Cytolethal distending toxin (CDT)-negative Campylobacter jejuni strains and anti-CDT neutralising antibodies induced during human infection but not chicken colonisation

The cytolethal distending toxin (CDT) of Campylobacter jejuni was detectable, using an in vitro assay, in most but not all of 24 strains tested. The reason for the absence of toxin activity in these naturally occurring CDT-negative C. jejuni strains was then investigated at the genetic level. CDT is encoded by three highly conserved genes, cdtA, -B, and -C. In the CDT-negative strains, two types of mutation were identified. The CDT activities of C. jejuni strains possessing both types of mutation were successfully complemented with the functional genes of C. jejuni 11168. The first type of mutation comprised a 667-bp deletion across cdtA and cdtB and considerable degeneration in the remainder of the cdt locus. Using a PCR technique to screen for this deletion, this mutation occurred in fewer than 3% of 147 human, veterinary, and environmental strains tested. The second type of mutation involved at least four nonsynonymous nucleotide changes, but only the replacement of proline with serine at CdtB position 95 was considered important for CDT activity. This was confirmed by site-directed mutagenesis. This type of mutation also occurred in fewer than 3% of strains as determined using a LightCycler biprobe assay. The detection of two CDT-negative clinical isolates raised questions about the role of CDT in some cases of human campylobacteriosis. To determine if anti-CDT antibodies are produced in human infection, a toxin neutralization assay was developed and validated using rabbit antisera. Pooled human sera from infected patients neutralized the toxin, indicating expression and immunogenicity during infection. However, no neutralizing antibodies were detected in colonized chickens despite the expression of CDT in the avian gut as indicated by reverse transcription-PCR

Exploring the efficacy of different electric field models in driving a model of the plasmasphere

The dynamics of the plasmasphere are strongly controlled by the inner magnetospheric electric field. In order to capture realistically the erosion of the nightside plasmapause and the formation of the drainage plume in a model of the plasmasphere, the electric field must be accurate. This study investigates how well five different electric field models drive the Dynamic Global Core Plasma Model during eight storm periods. The five electric field models are the Volland‐Stern analytic formula with Maynard‐Chen Kp dependence, two versions of the Weimer statistical models (96 and 05), and two versions of the Assimilative Mapping of Ionospheric Electrodynamics (AMIE) technique using magnetometer and DMSP satellite data. Manually extracted plasmapause locations from images taken by the EUV instrument on the Imager for Magnetopause‐to‐Aurora Global Exploration (IMAGE) satellite, as described by Goldstein et al. (2005), were compared to the simulation results throughout the main phase of the eight events. Three methods of calculating the plasmapause were employed to determine the best fit to EUV data, using the maximum gradient, a constant density contour (fit method), and the location in which the modeled density fell significantly below the specified saturation density for the given radial position (saturation method). It was found that the simulations driven by the Weimer (1996) model produced the best fit overall and that the fit and saturation methods worked best for matching the model results to the observations. Key Points The Weimer [1996] model works quite well for driving the plasmasphere A saturation technique for determining the plasmapause location in introduced Plasmapause determined by IMAGE may not be the steepest gradient in densityPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108010/1/jgra51094.pd

Spin Readout and Initialization in a Semiconductor Quantum Dot

Electron spin qubits in semiconductors are attractive from the viewpoint of long coherence times. However, single spin measurement is challenging. Several promising schemes incorporate ancillary tunnel couplings that may provide unwanted channels for decoherence. Here, we propose a novel spin-charge transduction scheme, converting spin information to orbital information within a single quantum dot by microwave excitation. The same quantum dot can be used for rapid initialization, gating, and readout. We present detailed modeling of such a device in silicon to confirm its feasibility.Comment: Published versio

Screening effects in the electron-optical phonon interaction

We show that recently reported unusual hardening of optical phonons renormalized by the electron-phonon interaction is due to the neglect of screening effects. When the electron-ion interaction is properly screened optical phonons soften in three dimension. It is important that for short-wavelength optical phonons screening is static while for long-wavelength optical phonons screening is dynamic. In two-dimensional and one-dimensional cases due to crossing of the nonperturbed optical mode with gapless plasmons the spectrum of renormalized optical phonon-plasmon mode shows split momentum dependence.Comment: 7 page

Farm level risk factors for fluoroquinolone resistance in E. coli and thermophilic Campylobacter spp. on poultry farms

