Assessing the impact of tailored biosecurity advice on farmer behaviour and pathogen presence in beef herds in England and Wales

The term ‘biosecurity’ encompasses many measures farmers can take to reduce the risk of pathogen incursion or spread. As the best strategy will vary between settings, veterinarians play an important role in assessing risk and providing advice, but effectiveness requires farmer acceptance and implementation. The aim of this study was to assess the effectiveness of specifically-tailored biosecurity advice packages in reducing endemic pathogen presence on UK beef suckler farms. One hundred and sixteen farms recruited by 10 veterinary practices were followed for three years. Farms were randomly allocated to intervention (receiving specifically-tailored advice, with veterinarians and farmers collaborating to develop an improved biosecurity strategy) or control (receiving general advice) groups. A spreadsheet-based tool was used annually to attribute a score to each farm reflecting risk of entry or spread of bovine viral diarrhoea virus (BVDV), bovine herpesvirus-1 (BHV1), Mycobacterium avium subsp. paratuberculosis (MAP), Leptospira interrogans serovar hardjo (L. hardjo) and Mycobacterium bovis (M. bovis). Objectives of these analyses were to identify evidence of reduction in risk behaviours during the study, as well as evidence of reductions in pathogen presence, as indications of effectiveness. Risk behaviours and pathogen prevalences were examined across study years, and on intervention compared with control farms, using descriptive statistics and multilevel regression. There were significant reductions in risk scores for all five pathogens, regardless of intervention status, in every study year compared with the outset. Animals on intervention farms were significantly less likely than those on control farms to be seropositive for BVDV in years 2 and 3 and for L. hardjo in year 3 of the study. Variations by study year in animal-level odds of seropositivity to BHV1 or MAP were not associated with farm intervention status. All farms had significantly reduced odds of BHV1 seropositivity in year 2 than at the outset. Variations in farm-level MAP seropositivity were not associated with intervention status. There were increased odds of M. bovis on intervention farms compared with control farms at the end of the study. Results suggest a structured annual risk assessment process, conducted as a collaboration between veterinarian and farmer, is valuable in encouraging improved biosecurity practices. There were some indications, but not conclusive evidence, that tailored biosecurity advice packages have potential to reduce pathogen presence. These findings will inform development of a collaborative approach to biosecurity between veterinarians and farmers, including adoption of cost-effective strategies effective across pathogens

13C-Labeling technique for metabolic network and flux analysis: Theory and applications

Applied Science

The relevance of respiratory viral infections in the exacerbations of chronic obstructive pulmonary disease-a systematic review

BACKGROUND: Despite the increasing knowledge on the role of viruses in exacerbations of COPD (AECOPD), it is less clear which viruses are involved and to what extent they contribute to exacerbations. This review aims to systematically combine and evaluate the available literature of the prevalence of respiratory viruses in patients with AECOPD, detected by PCR. METHODS: An electronic search strategy was performed on PubMed and Embase and reference lists were screened for eligible studies. Cross-sectional, prospective studies and case-control studies were included. The primary outcome measure was the prevalence of respiratory viruses (adenovirus, bocavirus, coronavirus, EBV, hMPV, influenza, parainfluenza, rhino-/enterovirus, RSV) in respiratory secretions of patients during an AECOPD. Secondary outcomes were the odds of the presence of the viruses in different respiratory secretions and the odds of the presence of viruses in upper and lower respiratory tract (URT/LRT) samples. RESULTS: Nineteen studies with 1728 patients were included. Rhino-/enteroviruses (16.39%), RSV (9.90%) and influenza (7.83%) were the most prevalent viruses detected with lower detection rates of coronaviruses (4.08%) and parainfluenza (3.35%). Adenovirus (2.07%), hMPV (2.78%) and bocaviruses (0.56%) appear to be rare causative agents of AECOPD. Definitive conclusions regarding the role of EBV cannot be made. Seven of the eight analyzed viruses had a higher prevalence in LRT samples. Coronaviruses were detected more frequently in the URT. CONCLUSIONS: Respiratory viruses are frequently detected in both URT and LRT samples in AECOPD with rhino-/enteroviruses, RSV and influenza viruses the most prevalent viruses. Detection rates vary between the two sites for different viruses

Efficient modeling of 13C-labeling distributions in microorganisms

Applied Science

Metabolite and reaction inference based on enzyme specificities

Motivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. In this paper, we propose to model enzyme aspecificity by predicting whether an input compound is likely to be transformed by a certain enzyme. Such a predictor has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. Results: We have developed a system for metabolite and reaction inference based on enzyme specificities (MaRIboES). It employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA. Leave-one-out cross-validation shows that 80% of known reactions are predicted well. Application to the yeast glycolytic and pentose phosphate pathways predicts a large number of known and new reactions, often leading to the formation of novel compounds, as well as a number of interesting bypasses and cross-links.Electrical Engineering, Mathematics and Computer Scienc

Demonstration of MHz frequency domain multiplexing readout of 37 transition edge sensors for high-resolution x-ray imaging spectrometers

We report on the development and demonstration of a MHz frequency domain multiplexing (FDM) technology to read out arrays of cryogenic transition edge sensor (TES) X-ray microcalorimeters. In our FDM scheme, TESs are AC-biased at different resonant frequencies in the low MHz range through an array of high-$Q$ LC resonators. The current signals of all TESs are summed at superconducting quantum interference devices (SQUIDs). We have demonstrated multiplexing for a readout of 31 pixels using room temperature electronics, high-$Q$ LC filters and TES arrays developed at SRON, and SQUID arrays from VTT. We repeated this on a second setup with 37 pixels. The summed X-ray spectral resolutions $@$ 5.9 keV are $\Delta E_{\rm 31 pix ~MUX}=2.14\pm0.03$ eV and $\Delta E_{\rm 37 pix ~MUX}=2.23\pm0.03$ eV. The demonstrated results are comparable with other multiplexing approaches. There is potential to further improve the spectral resolution and to increase the number of multiplexed TESs, and to open up applications for TES X-ray microcalorimeters.Comment: 6 pages, 3 figures, accepted for publication on Applied physics letter

Metabolic Flux Analysis of Mammalian Cells

Metabolic flux analysis has become a standard tool for analyzing metabolism and optimizing bioprocesses. Metabolic flux analysis makes use of a metabolic reaction network in combination with extra-cellular measurements and mass balancing to calculate flux distributions in metabolism. It is a useful tool to analyze metabolism of cells and can be used to optimize the bioprocess in terms of medium design and metabolic engineering of the cells. In this chapter first the fundamental aspects of metabolic networks and the mathematical methods are described. Next a metabolic model for mammalian cells is discussed, Finally, applications of metabolic flux balancing are reviewed. Further extension of the metabolic network models, possibly towards genome-scale models, will further increase the value of these model