Discovering unique tobacco use patterns among Alaska Native people

Background . Alaska Native people are disproportionately impacted by tobacco-related diseases in comparison to non-Native Alaskans. Design. We used Alaska's Behavioral Risk Factor Surveillance System (BRFSS) to describe tobacco use among more than 4,100 Alaska Native adults, stratified by geographic region and demographic groups. Results . Overall tobacco use was high: approximately 2 out of every 5 Alaska Native adults reported smoking cigarettes (41.2%) and 1 in 10 reported using smokeless tobacco (SLT, 12.3%). A small percentage overall (4.8%) reported using iq'mik, an SLT variant unique to Alaska Native people. When examined by geographic region, cigarette smoking was highest in remote geographic regions; SLT use was highest in the southwest region of the state. Use of iq'mik was primarily confined to a specific area of the state; further analysis showed that 1 in 3 women currently used iq'mik in this region. Conclusion . Our results suggest that different types of tobacco use are epidemic among diverse Alaska Native communities. Our results also illustrate that detailed analysis within racial/ethnic groups can be useful for public health programme planning to reduce health disparities

Motives and comprehension in a public goods game with induced emotions

This study analyses the sensitivity of public goods contributions through the lens of psychological motives. We report the results of a public goods experiment in which subjects were induced with the motives of care and anger through autobiographical recall. Subjects' preferences, beliefs, and perceptions under each motive are compared with those of subjects experiencing a neutral autobiographical recall control condition. We find, but only for those subjects with the highest comprehension of the game, that care elicits significantly higher contributions than anger, with the control treatment in between. This positive influence of the care motive on unconditional giving is accounted for partly by preferences for giving and partly by the beliefs concerning greater contributions by others. Anger also affects attention to own and other's payoffs (using mouse tracking) and perceptions of the game's incentive structure (cooperative or competitive)

Manganese as a Probe of Fungal Degradation of Wood

Transition state metals, such as manganese (Mn) and iron (Fe), have been reported to be involved in fungal degradation of wood (Ellis, 1959; Shortl

Isolation, Characterization, and Stability of Discretely-Sized Nanolipoprotein Particles Assembled with Apolipophorin-III

Background: Nanolipoprotein particles (NLPs) are discoidal, nanometer-sized particles comprised of self-assembled phospholipid membranes and apolipoproteins. NLPs assembled with human apolipoproteins have been used for myriad biotechnology applications, including membrane protein solubilization, drug delivery, and diagnostic imaging. To expand the repertoire of lipoproteins for these applications, insect apolipophorin-III (apoLp-III) was evaluated for the ability to form discretely-sized, homogeneous, and stable NLPs. Methodology: Four NLP populations distinct with regards to particle diameters (ranging in size from 10 nm to.25 nm) and lipid-to-apoLp-III ratios were readily isolated to high purity by size exclusion chromatography. Remodeling of the purified NLP species over time at 4uC was monitored by native gel electrophoresis, size exclusion chromatography, and atomic force microscopy. Purified 20 nm NLPs displayed no remodeling and remained stable for over 1 year. Purified NLPs with 10 nm and 15 nm diameters ultimately remodeled into 20 nm NLPs over a period of months. Intra-particle chemical cross-linking of apoLp-III stabilized NLPs of all sizes. Conclusions: ApoLp-III-based NLPs can be readily prepared, purified, characterized, and stabilized, suggesting their utilit

Towards realistic benchmarks for multiple alignments of non-coding sequences

<p><b>Abstract</b></p> <p>Background</p> <p>With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based benchmarks have been proposed to meet this necessity, especially for non-coding sequences. However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks.</p> <p>Results</p> <p>We find that the conventional simulation approach, which relies on empirically estimated values for various parameters such as substitution rate or insertion/deletion rates, is unable to generate synthetic sequences reflecting the broad genomic variation in conservation levels. We tackle this problem with a new method for simulating non-coding sequence evolution, by relying on genome-wide distributions of evolutionary parameters rather than their averages. We then generate synthetic data sets to mimic orthologous sequences from the <it>Drosophila </it>group of species, and show that these data sets truly represent the variability observed in genomic data in terms of the difficulty of the alignment task. This allows us to make significant progress towards estimating the alignment accuracy of current tools in an absolute sense, going beyond only a relative assessment of different tools. We evaluate six widely used multiple alignment tools in the context of <it>Drosophila </it>non-coding sequences, and find the accuracy to be significantly different from previously reported values. Interestingly, the performance of most tools degrades more rapidly when there are more insertions than deletions in the data set, suggesting an asymmetric handling of insertions and deletions, even though none of the evaluated tools explicitly distinguishes these two types of events. We also examine the accuracy of two existing tools for annotating insertions versus deletions, and find their performance to be close to optimal in <it>Drosophila </it>non-coding sequences if provided with the true alignments.</p> <p>Conclusion</p> <p>We have developed a method to generate benchmarks for multiple alignments of <it>Drosophila </it>non-coding sequences, and shown it to be more realistic than traditional benchmarks. Apart from helping to select the most effective tools, these benchmarks will help practitioners of comparative genomics deal with the effects of alignment errors, by providing accurate estimates of the extent of these errors.</p

