A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

We describe a novel coarse grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a viscoelastic continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obtained for proteins in general from atomistic molecular dynamics simulations

Performance Control in Wireless Sensor Networks

Most of the currently deployed wireless sensor networks applications do not require performance control. The goal of the GINSENG project is sensor networks that meet application-specific performance targets, in particular with respect to latency and reliability. We present scenarios within the GALP oil re¿nery where the system will be deployed and some initial technical insights with respect to deterministic communication

Randomised trial of once-daily vilanterol in children with asthma on inhaled corticosteroid therapy

GSK (ClinicalTrials.gov identifier NCT01573767

Stacking fault-associated polarized surface-emitted photoluminescence from zincblende InGaN/GaN quantum wells

Zincblende InGaN/GaN quantum wells offer a potential improvement to the efficiency of green light emission by removing the strong electric fields present in similar structures. However, a high density of stacking faults may have an impact on the recombination in these systems. In this work, scanning transmission electron microscopy and energy-dispersive x-ray measurements demonstrate that one dimensional nanostructures form due to indium segregation adjacent to stacking faults. In photoluminescence experiments these structures emit visible light which is optically polarised up to 86% at 10K and up to 75% at room temperature. The emission redshifts and broadens as the well width increases from 2nm to 8nm. Photoluminescence excitation measurements indicate that carriers are captured by these structures from the rest of the quantum wells and recombine to emit light polarised along the length of these nanostructures

Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of false-positive GM plants linked to Cauliflower mosaic virus (CaMV) infection.

BACKGROUND:Most genetically modified (GM) plants contain a promoter, P35S, from the plant virus, Cauliflower mosaic virus (CaMV), and many have a terminator, TNOS, derived from the bacterium, Agrobacterium tumefaciens. Assays designed to detect GM plants often target the P35S and/or TNOS DNA sequences. However, because the P35S promoter is derived from CaMV, these detection assays can yield false-positives from non-GM plants infected by this naturally-occurring virus. RESULTS:Here we report the development of an assay designed to distinguish CaMV-infected plants from GM plants in a single multiplexed quantitative PCR (qPCR) reaction. Following initial testing and optimization via PCR and singleplex-to-multiplex qPCR on both plasmid and plant DNA, TaqMan qPCR probes with different fluorescence wavelengths were designed to target actin (a positive-control plant gene), P35S, P3 (a CaMV-specific gene), and TNOS. We tested the specificity of our quadruplex qPCR assay using different DNA extracts from organic watercress and both organic and GM canola, all with and without CaMV infection, and by using commercial and industrial samples. The limit of detection (LOD) of each target was determined to be 1% for actin, 0.001% for P35S, and 0.01% for both P3 and TNOS. CONCLUSIONS:This assay was able to distinguish CaMV-infected plants from GM plants in a single multiplexed qPCR reaction for all samples tested in this study, suggesting that this protocol is broadly applicable and readily transferrable to any interested parties with a qPCR platform

Risk factors for hospital admission with RSV bronchiolitis in England: a population-based birth cohort study.

OBJECTIVE: To examine the timing and duration of RSV bronchiolitis hospital admission among term and preterm infants in England and to identify risk factors for bronchiolitis admission. DESIGN: A population-based birth cohort with follow-up to age 1 year, using the Hospital Episode Statistics database. SETTING: 71 hospitals across England. PARTICIPANTS: We identified 296618 individual birth records from 2007/08 and linked to subsequent hospital admission records during the first year of life. RESULTS: In our cohort there were 7189 hospital admissions with a diagnosis of bronchiolitis, 24.2 admissions per 1000 infants under 1 year (95%CI 23.7-24.8), of which 15% (1050/7189) were born preterm (47.3 bronchiolitis admissions per 1000 preterm infants (95% CI 44.4-50.2)). The peak age group for bronchiolitis admissions was infants aged 1 month and the median was age 120 days (IQR = 61-209 days). The median length of stay was 1 day (IQR = 0-3). The relative risk (RR) of a bronchiolitis admission was higher among infants with known risk factors for severe RSV infection, including those born preterm (RR = 1.9, 95% CI 1.8-2.0) compared with infants born at term. Other conditions also significantly increased risk of bronchiolitis admission, including Down's syndrome (RR = 2.5, 95% CI 1.7-3.7) and cerebral palsy (RR = 2.4, 95% CI 1.5-4.0). CONCLUSIONS: Most (85%) of the infants who are admitted to hospital with bronchiolitis in England are born at term, with no known predisposing risk factors for severe RSV infection, although risk of admission is higher in known risk groups. The early age of bronchiolitis admissions has important implications for the potential impact and timing of future active and passive immunisations. More research is needed to explain why babies born with Down's syndrome and cerebral palsy are also at higher risk of hospital admission with RSV bronchiolitis

