Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large

Conifers are resistant to attack from a large number of potential herbivores or pathogens. Previous molecular and biochemical characterization of selected conifer defence systems support a model of multigenic, constitutive and induced defences that act on invading insects via physical, chemical, biochemical or ecological (multitrophic) mechanisms. However, the genomic foundation of the complex defence and resistance mechanisms of conifers is largely unknown. As part of a genomics strategy to characterize inducible defences and possible resistance mechanisms of conifers against insect herbivory, we developed a cDNA microarray building upon a new spruce (Picea spp.) expressed sequence tag resource. This first-generation spruce cDNA microarray contains 9720 cDNA elements representing c. 5500 unique genes. We used this array to monitor gene expression in Sitka spruce (Picea sitchensis) bark in response to herbivory by white pine weevils (Pissodes strobi, Curculionidae) or wounding, and in young shoot tips in response to western spruce budworm (Choristoneura occidentalis, Lepidopterae) feeding. Weevils are stem-boring insects that feed on phloem, while budworms are foliage feeding larvae that consume needles and young shoot tips. Both insect species and wounding treatment caused substantial changes of the host plant transcriptome detected in each case by differential gene expression of several thousand array elements at 1 or 2 d after the onset of treatment. Overall, there was considerable overlap among differentially expressed gene sets from these three stress treatments. Functional classification of the induced transcripts revealed genes with roles in general plant defence, octadecanoid and ethylene signalling, transport, secondary metabolism, and transcriptional regulation. Several genes involved in primary metabolic processes such as photosynthesis were down-regulated upon insect feeding or wounding, fitting with the concept of dynamic resource allocation in plant defence. Refined expression analysis using gene-specific primers and real-time PCR for selected transcripts was in agreement with microarray results for most genes tested. This study provides the first large-scale survey of insect-induced defence transcripts in a gymnosperm and provides a platform for functional investigation of plant-insect interactions in spruce. Induction of spruce genes of octadecanoid and ethylene signalling, terpenoid biosynthesis, and phenolic secondary metabolism are discussed in more detail.

Design of decoupling networks for circulant symmetric antenna arrays

Small element spacing in compact arrays results in strong mutual coupling between array elements. Performance degradation associated with the strong coupling can be avoided through the introduction of a decoupling network consisting of interconnected reactive elements. We present a systematic design procedure for decoupling networks of symmetrical arrays with more than three elements and characterized by circulant scattering parameter matrices. The elements of the decoupling network are obtained through repeated decoupling of the characteristic eigenmodes of the array, which allows the calculation of element values using closed-form expressions.

Single-layer decoupling networks for circulant symmetric arrays

Reduced element spacing in antenna arrays gives rise to strong mutual coupling between array elements and may cause significant performance degradation. These effects can be alleviated by introducing a decoupling network consisting of interconnected reactive elements. The existing design approach for the synthesis of a decoupling network for circulant symmetric arrays allows calculation of element values using closed-form expressions, but the resulting circuit configuration requires multilayer technology for implementation. In this paper, a new structure for the decoupling of circulant symmetric arrays of more than four elements is presented. Element values are no longer obtained in closed form, but the resulting circuit is much simpler and can be implemented on a single layer.

Microstrip decoupling networks for low-order multi-port arrays with reduced element spacing

An array of monopole elements with reduced element spacing of λ/6 to λ/20 is considered for application in digital beam-forming and direction-finding. The small element spacing introduces strong mutual coupling between the array elements. This paper discusses that decoupling can be achieved analytically for arrays with three elements and describes Kuroda’s identities to realize the lumped elements of the derived decoupling network. Design procedures and equations are proposed. Experimental results are presented. The decoupled array has a bandwidth of 1% and a superdirective radiation pattern.

Performance enhancement of smart antennas with reduced element spacing

This paper addresses the problem of degradations in adaptive digital beam-forming (DBF) systems caused by mutual coupling between array elements. The focus is on compact arrays with reduced element spacing and, hence, strongly coupled elements. Deviations in the radiation patterns of coupled and (theoretically) uncoupled elements can be compensated for by weight-adjustments in DBF, but SNR degradation due to impedance mismatches cannot be compensated for via signal processing techniques. It is shown that this problem can be overcome via the implementation of a RF-decoupling-network. SNR enhancement is achieved at the cost of a reduced frequency bandwidth and an increased sensitivity to dissipative losses in the antenna and matching network structure.

