Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks.

Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended and paired end strings to a reference remains computationally demanding. Further tailoring Bioinformatics tools to each new task or scanner remains highly skilled and labour intensive. With this in mind, we recently demonstrated a genetic programming based automated technique which generated a version of the state-of-the-art alignment tool Bowtie2 which was considerably faster on short sequences produced by a scanner at the Broad Institute and released as part of The Thousand Genome Project

Genetic programming for mining DNA chip data from cancer patients

In machine learning terms DNA (gene) chip data is unusual in having thousands of attributes (the gene expression values) but few (<100) records (the patients). A GP based method for both feature selection and generating simple models based on a few genes is demonstrated on cancer data

Assessing the effect of a single dose florfenicol treatment in feedlot cattle on the antimicrobial resistance patterns in faecal Escherichia coli

The objective of this clinical trial was to examine the effect of a single dose of florfenicol on antimicrobial resistance patterns in faecal E. coli of feedlot steers. Steers (n = 370), were purchased from two sources and housed in outdoor concrete floored pens. Two cattle from each pen (n = 42 pens, 84 cattle) were randomly selected for faecal sampling at study day 1, 14, 28, and 42. One sampled animal from each of 21 pens was randomly selected to receive a single 39.6 mg/kg dose of florfenicol subcutaneously at study day 11. Ten lactose positive colonies were isolated from faecal swabs and tested for antimicrobial resistance to 11 antimicrobials using the disk diffusion method. Zones of inhibition were grouped using cluster analysis and clusters were ordered by increasing multiple resistance. A cumulative logistic regression model using generalized estimating equations was used to assess factors associated with increasing levels of multiple resistance. Immediately post-treatment, all isolates obtained from treated cattle belonged to multiple resistant clusters containing chloramphenicol resistance. Though less pronounced in later sampling, resistance to chloramphenicol and other antimicrobials persisted. Antimicrobial treatment, sampling time and animal source, as well as interactions between these variables, were important predictors of the odds of E. coli belonging to a more resistant cluster. A very clear but transitory shift to increasingly multiple resistant faecal E. coli in response to florfenicol treatment was observed. There was no indication of horizontal transfer of resistant E. coli between steers. Level of resistance was influenced by complex interaction of animal source and previous managemen

Icosahedral quasicrystal and 1/1 cubic approximant in Au-Al-Yb alloys

A P-type icosahedral quasicrystal is formed in Au-Al-Yb alloy of which 6-dimensional lattice parameter a6D = 7.448 {\AA}. The composition of the quasicrystal was analyzed to be Au51Al34Yb15. This quasicrystal is formed in as-cast alloys, and is regarded as metastable because of decomposition into other crystalline phases by annealing at 700 \degree C. Among Tsai-type quasicrystals, this quasicrystal is situated just between Zn-Sc group with smaller a6D and larger Cd-Yb group. Intermediate valence of Yb recently observed in this quasicrystal may be due to this unique situation, namely smaller major component Au-Al than in Cd-Yb. The predominant phase in the annealed specimen is a 1/1 cubic approximant with lattice parameter a = 14.500 {\AA} belonging to the space group Im-3 . This phase is stable at the composition Au51Al35Yb14 at 700 \degree C. Rietveld structural analysis indicated that the crystal structure is understood as periodic arrangement of Tsai-type clusters each including four Au-Al atoms at their centers. Chemical ordering of Au and Al is characteristics of this approximant.Comment: 20 pages including 1 table and 7 figure

Introduction to Translation.

We introduce here the inaugural issue of the new scientific journal Translation. The overarching aim of this endeavor is to establish a new forum for a broad spectrum of research in the area of protein synthesis in living systems ranging from structural biochemical, evolutionary and regulatory aspects of translation to the fundamental questions related to post-translational control of somatic phenomena in multicellular organisms including human behavior and health. The journal will publish high quality research articles, provide novel insights, ask provocative questions and discuss new hypothesis in this emerging field. Launching a new journal is always challenging. We hope that strong criteria for the peer-review process, transparency of the editorial policy and the scientific reputation of its founders, editors and editorial board assure the success of Translation; and we rely on continuing support of the scientific community in all aspects of the journal's activity