Genetic signal maximization using environmental regression

Joint analyses of correlated phenotypes in genetic epidemiology studies are common. However, these analyses primarily focus on genetic correlation between traits and do not take into account environmental correlation. We describe a method that optimizes the genetic signal by accounting for stochastic environmental noise through joint analysis of a discrete trait and a correlated quantitative marker. We conducted bivariate analyses where heritability and the environmental correlation between the discrete and quantitative traits were calculated using Genetic Analysis Workshop 17 (GAW17) family data. The resulting inverse value of the environmental correlation between these traits was then used to determine a new β coefficient for each quantitative trait and was constrained in a univariate model. We conducted genetic association tests on 7,087 nonsynonymous SNPs in three GAW17 family replicates for Affected status with the β coefficient fixed for three quantitative phenotypes and compared these to an association model where the β coefficient was allowed to vary. Bivariate environmental correlations were 0.64 (± 0.09) for Q1, 0.798 (± 0.076) for Q2, and −0.169 (± 0.18) for Q4. Heritability of Affected status improved in each univariate model where a constrained β coefficient was used to account for stochastic environmental effects. No genome-wide significant associations were identified for either method but we demonstrated that constraining β for covariates slightly improved the genetic signal for Affected status. This environmental regression approach allows for increased heritability when the β coefficient for a highly correlated quantitative covariate is constrained and increases the genetic signal for the discrete trait

Unified View of Scaling Laws for River Networks

Scaling laws that describe the structure of river networks are shown to follow from three simple assumptions. These assumptions are: (1) river networks are structurally self-similar, (2) single channels are self-affine, and (3) overland flow into channels occurs over a characteristic distance (drainage density is uniform). We obtain a complete set of scaling relations connecting the exponents of these scaling laws and find that only two of these exponents are independent. We further demonstrate that the two predominant descriptions of network structure (Tokunaga's law and Horton's laws) are equivalent in the case of landscapes with uniform drainage density. The results are tested with data from both real landscapes and a special class of random networks.Comment: 14 pages, 9 figures, 4 tables (converted to Revtex4, PRE ref added

Image analysis techniques for the study of turbulent flows

In this paper, a brief review of Digital Image Analysis techniques employed in Fluid Mechanics for the study of turbulent flows is given. Particularly the focus is on the techniques developed by the research teams the Author worked in, that can be considered relatively "low cost" techniques. Digital Image Analysis techniques have the advantage, when compared to the traditional techniques employing physical point probes, to be non-intrusive and quasi-continuous in space, as every pixel on the camera sensor works as a single probe: consequently, they allow to obtain two-dimensional or three-dimensional fields of the measured quantity in less time. Traditionally, the disadvantages are related to the frequency of acquisition, but modern high-speed cameras are typically able to acquire at frequencies from the order of 1 KHz to the order of 1 MHz. Digital Image Analysis techniques can be employed to measure concentration, temperature, position, displacement, velocity, acceleration and pressure fields with similar equipment and setups, and can be consequently considered as a flexible and powerful tool for measurements on turbulent flows

Splicing factor and exon profiling across human tissues

It has been shown that alternative splicing is especially prevalent in brain and testis when compared to other tissues. To test whether there is a specific propensity of these tissues to generate splicing variants, we used a single source of high-density microarray data to perform both splicing factor and exon expression profiling across 11 normal human tissues. Paired comparisons between tissues and an original exon-based statistical group analysis demonstrated after extensive RT-PCR validation that the cerebellum, testis, and spleen had the largest proportion of differentially expressed alternative exons. Variations at the exon level correlated with a larger number of splicing factors being expressed at a high level in the cerebellum, testis and spleen than in other tissues. However, this splicing factor expression profile was similar to a more global gene expression pattern as a larger number of genes had a high expression level in the cerebellum, testis and spleen. In addition to providing a unique resource on expression profiling of alternative splicing variants and splicing factors across human tissues, this study demonstrates that the higher prevalence of alternative splicing in a subset of tissues originates from the larger number of genes, including splicing factors, being expressed than in other tissues