Predictors of patient preference for either whole body magnetic resonance imaging (WB-MRI) or CT/ PET-CT for staging colorectal or lung cancer

Introduction: Whole body magnetic resonance imaging (WB-MRI) may be more efficient in staging cancers, but can be harder for patients to tolerate. We examined predictors of patient preference for WB-MRI vs. CT/ PET-CT for staging colorectal or lung cancer. Methods: Patients recruited prospectively to two multicenter trials comparing diagnostic accuracy of WB-MRI with standard staging scans were sent two questionnaires: the first, administered at trial registration, captured demographics, educational level, and comorbidities; the second, administered after staging completion, measured emotional distress (GHQ-12), positive mood (PANAS), perceived scan burden, patients’ beliefs about WB-MRI, and preference for either WB-MRI or CT (colorectal trial), WB-MRI or PET-CT (lung trial). Preference for WB-MRI or CT / PET-CT were analysed using logistic regression. Results: Baseline and post-staging questionnaires were completed by 97 and 107 patients respectively. Overall, 56/107 (52%) preferred WB-MRI over standard scans, and were more likely to have no additional comorbidities, higher positive mood, greater awareness of potential benefits of WB-MRI, and lower levels of perceived WB-MRI scan burden. In adjusted analyses, only awareness of potential WB-MRI benefits remained a significant predictor (OR: 1.516, 95% CIs 1.006 to 2.284, p=0.047). Knowledge that WB-MRI does not use radiation predicted preference (adjusted OR: 3.018, 95% CIs 1.099 to 8.288, p=0.032), yet only 45/107 (42%) patients were aware of this attribute. Conclusions: A small majority of patients undergoing staging of colorectal or lung cancer prefer WB-MRI to CT/ PET-CT. Raising awareness of the potential benefits of WB-MRI, notably lack of ionising radiation, could influence preference

Predictors of patient preference for either whole body magnetic resonance imaging (WB-MRI) or CT/ PET-CT for staging colorectal or lung cancer.

INTRODUCTION: Whole body magnetic resonance imaging (WB-MRI) may be more efficient in staging cancers, but can be harder for patients to tolerate. We examined predictors of patient preference for WB-MRI vs. CT/ PET-CT for staging colorectal or lung cancer. METHODS: Patients recruited prospectively to two multicentre trials comparing diagnostic accuracy of WB-MRI with standard staging scans were sent two questionnaires: the first, administered at trial registration, captured demographics, educational level and comorbidities; the second, administered after staging completion, measured emotional distress (GHQ-12), positive mood (PANAS), perceived scan burden, patients' beliefs about WB-MRI, and preference for either WB-MRI or CT (colorectal trial), WB-MRI or PET-CT (lung trial). Preference for WB-MRI or CT/ PET-CT was analysed using logistic regression. RESULTS: Baseline and post-staging questionnaires were completed by 97 and 107 patients, respectively. Overall, 56/107 (52%) preferred WB-MRI over standard scans and were more likely to have no additional comorbidities, higher positive mood, greater awareness of potential benefits of WB-MRI and lower levels of perceived WB-MRI scan burden. In adjusted analyses, only awareness of potential WB-MRI benefits remained a significant predictor (OR: 1.516, 95% CIs 1.006-2.284, P = 0.047). Knowledge that WB-MRI does not use radiation predicted preference (adjusted OR: 3.018, 95% CIs 1.099-8.288, P = 0.032), although only 45/107 (42%) patients were aware of this attribute. CONCLUSIONS: A small majority of patients undergoing staging of colorectal or lung cancer prefer WB-MRI to CT/ PET-CT. Raising awareness of the potential benefits of WB-MRI, notably lack of ionizing radiation, could influence preference

High-fidelity quantum driving

The ability to accurately control a quantum system is a fundamental requirement in many areas of modern science such as quantum information processing and the coherent manipulation of molecular systems. It is usually necessary to realize these quantum manipulations in the shortest possible time in order to minimize decoherence, and with a large stability against fluctuations of the control parameters. While optimizing a protocol for speed leads to a natural lower bound in the form of the quantum speed limit rooted in the Heisenberg uncertainty principle, stability against parameter variations typically requires adiabatic following of the system. The ultimate goal in quantum control is to prepare a desired state with 100% fidelity. Here we experimentally implement optimal control schemes that achieve nearly perfect fidelity for a two-level quantum system realized with Bose-Einstein condensates in optical lattices. By suitably tailoring the time-dependence of the system's parameters, we transform an initial quantum state into a desired final state through a short-cut protocol reaching the maximum speed compatible with the laws of quantum mechanics. In the opposite limit we implement the recently proposed transitionless superadiabatic protocols, in which the system perfectly follows the instantaneous adiabatic ground state. We demonstrate that superadiabatic protocols are extremely robust against parameter variations, making them useful for practical applications.Comment: 17 pages, 4 figure