SCAPA (Spacially Addressable Protein Array) – a Novel Protein Array for the Differential Profiling of Ligand-receptor Induced Signalling

While protein microarray technology has been successful in demonstrating its usefulness for large scale high-throughput proteome profiling, performance of antibody/antigen microarrays has been only moderately productive. Immobilization of either the capture antibodies or the protein samples on solid supports has severe drawbacks. Denaturation of the immobilized proteins as well as inconsistent orientation of antibodies/ligands on the arrays can lead to erroneous results. This has prompted a number of studies to address these challenges by immobilizing proteins on biocompatible surfaces, which has met with limited success. Our strategy relates to a multiplexed, sensitive and high-throughput method for the screening quantification of intracellular signalling proteins from a complex mixture of proteins. Each signalling protein to be monitored has its capture moiety linked to a specific oligo ‘tag’. The array involves the oligonucleotide hybridization-directed localization and identification of different signalling proteins simultaneously, in a rapid and easy manner. Antibodies have been used as the capture moieties for specific identification of each signaling protein. The method involves covalently partnering each antibody/protein molecule with a unique DNA or DNA derivatives oligonucleotide tag that directs the antibody to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array. Particular surface modifications and optimal conditions allowed high signal to noise ratio which is essential to the success of this approach.

Evaluating the directional effects of acoustic horn style hearing aids using the QuickSIN procedure

This paper evaluates the directional effects of two hearing devices – an antique London Dome horn style device and a constructed Cupped Hand. The comparisons were made using the Quick SIN (Speech in Noise) adaptive test which measures signal-to-noise ratio loss.

Very large inverse problems in atmosphere and ocean modelling

For the very large nonlinear dynamical systems that arise in a wide range of physical, biological and environmental problems, the data needed to initialize a numerical forecasting model are seldom available. To generate accurate estimates of the expected states of the system, both current and future, the technique of ‘data assimilation’ is used to combine the numerical model predictions with observations of the system measured over time. Assimilation of data is an inverse problem that for very large-scale systems is generally ill-posed. In four-dimensional variational assimilation schemes, the dynamical model equations provide constraints that act to spread information into data sparse regions, enabling the state of the system to be reconstructed accurately. The mechanism for this is not well understood. Singular value decomposition techniques are applied here to the observability matrix of the system in order to analyse the critical features in this process. Simplified models are used to demonstrate how information is propagated from observed regions into unobserved areas. The impact of the size of the observational noise and the temporal position of the observations is examined. The best signal-to-noise ratio needed to extract the most information from the observations is estimated using Tikhonov regularization theory. Copyright © 2005 John Wiley & Sons, Ltd.

Predictability and skill of boreal winter forecasts made with the ECMWF Seasonal Forecasting System II

The performance of boreal winter forecasts made with the European Centre for Medium-Range Weather Forecasts (ECMWF) System 11 Seasonal Forecasting System is investigated through analyses of ensemble hindcasts for the period 1987-2001. The predictability, or signal-to-noise ratio, associated with the forecasts, and the forecast skill are examined. On average, forecasts of 500 hPa geopotential height (GPH) have skill in most of the Tropics and in a few regions of the extratropics. There is broad, but not perfect, agreement between regions of high predictability and regions of high skill. However, model errors are also identified, in particular regions where the forecast ensemble spread appears too small. For individual winters the information provided by t-values, a simple measure of the forecast signal-to-noise ratio, is investigated. For 2 m surface air temperature (T2m), highest t-values are found in the Tropics but there is considerable interannual variability, and in the tropical Atlantic and Indian basins this variability is not directly tied to the El Nino Southern Oscillation. For GPH there is also large interannual variability in t-values, but these variations cannot easily be predicted from the strength of the tropical sea-surface-temperature anomalies. It is argued that the t-values for 500 hPa GPH can give valuable insight into the oceanic forcing of the atmosphere that generates predictable signals in the model. Consequently, t-values may be a useful tool for understanding, at a mechanistic level, forecast successes and failures. Lastly, the extent to which t-values are useful as a predictor of forecast skill is investigated. For T2m, t-values provide a useful predictor of forecast skill in both the Tropics and extratropics. Except in the equatorial east Pacific, most of the information in t-values is associated with interannual variability of the ensemble-mean forecast rather than interannual variability of the ensemble spread. For GPH, however, t-values provide a useful predictor of forecast skill only in the tropical Pacific region.

