Backstreaming from oil diffusion pumps Quarterly progress report, 1 Jan. - 31 Mar. 1966

Backstreaming from oil diffusion and turbo-molecular pump

More Mouldy Data: Another mycoplasma gene jumps the silicon barrier into the human genome

The human genome sequence database contains DNA sequences very like those of mycoplasma molds. It appears such moulds infect not only molecular Biology laboratories but were picked up by experimenters from contaminated samples and inserted into GenBank as if they were human. At least one mouldy EST (Expressed Sequence Tag) has transferred from public databases to commercial tools (Affymetrix HG-U133 plus 2.0 microarrays). We report a second example (DA466599) and suggest there is a need to clean up genomic databases but fear current tools will be inadequate to catch genes which have jumped the silicon barrier.Comment: data directory contains results of AF241217 and DA466599 blast runs by EBI in Cambridg

Backstreaming from oil diffusion pumps Final report, Dec. 1, 1963 - May 30, 1966

Backstreaming from oil diffusion and turbomolecular pump

Evolving DNA motifs to predict GeneChip probe performance

Background: Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results: Regular expressions can be automatically created from a Backus-Naur form (BNF) context-free grammar using strongly typed genetic programming. Conclusion: The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided. © 2009 Langdon and Harrison; licensee BioMed Central Ltd

Optimising Existing Software with Genetic Programming

We show genetic improvement of programs (GIP) can scale by evolving increased performance in a widely-used and highly complex 50000 line system. GISMOE found code that is 70 times faster (on average) and yet is at least as good functionally. Indeed it even gives a small semantic gain

Vlasov Simulations of Trapping and Inhomogeneity in Raman Scattering

We study stimulated Raman scattering (SRS) in laser-fusion conditions with the Eulerian Vlasov code ELVIS. Back SRS from homogeneous plasmas occurs in sub-picosecond bursts and far exceeds linear theory. Forward SRS and re-scatter of back SRS are also observed. The plasma wave frequency downshifts from the linear dispersion curve, and the electron distribution shows flattening. This is consistent with trapping and reduces the Landau damping. There is some acoustic ($\omega\propto k$) activity and possibly electron acoustic scatter. Kinetic ions do not affect SRS for early times but suppress it later on. SRS from inhomogeneous plasmas exhibits a kinetic enhancement for long density scale lengths. More scattering results when the pump propagates to higher as opposed to lower density.Comment: 4 pages, 6 figures. Submitted to "Journal of Plasmas Physics" for the conference proceedings of the 19th International Conference on Numerical Simulation of Plasma

Cognitive impairment among patients with multiple sclerosis:associations with employment and quality of life

OBJECTIVES To explore the relationship between cognitive impairment and conventional measures of disability in multiple sclerosis (MS), quality of life (QOL) and employment status using the brief international cognitive assessment for multiple sclerosis (BICAMS) in the routine outpatient clinic. METHODS 62 patients with MS were assessed on the BICAMS test battery for cognitive impairment. Data were obtained on employment status and a number of questionnaires completed including fatigue severity score, multiple sclerosis neuropsychological questionnaire, hospital anxiety and depression scale, the functional assessment of multiple sclerosis (FAMS) as well as on the EuroQOL five dimension questionnaire (EQ-5D). Other assessments include the patient activation measure and unidimensional self-efficacy scale for multiple sclerosis. RESULTS Cognitive assessment revealed 44 subjects (65%) had evidence of cognitive impairment on formal testing. In comparison with patients without evidence of cognitive impairment, cognitively impaired patients exhibited significantly higher rates of unemployment (p=0.009). The symbol digits modalities test was the most significant predictor of unemployment. Cognitive impairment was associated with lower QOL scores on the FAMS (p=0.001) and EQ-5D (p<0.001). CONCLUSIONS BICAMS provides a sensitive and easy to administer screening test for cognitive impairment within the outpatient setting. Cognitive impairment is common in our cohort of patients with MS attending outpatients and appears to be associated with increased rates of unemployment and lower measures of QOL

Simple Max-Min Ant Systems and the Optimization of Linear Pseudo-Boolean Functions

With this paper, we contribute to the understanding of ant colony optimization (ACO) algorithms by formally analyzing their runtime behavior. We study simple MAX-MIN ant systems on the class of linear pseudo-Boolean functions defined on binary strings of length 'n'. Our investigations point out how the progress according to function values is stored in pheromone. We provide a general upper bound of O((n^3 \log n)/ \rho) for two ACO variants on all linear functions, where (\rho) determines the pheromone update strength. Furthermore, we show improved bounds for two well-known linear pseudo-Boolean functions called OneMax and BinVal and give additional insights using an experimental study.Comment: 19 pages, 2 figure

Genetic improvement of GPU software

We survey genetic improvement (GI) of general purpose computing on graphics cards. We summarise several experiments which demonstrate four themes. Experiments with the gzip program show that genetic programming can automatically port sequential C code to parallel code. Experiments with the StereoCamera program show that GI can upgrade legacy parallel code for new hardware and software. Experiments with NiftyReg and BarraCUDA show that GI can make substantial improvements to current parallel CUDA applications. Finally, experiments with the pknotsRG program show that with semi-automated approaches, enormous speed ups can sometimes be had by growing and grafting new code with genetic programming in combination with human input