Optimizing care in osteoporosis: The Canadian quality circle project

<p>Abstract</p> <p>Background</p> <p>While the Osteoporosis Canada 2002 Canadian guidelines provided evidence based strategies in preventing, diagnosing, and managing this condition, publication and distribution of guidelines have not, in and of themselves, been shown to alter physicians clinical approaches. We hypothesize that primary care physicians enrolled in the Quality Circle project would change their patient management of osteoporosis in terms of awareness of osteoporosis risk factors and bone mineral density testing in accordance with the guidelines.</p> <p>Methods</p> <p>The project consisted of five Quality Circle phases that included: 1) Training & Baseline Data Collection, 2) First Educational Intervention & First Follow-Up Data Collection 3) First Strategy Implementation Session, 4) Final Educational Intervention & Final Follow-up Data Collection, and 5) Final Strategy Implementation Session. A total of 340 circle members formed 34 quality circles and participated in the study. The generalized estimating equations approach was used to model physician awareness of risk factors for osteoporosis and appropriate utilization of bone mineral density testing pre and post educational intervention (first year of the study). Odds ratios (OR) and 95% confidence intervals (95% CI) were calculated.</p> <p>Results</p> <p>After the 1^styear of the study, physicians' certainty of their patients' risk factor status increased. Certainty varied from an OR of 1.4 (95% CI: 1.1, 1.8) for prior vertebral fracture status to 6.3 (95% CI: 2.3, 17.9) for prior hip fracture status. Furthermore, bone mineral density testing increased in high risk as compared with low risk patients (OR: 1.4; 95% CI: 1.2, 1.7).</p> <p>Conclusion</p> <p>Quality Circle methodology was successful in increasing both physicians' awareness of osteoporosis risk factors and appropriate bone mineral density testing in accordance with the 2002 Canadian guidelines.</p

Resolving the ancestry of Austronesian-speaking populations

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The “out-of-Taiwan” model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion

Prediction of crop coefficients from fraction of ground cover and height. Background and validation using ground and remote sensing data

ReviewThe current study aims at reviewing and providing advances on methods for estimating and applying crop coefficients from observations of ground cover and vegetation height. The review first focuses on the relationships between single Kc and basal Kcb and various parameters including the fraction of ground covered by the canopy (fc), the leaf area index (LAI), the fraction of ground shaded by the canopy (fshad), the fraction of intercepted light (flight) and intercepted photosynthetic active radiation (fIPAR). These relationships were first studied in the 1970’s, for annual crops, and later, in the last decennia, for tree and vine perennials. Research has now provided a variety of methods to observe and measure fc and height (h) using both ground and remote sensing tools, which has favored the further development of Kc related functions. In the past, these relationships were not used predictively but to support the understanding of dynamics of Kc and Kcb in relation to the processes of evapotranspiration or transpiration, inclusive of the role of soil evaporation. Later, the approach proposed by Allen and Pereira (2009), the A&P approach, used fc and height (h) or LAI data to define a crop density coefficient that was used to directly estimate Kc and Kcb values for a variety of annual and perennial crops in both research and practice. It is opportune to review the A&P method in the context of a variety of studies that have derived Kc and Kcb values from field measured data with simultaneously observed ground cover fc and height. Applications used to test the approach include various tree and vine crops (olive, pear, and lemon orchards and vineyards), vegetable crops (pea, onion and tomato crops), field crops (barley, wheat, maize, sunflower, canola, cotton and soybean crops), as well as a grassland and a Bermudagrass pasture. Comparisons of Kcb values computed with the A &P method produced regression coefficients close to 1.0 and coefficients of determination≥0.90, except for orchards. Results indicate that the A&P approach can produce estimates of potential Kcb, using vegetation characteristics alone, within reasonable or acceptable error, and are useful for refining Kcb for conditions of plant spacing, size and density that differ from standard values. The comparisons provide parameters appropriate to applications for the tested crops. In addition, the A&P approach was applied with remotely sensed fc data for a variety of crops in California using the Satellite Irrigation Management Support (SIMS) framework. Daily SIMS crop ET (ETc-SIMS) produced Kcb values using the FAO56 and A&P approaches. Combination of satellite derived fc and Kcb values with ETo data from Spatial CIMIS (California Irrigation Management Information System) produced ET estimates that were compared with daily actual crop ET derived from energy balance calculations from micrometeorological instrumentation (ETc EB).Results produced coefficients of regression of 1.05 for field crops and 1.08 for woody crops, and R2 values of 0.81 and 0.91, respectively. These values suggest that daily ETc-SIMS -based ET can be accurately estimated within reasonable error and that the A&P approach is appropriate to support that estimation. It is likely that accuracy can be improved via progress in remote sensing determination of fc. Tabulated Kcb results and calculation parameters are presented in a companion paper in this Special Issueinfo:eu-repo/semantics/publishedVersio

