A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Evaluation of live-attenuated Salmonella vaccines expressing Campylobacter antigens for control of C. jejuni in poultry

Campylobacter jejuni is a zoonotic bacterial pathogen of worldwide importance. It is estimated that 460,000 human infections occur in the United Kingdom per annum and these involve acute enteritis and may be complicated by severe systemic sequelae. Such infections are frequently associated with the consumption of contaminated poultry meat and strategies to control C. jejuni in poultry are expected to limit pathogen entry into the food chain and the incidence of human disease. Toward this aim, a total of 840 Light Sussex chickens were used to evaluate a Salmonella enterica serovar Typhimurium ΔaroA vaccine expressing the C. jejuni amino acid binding protein CjaA as a plasmid-borne fusion to the C-terminus of fragment C of tetanus toxin. Chickens were given the vaccine at 1-day-old and two weeks later by oral gavage, then challenged after a further two weeks with C. jejuni. Across six biological replicates, statistically significant reductions in caecal C. jejuni of c. 1.4 log10 colony-forming units/g were observed at three and four weeks post-challenge relative to age-matched unvaccinated birds. Protection was associated with the induction of CjaA-specific serum IgY and biliary IgA. Protection was not observed using a vaccine strain containing the empty plasmid. Vaccination with recombinant CjaA subcutaneously at the same intervals significantly reduced the caecal load of C. jejuni at three and four weeks post-challenge. Taken together these data imply that responses directed against CjaA, rather than competitive or cross-protective effects mediated by the carrier, confer protection. The impact of varying parameters on the efficacy of the S. Typhimurium ΔaroA vaccine expressing TetC-CjaA was also tested. Delaying the age at primary vaccination had little impact on protection or humoral responses to CjaA. The use of the parent strain as carrier or changing the attenuating mutation of the carrier to ΔspaS or ΔssaU enhanced the protective effect, consistent with increased invasion and persistence of the vaccine strains relative to the ΔaroA mutant. Expression in the ΔaroA strain of a TetC fusion to Peb1A, but not TetC fusions to GlnH or ChuA, elicited protection against intestinal colonisation by C. jejuni that was comparable to that observed with the TetC-CjaA fusion. Our data are rendered highly relevant by use of the target host in large numbers and support the potential of CjaA- and Peb1A-based vaccines for control of C. jejuni in poultry. © 2009 Elsevier Ltd. All rights reserved.

Investigation of spatial repeatability using a tire force measuring mat

A portable mat for measuring the dynamic tire forces of commercial vehicles is described. The mat is 56 m long and 13 mm thick and has 141 capacitative strip sensors spaced at 0.4-m intervals. The accuracy of the mat for measuring dynamic tire forces generated by heavy commercial vehicles is assessed using an instrumented vehicle. The spatial repeatability of dynamic wheel loads generated by 14 uninstrumented articulated vehicles is investigated, and it is concluded that approximately half of the vehicles tested are likely to contribute to a repeatable pattern of road loading.

PARTIALLY COHERENT DYNAMIC PROGRAMMING ALGORITHM FOR CPM DETECTION.

A dynamic programming algorithm for joint data detection and carrier phase estimation of continuous-phase-modulated signal is presented. The intent is to combine the robustness of noncoherent detectors with the superior performance of coherent ones. The algorithm differs from the Viterbi algorithm only in the metric that it maximizes over the possible transmitted data sequences. This metric is influenced both by the correlation with the received signal and the current estimate of the carrier phase. Carrier-phase estimation is based on decision guiding, but there is no external phase-locked loop. Instead, the phase of the best complex correlation with the received signal over the last few signaling intervals is used. The algorithm is slightly more complex than the coherent Viterbi algorithm but does not require narrowband filtering of the recovered carrier, as earlier appproaches did, to achieve the same level of performance.

System model for studying fibre grating dispersion compensators

A complete optical system model has been developed and used to assess chirped fibre Bragg grating dispersion compensators. Gratings suitable for dispersion compensation in both laser based and modulator based optical communications systems have been modelled. A grating 10 cm in length has been shown to permit virtually dispersion free transmission over 425 km, when used in an externally modulated system. Long haul dispersion compensation using several 2 cm gratings spaced at intervals along the fibre is also modelled, illustrating viable 10Gbit/s transmission over a distance in excess of 168 km.

Probabilistic fault identification using vibration data and neural networks

Bayesian formulated neural networks are implemented using hybrid Monte Carlo method for probabilistic fault identification in cylindrical shells. Each of the 20 nominally identical cylindrical shells is divided into three substructures. Holes of (12±2) mm in diameter are introduced in each of the substructures and vibration data are measured. Modal properties and the Coordinate Modal Assurance Criterion (COMAC) are utilized to train the two modal-property-neural-networks. These COMAC are calculated by taking the natural-frequency-vector to be an additional mode. Modal energies are calculated by determining the integrals of the real and imaginary components of the frequency response functions over bandwidths of 12% of the natural frequencies. The modal energies and the Coordinate Modal Energy Assurance Criterion (COMEAC) are used to train the two frequency-response-function-neural-networks. The averages of the two sets of trained-networks (COMAC and COMEAC as well as modal properties and modal energies) form two committees of networks. The COMEAC and the COMAC are found to be better identification data than using modal properties and modal energies directly. The committee approach is observed to give lower standard deviations than the individual methods. The main advantage of the Bayesian formulation is that it gives identities of damage and their respective confidence intervals.

