Amount Of Variation In Rates Research Articles

CAFE 5 models variation in evolutionary rates among gene families.

Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, Computational Analysis of gene Family Evolution (CAFE), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. Here, we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modeling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. CAFE 5 source code, documentation, test data and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases. Supplementary data are available at Bioinformatics online.

Population based trends in procedures following sling surgery for urinary incontinence

To investigate practice patterns and variation associated with sling removal/revision and urethrolysis on a population level. We used CPT 4 codes and the State Ambulatory Surgery Database (SASD) to identify all ambulatory procedures for sling removal/revision and urethrolysis from 2004 to 2009 in Florida. Next, we calculated adjusted rates for these procedures and measured regional variation in rates at the level of the Hospital Service Area (HSA). During this time period, rates of secondary procedures following slings more than doubled from 3.2 per 100,000 to 6.5 per 100,000 population (p<0.001). There was a large amount of regional variation, with rates of these procedures varying more than 5-fold across HSAs. Regions that placed more slings did not necessarily have higher rates of secondary procedures following sling placement. The large amount of variability in rates of secondary procedures following slings signifies considerable uncertainty about the indications for these procedures. Further research is warranted to better explain potential sources for this variation in order to improve the quality of care surrounding midurethral sling placement and the recognition and treatment of its complications.

Altruism as an Organizational Problem: The Case of Organ Procurement

This article presents a social-organizational approach to explaining empirical variation in rates of altruism. The efforts of organizations are mostly responsible for much of the altruism seen today, and the substance of these efforts varies. Although research from social psychology and organizational studies suggests that altruistic action is sensitive to social context, the link between individual and organizational aspects of altruism has not been clearly articulated. In particular, our knowledge of “one-shot,” organizationally managed altruism is limited. I suggest that the factors of organizational resources, scope, and persistence are likely to generate higher rates of individual altruism in the absence of long-term relationships that encourage giving behavior. The approach is applied to the case of cadaveric organ procurement in the United States. The analysis highlights the central role of organ procurement organizations (OPOs). Quantitative analysis of OPO procurement rates shows that, while demographic characteristics are important, OPO resources and scope are important predictors of procurement. The findings strongly suggest that the ability of organizations to produce contexts for giving explains a substantial amount of variation in rates of one-shot altruism.

Substitution-rate variation among sites and the estimation of transition bias.

Substitution-rate variation among sites and differences in the probabilities of change among the four nucleotides are conflated in DNA sequence comparisons. When variation in rate exists among sites but is ignored, biases in the rates of change among nucleotides are underestimated. This paper provides a quantification of this effect when the observed proportions of transitions, P, and transversions, Q, between two sequences are used to estimate transition bias. The utility of P/Q as an estimator is examined both with and without rate variation among sites. A gamma-distributed-rates model is used to illustrate the effect that variation among sites has on estimates of transition bias, but it is argued that the basic results should hold for any pattern of rate variation. Naive estimates of the extent of transition bias, those that ignore rate variation when it is present, can seriously underestimate its true value. The extent of this underestimation increases with the amount of rate variation among sites. An example using human mitochondrial DNA shows that a simple comparison of the proportions of transitions and transversions in recently diverged sequences underestimates the level of transition bias by approximately 15%. This does not depend on the use of P/Q to estimate transition bias; maximum-likelihood methods give similar results.