Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis

Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.

Epidemiological analysis of methicillin-resistant Staphylococcus aureus isolates from adult patients with cystic fibrosis

Using pulsed-field gel electrophoresis, we genotyped 21 methicillin-resistant Staphylococcus aureus isolates from patients attending an adult cystic fibrosis unit. Eleven patients exhibited pulsotypes related to 2 locally endemic strains. Eleven chronically colonized patients were assessed over a period of up to 2 years, and all demonstrated a retention of strain type.

Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of,300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.

Identification of putative markers of triclabendazole resistance by a genome-wide analysis of genetically recombinant Fasciola hepatica

Despite years of investigation into triclabendazole (TCBZ) resistance in Fasciola hepatica, the genetic mechanisms responsible remain unknown. Extensive analysis of multiple triclabendazole-susceptible and -resistant isolates using a combination of experimental in vivo and in vitro approaches has been carried out, yet few, if any, genes have been demonstrated experimentally to be associated with resistance phenotypes in the field. In this review we summarize the current understanding of TCBZ resistance from the approaches employed to date. We report the current genomic and genetic resources for F. hepatica that are available to facilitate novel functional genomics and genetic experiments for this parasite in the future. Finally, we describe our own non-biased approach to mapping the major genetic loci involved in conferring TCBZ resistance in F. hepatica.

Analysis of a three-dimensional flow generated by a linear aerospike

Linear aerospike nozzles are envisaged as a possible means to improve launcher engine performance. One of the most interesting properties of these nozzles is the possibility of a good integration with the vehicle. To improve the knowledge of the flow-field and performance of aerospike nozzles, they are studied numerically, with particular attention to the differences between the basic two-dimensional nozzle, usually considered in the design phase, and the more realistic three-dimensional nozzle. The study considers also the effect of flight condition, which cannot be neglected because of the characteristic external expansion of aerospike nozzles.

Statistical Analysis of Small Ellerman Bomb Events

The properties of Ellerman bombs (EBs), small-scale brightenings in the Hα line wings, have proved difficult to establish because their size is close to the spatial resolution of even the most advanced telescopes. Here, we aim to infer the size and lifetime of EBs using high-resolution data of an emerging active region collected using the Interferometric BIdimensional Spectrometer (IBIS) and Rapid Oscillations of the Solar Atmosphere (ROSA) instruments as well as the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO). We develop an algorithm to track EBs through their evolution, finding that EBs can often be much smaller (around 0.3″) and shorter-lived (less than one minute) than previous estimates. A correlation between G-band magnetic bright points and EBs is also found. Combining SDO/HMI and G-band data gives a good proxy of the polarity for the vertical magnetic field. It is found that EBs often occur both over regions of opposite polarity flux and strong unipolar fields, possibly hinting at magnetic reconnection as a driver of these events.The energetics of EB events is found to follow a power-law distribution in the range of a nanoflare (1022-25 ergs).

Resistivity and Induced Polarization Monitoring of Biogas combined with Microbial Ecology on a Brown field Site

The accumulation of biogenic greenhouse gases (methane, carbon dioxide) in organic sediments is an important factor in the redevelopment and risk management of many brownfield sites. Good practice with brownfield site characterization requires the identification of free-gas phases and pathways that allow its migration and release at the ground surface. Gas pockets trapped in the subsurface have contrasting properties with the surrounding porous media that favor their detection using geophysical methods. We have developed a case study in which pockets of gas were intercepted with multilevel monitoring wells, and their lateral continuity was monitored over time using resistivity. We have developed a novel interpretation procedure based on Archie’s law to evaluate changes in water and gas content with respect to a mean background medium. We have used induced polarization data to account for errors in applying Archie’s law due to the contribution of surface conductivity effects. Mosaics defined by changes in water saturation allowed the recognition of gas migration and groundwater infiltration routes and the association of gas and groundwater fluxes. The inference on flux patterns was analyzed by taking into account pressure measurements in trapped gas reservoirs and by metagenomic analysis of the microbiological content, which was retrieved from suspended sediments in groundwater sampled in multilevel monitoring wells. A conceptual model combining physical and microbiological subsurface processes suggested that biogas trapped at depth may have the ability to quickly travel to the surface.

Genetic diversity of root-associated fungal endophytes from Calluna vulgaris at contrasting field sites

A total of 107 putative ericoid mycorrhizal endophytes were isolated from hair roots of Calluna vulgaris from two abandoned arsenic/copper mine sites and a natural heathland site in southwest England. The endophytes were initially grouped as 14 RFLP types, based on the results of ITS-RFLP analysis using the restriction endonucleases Hinf I, Rsa I and Hae III. ITS sequences were obtained for representative isolates from each RFLP type and compared phylogenetically with sequences for known ericoid mycorrhizal endophytes and selected ascomycetes. The majority of endophyte isolates (62-92%) from each site were identified as Hymenoscyphus ericae, but a number of other less common mycorrhizal RFLP types were also identified, all of which appear to have strong affinities with the order Leotiales. None of the less common RFLP types was isolated from C. vulgaris at more than one field site. Neighbour-joining analysis indicated similarities between the endophytes from C. vulgaris and mycorrhizal endophytes isolated from other Ericaceae and Epacridaceae hosts in North America and Australia.

How individual participant data meta-analyses have influenced trial design, conduct, and analysis

OBJECTIVES: To demonstrate how individual participant data (IPD) meta-analyses have impacted directly on the design and conduct of trials and highlight other advantages IPD might offer.

