Signature-tagged transposon mutagenesis studies demonstrate the dynamic nature of cecal colonization of 2-week-old chickens by Campylobacter jejuni.

We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of Campylobacter jejuni and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the C. jejuni NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.

The role of androgens in fetal growth: observational study in two genetic models of disordered androgen signalling.

OBJECTIVE: To examine the role of androgens on birth weight in genetic models of altered androgen signalling. SETTING: Cambridge Disorders of Sex Development (DSD) database and the Swedish national screening programme for congenital adrenal hyperplasia (CAH). PATIENTS: (1) 29 girls with XY karyotype and mutation positive complete androgen insensitivity syndrome (CAIS); (2) 43 girls and 30 boys with genotype confirmed CAH. MAIN OUTCOME MEASURES: Birth weight, birth weight-for-gestational-age (birth weight standard deviation score (SDS)) calculated by comparison with national references. RESULTS: Mean birth weight SDS in CAIS XY infants was higher than the reference for girls (mean, 95% CI: 0.4, 0.1 to 0.7; p=0.02) and was similar to the national reference for boys (0.1, -0.2 to 0.4). Birth weight SDS in CAH girls was similar to the national reference for girls (0.0, -0.2 to 0.2) and did not vary by severity of gene mutation. Birth weight SDS in CAH boys was also similar to the national reference for boys (0.2, -0.2 to 0.6). CONCLUSION: CAIS XY infants have a birth weight distribution similar to normal male infants and birth weight is not increased in infants with CAH. Alterations in androgen signalling have little impact on birth weight. Sex dimorphism in birth size is unrelated to prenatal androgen exposure.

Anharmonic surface interactions for biomolecular screening and characterization.

The acoustic response of conventional mechanical oscillators, such as a piezoelectric crystal, is predominantly harmonic at modest amplitudes. However, here, we observe from the electrical response that significant motional anharmonicity is introduced in the presence of attached analyte. Experiments were conducted with streptavidin-coated polystyrene microbeads of various sizes attached to a quartz crystal resonator via specific and nonspecific molecular tethers in liquid. Quantitative analysis reveals that the deviation of odd Fourier harmonics of the response caused by introduction of microbeads as a function of oscillation amplitude presents a unique signature of the molecular tether. Hence, the described anharmonic detection technique (ADT) based on this function allows screening of biomolecules and provides an additional level of selectivity in receptor-based detection that is often associated with nonspecific interactions. We also propose methods to extract mechanical force-extension characteristics of the molecular tether and activation energy using this technique.

Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores.

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks.

Development and validation of a new method for measuring friction between skin and nonwoven materials.

A new method for measuring the coefficient of friction between nonwoven materials and the curved surface of the volar forearm has been developed and validated. The method was used to measure the coefficient of static friction for three different nonwoven materials on the normal (dry) and over-hydrated volar forearms of five female volunteers (ages 18-44). The method proved simple to run and had good repeatability: the coefficient of variation (standard deviation expressed as a percentage of the mean) for triplets of repeat measurements was usually (80 per cent of the time) less than 10 per cent. Measurements involving the geometrically simpler configuration of pulling a weighted fabric sample horizontally across a quasi-planar area of volar forearm skin proved experimentally more difficult and had poorer repeatability. However, correlations between values of coefficient of static friction derived using the two methods were good (R = 0.81 for normal (dry) skin, and 0.91 for over-hydrated skin). Measurements of the coefficient of static friction for the three nonwovens for normal (dry) and for over-hydrated skin varied in the ranges of about 0.3-0.5 and 0.9-1.3, respectively. In agreement with Amontons' law, coefficients of friction were invariant with normal pressure over the entire experimental range (0.1-8.2 kPa).

Fundamental limits on the suppression of molecular fluctuations.

