Automated DNA Motif Discovery

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene. Keywords: pseudogene, short and microRNAs, non-coding transcripts, systems biology, machine learning, Bioinformatics, motif, regular expression, strongly typed genetic programming, context-free grammar.Comment: 12 pages, 2 figure

Can a computerised training paradigm assist people with intellectual disabilities to learn cognitive mediation skills? A randomised experiment

Aims: The aim was to examine whether specific skills required for cognitive behavioural therapy (CBT) could be taught using a computerised training paradigm with people who have intellectual disabilities (IDs). Training aimed to improve: a) ability to link pairs of situations and mediating beliefs to emotions, and b) ability to link pairs of situations and emotions to mediating beliefs. Method: Using a single-blind mixed experimental design, sixty-five participants with IDs were randomised to receive either computerised training or an attention-control condition. Cognitive mediation skills were assessed before and after training. Results: Participants who received training were significantly better at selecting appropriate emotions within situation-beliefs pairs, controlling for baseline scores and IQ. Despite significant improvements in the ability of those who received training to correctly select intermediating beliefs for situation-feelings pairings, no between-group differences were observed at post-test. Conclusions: The findings indicated that computerised training led to a significant improvement in some aspects of cognitive mediation for people with IDs, but whether this has a positive effect upon outcome from therapy is yet to be established

Electromagnetic "particle-in-cell" plasma simulation

''PIC'' simulation tracks particles through electromagnetic fields calculated self-consistently from the charge and current densities of the particles themselves, external sources, and boundaries. Already used extensively in plasma physics, such simulations have become useful in the design of accelerators and their r.f. sources. 5 refs

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

Popular Music Lyrics and Adolescent Sexual Behavior and Attitudes

This study examines the possible links between music lyrics and adolescent sexual health and behavior. This relationship is first explored through a content analysis of sexual content of popular music lyrics. The findings generally support those of previous content analyses that find sexual content to be increasing, to be used regardless of gender of singer, and to be higher among some genres than others. The study also offers unexpected evidence of a link between lyrical content and cultural happenings that was not formally sought as part of the original study. The study secondly seeks to discover any correlations between sexual content of lyrics and national social indicators of adolescent sexual behavior. Few findings of significance emerged, and future research may wish to examine why expected negative media effects do not reveal themselves at the national leve

Popular Music Lyrics and Adolescent Sexual Behavior and Attitudes

This study examines the possible links between music lyrics and adolescent sexual health and behavior. This relationship is first explored through a content analysis of sexual content of popular music lyrics. The findings generally support those of previous content analyses that find sexual content to be increasing, to be used regardless of gender of singer, and to be higher among some genres than others. The study also offers unexpected evidence of a link between lyrical content and cultural happenings that was not formally sought as part of the original study. The study secondly seeks to discover any correlations between sexual content of lyrics and national social indicators of adolescent sexual behavior. Few findings of significance emerged, and future research may wish to examine why expected negative media effects do not reveal themselves at the national leve

Using Action Research Methodologies In Building a Frame for Practicing Research

I discuss action research methodologies and nuances to recount how my research with art educators using critical encounters with visual culture and senior artists, facilitated gaining a broader view of place. During the study, I recognized my first-person voice operating critically and analyzing paradoxes found in the dialogue and data, which was in conflict with my second-person relationships with participants, insofar as we shared a way of knowing that values multiple forms of participant learning. I used these disjunctures to challenge my outdated notions of what it means to “do” research and learned that action research practice offers multiple insights into working in relation to participants and to myself. I describe the variations of action research employed to frame and to facilitate the study within the events of the workshop which suggested insights into what direction the analysis of the research should take. I conclude with describing participants’ learning through the action of the research. My objectives were refocused by the events of learning in and through the action of the research

An efficient frequency-independent numerical method for computing the far-field pattern induced by polygonal obstacles

For problems of time-harmonic scattering by rational polygonal obstacles, embedding formulae express the far-field pattern induced by any incident plane wave in terms of the far-field patterns for a relatively small (frequency-independent) set of canonical incident angles. Although these remarkable formulae are exact in theory, here we demonstrate that: (i) they are highly sensitive to numerical errors in practice, and; (ii) direct calculation of the coefficients in these formulae may be impossible for particular sets of canonical incident angles, even in exact arithmetic. Only by overcoming these practical issues can embedding formulae provide a highly efficient approach to computing the far-field pattern induced by a large number of incident angles. Here we propose solutions for problems (i) and (ii), backed up by theory and numerical experiments. Problem (i) is solved using techniques from computational complex analysis: we reformulate the embedding formula as a complex contour integral and prove that this is much less sensitive to numerical errors. In practice, this contour integral can be efficiently evaluated by residue calculus. Problem (ii) is addressed using techniques from numerical linear algebra: we oversample, considering more canonical incident angles than are necessary, thus expanding the space of valid coefficients vectors. The coefficients vectors can then be selected using either a least squares approach or column subset selection