A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH

BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples.

RESULTS: In this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC outliers that might indicate microevents. These microevents were validated by the oligo platform results.

CONCLUSION: This article presents a genome-wide statistical validation of the oligo array platform on a large set of patient samples and demonstrates statistically its superiority over the BAC platform for the Identification of chromosomic events. Taking advantage of a large set of human samples treated by the two technologies, a statistical model has been developed to show that the BAC platform could also detect microevents.

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.

Increasing the TRL of an L band Retrodirective array for Type Approved SATCOM applications

Retrodirective, self-steering, antennas have the advantage of being able to automatically return a signal back in the direction along from which it originated. The tracking is real time and is carried out in the analogue domain which results in simple circuits which can be accommodated, planar-form, behind the antenna elements. The main objective of this paper is to detail the continuation of the work on L band retrodirective antennas which has the ambition of increasing the TRL such that a minimal viable product can be produced, suitable for type approval as an L band SATCOM user terminal. The focus will be the technical challenges that have arisen as the retrodirective antenna is moved up the TRL chain. Some of these aspects include the ability to track very weak modulated signals (S/N tending to 0dB), TX/RX filter and duplexer specifications, PA and LNA considerations. The resultant retrodirective architecture will be compared against typical specifications of L band satellite ground terminals, showing that the retrodirective antenna offers a simple and effective real time tracking antenna architecture.

Application of the pMHC Array to Characterise Tumour Antigen Specific T Cell Populations in Leukaemia Patients at Disease Diagnosis

Immunotherapy treatments for cancer are becoming increasingly successful, however to further improve our understanding of the T-cell recognition involved in effective responses and to encourage moves towards the development of personalised treatments for leukaemia immunotherapy, precise antigenic targets in individual patients have been identified. Cellular arrays using peptide-MHC (pMHC) tetramers allow the simultaneous detection of different antigen specific T-cell populations naturally circulating in patients and normal donors. We have developed the pMHC array to detect CD8+ T-cell populations in leukaemia patients that recognise epitopes within viral antigens (cytomegalovirus (CMV) and influenza (Flu)) and leukaemia antigens (including Per Arnt Sim domain 1 (PASD1), MelanA, Wilms' Tumour (WT1) and tyrosinase). We show that the pMHC array is at least as sensitive as flow cytometry and has the potential to rapidly identify more than 40 specific T-cell populations in a small sample of T-cells (0.8-1.4 x 106). Fourteen of the twenty-six acute myeloid leukaemia (AML) patients analysed had T cells that recognised tumour antigen epitopes, and eight of these recognised PASD1 epitopes. Other tumour epitopes recognised were MelanA (n = 3), tyrosinase (n = 3) and WT1126-134 (n = 1). One of the seven acute lymphocytic leukaemia (ALL) patients analysed had T cells that recognised the MUC1950-958 epitope. In the future the pMHC array may be used provide point of care T-cell analyses, predict patient response to conventional therapy and direct personalised immunotherapy for patients.

Validation of a high-throughput immunobead array technique for multiplex detection of three foodborne pathogens in chicken products

This study rigorously evaluated a previously developed immunobead array method to simultaneously detect three important foodborne pathogens, Campylobacter jejuni, Listeria monocytogenes, and Salmonella spp., for its actual application in routine food testing. Due to the limitation of the detection limit of the developed method, an enrichment step was included in this study by using Campylobacter Enrichment Broth for C. jejuni and Universal Pre-enrichment Broth for L. monocytogenes and Salmonella spp.. The findings show that the immunobead array method was capable of detecting as low as 1 CFU of the pathogens spiked in the culture media after being cultured for 24 hours for all three pathogens. The immunobead array method was further evaluated for its pathogen detection capabilities in ready-to-eat (RTE) and ready-to-cook (RTC) chicken samples and proven to be able to detect as low as 1 CFU of the pathogens spiked in the food samples after being cultured for 24 hours in the case of Salmonella spp., and L. monocytogenes and 48 hours in the case of C. jejuni. The method was subsequently validated with three types of chicken products (RTE, n=30; RTC, n=20; raw chicken, n=20) and was found to give the same results as the conventional plating method. Our findings demonstrated that the previously developed immunobead array method could be used for actual food testing with minimal enrichment period of only 52 hours, whereas the conventional ISO protocols for the same pathogens take 90-144 hours. The immunobead array was therefore an inexpensive, rapid and simple method for the food testing.

SATCOM Retrodirective Array

We present an in depth look at the challenges involved in using analogue retrodirective arrays for satellite communications. The main technical issues surrounding the development of a retrodirective (self-steering) Satellite Communications (SATCOM) system are given and techniques for mitigating these issues provided. Detailed results are given for a prototype high performance circularly polarized retrodirective array architecture suitable for mounting on an un-stabilized mobile platform. The paper concludes with practical retrodirective L-band array results with the array used to acquire actual broadband satellite data signals from a commercial L-band satellite system. Received satellite signals as low as -130dBm at the antenna elements are tracked. Accurate self-tracking occurs over the azimuth range of up to +/- 40 degrees.

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.