A Spectral Iteration Technique For The Analysis Of Yagi-Uda Arrays

The paper present a spectral iteration technique for the analysis of linear arrays of unequally spaced dipoles of unequal lengths. As an example, the Yagi-Uda array is considered for illustration. Analysis is carried out in both the spatial as well as the spectral domains, the two being linked by the Fourier transform. The fast Fourier transform algorithm is employed to obtain an iterative solution to the electric field integral equation and the need for matrix inversion is circumvented. This technique also provides a convenient means for testing the satisfaction of the boundary conditions on the array elements. Numerical comparison of the input impedance and radiation pattern have been made with results deduced elsewhere by other methods. The computational efficency of this technique has been found to be significant for large arrays.

Differential Diffractive Reflectance Modulation Sensing

We fabricated a reflectance based sensor which relies on the diffraction pattern generated from a bio-microarray where an underlying thin film structure enhances the diffracted intensity from molecular layers. The zero order diffraction represents the background signal and the higher orders represent the phase difference between the array elements and the background. By taking the differential ratio of the first and zero order diffraction signals we get a quantitative measure of molecular binding while simultaneously rejecting common mode fluctuations. We improved the signal-to-noise ratio by an order of magnitude with this ratiometric approach compared to conventional single channel detection. In addition, we use a lithography based approach for fabricating microarrays which results in spot sizes as small as 5 micron diameter unlike the 100 micron spots from inkjet printing and is therefore capable of a high degree of multiplexing. We will describe the real-time measurement of adsorption of charged polymers and bulk refractometry using this technique. The lack of moving parts for point scanning of the microarray and the differential ratiometric measurements using diffracted orders from the same probe beam allows us to make real-time measurements in spite of noise arising from thermal or mechanical fluctuations in the fluid sample above the sensor surface. Further, the lack of moving parts leads to considerable simplification in the readout hardware permitting the use of this technique in compact point of care sensors.

Microfabrication of electrode patterns for high-frequency ultrasound transducer arrays.

High-frequency ultrasound is needed for medical imaging with high spatial resolution. A key issue in the development of ultrasound imaging arrays to operate at high frequencies (≥30 MHz) is the need for photolithographic patterning of array electrodes. To achieve this directly on 1-3 piezocomposite, the material requires not only planar, parallel, and smooth surfaces, but also an epoxy composite filler that is resistant to chemicals, heat, and vacuum. This paper reports, first, on the surface finishing of 1-3 piezocomposite materials by lapping and polishing. Excellent surface flatness has been obtained, with an average surface roughness of materials as low as 3 nm and step heights between ceramic/polymer of ∼80 nm. Subsequently, high-frequency array elements were patterned directly on top of these surfaces using a photolithography process. A 30-MHz linear array electrode pattern with 50-μm element pitch has been patterned on the lapped and polished surface of a high-frequency 1-3 piezocomposite. Excellent electrode edge definition and electrical contact to the composite were obtained. The composite has been lapped to a final thickness of ∼55 μm. Good adhesion of electrodes on the piezocomposite has been achieved and electrical impedance measurements have demonstrated their basic functionality. The array was then packaged, and acoustic pulse-echo measurements were performed. These results demonstrate that direct patterning of electrodes by photolithography on 1-3 piezocomposite is feasible for fabrication of high-frequency ultrasound arrays. Furthermore, this method is more conducive to mass production than other reported array fabrication techniques.

Nanoscale-accuracy transfer printing of ultra-thin AlInGaN light-emitting diodes onto mechanically flexible substrates

The transfer printing of 2 μm-thick aluminum indium gallium nitride (AlInGaN) micron-size light-emitting diodes with 150 nm (±14 nm) minimum spacing is reported. The thin AlInGaN structures were assembled onto mechanically flexible polyethyleneterephthalate/polydimethylsiloxane substrates in a representative 16 × 16 array format using a modified dip-pen nano-patterning system. Devices in the array were positioned using a pre-calculated set of coordinates to demonstrate an automated transfer printing process. Individual printed array elements showed blue emission centered at 486 nm with a forward-directed optical output power up to 80 μW (355 mW/cm 2) when operated at a current density of 20 A/cm2. © 2013 AIP Publishing LLC.

Artificial surfaces of intertwined square spirals:A CPW model

Intertwining planar spirals arranged in doubly periodic arrays enables a substantially subwavelength response of the unit cell smaller than 1/40 of wavelength with large fractional bandwidths. These properties are important for application at low frequencies, conformal curved surfaces, or with compact radiators. It is shown that interleaving counter-wound spiral arms extended into adjacent unit cells dramatically increase the array equivalent capacitance while reducing the inductance. A coplanar waveguide (CPW) model has been developed to analytically estimate the equivalent capacitance and inductance of intertwined spiral array elements in terms of their geometrical parameters. The proposed CPW model is shown to provide an accurate prediction of the fundamental resonance frequency and can be instrumental in the design of the arrays for a specified frequency response. © 2012 IEEE.