The Role of Medical Language in Changing Public Perceptions of Illness

This study was designed to investigate the impact of medical terminology on perceptions of disease. Specifically, we look at the changing public perceptions of newly medicalized disorders with accompanying newly medicalized terms (e.g. impotence has become erectile dysfunction disorder). Does using “medicalese” to label a recently medicalized disorder lead to a change in the perception of that condition? Undergraduate students (n = 52) rated either the medical or lay label for recently medicalized disorders (such as erectile dysfunction disorder vs. impotence) and established medical conditions (such as a myocardial infarction vs. heart attack) for their perceived seriousness, disease representativeness and prevalence. Students considered the medical label of the recently medicalized disease to be more serious (mean = 4.95 (SE = .27) vs. mean = 3.77 (SE = .24) on a ten point scale), more representative of a disease (mean = 2.47 (SE = .09) vs. mean = 1.83 (SE = .09) on a four point scale), and have lower prevalence (mean = 68 (SE = 12.6) vs. mean = 122 (SE = 18.1) out of 1,000) than the same disease described using common language. A similar pattern was not seen in the established medical conditions, even when controlled for severity. This study demonstrates that the use of medical language in communication can induce bias in perception; a simple switch in terminology results in a disease being perceived as more serious, more likely to be a disease, and more likely to be a rare condition. These findings regarding the conceptualization of disease have implications for many areas, including medical communication with the public, advertising, and public policy

Dropout in a longitudinal, cohort study of urologic disease in community men

BACKGROUND: Reasons for attrition in studies vary, but may be a major concern in long-term studies if those who drop out differ systematically from those who continue to participate. Factors associated with dropout were evaluated in a twelve-year community-based, prospective cohort study of urologic disease in men. METHODS: During 1989–1991, 2,115 randomly selected Caucasian men, ages 40–79 years from Olmsted County, Minnesota were enrolled and followed with questionnaires biennially; 332 men were added in follow-up. A random subset (~25%) received a urologic examination. Baseline characteristics including age, benign prostatic hyperplasia (BPH) symptoms, comorbidities, and socioeconomic factors were compared between subjects who did and did not participate after the twelfth year of follow-up. RESULTS: Of the 2,447 men, 195 died and were excluded; 682 did not participate in 2002. Compared with men in the 40–49 year age group, men ≥ 70 years of age at baseline had a greater relative odds of dropout, 2.65 (95% CI: 1.93, 3.63). In age-adjusted analyses, relative to men without stroke, men who had suffered a stroke had a higher odds of dropout, age-adjusted OR 3.07 (95% CI: 1.49, 6.33). Presence of at least one BPH symptom was not associated with dropout, (age-adjusted OR 1.12 (95% CI: 0.93, 1.36)). CONCLUSION: These results provide assurance that dropout was not related to primary study outcomes. However, factors associated with dropout should be taken into account in analyses where they may be potential confounders