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

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

Swearing as a response to pain: A cross-cultural comparison of British and Japanese participants

Background and aims: Research suggests swearing can moderate pain perception. The present study assessed whether changes in pain perception due to swearing reflect a "scripting" effect by comparing swearing as a response to pain in native English and Japanese speakers. Cognitive psychology denotes a 'script' to be a sequence of learnt behaviours expected for given situations. Japanese participants were included as they rarely, if ever, swear as a response to pain and therefore do not possess an available script for swearing in the context of pain. It was hypothesised that Japanese participants would demonstrate less tolerance and more sensitivity to pain than English participants, and - due to a lack of an available script of swearing in response to pain - that Japanese participants would not experience swearword mediated hypoalgesia. Methods: Fifty-six native English (mean age = 23 years) and 39 Japanese (mean age = 21) speakers completed a cold-pressor task whilst repeating either a swear on control word. A 2 (culture; Japanese, British). ×. 2 (word; swear; non-swear) design explored whether Japanese participants showed the same increase in pain tolerance and experienced similar levels of perceived pain when a swearing intervention was used as British participants. Pain tolerance was assessed by the number of seconds participants could endure of cold-pressor exposure and self-report pain measurements. Levels of perceived pain were assessed using a 120-mm horizontal visual analogue scale anchored by descriptors in the participant's native language of "no pain" (left) and "terrible pain" (right). The participant was asked to mark a 10. mm vertical line to indicate overall pain intensity. The score was measured from the zero anchor to the participant's mark. Results: Japanese participants reported higher levels of pain (p <. 0.005) and displayed lower pain tolerance than British participants (p <. 0.05). Pain tolerance increased in swearers regardless of cultural background (p <. 0.001) and no interaction was found between word group and culture (p = 0.96), thereby suggesting that swearing had no differential effect related to the cultural group of the participant. Conclusions: The results replicate previous findings that swearing increases pain tolerance and that individuals from an Asian ethnic background experience greater levels of perceived pain than those from a Caucasian ethnic background. However, these results do not support the idea of pain perception modification due to a "scripting" effect. This is evidenced as swearword mediated hypoalgesia occurs irrespective of participant cultural background. Rather, it is suggested that modulation of pain perception may occur through activation of descending inhibitory neural pain mechanisms. Implications: As swearing can increase pain tolerance in both Japanese and British people, it may be suggested that swearword mediated hypoalgesia is a universal phenomenon that transcends socio-cultural learnt behaviours. Furthermore, swearing could be encouraged as an intervention to help people cope with acute painful stimuli