Phenomenology of Resonance Reflectance by Intertwined Spiral Arrays

The physical mechanisms underlying the dramatic reduction of the unit cell electrical size along with broadening fractional bandwidths provided by intertwined spiral arrays are discussed. Based upon this insight, a multi-strip transmission line (MTL) model is developed to analytically estimate the equivalent capacitance and inductance of intertwined spiral array elements in terms of their geometrical parameters. The proposed MTL model enables an accurate prediction of the fundamental resonance characteristics and provides a valuable tool for design of the arrays with the specified frequency response.

Design and Qualitative/Quantitative Analysis of Multi-Agent Spatial Simulation Library

Thesis (Master's)--University of Washington, 2012

Comparison Study of Pattern Synthesis Techniques Using Neural Networks

In this paper, a comparison study among three neuralnetwork algorithms for the synthesis of array patterns is presented. The neural networks are used to estimate the array elements' excitations for an arbitrary pattern. The architecture of the neural networks is discussed and simulation results are presented. Two new neural networks, based on radial basis functions (RBFs) and wavelet neural networks (WNNs), are introduced. The proposed networks offer a more efficient synthesis procedure, as compared to other available techniques

Using GPUs for beamforming acceleration on SAFT imaging

SAFT techniques are based on the sequential activation, in emission and reception, of the array elements and the post-processing of all the received signals to compose the image. Thus, the image generation can be divided into two stages: (1) the excitation and acquisition stage, where the signals received by each element or group of elements are stored; and (2) the beamforming stage, where the signals are combined together to obtain the image pixels. The use of Graphics Processing Units (GPUs), which are programmable devices with a high level of parallelism, can accelerate the computations of the beamforming process, that usually includes different functions such as dynamic focusing, band-pass filtering, spatial filtering or envelope detection. This work shows that using GPU technology can accelerate, in more than one order of magnitude with respect to CPU implementations, the beamforming and post-processing algorithms in SAFT imaging. ©2009 IEEE.

HIGH PERFORMANCE, LOW COST SUBSPACE DECOMPOSITION AND POLYNOMIAL ROOTING FOR REAL TIME DIRECTION OF ARRIVAL ESTIMATION: ANALYSIS AND IMPLEMENTATION

This thesis develops high performance real-time signal processing modules for direction of arrival (DOA) estimation for localization systems. It proposes highly parallel algorithms for performing subspace decomposition and polynomial rooting, which are otherwise traditionally implemented using sequential algorithms. The proposed algorithms address the emerging need for real-time localization for a wide range of applications. As the antenna array size increases, the complexity of signal processing algorithms increases, making it increasingly difficult to satisfy the real-time constraints. This thesis addresses real-time implementation by proposing parallel algorithms, that maintain considerable improvement over traditional algorithms, especially for systems with larger number of antenna array elements. Singular value decomposition (SVD) and polynomial rooting are two computationally complex steps and act as the bottleneck to achieving real-time performance. The proposed algorithms are suitable for implementation on field programmable gated arrays (FPGAs), single instruction multiple data (SIMD) hardware or application specific integrated chips (ASICs), which offer large number of processing elements that can be exploited for parallel processing. The designs proposed in this thesis are modular, easily expandable and easy to implement. Firstly, this thesis proposes a fast converging SVD algorithm. The proposed method reduces the number of iterations it takes to converge to correct singular values, thus achieving closer to real-time performance. A general algorithm and a modular system design are provided making it easy for designers to replicate and extend the design to larger matrix sizes. Moreover, the method is highly parallel, which can be exploited in various hardware platforms mentioned earlier. A fixed point implementation of proposed SVD algorithm is presented. The FPGA design is pipelined to the maximum extent to increase the maximum achievable frequency of operation. The system was developed with the objective of achieving high throughput. Various modern cores available in FPGAs were used to maximize the performance and details of these modules are presented in detail. Finally, a parallel polynomial rooting technique based on Newton’s method applicable exclusively to root-MUSIC polynomials is proposed. Unique characteristics of root-MUSIC polynomial’s complex dynamics were exploited to derive this polynomial rooting method. The technique exhibits parallelism and converges to the desired root within fixed number of iterations, making this suitable for polynomial rooting of large degree polynomials. We believe this is the first time that complex dynamics of root-MUSIC polynomial were analyzed to propose an algorithm. In all, the thesis addresses two major bottlenecks in a direction of arrival estimation system, by providing simple, high throughput, parallel algorithms.