzed responses to canopy gaps, long viewed as a key variable responsible for species coexistence. Methodology/Principal Findings: A longitudinal intervention analysis of individual responses to experimental canopy gaps with 12 yr of pre-treatment and 8 yr post-treatment responses showed that species-level responses are positively correlated – species that grow fast on average in the understory also grow fast on average in response to gap formation. In other words, there is no tradeoff. However, the joint distribution of individual responses to understory and gap showed a negative correlation – species having individuals that respond most to gaps when previously growing slowly also have individuals that respond least to gaps when previously growing rapidly (e.g., Morus rubra), and vice versa (e.g., Quercus prinus). Conclusions/Significance: Because competition occurs at the individual scale, not the species scale, aggregated speciesleve

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

<p>Abstract</p> <p>Background</p> <p>In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low <it>p</it>-value. However, the interpretation of each single <it>p</it>-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, <it>game theory </it>has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions.</p> <p>Results</p> <p>In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called <it>Comparative Analysis of Shapley value </it>(shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability.</p> <p>Conclusion</p> <p>CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways.</p

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

Numerous genetic loci have been associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N = 74,064) and follow-up studies (N = 48,607), we identified at genome-wide significance (P = 2.7 × 10(-8) to P = 2.3 × 10(-13)) four new PP loci (at 4q12 near CHIC2, 7q22.3 near PIK3CG, 8q24.12 in NOV and 11q24.3 near ADAMTS8), two new MAP loci (3p21.31 in MAP4 and 10q25.3 near ADRB1) and one locus associated with both of these traits (2q24.3 near FIGN) that has also recently been associated with SBP in east Asians. For three of the new PP loci, the estimated effect for SBP was opposite of that for DBP, in contrast to the majority of common SBP- and DBP-associated variants, which show concordant effects on both traits. These findings suggest new genetic pathways underlying blood pressure variation, some of which may differentially influence SBP and DBP

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion