Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays.

Introduction Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by chronic joint inflammation of unknown cause in children. JIA is an autoimmune disease and small numbers of auto-antibodies have been reported in JIA patients. The identification of antibody markers could improve the existing clinical management of patients. Methods A pilot study was performed on the application of a high-throughput platform, nucleic acid programmable protein arrays (NAPPA), to assess the levels of antibodies present in the systemic circulation and synovial joint of a small cohort of juvenile arthritis patients. Plasma and synovial fluid from ten JIA patients was screened for antibodies against 768 proteins on NAPPA. Results Quantitative reproducibility of NAPPA was demonstrated with >0.95 intra- and inter- array correlations. A strong correlation was also observed for the levels of antibodies between plasma and synovial fluid across the study cohort (r=0.96). Differences in the levels of 18 antibodies were revealed between sample types across all patients. Patients were segregated into two clinical subtypes with distinct antibody signatures by unsupervised hierarchical cluster analysis. Conclusions NAPPA provides a high-throughput quantitatively reproducible platform to screen for disease specific autoantibodies at the proteome level on a microscope slide. The strong correlation between the circulating antibody levels and those of the inflamed joint represents a novel finding and provides confidence to use plasma for discovery of autoantibodies in JIA, thus circumventing the challenges associated with joint aspiration. We expect that autoantibody profiling of JIA patients on NAPPA could yield antibody markers that can act as criteria to stratify patients, predict outcomes and understand disease etiology at the molecular level.

A hardware solution on multi-field packet classification

In this paper, a hardware solution for packet classification based on multi-fields is presented. The proposed scheme focuses on a new architecture based on the decomposition method. A hash circuit is used in order to reduce the memory space required for the Recursive Flow Classification (RFC) algorithm. The implementation results show that the proposed architecture achieves significant performance advantage that is comparable to that of some well-known algorithms. The solution is based on Altera Stratix III FPGA technology.

Programmable image processing chip

A new high performance, programmable image processing chip targeted at video and HDTV applications is described. This was initially developed for image small object recognition but has much broader functional application including 1D and 2D FIR filtering as well as neural network computation. The core of the circuit is made up of an array of twenty one multiplication-accumulation cells based on systolic architecture. Devices can be cascaded to increase the order of the filter both vertically and horizontally. The chip has been fabricated in a 0.6 µ, low power CMOS technology and operates on 10 bit input data at over 54 Megasamples per second. The introduction gives some background to the chip design and highlights that there are few other comparable devices. Section 2 gives a brief introduction to small object detection. The chip architecture and the chip design will be described in detail in the later sections.

Simulations of magnetic microstructure in thin film elements used for programmable motion of magnetic particles

The results of two-dimensional micromagnetic modeling of magnetization patterns in Permalloy ellipses under the influence of rotating constant-amplitude magnetic fields are discussed. Ellipses of two different lateral sizes have been studied, 0.5m x 1.5m and 1m x 3m. The amplitude of the rotating magnetic field was varied between simulations with the condition that it must be large enough to saturate or nearly saturate the ellipse with the field applied along the long axis of the ellipse. For the smaller ellipse size it is found that the magnetization pattern forms an S state and the direction of the net magnetization lags behind the direction of the applied field. At a critical angle of the rotating magnetic field the direction of the magnetization switches by a large angle to a new S state. Both the critical angle and the angle interval of the switch depend on field amplitude. For this new state, it is instead the applied field direction that lags behind the magnetization direction. The transient magnetization patterns correspond to multi-domain patterns including two vortices, but this state never exists for the equilibrated magnetization patterns. The behavior of the larger ellipse in rotating field is different. With the field applied along the long-axis of the ellipse, the magnetization of the ellipse is nearly saturated with a vortex close to each apex of the ellipse. As the field is rotated, this magnetization pattern remains and the net-magnetization direction lags behind the direction of the field until for a certain angle of the applied field an equilibrium multi-domain state is created. Comparisons are made with corresponding experimental results obtained by performing in-field magnetic force microscopy on Permalloy ellipses.

Programmable motion and separation of single magnetic particles on patterned magnetic surfaces

Motion of single micrometer-sized magnetic particles on patterned magnetic surfaces is controlled by a rotating magnetic field (see Figure and cover). Patterns of thin-film magnetic elements are tailored to form transport lines. Individual particles are separated by adding junctions to the transport lines. The method can improve existing applications in biotechnology and generate new ones in life sciences.

Surface-Enhanced Raman Scattering from Metallic Nanostructures: Bridging the Gap between the Near-Field and Far-Field Responses

We present here a detailed study of the complex relationship between the electromagnetic near-field and far-field responses of "real" nanostructured metallic surfaces. The near-field and far-field responses are specified in terms of (spectra of) the surface-enhanced Raman-scattering enhancement factor (SERS EF) and optical extinction, respectively. First, it is shown that gold nanorod- and nanotube-array substrates exhibit three distinct localized surface plasmon resonances (LSPRs): a longitudinal, a transverse, and a cavity mode. The cavity mode simultaneously has the largest impact on the near-field behavior (as observed through the SERS EF) and the weakest optical interaction: It has a "near-field-type" character. The transverse and longitudinal modes have a significant impact on the far-field behavior but very little impact on SERS: They have a "far-field-type" character. We confirm the presence of the cavity mode using a combination of SERS EF spectra, electron microscopy, and electromagnetic modeling and thus clearly illustrate and explain the (lack of) correlation between the SERS EF spectra and the optical response in terms of the contrasting character of the three LSPRs. In doing so, we experimentally demonstrate that, for a surface that supports multiple LSPRs, the near-field and far-field properties can in fact be tuned almost independently. It is further demonstrated that small changes in geometrical parameters that tune the spectral location of the LPSRs can also drastically influence the character of these modes, resulting in certain unusual behavior, such as the far-field resonance redshift as the near-field resonance blueshifts. DOI: 10.1103/PhysRevX.3.011001

Performance analysis of an infinite array linear clustered plug nozzle

The effects of module shape, module design, three dimensional flow field generated by modules, and partition of primary nozzle on the performance of an infinite array linear clustered plug nozzle are discussed. The module shape is a critical element for nozzle performance and the partition of the primary nozzle with round-to square modules causes a vacuum thrust reduction with respect to two-dimensional model. The performance analysis of different module configuration allows weighing separately the role of clustering and the role of module design. In operating conditions characterized by turned off modules the performance loss is larger, but the difference due to the module shape are smaller and mostly due to the module contribution. The performance of the plug nozzle can be improved by module design, which reduces the module exit flow nonuniformity.

Pilot Tone Actuated Antenna Array Pattern Reconfiguration

A new strategy for remote reconfiguration of an antenna array far field radiation pattern is described. The scheme uses a pilot tone co-transmitted with a carrier signal from a location distant from that of a receive antenna array whose far field pattern is to be reconfigured. By mixing the co-transmitted signals locally at each antenna element in the array an IF signal is formed which defines an equivalent array spacing that can be made variable by tuning the frequency of the pilot tone with respect to the RF carrier. This makes the antenna array factor hence far field spatial characteristic reconfigurable on receive. For a 10 x 1 microstrip patch element array we show that the receive pattern can be made to vary from 35 to 10 degrees half power beam width as the difference frequency between the pilot and the carrier at 2.45 GHz varies between 10 MHz and 500 MHz carrier.

A Spherical Array Approach for Simulation of Binaural Impulse Responses using the Finite Difference Time Domain Method

The finite difference time domain (FDTD) method has direct applications in musical instrument modeling, simulation of environmental acoustics, room acoustics and sound reproduction paradigms, all of which benefit from auralization. However, rendering binaural impulse responses from simulated
data is not straightforward to accomplish as the calculated pressure at FDTD grid nodes does not contain any directional information. This paper addresses this issue by introducing a spherical array to capture sound pressure on a finite difference grid, and decomposing it into a plane-wave density
function. Binaural impulse responses are then constructed in the spherical harmonics domain by combining the decomposed grid data with free field head-related transfer functions. The effects of designing a spherical array in a Cartesian grid are studied, and emphasis is given to the relationships
between array sampling and the spatial and spectral design parameters of several finite-difference
schemes.

Binaural Reproduction of Finite Difference Simulations Using Spherical Array Processing

Due to its efficiency and simplicity, the finite-difference time-domain method is becoming a popular choice for solving wideband, transient problems in various fields of acoustics. So far, the issue of extracting a binaural response from finite difference simulations has only been discussed in the context of embedding a listener geometry in the grid. In this paper, we propose and study a method for binaural response rendering based on a spatial decomposition of the sound field. The finite difference grid is locally sampled using a volumetric array of receivers, from which a plane wave density function is computed and integrated with free-field head related transfer functions, in the spherical harmonics domain. The volumetric array is studied in terms of numerical robustness and spatial aliasing. Analytic formulas that predict the performance of the array are developed, facilitating spatial resolution analysis and numerical binaural response analysis for a number of finite difference schemes. Particular emphasis is placed on the effects of numerical dispersion on array processing and on the resulting binaural responses. Our method is compared to a binaural simulation based on the image method. Results indicate good spatial and temporal agreement between the two methods.

FPGA Soft-core Processors, Compiler and Hardware Optimizations validated using HOG

There is demand for an easily programmable, high performance image processing platform based on FPGAs. In previous work, a novel, high performance processor - IPPro was developed and a Histogram of Orientated Gradients (HOG) algorithm study undertaken on a Xilinx Zynq platform. Here, we identify and explore a number of mapping strategies to improve processing efficiency for soft-cores and a number of options for creation of a division coprocessor. This is demonstrated for the revised high definition HOG implementation on a Zynq platform, resulting in a performance of 328 fps which represents a 146% speed improvement over the original realization and a tenfold reduction in energy.

FPGA based Streaming Image Processing Processor (SIPPro) architecture to accelerate data intensive applications

Current data-intensive image processing applications push traditional embedded architectures to their limits. FPGA based hardware acceleration is a potential solution but the programmability gap and time consuming HDL design flow is significant. The proposed research approach to develop “FPGA based programmable hardware acceleration platform” that uses, large number of Streaming Image processing Processors (SIPPro) potentially addresses these issues. SIPPro is pipelined in-order soft-core processor architecture with specific optimisations for image processing applications. Each SIPPro core uses 1 DSP48, 2 Block RAMs and 370 slice-registers, making the processor as compact as possible whilst maintaining flexibility and programmability. It is area efficient, scalable and high performance softcore architecture capable of delivering 530 MIPS per core using Xilinx Zynq SoC (ZC7Z020-3). To evaluate the feasibility of the proposed architecture, a Traffic Sign Recognition (TSR) algorithm has been prototyped on a Zedboard with the color and morphology operations accelerated using multiple SIPPros. Simulation and experimental results demonstrate that the processing platform is able to achieve a speedup of 15 and 33 times for color filtering and morphology operations respectively, with a significant reduced design effort and time.

Characterisation of a two-dimensional liquid-filled ion chamber detector array using flattened and unflattened beams for small fields, small MUs and high dose-rates

In this study, the PTW 1000SRS array with Octavius 4D phantom was characterised for FF and FFF beams. MU linearity, field size, dose rate, dose per pulse (DPP) response and dynamic conformal arc treatment accuracy of the 1000SRS array were assessed for 6MV, 6FFF and 10FFF beams using a Varian TrueBeam STx linac. The measurements were compared with a pinpoint IC, microdiamond IC and EBT3 Gafchromic film. Measured dose profiles and FWHMs were compared with film measurements. Verification of FFF volumetric modulated arc therapy (VMAT) clinical plans were assessed using gamma analysis with 3%/3 mm and 2%/2 mm tolerances (10% threshold). To assess the effect of cross calibration dose rate, clinical plans with different dose rates were delivered and analysed. Output factors agreed with film measurements to within 4.5% for fields between 0.5 and 1 cm and within 2.7% for field sizes between 1.5 and 10 cm and were highly correlated with the microdiamond IC detector. Field sizes measured with the 1000SRS array were within 0.5 mm of film measurements. A drop in response of up to 1.8%, 2.4% and 5.2% for 6MV, 6FFF and 10FFF beams respectively was observed with increasing nominal dose rate. With an increase in DPP, a drop of up to 1.7%, 2.4% and 4.2% was observed in 6MV, 6FFF and 10FFF respectively. The differences in dose following dynamic conformal arc deliveries were less than 1% (all energies) from calculated. Delivered VMAT plans showed an average pass percentage of 99.5(±0.8)% and 98.4(±3.4)% with 2%/2 mm criteria for 6FFF and 10FFF respectively. A drop to 97.7(±2.2)% and 88.4(±9.6)% were observed for 6FFF and 10FFF respectively when plans were delivered at the minimum dose rate and calibrated at the maximum dose rate. Calibration using a beam with the average dose rate of the plan may be an efficient method to overcome the dose rate effects observed by the 1000SRS array.

Investigating Tools used to Analyse the Impact of a Wave Farm on the surrounding Wave Field

For wave energy to become commercially viable, it is predicted that wave energy converters (WECs) will need to be installed in large wave farms. This will required an extensive environmental impact study. Assessments of impacts of these sites requires prior numerical modelling however the available tools have not been fully validated.
This project investigates the area surrounding an array of five scaled WEC models using experimental techniques. It then assesses the suitability of numerical tools to be validated with this experimental data. Validated numerical tools could then be used to predict parameters relating to the models such as reflection and transmission coefficients.
The physical aspect of this project was conducted in the Portaferry wave basin owned by Queen’s University Belfast. The device studied was a bottom hinged oscillating wave surge converter (OWSC) which penetrates the surface (similar to the Oyster device). The models were tested at 40th scale.

Feature Study on a Programmable Network Traffic Classifier

Monitoring and tracking of IP traffic flows are essential for network services (i.e. packet forwarding). Packet header lookup is the main part of flow identification by determining the predefined matching action for each incoming flow. In this paper, an improved header lookup and flow rule update solution is investigated. A detailed study of several well-known lookup algorithms reveals that searching individual packet header field and combining the results achieve high lookup speed and flexibility. The proposed hybrid lookup architecture is comprised of various lookup algorithms, which are selected based on the user applications and system requirements.