A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water

Background: Water and High Purity Water (HPW) distribution systems can be contaminated with human pathogenic microorganisms. This biocontamination may pose a risk to human health as HPW is commonly used in the industrial, pharmaceutical and clinical sectors. Currently, routine microbiological testing of HPW is performed using slow and labour intensive traditional microbiological based techniques. There is a need to develop a rapid culture independent methodology to quantitatively detect and identify biocontamination associated with HPW. Results: A novel internally controlled 5-plex real-time PCR Nucleic Acid Diagnostics assay (NAD), was designed and optimised in accordance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, to rapidly detect, identify and quantify the human pathogenic bacteriaStenotrophomonas maltophilia, Burkholderia species, Pseudomonas aeruginosa and Serratia marcescenswhich are commonly associated with the biocontamination of water and water distribution systems. The specificity of the 5-plex assay was tested against genomic DNA isolated from a panel of 95 microorganisms with no cross reactivity observed. The analytical sensitivities of the S. maltophilia, B. cepacia, P. aeruginosa and the S. marcescens assays are 8.5, 5.7, 3.2 and 7.4 genome equivalents respectively. Subsequently, an analysis of HPW supplied by a Millipore Elix 35 water purification unit performed using standard microbiological methods revealed high levels of naturally occurring microbiological contamination. Five litre water samples from this HPW delivery system were also filtered and genomic DNA was purified directly from these filters. These DNA samples were then tested using the developed multiplex real-time PCR NAD assay and despite the high background microbiological contamination observed, both S. maltophilia andBurkholderia species were quantitatively detected and identified. At both sampling points the levels of both S. maltophilia and Burkholderia species present was above the threshold of 10 cfu/100 ml recommended by both EU and US guidelines. Conclusions: The novel culture independent methodology described in this study allows for rapid (<5 h), quantitative detection and identification of these four human pathogens from biocontaminated water and HPW distribution systems. We propose that the described NAD assay and associated methodology could be applied to routine testing of water and HPW distribution systems to assure microbiological safety and high water quality standards

Does early intervention improve outcomes in physiotherapy management of lumbar radicular syndrome? A mixed-methods study protocol.

INTRODUCTION: Lumbar radicular syndrome (LRS) can be a painful and debilitating condition. The optimum management strategies and their timing remain elusive despite extensive research. Surgery provides good short-term outcomes but has concomitant risks and costs. Physiotherapy is commonly practised for patients with LRS but its effects remain equivocal and there is a lack of consensus on the type, duration and timing of physiotherapy intervention. There is a lack of high-quality evidence into new and innovative management strategies and the timings of those strategies for LRS. This pilot trial is an essential preliminary to a definitive randomised controlled trial (RCT) assessing the effectiveness and cost-effectiveness of early physiotherapy intervention for patients with LRS. The study will test the protocol, the intervention, the use of outcome measures and the ability to set-up and run the trial to enable refinement of a future definitive RCT. METHODS AND ANALYSIS: This is a mixed-methods study encompassing an external pilot RCT with integrated qualitative interviews with patients, clinicians and other key stakeholders. 80 patients will be recruited from primary care and randomised, after consent into 1 of 2 groups. Both groups will receive individually tailored, goal orientated physiotherapy. The usual care group will begin their physiotherapy 6 weeks after randomisation and the intervention group at 2 weeks after randomisation. Outcome measures will primarily be feasibility parameters including the ability to recruit and retain patients and to deliver the intervention. Data will be collected at baseline, and 6, 12 and 26 weeks following randomisation. ETHICS AND DISSEMINATION: The study has received favourable ethical review from the East of Scotland Research Ethics Service (EoSRES) on the 20 August 2015 (15/ES/0130). Recruitment began on the 1 March 2016 and is expected to close in January 2017. Data collection is anticipated to be complete in July 2017. The study results will be made available to participants, clinicians involved in the study and the wider clinical community through publication in a peer reviewed journal and at conference presentations. TRIAL REGISTRATION NUMBER: ISRCTN: 25018352, Pre-results; Clinical Trials.Gov: NCT02618278 Document version V1.1 23.9.2016

Cancer Informatics in the U.K.: The NCRI Informatics Initiative

The arrival of high-throughput technologies in cancer science and medicine has made the possibility for knowledge generation greater than ever before. However, this has brought with it real challenges as researchers struggle to analyse the avalanche of information available to them. A unique U.K.-based initiative has been established to promote data sharing in cancer science and medicine and to address the technical and cultural issues needed to support this

Biomass burning aerosol over the Amazon: analysis of aircraft, surface and satellite observations using a global aerosol model

