Production of positive controls for calcivirus-specific PCR using recombinant baculiovirus technology

Recent advances in our knowledge of the genetic structure of human caliciviruses (HuCVs) and small round-structured viruses (SRSVs) have led to the development of polymerase chain reaction (PCR)-based molecular tests specific for these viruses. These methods have been developed to detect a number of human pathogenic viruses in environmental samples including water, sewage and shellfish. HuCVs and SRSVs are not culturable, and no animal model is currently available. Therefore there is no convenient method of preparing viruses for study or for reagent production. One problem facing those attempting to use PCR-based methods for the detection of HuCVs and SRSVs is the lack of a suitable positive control substrate. This is particularly important when screening complex samples in which the levels of inhibitors present may significantly interfere with amplificiation. Regions within the RNA polymerase regions of two genetically distinct human caliciviruses have been amplified and used to produce recombinant baculoviruses which express RNA corresponding to the calicivirus polymerase. This RNA is being investigated as a positive control substrate for PCR testing, using current diagnostic primer sets. Recombinant baculovirus technology will enable efficient and cost-effective production of large quantities of positive control RNA with a specific known genotype. We consider the development of these systems as essential for successful screening and monitoring applications

Spurious PIV vector correction using Linear Stochastic Estimation

Techniques for the experimental determination of velocity fields such as particle image velocimetry (PIV) can often be hampered by spurious vectors or sparse regions of measurement which may occur due to a number of reasons. Commonly used methods for detecting and replacing erroneous values are often based on statistical measures of the surrounding vectors and may be influenced by further poor data quality in the region. A new method is presented in this paper using Linear Stochastic Estimation for vector replacement (LSEVR) which allows for increased flexibility in situations with regions of spurious vectors. LSEVR is applied to PIV dataset to demonstrate and assess its performance relative to commonly used bilinear and bicubic interpolation methods. For replacement of a single vector, all methods performed well, with LSEVR having an average error of 11% in comparison to 14% and 18% for bilinear and bicubic interpolation respectively. A more significant difference was found in replacement of clusters of vectors which showed average vector angle errors of 10°, 9° and 6° for bilinear, bicubic and LSEVR respectively. Error in magnitude was 3% for both interpolation techniques and 1% for LSEVR showing a clear benefit to using LSEVR for conditions that require multiple clustered vectors to be replaced

Support for the global feasibility of the Ages and Stages Questionnaire as developmental screener

Objective: To investigate the psychometric properties of the Dutch version of the 48 months Ages and Stages Questionnaire (D_ASQ_48). Design: Prospective cohort study of a community-based sample of children born in 2002 and 2003 whose parents filled out the D_ASQ_48 and a questionnaire on school status at 60 months. The ASQ was translated into Dutch and back-translated into English by three independent translators. Setting: Well Child Centers covering 25% of the Netherlands. Participants: Parents of 1510 preterm and 562 term children born in 2002-2003 attending routine Well Child visits at age 45-50 months. Main outcome measures: Reliability, validity and mean population scores for D_ASQ_48 compared to other countries. Results: Mean population scores for the D_ASQ_48 were mostly similar to those in the USA, Norway and Korea. Exceptions (effect sizes of difference >0.5) were problem solving (USA) and fine motor (Korea). Reliability was good for the total score (Cronbach alpha 0.79) and acceptable for all domains (0.61-0.74). As expected, infants born at gestational age Conclusions: The good psychometric properties of the Dutch ASQ_48 and the small differences when compared to other countries support its usefulness in the early detection of developmental problems amongst children worldwide. (C) 2009 Elsevier Ireland Ltd. All rights reserved

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms

Analysis of bilinear oscillators under harmonic loading using nonlinear output frequency response functions