Estimating bottom properties with a vector sensor array during MakaiEx 2005

Nowadays, vector sensors which measure both acoustic pressure and particle velocity begin to be available in underwater acoustic systems, normally configured as vector sensor arrays (VSA). The spatial filtering capabilities of a VSA can be used, with advantage over traditional pressure only hydrophone arrays, for estimating acoustic field directionality as well as arrival times and spectral content, which could open up the possibility for its use in bottom properties' estimation. An additional motivation for this work is to test the possibility of using high frequency probe signals (say above 2 kHz) for reducing size and cost of actual sub bottom profilers and current geoacoustic inversion methods. This work studies the bottom related structure of the VSA acquired signals, regarding the emitted signal waveform, frequency band and source-receiver geometry in order to estimate bottom properties, specially bottom reflection coefficient characteristics. Such a system was used during the Makai 2005 experiment, off Kauai I., Hawai (USA) to receive precoded signals in a broad frequency band from 8 up to 14 kHz. The agreement between the observed and the modelled acoustic data is discussed and preliminary results on the bottom reflection estimation are presented.

Source localization with vector sensor array during the makai experiment

Vector sensors measure both the acoustic pressure and the three components of particle velocity. Because of this, a vector sensor array (VSA) has the advantage of being able to provide substantially higher directivity with a much smaller aperture than an array of traditional scalar (pressure only) hydrophones. Although several, most of them theoretic, works were published from early nineties, only in the last years due to improvements and availability of vector sensor technology, the interest on field experiments with VSA increased in the scientific community. During the Makai Experiment, that took place off the coast of Kauai I., Hawaii, in September 2005, real data were collected with a 4 element vertical VSA. These data will be discussed in the present paper. The acoustic signals were emitted from a near source (low frequency ship noise) and two high frequency controlled acoustic sources located within a range of 2km from the VSA. The advantages of the VSA over traditional scalar hydrophone arrays in source localization will be addressed using conventional beamforming.

Microstrip antenna array for multiband dedicated short range communications systems

Dedicated Short Range Communications (DSRC) is the key enabling technology for the present and future vehicular communication for various applications, such as safety improvement and traffic jam mitigation. This paper describes the development of a microstrip antenna array for the roadside equipment of a DSRC system, whose characteristics are according with the vehicular communications standards. The proposed antenna, with circular polarization, has a wide bandwidth, enough to cover the current European DSRC 5.8 GHz band and the future 5.9 GHz band for next generation DSRC communications. (C) 2011 Wiley Periodicals, Inc. Microwave Opt Technol Lett 53: 2794-2796, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.26394

Non-uniform microstrip antenna array for RX DSRC communications

The urgent need to mitigate traffic problems such as accidents, road hazards, pollution and traffic jam have strongly driven the development of vehicular communications. DSRC (Dedicated Short Range Communications) is the technology of choice in vehicular communications, enabling real time information exchange among vehicles V2V (Vehicle-to-Vehicle) and between vehicles and infrastructure V2I (Vehicle-Infrastructure). This paper presents a receiving antenna for a single lane DSRC control unit. The antenna is a non-uniform array with five microstrip patches. The obtained beam width, bandwidth and circular polarization quality, among other characteristics, are compatible with the DSRC standards, making this antenna suitable for this application. © 2014 IEEE.

The impact of different power dividers used in a non-uniform planar antenna array

Wireless communications are widely used for various applications, requiring antennas with different features. Often, to achieve the desired radiation pattern, is necessary to employ antenna arrays, using non-uniform excitation on its elements. Power dividers can be used and the best known are the T-junction and the Wilkinson power divider, whose main advantage is the isolation between output ports. In this paper the impact of this isolation on the overall performance of a circularly polarized planar antenna array using non-uniform excitation is investigated. Results show a huge decrease of the array bandwidths either in terms of return loss or in polarization, without resistors. © 2014 IEEE.

Detect and pointing algorithm's performance for a planar smart antenna array: a review

An adaptive antenna array combines the signal of each element, using some constraints to produce the radiation pattern of the antenna, while maximizing the performance of the system. Direction of arrival (DOA) algorithms are applied to determine the directions of impinging signals, whereas beamforming techniques are employed to determine the appropriate weights for the array elements, to create the desired pattern. In this paper, a detailed analysis of both categories of algorithms is made, when a planar antenna array is used. Several simulation results show that it is possible to point an antenna array in a desired direction based on the DOA estimation and on the beamforming algorithms. A comparison of the performance in terms of runtime and accuracy of the used algorithms is made. These characteristics are dependent on the SNR of the incoming signal.

Printed nonuniform antenna array for WI-FI sectorized communications

Wireless networks have joined to the sports venues, offering to the public a set of facilities, such as the access to email, news, and also to use the social networking, uploading their photos. New challenges have emerged to provide Wi-Fi in this densely populated stadiums, such as increasing capacity and coverage. In this article, an access point antenna array to cover a sector of a stadium is presented. Its structure, designed in a low cost material allows to reduce the total manufacturing costs, an important factor due to the large number of antennas required in these venues. The material characteristic, the broad bandwidth of operation (300 MHz), along with to the low side lobe levels, important to reduce interference between sectors, makes this antenna well-positioned for wireless communications in these particular locals. (c) 2015 Wiley Periodicals, Inc. Microwave Opt Technol Lett 57:2037-2041, 2015.