Negative feedback is common in biological processes and can increase a system's stability to internal and external perturbations. But at the molecular level, control loops always involve signalling steps with finite rates for random births and deaths of individual molecules. Here we show, by developing mathematical tools that merge control and information theory with physical chemistry, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically, the minimum standard deviation in abundances decreases with the quartic root of the number of signalling events, making it extremely expensive to increase accuracy. Our results are formulated in terms of experimental observables, and existing data show that cells use brute force when noise suppression is essential; for example, regulatory genes are transcribed tens of thousands of times per cell cycle. The theory challenges conventional beliefs about biochemical accuracy and presents an approach to the rigorous analysis of poorly characterized biological systems.

Electroosmotic flow analysis of a branched U-turn nanofluidic device.

In this paper, we present the analysis of electroosmotic flow in a branched -turn nanofluidic device, which we developed for detection and sorting of single molecules. The device, where the channel depth is only 150 nm, is designed to optically detect fluorescence from a volume as small as 270 attolitres (al) with a common wide-field fluorescent setup. We use distilled water as the liquid, in which we dilute 110 nm fluorescent beads employed as tracer-particles. Quantitative imaging is used to characterize the pathlines and velocity distribution of the electroosmotic flow in the device. Due to the device's complex geometry, the electroosmotic flow cannot be solved analytically. Therefore we use numerical flow simulation to model our device. Our results show that the deviation between measured and simulated data can be explained by the measured Brownian motion of the tracer-particles, which was not incorporated in the simulation.

Friction of sliding surfaces carrying adsorbed lubricant layers

In concentrated contacts the behaviour of lubricants is much modified by the high local pressures: changes can arise both from molecular ordering within the very thin film lubricant layers present at the interface as well as from the deposition on the component surfaces of more solid-like polymeric boundary layers. These 'third bodies' separating the solid surfaces may have rheological or mechanical properties very different from those observed in the bulk. Classical elasto-hydrodynamic theory considers the entrapped lubricant to exhibit a piezo-viscous behaviour while the conventional picture of more solid boundary lubricant layers views their shear strength r as being linearly dependent on local pressure p, so that T = TO + ap where TO and a are constants. If TO is relatively small, then the coefficient of friction \i = T Ip ~ a and so Amonton's laws are recovered. However, the properties of adsorbed or deposited surface films, or indeed other third bodies such as debris layers, may be more complex than this. A preliminary study has looked quantitatively at the influence of the pressure dependence of the shear strength of any surface layer on the overall friction coefficient of a contact which is made up of an array of asperities whose height varies in a Gaussian manner. Individual contact points may be elastic or plastic. The analysis results in plots of coefficient of friction versus the service or load parameter PIH&NRa where P is the nominal pressure on the contact, HS the hardness of the deforming surface, N the asperity density, R the mean radius of curvature of the asperities, and a is the standard deviation of their height distribution. In principle, any variation oft withp can be incorporated into the model; however, in this initial study we have used data on colloidal suspensions from the group at the Ecole Centrale de Lyon as well as examining the effect of functional relationships of somewhat greater complexity than a simple linear form. Results of the analysis indicate that variations in fj. are possible as the load is varied which depend on the statistical spread of behaviour at individual asperity contacts. The value of this analysis is that it attempts to combine the behaviour of films on the molecular scale with the topography of real engineering surfaces and so give an indication of the effects at the full-size or macro-scale that can be achieved by chemical or molecular surface engineering.

Studies of inverter ratings of BDFM adjustable speed drive or generator systems

This paper discusses the inverter ratings of Brushless Doubly-Fed Machine (BDFM) adjustable speed drive (ASD) or generator (ASG) systems. Based on the per phase equivalent circuit model, the ratings of the two inverters in a bidirectional converter are evaluated individually. An approach to minimise the total inverter rating is presented, taking into account power factor constraints of the power grid. The effects of speed deviation and control winding excitation on the inverter ratings are discussed. Predictions of inverter ratings are presented with experimental verification. A design example is also provided in which the total inverter rating is minimised for a practical BDFM based ASG system. © 2005 IEEE.