In this paper, the new concept of Nonlinear Output Frequency Response Functions (NOFRFs) is extended to the harmonic input case, an input-independent relationship is found between the NOFRFs and the Generalized Frequency Response Functions (GFRFs). This relationship can greatly simplify the application of the NOFRFs. Then, beginning with the demonstration that a bilinear oscillator can be approximated using a polynomial type nonlinear oscillator, the NOFRFs are used to analyze the energy transfer phenomenon of bilinear oscillators in the frequency domain. The analysis provides insight into how new frequency generation can occur using bilinear oscillators and how the sub-resonances occur for the bilinear oscillators, and reveals that it is the resonant frequencies of the NOFRFs that dominate the occurrence of this well-known nonlinear behaviour. The results are of significance for the design and fault diagnosis of mechanical systems and structures which can be described by a bilinear oscillator model

E-menus – Managing Choice Options in Hospital Foodservice

This study examined an initiative in which e-menus and touch screen technology were piloted in a large UK hospital, with the aim of improving food service and satisfaction. Current practice often means that patients may receive the wrong meals, resulting in dissatisfaction and plate waste. An alternative approach is for patients to use electronic menus (e-menus) to make their order, using touch screen technology on the TVs, which in many hospitals are provided at every bedside. A pre-test, post-test questionnaire, which elicited scaled responses and written comments (n=90) was administered to a comparable group of patients. Results from both types of data suggested that most patients used e-menus effectively, although for older patients, it was more challenging. However the biggest difference in the effectiveness of the new technology was between the wards, which also showed substantial differences in service standards. It is concluded that e-menus are an effective way of imparting information about the food, and that they tend to produce greater satisfaction in recipients. However, the results suggest that more training of foodservice staff will be required in order to make the most of initiatives of this kind

Antibody-mediated protection against MERS-CoV in the murine model

Murine antisera with neutralising activity for the coronavirus causative of Middle East respiratory syndrome (MERS) were induced by immunisation of Balb/c mice with the receptor binding domain (RBD) of the viral Spike protein. The murine antisera induced were fully-neutralising in vitro for two separate clinical strains of the MERS coronavirus (MERS-CoV). To test the neutralising capacity of these antisera in vivo, susceptibility to MERS-CoV was induced in naive recipient Balb/c mice by the administration of an adenovirus vector expressing the human DPP4 receptor (Ad5-hDPP4) for MERS-CoV, prior to the passive transfer of the RBD-specific murine antisera to the transduced mice. Subsequent challenge of the recipient transduced mice by the intra-nasal route with a clinical isolate of the MERS-CoV resulted in a significantly reduced viral load in their lungs, compared with transduced mice receiving a negative control antibody. The murine antisera used were derived from mice which had been primed sub-cutaneously with a recombinant fusion of RBD with a human IgG Fc tag (RBD-Fc), adsorbed to calcium phosphate microcrystals and then boosted by the oral route with the same fusion protein in reverse micelles. The data gained indicate that this dual-route vaccination with novel formulations of the RBD-Fc, induced systemic and mucosal anti-viral immunity with demonstrated in vitro and in vivo neutralisation capacity for clinical strains of MERS-CoV

Multidimensional quantum solitons with nondegenerate parametric interactions: Photonic and Bose-Einstein condensate environments

We consider the quantum theory of three fields interacting via parametric and repulsive quartic couplings. This can be applied to treat photonic chi((2)) and chi((3)) interactions, and interactions in atomic Bose-Einstein condensates or quantum Fermi gases, describing coherent molecule formation together with a-wave scattering. The simplest two-particle quantum solitons or bound-state solutions of the idealized Hamiltonian, without a momentum cutoff, are obtained exactly. They have a pointlike structure in two and three dimensions-even though the corresponding classical theory is nonsingular. We show that the solutions can be regularized with a momentum cutoff. The parametric quantum solitons have much more realistic length scales and binding energies than chi((3)) quantum solitons, and the resulting effects could potentially be experimentally tested in highly nonlinear optical parametric media or interacting matter-wave systems. N-particle quantum solitons and the ground state energy are analyzed using a variational approach. Applications to atomic/molecular Bose-Einstein condensates (BEC's) are given, where we predict the possibility of forming coupled BEC solitons in three space dimensions, and analyze superchemistry dynamics

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR