Spectrophotometer-Integrating-Sphere System for Computing Solar Absorptance

A commercially available ultraviolet, visible, near-infrared spectrophotometer was modified to utilize an 8-inch-diameter modified Edwards-type integrated sphere. Software was written so that the reflectance spectra could be used to obtain solar absorptance values of 1-inch-diameter specimens. A descriptions of the system, spectral reflectance, and software for calculation of solar absorptance from reflectance data are presented

Hierarchical modeling in association studies of multiple phenotypes

The genetic study of disease-associated phenotypes has become common because such phenotypes are often easier to measure and in many cases are under greater genetic control than the complex disease itself. Some disease-associated phenotypes are rare, however, making it difficult to evaluate their effects due to small informative sample sizes. In addition, analyzing numerous phenotypes introduces the issue of multiple comparisons. To address these issues, we have developed a hierarchical model (HM) for multiple phenotypes that provides more accurate effect estimates with a lower false-positive rate. We evaluated the validity and power of HM in association studies of multiple phenotypes using randomly selected cases and controls from the simulated data set in the Genetic Analysis Workshop 14. In particular, we first analyzed the association between each of the 12 subclinical phenotypes and single-nucleotide polymorphisms within the known causal loci using a conventional logistic regression model (LRM). Then we added a second-stage model by regressing all of the logistic coefficients of the phenotypes obtained from LRM on a Z matrix that incorporates the clinical correlation of the phenotypes. Specially, the 12 phenotypes were grouped into 3 clusters: 1) communally shared emotions; 2) behavioral related; and 3) anxiety related. A semi-Bayes HM effect estimate for each phenotype was calculated and compared with those from LRM. We observed that using HM to evaluate the association between SNPs and multiple related phenotypes slightly increased power for detecting the true associations and also led to fewer false-positive results

Parallel biocomputing

<p>Abstract</p> <p>Background</p> <p>With the advent of high throughput genomics and high-resolution imaging techniques, there is a growing necessity in biology and medicine for parallel computing, and with the low cost of computing, it is now cost-effective for even small labs or individuals to build their own personal computation cluster.</p> <p>Methods</p> <p>Here we briefly describe how to use commodity hardware to build a low-cost, high-performance compute cluster, and provide an in-depth example and sample code for parallel execution of R jobs using MOSIX, a mature extension of the Linux kernel for parallel computing. A similar process can be used with other cluster platform software.</p> <p>Results</p> <p>As a statistical genetics example, we use our cluster to run a simulated eQTL experiment. Because eQTL is computationally intensive, and is conceptually easy to parallelize, like many statistics/genetics applications, parallel execution with MOSIX gives a linear speedup in analysis time with little additional effort.</p> <p>Conclusions</p> <p>We have used MOSIX to run a wide variety of software programs in parallel with good results. The limitations and benefits of using MOSIX are discussed and compared to other platforms.</p

An empirical evaluation of the common disease-common variant hypothesis

While genome-wide linkage studies have been successful in mapping variants underlying rare monogenic disorders, genome-wide association studies may be more appropriate for detecting common variants of modest effects that underlie common disorders. To this end, we were interested in determining whether genetic variants associated with a phenotype differed depending on whether they were within or outside of regions linked to the phenotype. In particular, we compared allele frequencies and effect sizes between associated single-nucleotide polymorphisms within and outside of linkage regions using the Genetic Analysis Workshop 15 Problem 1. We did not find any statistically significant differences between these two sets. However, our power calculations show that these results may be inconclusive

Comprehensive Approach to Analyzing Rare Genetic Variants

Recent findings suggest that rare variants play an important role in both monogenic and common diseases. Due to their rarity, however, it remains unclear how to appropriately analyze the association between such variants and disease. A common approach entails combining rare variants together based on a priori information and analyzing them as a single group. Here one must make some assumptions about what to aggregate. Instead, we propose two approaches to empirically determine the most efficient grouping of rare variants. The first considers multiple possible groupings using existing information. The second is an agnostic “step-up” approach that determines an optimal grouping of rare variants analytically and does not rely on prior information. To evaluate these approaches, we undertook a simulation study using sequence data from genes in the one-carbon folate metabolic pathway. Our results show that using prior information to group rare variants is advantageous only when information is quite accurate, but the step-up approach works well across a broad range of plausible scenarios. This agnostic approach allows one to efficiently analyze the association between rare variants and disease while avoiding assumptions required by other approaches for grouping such variants

Comparison of missing data approaches in linkage analysis

BACKGROUND: Observational cohort studies have been little used in linkage analyses due to their general lack of large, disease-specific pedigrees. Nevertheless, the longitudinal nature of such studies makes them potentially valuable for assessing the linkage between genotypes and temporal trends in phenotypes. The repeated phenotype measures in cohort studies (i.e., across time), however, can have extensive missing information. Existing methods for handling missing data in observational studies may decrease efficiency, introduce biases, and give spurious results. The impact of such methods when undertaking linkage analysis of cohort studies is unclear. Therefore, we compare here six methods of imputing missing repeated phenotypes on results from genome-wide linkage analyses of four quantitative traits from the Framingham Heart Study cohort. RESULTS: We found that simply deleting observations with missing values gave many more nominally statistically significant linkages than the other five approaches. Among the latter, those with similar underlying methodology (i.e., imputation- versus model-based) gave the most consistent results, although some discrepancies remained. CONCLUSION: Different methods for addressing missing values in linkage analyses of cohort studies can give substantially diverse results, and must be carefully considered to protect against biases and spurious findings

Impact of Meat Consumption, Preparation, and Mutagens on Aggressive Prostate Cancer

The association between meat consumption and prostate cancer remains unclear, perhaps reflecting heterogeneity in the types of tumors studied and the method of meat preparation—which can impact the production of carcinogens.We address both issues in this case-control study focused on aggressive prostate cancer (470 cases and 512 controls), where men reported not only their meat intake but also their meat preparation and doneness level on a semi-quantitative food-frequency questionnaire. Associations between overall and grilled meat consumption, doneness level, ensuing carcinogens and aggressive prostate cancer were assessed using multivariate logistic regression.Higher consumption of any ground beef or processed meats were positively associated with aggressive prostate cancer, with ground beef showing the strongest association (OR = 2.30, 95% CI:1.39–3.81; P-trend = 0.002). This association primarily reflected intake of grilled or barbequed meat, with more well-done meat conferring a higher risk of aggressive prostate cancer. Comparing high and low consumptions of well/very well cooked ground beef to no consumption gave OR's of 2.04 (95% CI:1.41–2.96) and 1.51 (95% CI:1.06–2.14), respectively. In contrast, consumption of rare/medium cooked ground beef was not associated with aggressive prostate cancer. Looking at meat mutagens produced by cooking at high temperatures, we detected an increased risk with 2-amino-3,8-Dimethylimidazo-[4,5-f]Quinolaxine (MelQx) and 2-amino-3,4,8-trimethylimidazo(4,5-f)qunioxaline (DiMelQx), when comparing the highest to lowest quartiles of intake: OR = 1.69 (95% CI:1.08–2.64;P-trend = 0.02) and OR = 1.53 (95% CI:1.00–2.35; P-trend = 0.005), respectively.Higher intake of well-done grilled or barbequed red meat and ensuing carcinogens could increase the risk of aggressive prostate cancer

Emil Brunner

Swiss theologian Emil Brunner (1899-1966) developed a liberal Protestant theology of the family, contrary to the more traditional biblical views of his compatriot Karl Barth. Brunner treated the family as a natural order of creation, alongside the state and economy. The family has a natural monogamous structure and a built-in set of spousal and parental rights and duties that cannot be invaded by other social spheres or reconstructed by family members or liberal reformers. The state has to protect and enforce these family rights and duties as a matter of justice, but Christians should honor them spontaneously in expression of agapic love. Brunner prized children and their rights, and he called the union of husband, wife, and child, a “trinitarian union” built on the foundation of mutual natural attraction and as a reflection of the triune Godhead. But he insisted that marital sex was a unique expression of love not just a means to a procreative end, and he firmly rejected as unrealistic the procreative perfectionism of some parts of the Catholic tradition. A marital couple without children was a complete family, he believed, just as a widow(er) or divorcee with children remained a complete family

Christianity's Mixed Contributions to Children's Rights: Traditional Teachings, Modern Doubts

The United States is the only nation, besides Somalia, not to ratify the 1989 United Nations Convention on Human Rights. This is ironic, given the leading role that American lawyers and diplomats played in creating the Convention. The leading opponents to ratification, it turns out, are conservative Christians who object to the idea of children’s rights altogether, or at least to international human rights protection of the child, and see these rights as a liberal threat to parental rights to nurture, educate, and discipline their own children. We argue, however, that many of these modern objections to children’s rights are misplaced, and fail to appreciate the classical and Christian roots of children’s rights and parental duties in the Western tradition. We call upon churches and states alike to embrace children’s rights more fully, and to offer at least qualified acceptance of the UN Convention