Stray light analysis of SALEX instrument

Discrepancies between recent global earth albedo anomaly data obtained from the climate models, space and ground observations call for a new and better earth reflectance measurement technique. The SALEX (Space Ashen Light Explorer) instrument is a space-based visible and IR instrument for precise estimation of the global earth albedo by measuring the ashen light reflected off the shadowy side of the Moon from the low earth orbit. The instrument consists of a conventional 2-mirror telescope, a pair of a 3-mirror visible imager and an IR bolometer. The performance of this unique multi-channel optical system is sensitive to the stray light contamination due to the complex optical train incorporating several reflecting and refracting elements, associated mounts and the payload mechanical enclosure. This could be further aggravated by the very bright and extended observation target (i.e. the Moon). In this paper, we report the details of extensive stray light analysis including ghosts and cross-talks, leading to the optimum set of stray light precautions for the highest signal-to-noise ratio attainable.

Liquid matrices for analyses by UV-MALDI mass spectrometry

Data are presented for a pH-adjustable liquid UV-matrix-assisted laser desorption ionization (MALDI) matrix for mass spectrometry analysis. The liquid matrix system possesses high analytical sensitivity within the same order of magnitude as that achievable by the commonly used solid UV-MALDI matrices such as 2,5-dihydroxybenzoic acid but with improved spot homogeneity and reproducibility. The pH of the matrix has been adjusted by the addition of up to 0.35% trifluoroacetic acid and up to 200 mM ammonium bicarbonate, achieving an on-target pH range of 3.5-8.6. Alteration of the pH does not seem to affect the overall sample signal intensity or signal-to-noise ratio achievable, nor does it affect the individual peptide ion signals from a mixture of peptides with varying isoelectric points (p1). In addition, the pH adjustment has allowed for the performance of a tryptic digest within the diluted pH-optimized liquid matrix.

On the design of opportunistic cooperative transmission strategies with partial CSI information

The aim of this paper is to study the impact of channel state information on the design of cooperative transmission protocols. This is motivated by the fact that the performance gain achieved by cooperative diversity comes at the price of the extra bandwidth resource consumption. Several opportunistic relaying strategies are developed to fully utilize the different types of a priori channel information. The information-theoretic measures such as outage probability and diversity-multiplexing tradeoff are developed for the proposed protocols. The analytical and numerical results demonstrate that the use of such a priori information increases the spectral efficiency of cooperative diversity, especially at low signal-to-noise ratio.

Apodisation, denoising and system identification techniques for THz transients in the wavelet domain

This work describes the use of a quadratic programming optimization procedure for designing asymmetric apodization windows to de-noise THz transient interferograms and compares these results to those obtained when wavelet signal processing algorithms are adopted. A systems identification technique in the wavelet domain is also proposed for the estimation of the complex insertion loss function. The proposed techniques can enhance the frequency dependent dynamic range of an experiment and should be of particular interest to the THz imaging and tomography community. Future advances in THz sources and detectors are likely to increase the signal-to-noise ratio of the recorded THz transients and high quality apodization techniques will become more important, and may set the limit on the achievable accuracy of the deduced spectrum.

Classification of lactose and mandelic acid THz spectra using subspace and wavelet-packet algorithms

This work compares classification results of lactose, mandelic acid and dl-mandelic acid, obtained on the basis of their respective THz transients. The performance of three different pre-processing algorithms applied to the time-domain signatures obtained using a THz-transient spectrometer are contrasted by evaluating the classifier performance. A range of amplitudes of zero-mean white Gaussian noise are used to artificially degrade the signal-to-noise ratio of the time-domain signatures to generate the data sets that are presented to the classifier for both learning and validation purposes. This gradual degradation of interferograms by increasing the noise level is equivalent to performing measurements assuming a reduced integration time. Three signal processing algorithms were adopted for the evaluation of the complex insertion loss function of the samples under study; a) standard evaluation by ratioing the sample with the background spectra, b) a subspace identification algorithm and c) a novel wavelet-packet identification procedure. Within class and between class dispersion metrics are adopted for the three data sets. A discrimination metric evaluates how well the three classes can be distinguished within the frequency range 0. 1 - 1.0 THz using the above algorithms.

On the performance of opportunistic cooperative wireless networks

The aim of this paper is to study the impact of channel state information on the design of cooperative transmission protocols. This is motivated by the fact that the performance gain achieved by cooperative diversity comes at the price of the extra bandwidth resource consumption. Several opportunistic relaying strategies are developed to fully utilize the different types of a priori channel information. The analytical and numerical results demonstrate that the use of such a priori information increases the spectral efficiency of cooperative diversity, especially at low signal-to-noise ratio.

