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.

Stall warning by blade pressure signature analysis

At low mass flow rates axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past - primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focussed on the level of irregularity in the blade passing signature in the rotor tip region. In general, this irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of the flow irregularity, but little effort has been made to characterise the irregularity, or to understand its underlying causes. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity which accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether this irregularity observed in the pre-stall flow field is due to random turbulence, or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity will not be viable in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. Copyright © 2011 by ASME.

Electron spin resonance signature of the oxygen vacancy in HfO 2

The oxygen vacancy has been inferred to be the critical defect in HfO 2, responsible for charge trapping, gate threshold voltage instability, and Fermi level pinning for high work function gates, but it has never been conclusively identified. Here, the electron spin resonance g tensor parameters of the oxygen vacancy are calculated, using methods that do not over-estimate the delocalization of the defect wave function, to be g xx = 1.918, g yy = 1.926, g zz = 1.944, and are consistent with an observed spectrum. The defect undergoes a symmetry lowering polaron distortion to be localized mainly on a single adjacent Hf ion. © 2012 American Institute of Physics.

Stall Warning by Blade Pressure Signature Analysis

At low mass flow rates, axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past---primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focused on the level of irregularity in the blade passing signature in the rotor tip region. In general, the irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of flow irregularity, but little effort has been made to characterize the irregularity itself, or to understand its underlying cause. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance size and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity that accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether the irregularity observed in the prestall flow field is due to random turbulence or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity would be difficult to implement in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. © 2013 American Society of Mechanical Engineers.

Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data

We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/

Determining vibration signature of a defective planet bearing in a wind turbine epicyclic gearbox

Planet bearings of wind turbine epicyclic gearboxes are considered as one of the most critical components due to their high failure rate. In order to develop effective vibration based detection algorithms for these bearings, a thorough understanding of their vibration signature is required. In this paper, we investigate the vibration behaviour of an epicyclic gearbox in the presence of a defective planet bearing both theoretically and experimentally. We also identify different sources of modulation sidebands using an analytical model which includes ring gear flexibility and planet bearing defects. The findings from this work will help engineers to develop more effective fault detection algorithms.

The neural signature of escalating frustration in humans.

Mammalian studies show that frustration is experienced when goal-directed activity is blocked. Despite frustration's strongly negative role in health, aggression and social relationships, the neural mechanisms are not well understood. To address this we developed a task in which participants were blocked from obtaining a reward, an established method of producing frustration. Levels of experienced frustration were parametrically varied by manipulating the participants' motivation to obtain the reward prior to blocking. This was achieved by varying the participants' proximity to a reward and the amount of effort expended in attempting to acquire it. In experiment 1, we confirmed that proximity and expended effort independently enhanced participants' self-reported desire to obtain the reward, and their self-reported frustration and response vigor (key-press force) following blocking. In experiment 2, we used functional magnetic resonance imaging (fMRI) to show that both proximity and expended effort modulated brain responses to blocked reward in regions implicated in animal models of reactive aggression, including the amygdala, midbrain periaqueductal grey (PAG), insula and prefrontal cortex. Our findings suggest that frustration may serve an energizing function, translating unfulfilled motivation into aggressive-like surges via a cortical, amygdala and PAG network.