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

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

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

O,N,N-Pincer ligand effects on oxidatively induced carbon–chlorine coupling reactions at palladium

The syntheses of two families of sterically tuneable O,N,N pro-ligands are reported, namely the 2-(phenyl-2′-ol)-6-imine-pyridines, 2-(C6H4-2′-OH),6-(CMe[double bond, length as m-dash]NAr)C5H3N [Ar = 4-i-PrC6H4 (HL1a), 2,6-i-Pr2C6H3 (HL1b)] and the 2-(phenyl-2′-ol)-6-(amino-prop-2-yl)pyridines, 2-(C6H4-2′-OH),6-(CMe2NHAr)C5H3N [Ar = 4-i-PrC6H4 (HL2a), 2,6-i-Pr2C6H3 (HL2b)], using straightforward synthetic approaches and in reasonable overall yields. Interaction of HL1a/c and HL2a/b with palladium(II) acetate affords the O,N,N-pincer complexes, [{2-(C6H4-2′-O)-6-(CMe[double bond, length as m-dash]NAr)C5H3N}Pd(OAc)] (Ar = 4-i-PrC6H4 (1a), 2,6-i-Pr2C6H3 (1b)) and [{2-(C6H4-2′-O)-6-(CMe2NHAr)C5H3N}Pd(OAc)] (Ar = 4-i-PrC6H4 (2a), 2,6-i-Pr2C6H3 (2b)), which can be readily converted to their chloride derivatives, [{2-(C6H4-2′-O)-6-(CMe[double bond, length as m-dash]NAr)C5H3N}PdCl] (Ar = 4-i-PrC6H4 (3a), 2,6-i-Pr2C6H3 (3b)) and [{2-(C6H4-2′-O)-6-(CMe2NHAr)C5H3N}PdCl] (Ar = 4-i-PrC6H4 (4a), 2,6-i-Pr2C6H3 (4b)), respectively, on reaction with an aqueous sodium chloride solution. Treating each of 3a, 3b, 4a and 4b with two equivalents of di-p-tolyliodonium triflate at 100 °C in a toluene/acetonitrile mixture affords varying amounts of 4-chlorotoluene along with the 4-iodotoluene by-product with the conversions highly dependent on the steric and backbone properties of the pincer complex employed (viz.4a > 3a > 4b > 3b); notably, the least sterically bulky and most flexible amine-containing 4a reaches 90% conversion to 4-chlorotoluene in 15 h as opposed to 17% for imine-containing 3b. In the case of 3a, the inorganic palladium species recovered from the reaction has been identified as the Pd(II) salt [{2-(C6H4-2′-O)-6-(CMe[double bond, length as m-dash]N(4-i-PrC6H4)C5H3N}Pd(NCMe)][O3SCF3] (5a), which was independently prepared by the reaction of 3a with silver triflate in acetonitrile. Single crystal X-ray structures are reported for HL1a, HL2a, 1a, 1b, 2a, 2b, 3a and 5a

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