A method for estimating the turbulent kinetic energy dissipation rate from a vertically pointing Doppler lidar, and independent evaluation from balloon-borne in situ measurements

A method of estimating dissipation rates from a vertically pointing Doppler lidar with high temporal and spatial resolution has been evaluated by comparison with independent measurements derived from a balloon-borne sonic anemometer. This method utilizes the variance of the mean Doppler velocity from a number of sequential samples and requires an estimate of the horizontal wind speed. The noise contribution to the variance can be estimated from the observed signal-to-noise ratio and removed where appropriate. The relative size of the noise variance to the observed variance provides a measure of the confidence in the retrieval. Comparison with in situ dissipation rates derived from the balloon-borne sonic anemometer reveal that this particular Doppler lidar is capable of retrieving dissipation rates over a range of at least three orders of magnitude. This method is most suitable for retrieval of dissipation rates within the convective well-mixed boundary layer where the scales of motion that the Doppler lidar probes remain well within the inertial subrange. Caution must be applied when estimating dissipation rates in more quiescent conditions. For the particular Doppler lidar described here, the selection of suitably short integration times will permit this method to be applicable in such situations but at the expense of accuracy in the Doppler velocity estimates. The two case studies presented here suggest that, with profiles every 4 s, reliable estimates of ϵ can be derived to within at least an order of magnitude throughout almost all of the lowest 2 km and, in the convective boundary layer, to within 50%. Increasing the integration time for individual profiles to 30 s can improve the accuracy substantially but potentially confines retrievals to within the convective boundary layer. Therefore, optimization of certain instrument parameters may be required for specific implementations.

An ultra-wide passband (5-30µm) filter for FTIR studies of Photosystem II

This paper reports on the design and manufacture of an ultra-wide (5-30µm) infrared edge filter for use in FTIR studies of the low frequency vibrational modes of metallo-proteins. We present details of the spectral design and manufacture of such a filter which meets the demanding bandwidth and transparency requirements of the application, and spectra that present the new data possible with such a filter. A design model of the filter and the materials used in its construction has been developed capable of accurately predicting spectral performance at both 300K and at the reduced operating temperature at 200K. This design model is based on the optical and semiconductor properties of a multilayer filter containing PbTe (IV-VI) layer material in combination with the dielectric dispersion of ZnSe (II-VI) deposited on a CdTe (II-VI) substrate together with the use of BaF2 (II-VII) as an antireflection layer. Comparisons between the computed spectral performance of the model and spectral measurements from manufactured coatings over a wavelength range of 4-30µm and temperature range 300-200K are presented. Finally we present the results of the FTIR measurements of Photosystem II showing the improvement in signal to noise ratio of the measurement due to using the filter, together with a light induced FTIR difference spectrum of Photosystem II.

Evaluation of peak-picking algorithms for protein mass spectrometry

Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods is illustrated and discussed in a practical context using a mass spectral data set created with MALDI-TOF technology. Sensitivity and specificity are investigated using a manually defined reference set of peaks. As an additional criterion, the robustness of the three methods is assessed by a perturbation analysis and illustrated using ROC curves.

Signal detection for orthogonal space-time block coding over time-selective fading channels: the H(i) systems

One major assumption in all orthogonal space-time block coding (O-STBC) schemes is that the channel remains static over the length of the code word. However, time-selective fading channels do exist, and in such case conventional O-STBC detectors can suffer from a large error floor in the high signal-to-noise ratio (SNR) cases. As a sequel to the authors' previous papers on this subject, this paper aims to eliminate the error floor of the H(i)-coded O-STBC system (i = 3 and 4) by employing the techniques of: 1) zero forcing (ZF) and 2) parallel interference cancellation (PIC). It is. shown that for an H(i)-coded system the PIC is a much better choice than the ZF in terms of both performance and computational complexity. Compared with the, conventional H(i) detector, the PIC detector incurs a moderately higher computational complexity, but this can well be justified by the enormous improvement.

Signal detection for orthogonal space-time block coding over time-selective fading channels: a PIC approach for the Gi Systems

One major assumption in all orthogonal space-time block coding (O-STBC) schemes is that the channel remains static over the entire length of the codeword. However, time selective fading channels do exist, and in such case the conventional O-STBC detectors can suffer from a large error floor in the high signal-to-noise ratio (SNR) cases. This paper addresses such an issue by introducing a parallel interference cancellation (PIC) based detector for the Gi coded systems (i=3 and 4).