Fragmentation and plasmid strand breaks in pure and gold-doped DNA irradiated by beams of fast hydrogen atoms

The results of an investigation into the damage caused to dry plasmid DNA after irradiation by fast (keV) hydrogen atoms are presented. Agarose gel electrophoresis was used to assess single and double strand break yields as a function of dose in dry DNA samples deposited on a mica substrate. Damage levels were observed to increase with beam energy. Strand break yields demonstrated a considerable dependence on sample structure and the method of sample preparation. Additionally, the effect of high-Z nanoparticles on damage levels was investigated by irradiating DNA samples containing controlled amounts of gold nanoparticles. In contrast to previous (photonic) studies, no enhancement of strand break yields was observed with the particles showing a slight radioprotective effect. A model of DNA damage as a function of dose has been constructed in terms of the probability for the creation of single and double strand breaks, per unit ion flux. This model provides quantitative conclusions about the effects of both gold nanoparticles and the different buffers used in performing the assays and, in addition, infers the proportion of multiply damaged fragments.

A fast multi-output RBF neural network construction method

This paper investigates the center selection of multi-output radial basis function (RBF) networks, and a multi-output fast recursive algorithm (MFRA) is proposed. This method can not only reveal the significance of each candidate center based on the reduction in the trace of the error covariance matrix, but also can estimate the network weights simultaneously using a back substitution approach. The main contribution is that the center selection procedure and the weight estimation are performed within a well-defined regression context, leading to a significantly reduced computational complexity. The efficiency of the algorithm is confirmed by a computational complexity analysis, and simulation results demonstrate its effectiveness. (C) 2010 Elsevier B.V. All rights reserved.

Fast, copper-free click chemistry: a convenient solid-phase approach to oligonucleotide conjugation

Solid-phase oligonucleotide conjugation by nitrile oxide-alkyne click cycloaddition chemistry has been successfully demonstrated; the reaction, compatible with all nucleobases, requires no metal catalyst and proceeds under physiological conditions.

Impure Thinking Practices and Clinical Acts: The Sonorous Becomings of Heidi Fast

This article introduces the recent sound works of Heidi Fast, a Finnish voice and performance artist. Fast’s creative practice operates between art and philosophy, and articulates several ‘zones of becoming’: what Fast designates as ‘the clinical’, ‘the virtual’ and ‘vocal thought-material’. Using a methodology of routing, the article shows how these zones emerge as aesthetic, ethical and political concerns within Fast’s work. Since 2005, Fast’s sound works have variously taken shape as miniature concerts, social sculptures, imaginary soundscapes and environmental music performances. Drawing upon the writings of theorists who have helped shape her practice, this article argues that Fast uses sound and voice to propose an ‘actualising philosophy’. This philosophy actualises virtualities (unrealised potentials), affecting transformative shifts through tiny mutations in perceptions and behaviours.

Effect of self-generated magnetic fields on fast-electron beam divergence in solid targets

The collimating effect of self-generated magnetic fields on fast-electron transport in solid aluminium targets irradiated by ultra-intense, picosecond laser pulses is investigated in this study. As the target thickness is varied in the range of 25 mu m to 1.4 mm, the maximum energies of protons accelerated from the rear surface are measured to infer changes in the fast-electron density and therefore the divergence of the fast-electron beam transported through the target. Purely ballistic spreading of the fast-electrons would result in a much faster decrease in the maximum proton energy with increasing target thickness than that measured. This implies that some degree of 'global' magnetic pinching of the fast-electrons occurs, particularly for thick (>400 mu m) targets. Numerical simulations of electron transport are in good agreement with the experimental data and show that the pinching effect of the magnetic field in thin targets is significantly reduced due to disruption of the field growth by refluxing fast-electrons.

Time of flight mass spectrometry for quantitative data analysis in fast transient studies using a Temporal Analysis of Products (TAP) reactor

A Time of flight (ToF) mass spectrometer suitable in terms of sensitivity, detector response and time resolution, for application in fast transient Temporal Analysis of Products (TAP) kinetic catalyst characterization is reported. Technical difficulties associated with such application as well as the solutions implemented in terms of adaptations of the ToF apparatus are discussed. The performance of the ToF was validated and the full linearity of the specific detector over the full dynamic range was explored in order to ensure its applicability for the TAP application. The reported TAP-ToF setup is the first system that achieves the high level of sensitivity allowing monitoring of the full 0-200 AMU range simultaneously with sub-millisecond time resolution. In this new setup, the high sensitivity allows the use of low intensity pulses ensuring that transport through the reactor occurs in the Knudsen diffusion regime and that the data can, therefore, be fully analysed using the reported theoretical TAP models and data processing.

Low power field programmable gate array implementation of fast digital signal processing algorithms: characterisation and manipulation of data locality

Dynamic power consumption is very dependent on interconnect, so clever mapping of digital signal processing algorithms to parallelised realisations with data locality is vital. This is a particular problem for fast algorithm implementations where typically, designers will have sacrificed circuit structure for efficiency in software implementation. This study outlines an approach for reducing the dynamic power consumption of a class of fast algorithms by minimising the index space separation; this allows the generation of field programmable gate array (FPGA) implementations with reduced power consumption. It is shown how a 50% reduction in relative index space separation results in a measured power gain of 36 and 37% over a Cooley-Tukey Fast Fourier Transform (FFT)-based solution for both actual power measurements for a Xilinx Virtex-II FPGA implementation and circuit measurements for a Xilinx Virtex-5 implementation. The authors show the generality of the approach by applying it to a number of other fast algorithms namely the discrete cosine, the discrete Hartley and the Walsh-Hadamard transforms.

Generation and optimization of electron currents along the walls of a conical target for fast ignition

The interaction of an ultraintense laser pulse with a conical target is studied by means of numerical particle-in-cell simulations in the context of fast ignition. The divergence of the fast electron beam generated at the tip of the cone has been shown to be a crucial parameter for the efficient coupling of the ignition laser pulse to the precompressed fusion pellet. In this paper, we demonstrate that a focused hot electron beam is produced at the cone tip, provided that electron currents flowing along the surfaces of the cone sidewalls are efficiently generated. The influence of various interaction parameters over the formation of these wall currents is investigated. It is found that the strength of the electron flows is enhanced for high laser intensities, low density targets, and steep density gradients inside the cone. The hot electron energy distribution obeys a power law for energies of up to a few MeV, with the addition of a high-energy Maxwellian tail.

Ultra-fast processing of gigapixel Tissue MicroArray images using high performance computing.

BACKGROUND:
tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers. The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform.
METHODS:
a High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented in this study. Using an HP high performance cluster and a centralised dynamic load balancing approach, the simultaneous analysis of multiple tissue-cores were established. This was evaluated on Non-Small Cell Lung Cancer TMAs for complex analysis of tissue pattern and immunohistochemical positivity.
RESULTS:
the automated processing of a single TMA virtual slide containing 230 patient samples can be significantly speeded up by a factor of circa 22, bringing the analysis time to one minute. Over 90 TMAs could also be analysed simultaneously, speeding up multiplex biomarker experiments enormously.
CONCLUSIONS:
the methodologies developed in this paper provide for the first time a genuine high throughput analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research. This will have widespread implications in translational tissue based research.