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

BACKGROUND: This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available. RESULTS: We present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence surrounding them. We present tests where we applied the algorithm to the identification of conserved annotated sites in homologous promoters, as well as in distal regions like enhancers. CONCLUSION: Results of the tests show how the algorithm can provide fast and reliable predictions of conserved transcription factor binding sites regulating the transcription of a gene, with better performances than other available methods for the same task. We also show examples on how the algorithm can be successfully employed when promoter annotations of the genes investigated are missing, or when regulatory sites and regions are located far away from the genes

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

<p>Abstract</p> <p>Background</p> <p>The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity.</p> <p>Results</p> <p><monospace>PhyloSim</monospace> is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, <monospace>PhyloSim</monospace> can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing <monospace>PhyloSim</monospace> to be adapted to specific needs.</p> <p>Conclusions</p> <p>Close integration with <monospace>R</monospace> and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that <monospace>PhyloSim</monospace> will be useful to future studies involving simulated alignments.</p

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms.We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The new genome alignment algorithm demonstrates high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental gain and loss. We apply the new algorithm to a set of 23 genomes from the genera Escherichia, Shigella, and Salmonella. Analysis of whole-genome multiple alignments allows us to extend the previously defined concepts of core- and pan-genomes to include not only annotated genes, but also non-coding regions with potential regulatory roles. The 23 enterobacteria have an estimated core-genome of 2.46Mbp conserved among all taxa and a pan-genome of 15.2Mbp. We document substantial population-level variability among these organisms driven by segmental gain and loss. Interestingly, much variability lies in intergenic regions, suggesting that the Enterobacteriacae may exhibit regulatory divergence.The multiple genome alignments generated by our software provide a platform for comparative genomic and population genomic studies. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve

What do parents think about parental participation in school-based interventions on energy balance-related behaviours? a qualitative study in 4 countries

<p>Abstract</p> <p>Background</p> <p>Overweight and obesity in youth has increased dramatically. Therefore, overweight prevention initiatives should start early in life and target modifiable energy balance-related behaviours. Parental participation is often advocated as important for school-based interventions, however, getting parents involved in school-based interventions appears to be challenging based on earlier intervention experiences. The purpose of this study was to get insight into the determinants of and perspectives on parental participation in school-interventions on energy balance-related behaviours (physical activity, healthy eating, sedentary behaviours) in parents of ten- to twelve-year olds in order to develop an effective parental module for school-based interventions concerning energy balance-related behaviours.</p> <p>Methods</p> <p>Four countries (Belgium, Hungary, Norway and Spain) conducted the focus group research based on a standardised protocol and a semi-structured questioning route. A variation in parental socio-economic status (SES) and parental school involvement was taken into account when recruiting the parents. The audio taped interviews were transcribed, and a qualitative content analysis of the transcripts was conducted in each country.</p> <p>Results</p> <p>Seventeen focus group interviews were conducted with a total of 92 parents (12 men, 80 women). Physical activity was considered to be a joint responsibility of school and parents, nutrition as parent's responsibility but supported by the school, and prevention of sedentary behaviours as parent's sole responsibility. Parents proposed interactive and practical activities together with their child as the best way to involve them such as cooking, food tasting, nutrition workshops, walking or cycling tours, sport initiations together with their child. Activities should be cheap, on a convenient moment, focused on their children and not on themselves, not tutoring, not theoretical, and school-or home-based.</p> <p>Conclusions</p> <p>Parents want to be involved in activities related to energy balance-related behaviours if this implies 'doing things together' with their child at school or at home.</p