Ranking of microRNA target prediction scores by Pareto front analysis

Over the past ten years, a variety of microRNA target prediction methods has been developed, and many of the methods are constantly improved and adapted to recent insights into miRNA-mRNA interactions. In a typical scenario, different methods return different rankings of putative targets, even if the ranking is reduced to selected mRNAs that are related to a specific disease or cell type. For the experimental validation it is then difficult to decide in which order to process the predicted miRNA-mRNA bindings, since each validation is a laborious task and therefore only a limited number of mRNAs can be analysed. We propose a new ranking scheme that combines ranked predictions from several methods and - unlike standard thresholding methods - utilises the concept of Pareto fronts as defined in multi-objective optimisation. In the present study, we attempt a proof of concept by applying the new ranking scheme to hsa-miR-21, hsa-miR-125b, and hsa-miR-373 and prediction scores supplied by PITA and RNAhybrid. The scores are interpreted as a two-objective optimisation problem, and the elements of the Pareto front are ranked by the STarMir score with a subsequent re-calculation of the Pareto front after removal of the top-ranked mRNA from the basic set of prediction scores. The method is evaluated on validated targets of the three miRNA, and the ranking is compared to scores from DIANA-microT and TargetScan. We observed that the new ranking method performs well and consistent, and the first validated targets are elements of Pareto fronts at a relatively early stage of the recurrent procedure. which encourages further research towards a higher-dimensional analysis of Pareto fronts. (C) 2010 Elsevier Ltd. All rights reserved.

Rare occurrence of a bigeye tuna Thunnus obesus in British waters, with notes on other occurrences of sub-tropical tunas

A freshly dead bigeye tuna Thunnus obesus was washed ashore near Burry Port, Wales (51 degrees 40' N; 4 degrees 15' W) in August, 2006. This is only the third occasion that the species has been observed in British waters, and is the largest and most northerly recorded specimen.

Ion acceleration from the shock front induced by hole boring in ultraintense laser-plasma interactions

Ion-acceleration processes have been studied in ultraintense laser plasma interactions for normal incidence irradiation of solid deuterated targets via neutron spectroscopy. The experimental neutron spectra strongly suggest that the ions are preferentially accelerated radially, rather than into the bulk of the material from three-dimensional Monte Carlo fitting of the neutron spectra. Although the laser system has a 10(-7) contrast ratio, a two-dimensional magnetic hydrodynamics simulation shows that the laser pedestal generates a 10 mum scale length in the coronal plasma with a 3 mum scale-length plasma near the critical density. Two-dimensional particle-in-cell simulations, incorporating this realistic density profile, indicate that the acceleration of the ions is caused by a collisionless shock formation. This has implications for modeling energy transport in solid is caused by a collisionless shock formation. This has implications for modeling energy transport in solid density plasmas as well as cone-focused fast ignition using the next generation PW lasers currently under construction.

TAP studies of CO oxidation over CuMnO<sub>Xsub> and Au/CuMnO<sub>Xsub> catalysts

The mechanism of CO oxidation reactions over undoped and gold-doped CuMnOX (Hopcalite) catalysts has been examined using a temporal analysis of products (TAP) reactor Gold doping has been found to increase the activity of the mixed oxide catalyst significantly however using consecutive pulsing TAP experiments the presence of gold was not found to affect the contribution of the Langmuir-Hinshelwood mechanism Conversely gold doping was found to promote the Mars van Krevelen mechanism Using CO and O-2 multi-pulse TAP experiments the gold was found to modify the catalyst surface such that it stores much more oxygen that is active for the CO oxidation The CO multi-pulse experiments indicated that two distinct types of active oxygen species were found to be involved in the CO oxidation One type was observed in a similar amount on both doped and undoped catalysts and was associated with mixed oxide while the second type was only found on the gold-doped catalyst and was therefore clearly associated with the presence of gold on the catalyst surface The latter was found to be much less active than the oxygen inherent to the oxide but was at a concentration of approximately 10 times larger leading to the enhanced activity observed on gold doping (C) 2010 Elsevier Inc All rights reserved

Sub-Wavelength Profile 2-D Leaky-Wave Antennas With Two Periodic Layers

A fast and accurate analysis and synthesis technique for high-gain sub-wavelength 2-D Fabry-Perot leaky-wave antennas (LWA) consisting of two periodic metallodielectric arrays over a ground plane is presented. Full-wave method of moments (MoM) together with reciprocity is employed for the estimation of the near fields upon plane wave illumination and the extraction of the radiation patterns of the LWA. This yields a fast and rigorous tool for the characterisation of this type of antennas. A thorough convergence study for different antenna designs is presented and the operation principles of these antennas as well as the radiation characteristics are discussed. Moreover, design guidelines to tailor the antenna profile, the dimensions of the arrays as well as the antenna directivity and bandwidth are provided. A study on the radiation efficiency for antennas with different profiles is also presented and the trade off between directivity and radiation bandwidth is discussed. Numerical examples are given throughout to demonstrate the technique. A finite size antenna model is simulated using commercial software (CST Microstripes 2009) which validates the technique.

Regulation of cyclin D<sub>1sub> by the BRCA1-BARD1 complex

Background BRCA1 and cyclin D<sub>1sub> are both essential for normal breast development and mutation or aberration of their expression is associated with breast cancer [1,2]. Cyclin D<sub>1sub> is best known as a G<sub>1sub> cyclin where it regulates the G<sub>1sub> to S phase transition by acting as a rate-limiting subunit of CDK4/6 kinase activity. More recently, however, Stacey has demonstrated that cyclin D<sub>1sub> levels in G<sub>2sub>/M determine whether a cell continues to proliferate or exits the cell cycle [3]. The majority of BRCA1 in the cell is bound to BARD1 through their N-terminal RING domains. Heterodimerization is essential for the stability and correct localization of the complex and confers ubiquitin ligase activity to BRCA1. The importance of the ligase activity of BRCA1 to breast cancer development is inferred from the fact that N-terminal diseaseassociated mutations are proposed to reduce ligase activity [4]. Methods Protein–protein interactions were demonstrated using yeast-two-hybrid and coimmunoprecipitation. Protein levels were altered through overexpression, siRNA and antisense technology. The effect of proteasome inhibitors and cycloheximide treatment was also examined. Results We initially identified cyclin D<sub>1sub> as a binding partner of BARD1 in a yeast-two-hybrid screen and defined the minimal binding region as the N-terminus of BARD1. This interaction was confirmed in vivo by coimmunoprecipitation. The N-terminus of BARD1 also binds BRCA1 and imparts ubiquitin ligase activity to the complex. Covalent modification of proteins with ubiquitin is a common regulatory mechanism in eukaryotic cells. Traditionally polyubiquitin chains linked through lysine 48 target proteins for degradation by the 26 S proteasome. We have demonstrated that cyclin D<sub>1sub> protein levels are inversely related to BRCA1 and BARD1 levels in several model systems. Furthermore, regulation of cyclin D1 levels occurs through a post-transcriptional mechanism and requires the ligase activity of BRCA1. Interestingly, this phenomenon is cell-cycle regulated, occurring in G<sub>2sub>/M. Conclusion We propose that cyclin D<sub>1sub> is a potential substrate for BRCA1 ubiquitination and that this targets cyclin D<sub>1sub> for proteasomal-mediated degradation. Future work will focus on ascertaining the functional consequence of cyclin D<sub>1sub> regulation by the BRCA1–BARD1 complex; in particular, the impact of BRCA1, mediated through regulation of cyclin D<sub>1sub>, on the proliferation versus differentiation decision.