Fracture and energy partitioning in uncooked and cooked noodles

Humans perform fascinating science experiments at home on a daily basis when they undertake the modification of natural and naturally-derived materials by a cooking process prior to consumption. The material properties of such foods are of interest to food scientists (texture is often fundamental to food acceptability), oral biologists (foods modulate feeding behavior), anthropologists (cooking is probably as old as the genus Homo and distinguishes us from all other creatures) and dentists (foods interact with tooth and tooth replacement materials). Materials scientists may be interested in the drastic changes in food properties observed over relatively short cooking times. In the current study, the mechanical properties of one of the most common (and oldest at 4,000+ years) foods on earth, the noodle, were examined as a function of cooking time. Two types of noodles were studied, each made from natural materials (wheat flour, salt, alkali and water) by kneading dough and passing them through a pasta-making machine. These were boiled for between 2-14 min and tested at regular intervals from raw to an overcooked state. Cyclic tensile tests at small strain levels were used to examine energy dissipation characteristics. Energy dissipation was >50% per cycle in uncooked noodles, but decreased by an order of magnitude with cooking. Fractional dissipation values remained approximately constant at cooking times greater than 7 min. Overall, a greater effect of cooking was on viscoplastic dissipation characteristics rather than on fracture resistance. The results of the current study plot the evolution of a viscoplastic mixture into an essentially elastic material in the space of 7 minutes and have broad implications for understanding what cooking does to food materials. In particular, they suggest that textural assessment by consumers of the optimally cooked state of food has a definite physical definition. © 2007 Materials Research Society.

Prognosis of underground structures deterioration based on in-situ measurements

The stability of the underground structure is very important not only from the point of view of the structure itself, but also from the point of view of other structures. Therefore, the evaluation of the process of deterioration can help us very much. In the first part of the paper the ageing of the structures in the scope of their life cycle will be described. The whole process of deterioration is important but limited to certain time intervals and is able to give signals about changes in macro-scale. The second part of the paper is focused on the adaptation of new methods: micro technology of monitoring - such as MEMS (Micro Electrical Mechanical Systems) and wireless technologies for data transfer. It is obvious that such new technologies have to be assessed for the ability to deliver data continuously and for their safety and solidity. At the end of the paper the application of the measurements on the Prague metro's lining is mentioned. © 2007 Taylor & Francis Group.

Predicting surface vibration from underground railways through inhomogeneous soil

Noise and vibration from underground railways is a major source of disturbance to inhabitants near subways. To help designers meet noise and vibration limits, numerical models are used to understand vibration propagation from these underground railways. However, the models commonly assume the ground is homogeneous and neglect to include local variability in the soil properties. Such simplifying assumptions add a level of uncertainty to the predictions which is not well understood. The goal of the current paper is to quantify the effect of soil inhomogeneity on surface vibration. The thin-layer method (TLM) is suggested as an efficient and accurate means of simulating vibration from underground railways in arbitrarily layered half-spaces. Stochastic variability of the soils elastic modulus is introduced using a KL expansion; the modulus is assumed to have a log-normal distribution and a modified exponential covariance kernel. The effect of horizontal soil variability is investigated by comparing the stochastic results for soils varied only in the vertical direction to soils with 2D variability. Results suggest that local soil inhomogeneity can significantly affect surface velocity predictions; 90 percent confidence intervals showing 8 dB averages and peak values up to 12 dB are computed. This is a significant source of uncertainty and should be considered when using predictions from models assuming homogeneous soil properties. Furthermore, the effect of horizontal variability of the elastic modulus on the confidence interval appears to be negligible. This suggests that only vertical variation needs to be taken into account when modelling ground vibration from underground railways. © 2012 Elsevier Ltd. All rights reserved.

Phase synchronization between stratospheric and tropospheric quasi-biennial and semi-annual oscillations

A combination of singular systems analysis and analytic phase techniques are used to investigate the possible occurrence in observations of coherent synchronization between quasi-biennial and semi-annual oscillations (QBOs; SAOs) in the stratosphere and troposphere. Time series of zonal mean zonal winds near the Equator are analysed from the ERA-40 and ERA-interim reanalysis datasets over a ∼ 50-year period. In the stratosphere, the QBO is found to synchronize with the SAO almost all the time, but with a frequency ratio that changes erratically between 4:1, 5:1 and 6:1. A similar variable synchronization is also evident in the tropical troposphere between semi-annual and quasi-biennial cycles (known as TBOs). Mean zonal winds from ERA-40 and ERA-interim, and also time series of indices for the Indian and West Pacific monsoons, are commonly found to exhibit synchronization, with SAO/TBO ratios that vary between 4:1 and 7:1. Coherent synchronization between the QBO and tropical TBO does not appear to persist for long intervals, however. This suggests that both the QBO and tropical TBOs may be separately synchronized to SAOs that are themselves enslaved to the seasonal cycle, or to the annual cycle itself. However, the QBO and TBOs are evidently only weakly coupled between themselves and are frequently found to lose mutual coherence when each changes its frequency ratio to its respective SAO. This suggests a need to revise a commonly cited paradigm that advocates the use of stratospheric QBO indices as a predictor for tropospheric phenomena such as monsoons and hurricanes. © 2012 Royal Meteorological Society.