High-throughput discovery of post-transcriptional cis-regulatory elements

Validation of 8mers found in the main screen. (PDF 280 kb

Model-based object recognition from a complex binary imagery using genetic algorithm

This paper describes a technique for model-based object recognition in a noisy and cluttered environment, by extending the work presented in an earlier study by the authors. In order to accurately model small irregularly shaped objects, the model and the image are represented by their binary edge maps, rather then approximating them with straight line segments. The problem is then formulated as that of finding the best describing match between a hypothesized object and the image. A special form of template matching is used to deal with the noisy environment, where the templates are generated on-line by a Genetic Algorithm. For experiments, two complex test images have been considered and the results when compared with standard techniques indicate the scope for further research in this direction

Effective Interactions and Volume Energies in Charge-Stabilized Colloidal Suspensions

Charge-stabilized colloidal suspensions can be conveniently described by formally reducing the macroion-microion mixture to an equivalent one-component system of pseudo-particles. Within this scheme, the utility of a linear response approximation for deriving effective interparticle interactions has been demonstrated [M. J. Grimson and M. Silbert, Mol. Phys. 74, 397 (1991)]. Here the response approach is extended to suspensions of finite-sized macroions and used to derive explicit expressions for (1) an effective electrostatic pair interaction between pseudo-macroions and (2) an associated volume energy that contributes to the total free energy. The derivation recovers precisely the form of the DLVO screened-Coulomb effective pair interaction for spherical macroions and makes manifest the important influence of the volume energy on thermodynamic properties of deionized suspensions. Excluded volume corrections are implicitly incorporated through a natural modification of the inverse screening length. By including nonlinear response of counterions to macroions, the theory may be generalized to systematically investigate effective many-body interactions.Comment: 13 pages (J. Phys.: Condensed Matter, in press

Stability of Colloidal Quasicrystals

Freezing of charge-stabilized colloidal suspensions and relative stabilities of crystals and quasicrystals are studied using thermodynamic perturbation theory. Macroion interactions are modelled by effective pair potentials combining electrostatic repulsion with polymer-depletion or van der Waals attraction. Comparing free energies -- counterion terms included -- for elementary crystals and rational approximants to icosahedral quasicrystals, parameters are identified for which one-component quasicrystals are stabilized by a compromise between packing entropy and cohesive energy.Comment: 6 pages, 4 figure

Identity-by-descent estimation with population- and pedigree-based imputation in admixed family data

Background: In the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, although both family- and population-based imputation methods have been proposed. With the recent surge of family-based designs, family-based imputation has become more important. Imputation methods for both designs are based on identity-by-descent (IBD) information. Apart from imputation, the use of IBD information is also common for several types of genetic analysis, including pedigree-based linkage analysis. Methods: We compared the performance of several family- and population-based imputation methods in large pedigrees provided by Genetic Analysis Workshop 19 (GAW19). We also evaluated the performance of a new IBD mapping approach that we propose, which combines IBD information from known pedigrees with information from unrelated individuals. Results: Different combinations of the imputation methods have varied imputation accuracies. Moreover, we showed gains from the use of both known pedigrees and unrelated individuals with our IBD mapping approach over the use of known pedigrees only. Conclusions: Our results represent accuracies of different combinations of imputation methods that may be useful for data sets similar to the GAW19 pedigree data. Our IBD mapping approach, which uses both known pedigree and unrelated individuals, performed better than classical linkage analysis

Counterion Penetration and Effective Electrostatic Interactions in Solutions of Polyelectrolyte Stars and Microgels

Counterion distributions and effective electrostatic interactions between spherical macroions in polyelectrolyte solutions are calculated via second-order perturbation (linear response) theory. By modelling the macroions as continuous charge distributions that are permeable to counterions, analytical expressions are obtained for counterion profiles and effective pair interactions in solutions of star-branched and microgel macroions. The counterions are found to penetrate stars more easily than microgels, with important implications for screening of bare macroion interactions. The effective pair interactions are Yukawa in form for separated macroions, but are softly repulsive and bounded for overlapping macroions. A one-body volume energy, which depends on the average macroion concentration, emerges naturally in the theory and contributes to the total free energy.Comment: 15 pages, 5 figure

Hysteresis and the dynamic phase transition in thin ferromagnetic films

Hysteresis and the non-equilibrium dynamic phase transition in thin magnetic films subject to an oscillatory external field have been studied by Monte Carlo simulation. The model under investigation is a classical Heisenberg spin system with a bilinear exchange anisotropy in a planar thin film geometry with competing surface fields. The film exhibits a non-equilibrium phase transition between dynamically ordered and dynamically disordered phases characterized by a critical temperature Tcd, whose location of is determined by the amplitude H0 and frequency w of the applied oscillatory field. In the presence of competing surface fields the critical temperature of the ferromagnetic-paramagnetic transition for the film is suppressed from the bulk system value, Tc, to the interface localization-delocalization temperature Tci. The simulations show that in general Tcd < Tci for the model film. The profile of the time-dependent layer magnetization across the film shows that the dynamically ordered and dynamically disordered phases coexist within the film for T < Tcd. In the presence of competing surface fields, the dynamically ordered phase is localized at one surface of the film.Comment: PDF file, 21 pages including 8 figure pages; added references,typos added; to be published in PR

Business in Engineering Education: Issues, Identities, Hybrids, and Limits

This chapter explores how engineering students are broadened in their education through the teaching of non-engineering subjects, such as business subjects, in order to develop critical thinking skills and self-knowledge of what it means to be an engineer. The goal of the chapter is to provide a commentary on the level of interaction, from design of courses to design of curricula, between business faculty and engineering faculty, and the results of that interaction. This chapter sets out to (i) explore whether there appears to be a place in engineering education curricula for reflective critique of assumptions related to business thinking, and why; (ii) discover what kinds of business issues are reflected in engineering education curricula, and for what purpose; (iii) explore the degree of business hybridization in engineering degree programs; (iv) ask who teaches business issues within engineering education? To this end a taxonomy of engineering enlightenment is proposed, and this is used to discuss evidence of broadening with engineering curricula. The approach adopted is to describe all relevant engineering degree programs in Ireland, based on their publicly available program information; examine the accreditation reports for these same programs; and then survey deans from colleges or schools of business to examine whether the business college/school is involved in the education of engineering students in the institution or university. If yes, how the business college or relevant business faculty are engaged in the design of engineering curricula. In order to enable a comparative discussion, the chapter will focus on Irish engineering programs that seek accreditation from Engineers Ireland for professional engineering. A number of hybrid engineering programs of study are also explored, and their apparent strengths discussed, including hybridity limits