High incidence of cryptic repeated elements in microsatellite flanking regions of galatheid genomes and its evolutionary implications

During the development of PCR primer sets for icrosatellite marker loci from enriched genomic libraries for three squat lobster species from Galatheidae (Decapoda: Anomura); Munida rugosa (Fabricius, 1775), M. sarsi (Huus, 1935), and Galathea strigosa (Linnaeus, 1761) (collectively known as squat lobsters), a number of unforeseen problems were encountered. These included PCR amplification failure, lack of amplification consistency, and the amplification of multiple fragments. Careful examination of microsatellite containing sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. BLAST analysis of these and other VNTR containing sequences (N 5 252) indicates that these cryptic elements can be grouped into families based upon sequence similarities. The unique features characterising these families suggest that different molecular mechanisms are involved. Of particular relevance is the association of microsatellites with mobile elements. This is the first reported observation of this phenomenon in crustaceans, and it also helps to explain why microsatellite primer development in galatheids has been relatively unsuccessful to date. We suggest a number of steps that can be used to identify similar problems in microsatellite marker development for other species, and also alternative approaches for both marker development and for the study of molecular evolution of species characterised by complex genome organisation. More specifically, we argue that new generation sequencing methodologies, which capitalise on parallel and multiplexed sequencing may pave the way forward for future crustacean research.

Introduction to Domain-Driven Data Mining Special Section

In the last decade, data mining has emerged as one of the most dynamic and lively areas in information technology. Although many algorithms and techniques for data mining have been proposed, they either focus on domain independent techniques or on very specific domain problems. A general requirement in bridging the gap between academia and business is to cater to general domain-related issues surrounding real-life applications, such as constraints, organizational factors, domain expert knowledge, domain adaption, and operational knowledge. Unfortunately, these either have not been addressed, or have not been sufficiently addressed, in current data mining research and development.Domain-Driven Data Mining (D3M) aims to develop general principles, methodologies, and techniques for modeling and merging comprehensive domain-related factors and synthesized ubiquitous intelligence surrounding problem domains with the data mining process, and discovering knowledge to support business decision-making. This paper aims to report original, cutting-edge, and state-of-the-art progress in D3M. It covers theoretical and applied contributions aiming to: 1) propose next-generation data mining frameworks and processes for actionable knowledge discovery, 2) investigate effective (automated, human and machine-centered and/or human-machined-co-operated) principles and approaches for acquiring, representing, modelling, and engaging ubiquitous intelligence in real-world data mining, and 3) develop workable and operational systems balancing technical significance and applications concerns, and converting and delivering actionable knowledge into operational applications rules to seamlessly engage application processes and systems.

A Scalable and Programmable Modular Traffic Manager Architecture

A key issue in the design of next generation Internet routers and switches will be provision of traffic manager (TM) functionality in the datapaths of their high speed switching fabrics. A new architecture that allows dynamic deployment of different TM functions is presented. By considering the processing requirements of operations such as policing and congestion, queuing, shaping and scheduling, a solution has been derived that is scalable with a consistent programmable interface. Programmability is achieved using a function computation unit which determines the action (e.g. drop, queue, remark, forward) based on the packet attribute information and a memory storage part. Results of a Xilinx Virtex-5 FPGA reference design are presented.

A scalable packet sorting circuit for high-speed WFQ packet scheduling

A novel implementation of a tag sorting circuit for a weighted fair queueing (WFQ) enabled Internet Protocol (IP) packet scheduler is presented. The design consists of a search tree, matching circuitry, and a custom memory layout. It is implemented using 130-nm silicon technology and supports quality of service (QoS) on networks at line speeds of 40 Gb/s, enabling next generation IP services to be deployed.

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.

Proteasome inhibitors in cancer therapy

The ubiquitin proteasome pathway plays a critical role in regulating many processes in the cell which are important for tumour cell growth and survival. Inhibition of proteasome function has emerged as a powerful strategy for anti-cancer therapy. Clinical validation of the proteasome as a therapeutic target was achieved with bortezomib and has prompted the development of a second generation of proteasome inhibitors with improved pharmacological properties. This review summarises the main mechanisms of action of proteasome inhibitors in cancer, the development of proteasome inhibitors as therapeutic agents and the properties and progress of next generation proteasome inhibitors in the clinic.

A Pipeline Interleaved Heterogeneous SIMD Soft Processor Array Architecture for MIMO-OFDM Detection

The most promising way to maintain reliable data transfer across the rapidly fluctuating channels used by next generation multiple-input multiple-output communications schemes is to exploit run-time variable modulation and antenna configurations. This demands that the baseband signal processing architectures employed in the communications terminals must provide low cost and high performance with runtime reconfigurability. We present a softcore-processor based solution to this issue, and show for the first time, that such programmable architectures can enable real-time data operation for cutting-edge standards
such as 802.11n; furthermore, by exploiting deep processing pipelines and interleaved task execution, the cost and performance of these architectures is shown to be on a par with traditional dedicated circuit based solutions. We believe this to be the first such programmable architecture to achieve this, and the combination of implementation efficiency and programmability makes this implementation style the most promising approach for hosting such dynamic architectures.

Electrical methods of controlling bacterial adhesion and biofilm on device surfaces.

This review will summarize the significant body of research within the field of electrical methods of controlling the growth of microorganisms. We examine the progress from early work using current to kill bacteria in static fluids to more realistic treatment scenarios such as flow-through systems designed to imitate the human urinary tract. Additionally, the electrical enhancement of biocide and antibiotic efficacy will be examined alongside recent innovations including the biological applications of acoustic energy systems to prevent bacterial surface adherence. Particular attention will be paid to the electrical engineering aspects of previous work, such as electrode composition, quantitative electrical parameters and the conductive medium used. Scrutiny of published systems from an electrical engineering perspective will help to facilitate improved understanding of the methods, devices and mechanisms that have been effective in controlling bacteria, as well as providing insights and strategies to improve the performance of such systems and develop the next generation of antimicrobial bioelectric materials.

Temporal characterization of attosecond pulses emitted from solid-density plasmas

The generation of high harmonics from solid-density plasmas promises the production of attosecond (as) pulses orders of magnitude brighter than those from conventional rare gas sources. However, while spatial and spectral emission of surface harmonics has been characterized in detail in many experiments proof that the harmonic emission is indeed phase locked and thus bunched in as-pulses has only been delivered recently (Nomura et al 2009 Nat. Phys. 5 124-8). In this paper, we discuss the experimental setup of our extreme ultraviolet (XUV) autocorrelation (AC) device in detail and show the first two-photon ionization and subsequent AC experiment using solid target harmonics. In addition, we describe a simple analytical model to estimate the chirp between the individual generated harmonics in the sub- and mildly relativistic regime and validate it using particle-in-cell (PIC) simulations. Finally, we propose several methods applicable to surface harmonics to extend the temporal pulse characterization to higher photon energies and for the reconstruction of the spectral phase between the individual harmonics. The experiments described in this paper prove unambiguously that harmonic emission from solid-density plasmas indeed occurs as a train of sub- femtosecond pulses and thus fulfills the most important property for a next-generation as-pulse source of unprecedented brightness.

FPGA based Soft-core SIMD Processing: A MIMO-OFDM Fixed-Complexity Sphere Decoder Case Study

To enable reliable data transfer in next generation Multiple-Input Multiple-Output (MIMO) communication systems, terminals must be able to react to fluctuating channel conditions by having flexible modulation schemes and antenna configurations. This creates a challenging real-time implementation problem: to provide the high performance required of cutting edge MIMO standards, such as 802.11n, with the flexibility for this behavioural variability. FPGA softcore processors offer a solution to this problem, and in this paper we show how heterogeneous SISD/SIMD/MIMD architectures can enable programmable multicore architectures on FPGA with similar performance and cost as traditional dedicated circuit-based architectures. When applied to a 4×4 16-QAM Fixed-Complexity Sphere Decoder (FSD) detector we present the first soft-processor based solution for real-time 802.11n MIMO.

A Kernel Interleaved Scheduling Method for Streaming Applications on Soft-core Vector Processors

Massively parallel networks of highly efficient, high performance Single Instruction Multiple Data (SIMD) processors have been shown to enable FPGA-based implementation of real-time signal processing applications with performance and
cost comparable to dedicated hardware architectures. This is achieved by exploiting simple datapath units with deep processing pipelines. However, these architectures are highly susceptible to pipeline bubbles resulting from data and control hazards; the only way to mitigate against these is manual interleaving of
application tasks on each datapath, since no suitable automated interleaving approach exists. In this paper we describe a new automated integrated mapping/scheduling approach to map algorithm tasks to processors and a new low-complexity list scheduling technique to generate the interleaved schedules. When applied to a spatial Fixed-Complexity Sphere Decoding (FSD) detector
for next-generation Multiple-Input Multiple-Output (MIMO) systems, the resulting schedules achieve real-time performance for IEEE 802.11n systems on a network of 16-way SIMD processors on FPGA, enable better performance/complexity balance than current approaches and produce results comparable to handcrafted implementations.

The Behavior of compressively loaded stiffener runout specimens - Part I: Experiments

The development of the next generation of civil and military transport aircraft will inevitably see an increased use of advanced carbon fibre composite material in the primary structure if performance targets are to be met. One concern in this development is the vulnerability of co-cured and co-bonded stiffened structures to through-thickness stresses at the skin-stiffener interfaces, particularly in stiffener runout regions. These regions are a consequence of the requirement to terminate stiffeners at cutouts, rib intersections, or other structural features which interrupt the stiffener load path.

This work presents the results of an experimental programme investigating the failure of thick-sectioned stiffener runout specimens loaded in uniaxial compression. For all tests, failure initiated at the edge of the runout and propagated across the skin-stiffener interface. It was found that the failure load of each specimen was greatly influenced by intentional changes in the geometric features of these specimens. High frictional forces at the edge of the runout were also deduced from a fractographic analysis, indicating a predominantly Mode II initial failure mode.

Failure of thick-skinned stiffener runout sections loaded in uniaxial compression

Recent efforts towards the development of the next generation of large civil and military transport aircraft within the European community have provided new impetus for investigating the potential use of composite material in the primary structure. One concern in this development is the vulnerability of co-cured stiffened structures to through-thickness stresses at the skin-stiffener interfaces particularly in stiffener runout regions. These regions are an inevitable consequence of the requirement to terminate stiffeners at cutouts, rib intersections or other structural features which interrupt the stiffener load path. In this respect, thickerskinned components are more vulnerable than thin-skinned ones. This work presents an experimental and numerical study of the failure of thick-sectioned stiffener runout specimens loaded in uniaxial compression. The experiments revealed that failure was initiated at the edge of the runout and propagated across the skin-stiffener interface. High frictional forces at the edge of the runout were also deduced from a fractographic analysis and it is postulated that these forces may enhance the fracture toughness of the specimens. Finite element analysis using an efficient thick-shell element and the Virtual Crack Closure Technique was able to qualitatively predict the crack growth characteristics for each specimen

Nanoscale Control of Phase Variants in Strain-Engineered BiFeO3

Development of magnetoelectric, electromechanical, and photovoltaic devices based on mixed-phase rhombohedral-tetragonal (R-T) BiFeO3 (BFO) systems is possible only if the control of the engineered R phase variants is realized. Accordingly, we explore the mechanism of a bias induced phase transformation in this system. Single point spectroscopy demonstrates that the T -> R transition is activated at lower voltages compared to T -> - T polarization switching. With phase field modeling, the transition is shown to be electrically driven. We further demonstrate that symmetry of formed R-phase rosettes can be broken by a proximal probe motion, allowing controlled creation of R variants with defined orientation. This approach opens a pathway to designing next-generation magnetoelectronic and data storage devices in the nanoscale.