Vegetation fires emit large quantities of aerosol into the atmosphere, impacting regional air quality and climate. Previous work has used comparisons of simulated and observed aerosol optical depth (AOD) in regions heavily impacted by fires to suggest that emissions of aerosol particles from fires may be underestimated by a factor of 2–5. Here we use surface, aircraft and satellite observations made over the Amazon during September 2012, along with a global aerosol model to improve understanding of aerosol emissions from vegetation fires. We apply three different satellite-derived fire emission datasets (FINN, GFED, GFAS) in the model. Daily mean aerosol emissions in these datasets vary by up to a factor of 3.7 over the Amazon during this period, highlighting the considerable uncertainty in emissions. We find variable agreement between the model and observed aerosol mass concentrations. The model reproduces observed aerosol concentrations over deforestation fires well in the western Amazon during dry season conditions with FINN or GFED emissions and during dry–wet transition season conditions with GFAS emissions. In contrast, the model underestimates aerosol concentrations over savanna fires in the Cerrado environment east of the Amazon Basin with all three fire emission datasets. The model generally underestimates AOD compared to satellite and ground stations, even when the model reproduces the observed vertical profile of aerosol mass concentration. We suggest it is likely caused by uncertainties in the calculation of AOD, which are as large as ∼90 %, with the largest sensitivities due to uncertainties in water uptake and relative humidity. Overall, we do not find evidence that particulate emissions from fires are systematically underestimated in the Amazon region and we caution against using comparison with AOD to constrain particulate emissions from fires

Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle

Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-L-phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the phenyl azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded phenyl azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks

Evaluation of the effectiveness and cost-effectiveness of Families for Health V2 for the treatment of childhood obesity : study protocol for a randomized controlled trial

Background: Effective programs to help children manage their weight are required. Families for Health focuses on a parenting approach, designed to help parents develop their parenting skills to support lifestyle change within the family. Families for Health V1 showed sustained reductions in overweight after 2 years in a pilot evaluation, but lacks a randomized controlled trial (RCT) evidence base. Methods/design: This is a multi-center, investigator-blind RCT, with parallel economic evaluation, with a 12-month follow-up. The trial will recruit 120 families with at least one child aged 6 to 11 years who is overweight (≥91st centile BMI) or obese (≥98th centile BMI) from three localities and assigned randomly to Families for Health V2 (60 families) or the usual care control (60 families) groups. Randomization will be stratified by locality (Coventry, Warwickshire, Wolverhampton). Families for Health V2 is a family-based intervention run in a community venue. Parents/carers and children attend parallel groups for 2.5 hours weekly for 10 weeks. The usual care arm will be the usual support provided within each NHS locality. A mixed-methods evaluation will be carried out. Child and parent participants will be assessed at home visits at baseline, 3-month (post-treatment) and 12-month follow-up. The primary outcome measure is the change in the children’s BMI z-scores at 12 months from the baseline. Secondary outcome measures include changes in the children’s waist circumference, percentage body fat, physical activity, fruit/vegetable consumption and quality of life. The parents’ BMI and mental well-being, family eating/activity, parent–child relationships and parenting style will also be assessed. Economic components will encompass the measurement and valuation of service utilization, including the costs of running Families for Health and usual care, and the EuroQol EQ-5D health outcomes. Cost-effectiveness will be expressed in terms of incremental cost per quality-adjusted life year gained. A de novo decision-analytic model will estimate the lifetime cost-effectiveness of the Families for Health program. Process evaluation will document recruitment, attendance and drop-out rates, and the fidelity of Families for Health delivery. Interviews with up to 24 parents and children from each arm will investigate perceptions and changes made. Discussion: This paper describes our protocol to assess the effectiveness and cost-effectiveness of a parenting approach for managing childhood obesity and presents challenges to implementation. Trial registration: Current Controlled Trials ISRCTN4503220

Sensitivity of air pollution exposure and disease burden to emission changes in China using machine learning emulation

Machine learning models can emulate chemical transport models, reducing computational costs and enabling more experimentation. We developed emulators to predict annual−mean fine particulate matter (PM(2.5)) and ozone (O(3)) concentrations and their associated chronic health impacts from changes in five major emission sectors (residential, industrial, land transport, agriculture, and power generation) in China. The emulators predicted 99.9% of the variance in PM(2.5) and O(3) concentrations. We used these emulators to estimate how emission reductions can attain air quality targets. In 2015, we estimate that PM(2.5) exposure was 47.4 μg m(−3) and O(3) exposure was 43.8 ppb, associated with 2,189,700 (95% uncertainty interval, 95UI: 1,948,000–2,427,300) premature deaths per year, primarily from PM(2.5) exposure (98%). PM(2.5) exposure and the associated disease burden were most sensitive to industry and residential emissions. We explore the sensitivity of exposure and health to different combinations of emission reductions. The National Air Quality Target (35 μg m(−3)) for PM(2.5) concentrations can be attained nationally with emission reductions of 72% in industrial, 57% in residential, 36% in land transport, 35% in agricultural, and 33% in power generation emissions. We show that complete removal of emissions from these five sectors does not enable the attainment of the WHO Annual Guideline (5 μg m(−3)) due to remaining air pollution from other sources. Our work provides the first assessment of how air pollution exposure and disease burden in China varies as emissions change across these five sectors and highlights the value of emulators in air quality research

Does early intervention improve outcomes in the physiotherapy management of lumbar radicular syndrome? Results of the POLAR pilot randomised controlled trial