Data on husbandry practices, performance, disease and drug use were collected during a cross-sectional survey of 89 poultry meat farms in England and Wales to provide information on possible risk factors for the occurrence of fluoroquinolone (FQ)-resistant bacteria. Faeces samples were used to classify farms as “affected” or “not affected” by FQ-resistant (FQr) Escherichia coli or Campylobacter spp. Risk factor analysis identified the use of FQ on the farms as having by far the strongest association, among the factors considered, with the occurrence of FQr bacteria. Resistant E. coli and/or Campylobacter spp. were found on 86% of the farms with a history of FQ use. However, a substantial proportion of farms with no history of FQ use also yielded FQr organisms, suggesting that resistant bacteria may transfer between farms. Further analysis suggested that for Campylobacter spp., on-farm hygiene, cleaning and disinfection between batches of birds and wildlife control were of most significance. By contrast, for E. coli biosecurity from external contamination was of particular importance, although the modelling indicated that other factors were likely to be involved. Detailed studies on a small number of sites showed that FQr E. coli can survive routine cleaning and disinfection. It appears difficult to avoid the occurrence of resistant bacteria when FQ are used on a farm, but the present findings provide evidence to support recommendations to reduce the substantial risk of the incidental acquisition of such resistance by farms where FQ are not used

Induced surface fluxes: A new framework for attributing Arctic sea ice volume balance biases to specific model errors

This is the final version. Available on open access from EGU via the DOI in this recordCode availability. The code used to create the fields of induced surface flux bias is written in Python and is provided as a Supplement (directory “ISF”). The code used to create Figs. 1–9, as well as Fig. B1, is also provided (directory “Figures”). In addition, the routines used to estimate errors in the ISF analysis are provided (directory “Analysis”). Finally, the code used to create Table 1 is provided (directory “Tables”). A set of auxiliary routines used by most of the above are also provided (directory “Library”). Most routines make use of the open-source Iris library, and several make use of the open-source Cartopy library.Data availability. Monthly mean ice thickness, ice fraction, snow thickness and surface radiation, as well as daily surface temperature and surface radiation, for the historical simulations of HadGEM2-ES, are available from the CMIP5 archive at https://cmip.llnl.gov/cmip5/data_portal.html (last access: February 2018). NSIDC ice concentration and melt onset data can be downloaded at http://nsidc.org/data/NSIDC-0051 (last access: May 2017; Cavalieri et al., 1996) and http://nsidc.org/data/NSIDC-0105 (last access: March 2016; Anderson et al., 2011) respectively. PIOMAS ice thickness data can be downloaded at http://psc.apl.uw.edu/research/projects/arctic-sea-ice-volume-anomaly/data/ (last access: March 2016; Zhang and Rothrock, 2003). ERAI surface radiation data can be downloaded at http://apps.ecmwf.int/datasets/data/interim-full-daily/levtype=sfc/ (last access: September 2016; Dee et al., 2011). ISCCP-FD surface radiation data are available at https://isccp.giss.nasa.gov/projects/browse_fc.html (last access: October 2015; Zhang et al., 2004). CERES surface radiation data are available at https://climatedataguide.ucar.edu/climate-data/ceres-ebaf. (last access: August 2014; Loeb et al., 2009)A new framework is presented for analysing the proximate causes of model Arctic sea ice biases, demonstrated with the CMIP5 model HadGEM2-ES (Hadley Centre Global Environment Model version 2 - Earth System). In this framework the Arctic sea ice volume is treated as a consequence of the integrated surface energy balance, via the volume balance. A simple model allows the local dependence of the surface flux on specific model variables to be described as a function of time and space. When these are combined with reference datasets, it is possible to estimate the surface flux bias induced by the model bias in each variable. The method allows the role of the surface albedo and ice thickness-growth feedbacks in sea ice volume balance biases to be quantified along with the roles of model bias in variables not directly related to the sea ice volume. It shows biases in the HadGEM2-ES sea ice volume simulation to be due to a bias in spring surface melt onset date, partly countered by a bias in winter downwelling longwave radiation. The framework is applicable in principle to any model and has the potential to greatly improve understanding of the reasons for ensemble spread in the modelled sea ice state. A secondary finding is that observational uncertainty is the largest cause of uncertainty in the induced surface flux bias calculation.Joint UK BEIS/Defra Met Office Hadley Centre Climate ProgrammeEuropean Union Horizon 2020Natural Environment Research Council (NERC

Cyclic oxidation of yttrium/ytterbium disilicate environmental barrier coatings

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The Use of Digital Imagery for the Assessment of Green Biomass in Native Pastures

A practice common to pasture research is the assessment of green leaf. In Australia, where the water use of plants is becoming an increasingly important issue due largely to its implications for dryland salinity, it is imperative that accurate and repeatable methods for characterising the amount of green leaf in pastures be used. The assessment of green leaf has been approached in many ways in the past with varying degrees of success and accuracy. The most accurate way is to physically harvest an area of pasture and separate the green component to make the relevant measurements. For many situations, this may not be suitable particularly due to the destructive, laborious nature of the activity. Many techniques have been tried but they vary in such areas as accuracy, the quantitative nature of the output, repeatability, destructiveness, complexity and labour and equipment expenses (\u27t Mannetje 2000). The project aim was to determine if digitally derived green cover measurements could act as a remote substitute for percentage green biomass in pastures