STUDY DESIGN AND SETTING: Potential examples of the impact of IPD meta-analyses on trials were identified at an international workshop, attended by individuals with experience in the conduct of IPD meta-analyses and knowledge of trials in their respective clinical areas. Experts in the field who did not attend were asked to provide any further examples. We then examined relevant trial protocols, publications, and Web sites to verify the impacts of the IPD meta-analyses. A subgroup of workshop attendees sought further examples and identified other aspects of trial design and conduct that may inform IPD meta-analyses.

RESULTS: We identified 52 examples of IPD meta-analyses thought to have had a direct impact on the design or conduct of trials. After screening relevant trial protocols and publications, we identified 28 instances where IPD meta-analyses had clearly impacted on trials. They have influenced the selection of comparators and participants, sample size calculations, analysis and interpretation of subsequent trials, and the conduct and analysis of ongoing trials, sometimes in ways that would not possible with systematic reviews of aggregate data. We identified additional potential ways that IPD meta-analyses could be used to influence trials.

CONCLUSIONS: IPD meta-analysis could be better used to inform the design, conduct, analysis, and interpretation of trials.

Energy and environmental forensic analysis for public buildings.

This paper outlines a forensic method for analysing the energy, environmental and comfort performance of a building. The method has been applied to a recently developed event space in an Irish public building, which was evaluated using on-site field studies, data analysis, building simulation and occupant surveying. The method allows for consideration of both the technological and anthropological aspects of the building in use and for the identification of unsustainable operational practice and emerging problems. The forensic analysis identified energy savings of up to 50%, enabling a more sustainable, lower-energy operational future for the building. The building forensic analysis method presented in this paper is now planned for use in other public and commercial buildings.

Memory Cost Analysis for OpenFlow Multiple Table Lookup

Multiple Table Lookup architectures in Software Defined Networking (SDN) open the door for exciting new network applications. The development of the OpenFlow protocol supported the SDN paradigm. However, the first version of the OpenFlow protocol specified a single table lookup model with the associated constraints in flow entry numbers and search capabilities. With the introduction of multiple table lookup in OpenFlow v1.1, flexible and efficient search to support SDN application innovation became possible. However, implementation of multiple table lookup in hardware to meet high performance requirements is non-trivial. One possible approach involves the use of multi-dimensional lookup algorithms. A high lookup performance can be achieved by using embedded memory for flow entry storage. A detailed study of OpenFlow flow filters for multi-dimensional lookup is presented in this paper. Based on a proposed multiple table lookup architecture, the memory consumption and update performance using parallel single field searches are evaluated. The results demonstrate an efficient multi-table lookup implementation with minimum memory usage.

Stochastic analysis of seepage under water-retaining structures

This paper investigated the problem of confined flow under dams and water retaining structuresusing stochastic modelling. The approach advocated in the study combined a finite elementsmethod based on the equation governing the dynamics of incompressible fluid flow through aporous medium with a random field generator that generates random hydraulic conductivity basedon lognormal probability distribution. The resulting model was then used to analyse confined flowunder a hydraulic structure. Cases for a structure provided with cutoff wall and when the wall didnot exist were both tested. Various statistical parameters that reflected different degrees ofheterogeneity were examined and the changes in the mean seepage flow, the mean uplift forceand the mean exit gradient observed under the structure were analysed. Results reveal that underheterogeneous conditions, the reduction made by the sheetpile in the uplift force and exit hydraulicgradient may be underestimated when deterministic solutions are used.

A Cyber-Physical Security Analysis of Synchronous-Islanded Microgrid Operation

Cyber-security research in the field of smart grids is often performed with a focus on either the power and control domain or the Information and Communications Technology (ICT) domain. The characteristics of the power equipment or ICT domain are commonly not collectively considered. This work provides an analysis of the physical effects of cyber-attacks on microgrids – a smart grid construct that allows continued power supply when disconnected from a main grid. Different types of microgrid operations are explained (connected, islanded and synchronous-islanding) and potential cyber-attacks and their physical effects are analyzed. A testbed that is based on physical power and ICT equipment is presented to validate the results in both the physical and ICT domain.

Tri-axial accelerometers quantify behaviour in the Eurasian badger (Meles meles): towards an automated interpretation of field data

The popularity of tri-axial accelerometer data loggers to quantify animal activity through the analysis of signature traces is increasing. However, there is no consensus on how to process the large data sets that these devices generate when recording at the necessary high sample rates. In addition, there have been few attempts to validate accelerometer traces with specific behaviours in non-domesticated terrestrial mammals.

A tool to include gamma analysis software into a quality assurance program

PURPOSE: To provide a tool to enable gamma analysis software algorithms to be included in a quality assurance (QA) program.

METHODS: Four image sets were created comprising two geometric images to independently test the distance to agreement (DTA) and dose difference (DD) elements of the gamma algorithm, a clinical step and shoot IMRT field and a clinical VMAT arc. The images were analysed using global and local gamma analysis with 2 in-house and 8 commercially available software encompassing 15 software versions. The effect of image resolution on gamma pass rates was also investigated.

RESULTS: All but one software accurately calculated the gamma passing rate for the geometric images. Variation in global gamma passing rates of 1% at 3%/3mm and over 2% at 1%/1mm was measured between software and software versions with analysis of appropriately sampled images.

CONCLUSION: This study provides a suite of test images and the gamma pass rates achieved for a selection of commercially available software. This image suite will enable validation of gamma analysis software within a QA program and provide a frame of reference by which to compare results reported in the literature from various manufacturers and software versions.