OBJECTIVE: To investigate the feasibility of undertaking a definitive randomised controlled trial (RCT). SETTING: This was a pilot, pragmatic superiority RCT with a qualitative element, recruiting from 14 general practitioner (GP) practices in England. PARTICIPANTS: Patients over 18 years of age presenting to their GP with unilateral lumbar radicular syndrome (LRS), defined as radicular pain and/or neurological symptoms originating from lumbar nerve roots, were eligible to participate in the study, those who did not have a clear understanding of the English language or had comorbidities preventing rehabilitation were ineligible. INTERVENTIONS: Participants were randomised into early intervention physiotherapy or usual care with the former receiving their treatment within 2 weeks after randomisation and the latter 6 weeks postrandomisation. Both groups received a patient-centred, goal-orientated physiotherapy programme specific to their needs. Participants received up to six treatment sessions over an 8-week period. OUTCOME MEASURES: Process outcomes to determine the feasibility of the study and an exploratory analysis of patient-reported outcomes, including self-rated disability, pain and general health, these were collected at baseline, 6, 12 and 26 weeks postrandomisation. RESULTS: 80 participants were recruited in 10 GP practices over 34 weeks and randomised to (early intervention physiotherapy n=42, usual care n=38). Follow-up rates at 26 weeks were 32 (84%) in the usual care and 36 (86%) in the early intervention physiotherapy group. The mean area under the curve (larger values indicating more disability) for the Oswestry Disability Index over the 26 weeks was 16.6 (SD 11.4) in the usual care group and 16.0 (SD 14.0) in the intervention group. A difference of -0.6 (95% CI -0.68 to 5.6) in favour of the intervention group. CONCLUSIONS: The results of the study suggest a full RCT is feasible and will provide evidence as to the optimal timing of physiotherapy for patients with LRS. TRIAL REGISTRATION NUMBER: NCT02618278, ISRCTN25018352

The climatic importance of uncertainties in regional aerosol-cloud radiative forcings over recent decades

This is the final version of the article. Available from American Meteorological Society via the DOI in this record.Regional patterns of aerosol radiative forcing are important for understanding climate change on decadal time scales. Uncertainty in aerosol forcing is likely to vary regionally and seasonally because of the short aerosol lifetime and heterogeneous emissions. Here the sensitivity of regional aerosol cloud albedo effect (CAE) forcing to 31 aerosol process parameters and emission fluxes is quantified between 1978 and 2008. The effects of parametric uncertainties on calculations of the balance of incoming and outgoing radiation are found to be spatially and temporally dependent. Regional uncertainty contributions of opposite sign cancel in global-mean forcing calculations, masking the regional importance of some parameters. Parameters that contribute little to uncertainty in Earth's global energy balance during recent decades make significant contributions to regional forcing variance. Aerosol forcing sensitivities are quantified within 11 climatically important regions, where surface temperatures are thought to influence large-scale climate effects. Substantial simulated uncertainty in CAE forcing in the eastern Pacific leaves open the possibility that apparent shifts in the mean ENSO state may result from a forced aerosol signal on multidecadal time scales. A likely negative aerosol CAE forcing in the tropical North Atlantic calls into question the relationship between Northern Hemisphere aerosol emission reductions and CAE forcing of sea surface temperatures in the main Atlantic hurricane development region on decadal time scales. Simulated CAE forcing uncertainty is large in the North Pacific, suggesting that the role of the CAE in altering Pacific tropical storm frequency and intensity is also highly uncertain.Data can be made available upon request from the corresponding author. L. A. Regayre is funded by a Doctoral Training Grant from the Natural Environment Research Council (NERC) and a CASE studentship with the Met Office Hadley Centre. B. B. B. Booth was supported by the Joint UK DECC/Defra Met Office Hadley Centre Climate Programme (GA01101). K. S. Carslaw acknowledges funding from the Royal Society Wolfson Award. We acknowledge funding from NERC under AEROS and GASSP Grants NE/G006172/1 and NE/J024252/1. This work made use of the facilities of N8 HPC provided and funded by the N8 consortium and EPSRC (EP/K000225/1). The Met Office Hadley Centre is coordinated by the University of Leeds and the University of Manchester. The authors thank three anonymous reviewers for their constructive comments on this article

Ensemble-Empirical-Mode-Decomposition based micro-Doppler signal separation and classification

The target echo signals obtained by Synthetic Aperture Radar (SAR) and Ground Moving Target Indicator (GMTI platforms are mainly composed of two parts, the micro-Doppler signal and the target body part signal. The wheeled vehicle and the track vehicle are classified according to the different character of their micro-Doppler signal. In order to overcome the mode mixing problem in Empirical Mode Decomposition (EMD), Ensemble Empirical Mode Decomposition (EEMD) is employed to decompose the original signal into a number of Intrinsic Mode Functions (IMF). The correlation analysis is then carried out to select IMFs which have a relatively high correlation with the micro-Doppler signal. Thereafter, four discriminative features are extracted and Support Vector Machine (SVM) classifier is applied for classification. The experimental results show that the features extracted after EEMD decomposition are effective, with up 90% success rate for classification using one feature. In addition, these four features are complementary in different target velocity and azimuth angles