The Speed of Adaptation in Large Asexual Populations

In large asexual populations, beneficial mutations have to compete with each other for fixation. Here, I derive explicit analytic expressions for the rate of substitution and the mean beneficial effect of fixed mutations, under the assumptions that the population size N is large, that the mean effect of new beneficial mutations is smaller than the mean effect of new deleterious mutations, and that new beneficial mutations are exponentially distributed. As N increases, the rate of substitution approaches a constant, which is equal to the mean effect of new beneficial mutations. The mean effect of fixed mutations continues to grow logarithmically with N. The speed of adaptation, measured as the change of log fitness over time, also grows logarithmically with N for moderately large N, and it grows double-logarithmically for extremely large N. Moreover, I derive a simple formula that determines whether at given N beneficial mutations are expected to compete with each other or go to fixation independently. Finally, I verify all results with numerical simulations.Comment: 33 pages, 6 figures. Minor changes in discussion. To appear in Genetic

Two-axis controller Patent

Two axis flight controller with potentiometer control shafts directly coupled to rotatable ball member

A Target Restricted Assembly Method (TRAM) for Phylogenomics

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon

Swearing as a Response to Pain: Assessing Hypoalgesic Effects of Novel “Swear” Words

Previous research showing that swearing alleviates pain is extended by addressing emotion arousal and distraction as possible mechanisms. We assessed the effects of a conventional swear word (“fuck”) and two new “swear” words identified as both emotion-arousing and distracting: “fouch” and “twizpipe.” A mixed sex group of participants (N = 92) completed a repeated measures experimental design augmented by mediation analysis. The independent variable was repeating one of four different words: “fuck” vs. “fouch” vs. “twizpipe” vs. a neutral word. The dependent variables were emotion rating, humor rating, distraction rating, cold pressor pain threshold, cold pressor pain tolerance, pain perception score, and change from resting heart rate. Mediation analyses were conducted for emotion, humor, and distraction ratings. For conventional swearing (“fuck”), confirmatory analyses found a 32% increase in pain threshold and a 33% increase in pain tolerance, accompanied by increased ratings for emotion, humor, and distraction, relative to the neutral word condition. The new “swear” words, “fouch” and “twizpipe,” were rated as more emotional and humorous than the neutral word but did not affect pain threshold or tolerance. Changes in heart rate and pain perception were absent. Our data replicate previous findings that repeating a swear word at a steady pace and volume benefits pain tolerance, extending this finding to pain threshold. Mediation analyses did not identify a pathway via which such effects manifest. Distraction appears to be of little importance but emotion arousal is worthy of future study

Graphs of Small Rank-width are Pivot-minors of Graphs of Small Tree-width

We prove that every graph of rank-width $k$ is a pivot-minor of a graph of tree-width at most $2k$. We also prove that graphs of rank-width at most 1, equivalently distance-hereditary graphs, are exactly vertex-minors of trees, and graphs of linear rank-width at most 1 are precisely vertex-minors of paths. In addition, we show that bipartite graphs of rank-width at most 1 are exactly pivot-minors of trees and bipartite graphs of linear rank-width at most 1 are precisely pivot-minors of paths.Comment: 16 pages, 7 figure

Storing fungicides safely

Growers who stocked up on fungicides for the 2005 growing season due to the threat of Asian soybean rust will likely be facing fungicide storage issues this winter, especially since it is likely that most products cannot be returned. The good news is that most fungicides have a shelf life of at least two years--and probably longer--assuming they are stored correctly. Optimum storage conditions are cool, dry conditions, away from sunlight. Storage temperatures should not go below freezing; however, if a fungicide does freeze, then slowly thaw it out at room temperature

Characterization of the OSSN Microbiome in HIV-1 Infected Patients

Purpose: Ocular surface squamous neoplasia (OSSN) is a rare cancer previously seen in elderly men. In Botswana there is an increase in OSSN and pterygia among young HIV-1 infected patients. Factors that determine the course of this cancer have not been characterized. Recent studies identified HPV, EBV, KSHV, HSV-1/2, and CMV in patient samples. We now characterize the microbiome associated with the disease that may contribute to its course. Results: Pyrosequencing identified viruses, bacteria, fungus and parasites. Analysis of shotgun cloning sequences showed a majority of infectious agents identified by pyrosequencing. Conclusion: HIV patients with OSSN in Botswana are infected with a range of infectious agents which may represent a unique microbiome. The persistent expressions of gene products by these agents some of which are oncogenic are likely to contribute to the oncogenic process and suggest that treatment modalities of the cancer should involve the screening for endemic agents