Boundary-layer suction system design for laminar-flying-wing aircraft

The present study aims to provide insight into the parameters affecting practical laminar-flow-control suction power requirements for a commercial laminar-flying-wing transport aircraft. It is shown that there is a minimum power requirement independent of the suction system design, associated with the stagnation pressure loss in the boundary layer. This requirement increases with aerofoil section thickness, but depends only weakly on Mach number and (for a thick, lightly loaded laminar flying wing) lift coefficient. Deviation from the optimal suction distribution, due to a practical chamber-based architecture, is found to have very little effect on the overall suction coefficient; hence, to a good approximation, the power penalty is given by the product of the optimal suction flow rate coefficient and the average skin pressure drop. In the spanwise direction, through suitable choice of chamber depth, the pressure drop due to frictional and inertial effects may be rendered negligible. Finally, if there are fewer pumps than chambers, the average pressure drop from the aerofoil surface to the pump collector ducts, rather than to the chambers, determines the power penalty. For the representative laminar-flying-wing aircraft parameters considered here, the minimum power associated with boundary-layer losses alone contributes some 80-90% of the total power requirement. © 2011 by the American Institute of Aeronautics and Astronautics, Inc.

Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks. © 2011 Elsevier B.V.

Robust airfoil design with respect to boundary layer transition

In order to disign an airfoil of which maximum lift coefficient (CL max) is not sensitive to location of forced top boundary layer transition. Taking maximizing mean value of CL max and minimizing standard deviation as biobjective, leading edge radius, manximum thickness and its location, maximum camber and its location as deterministic design variables, location of forced top boundary layer transition as stochastic variable, XFOIL as deterministic CFD solver, non-intrusive polynomial chaos as substitute of Monte Carlo method, we completed a robust airfoil design problem. Results demonstrate performance of initial airfoil is enhanced through reducing standard deviation of CL max. Besides, we also know maximum thickness has the most dominating effect on mean value of CL max, location of maximum thickness has the most dominating effect on standard deviation of CL max, maximum camber has a little effect on both mean value and standard deviation, and maximum camber is the only element of which increase can lead increase of mean value and standard deviation at the same time. Copyright © 2009 by the American Institute of Aeronautics and Astronautics, Inc.

Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach.

We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population. Most existing approaches for local ancestry estimation ignore the latent genetic relatedness between ancestral populations and treat them as independent. In this article, we exploit such information by building an inheritance model that describes both the ancestral populations and the admixed population jointly in a unified framework. Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each ancestral population and further extend it to generate the admixed population. Through an effective utilization of the population structural information under a principled nonparametric Bayesian framework, the resulting model is significantly less sensitive to the choice and the amount of training data for ancestral populations than state-of-the-art algorithms. We also improve the robustness under deviation from common modeling assumptions by incorporating population-specific scale parameters that allow variable recombination rates in different populations. Our method is applicable to an admixed population from an arbitrary number of ancestral populations and also performs competitively in terms of spurious ancestry proportions under a general multiway admixture assumption. We validate the proposed method by simulation under various admixing scenarios and present empirical analysis results from a worldwide-distributed dataset from the Human Genome Diversity Project.

Re-examination of the coefficient of determination (r2) using road materials engineering case studies

The analysis of scientific data is integral to materials engineering and science. The correlation between measured variables is often quantified by estimating the coefficient of determination or the r2 value. This is the recognised procedure for determining linear relationships. The authors review the derivation of the r2 value and derive an associated quantity, termed the relative deviation (RD), which is the ratio of the root mean square of the deviations about the fitted line to the root mean square of the deviations about the y bar line expressed as a percentage. The relative deviation has an advantage over the coefficient of determination in that it has greater numerical sensitivity to changes in the spread of data about the fitted line, especially when the scatter is small. In addition, the relative deviation is able to define, in percentage terms, the reduction in scatter when different independent variables are correlated with a common dependent variable. Four case studies in the materials field (aggregate crushing value, Atterberg limits, permeability and creep of asphalt) from work carried out at the Queensland Main Roads Department are presented to show the use of the new parameter RD.