Optimization and evaluation of an influenza A (H5) pseudotyped lentiviral particle-based serological assay

Background: Novel serological methods provide alternative options for sero-diagnosis, sero-epidemiology and for determining evidence of naturally acquired or vaccine induced immunity. Micro-neutralization tests are currently the gold standard for serological studies of highly pathogenic avian influenza in mammalian species but require handling live virus in a biosafety level (BSL) 3 environment. We previously reported the use of H5 pseudotyped lentiviral particles (H5pp) as an alternative to micro-neutralization tests in a BSL-2 setting (Nefkens et al., 2007). Objective: To optimize and evaluate this newly developed H5pp assay on relevant clinical specimens. Study design: We optimise and evaluate the performance of the H5pp assay using well-characterized sera from humans with confirmed H5N1 disease or controls. Results: The H5pp assay is a reliable serological method for the detection and quantification of neutralizing antibody to H5-viruses. Conclusion: H5pp provide a reliable and safe alternative for sero-diagnosis and sero-epidemiology of H5N1 infections in a BSL-2 setting. © 2009 Elsevier B.V. All rights reserved.postprin

In Situ Chemically-Selective Monitoring of Multiphase Displacement Processes in a Carbonate Rock Using 3D Magnetic Resonance Imaging.

Accurate monitoring of multiphase displacement processes is essential for the development, validation and benchmarking of numerical models used for reservoir simulation and for asset characterization. Here we demonstrate the first application of a chemically-selective 3D magnetic resonance imaging (MRI) technique which provides high-temporal resolution, quantitative, spatially resolved information of oil and water saturations during a dynamic imbibition core flood experiment in an Estaillades carbonate rock. Firstly, the relative saturations of dodecane ( S o ) and water ( S w ) , as determined from the MRI measurements, have been benchmarked against those obtained from nuclear magnetic resonance (NMR) spectroscopy and volumetric analysis of the core flood effluent. Excellent agreement between both the NMR and MRI determinations of S o and S w was obtained. These values were in agreement to 4 and 9% of the values determined by volumetric analysis, with absolute errors in the measurement of saturation determined by NMR and MRI being 0.04 or less over the range of relative saturations investigated. The chemically-selective 3D MRI method was subsequently applied to monitor the displacement of dodecane in the core plug sample by water under continuous flow conditions at an interstitial velocity of 1.27 × 10 - 6 m s - 1 ( 0.4 ft day - 1 ) . During the core flood, independent images of water and oil distributions within the rock core plug at a spatial resolution of 0.31 mm × 0.39 mm × 0.39 mm were acquired on a timescale of 16 min per image. Using this technique the spatial and temporal dynamics of the displacement process have been monitored. This MRI technique will provide insights to structure-transport relationships associated with multiphase displacement processes in complex porous materials, such as those encountered in petrophysics research.The authors would like to thank Royal Dutch Shell plc for funding this work. LFG, MDM and AJS also wish to thank EPSRC for financial support (EP/K039318/1)

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

Background: Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results: The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions: The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature

Hazard Analysis of Critical Control Points Assessment as a Tool to Respond to Emerging Infectious Disease Outbreaks

Highly pathogenic avian influenza virus (HPAI) strain H5N1 has had direct and indirect economic impacts arising from direct mortality and control programmes in over 50 countries reporting poultry outbreaks. HPAI H5N1 is now reported as the most widespread and expensive zoonotic disease recorded and continues to pose a global health threat. The aim of this research was to assess the potential of utilising Hazard Analysis of Critical Control Points (HACCP) assessments in providing a framework for a rapid response to emerging infectious disease outbreaks. This novel approach applies a scientific process, widely used in food production systems, to assess risks related to a specific emerging health threat within a known zoonotic disease hotspot. We conducted a HACCP assessment for HPAI viruses within Vietnam’s domestic poultry trade and relate our findings to the existing literature. Our HACCP assessment identified poultry flock isolation, transportation, slaughter, preparation and consumption as critical control points for Vietnam’s domestic poultry trade. Introduction of the preventative measures highlighted through this HACCP evaluation would reduce the risks posed by HPAI viruses and pressure on the national economy. We conclude that this HACCP assessment provides compelling evidence for the future potential that HACCP analyses could play in initiating a rapid response to emerging infectious diseases

Update on avian influenza A (H5N1) virus infection in humans

Avian influenza A (H5N1) viruses are entrenched among poultry in parts of Asia and Africa and continue to cause disease with high mortality in humans. This update summarizes recent information including research on the transmission and pathogenesis of the infection and on the current strategies for treatment and prevention. Copyright © 2008 Massachusetts Medical Society. All rights reserved.published_or_final_versio

Occupational exposures and genetic susceptibility to occupational exposures are related to sickness absence in the Lifelines cohort study

In this cross-sectional study, we investigated the association between occupational exposures and sickness absence (SA), the mediating role of respiratory symptoms, and whether genetic susceptibility to SA upon occupational exposures exists. Logistic regression was used to examine associations and structural equation modelling was used for mediation analyses. Genetic susceptibility was investigated by including interactions between occupational exposures and 11 candidate single nucleotide polymorphisms (SNPs). Biological dust, mineral dust, and pesticides exposure were associated with a lower prevalence of any SA (OR (95% CI) = 0.72 (0.58–0.89), 0.88 (0.78–0.99), and 0.70 (0.55–0.89), respectively) while gases/fumes exposure was associated with a higher prevalence of long-term SA (1.46 (1.11–1.91)). Subjects exposed to solvents and metals had a higher prevalence of any (1.14 (1.03–1.26) and 1.68 (1.26–2.24)) and long-term SA (1.26 (1.08–1.46) and 1.75 (1.15–2.67)). Chronic cough and chronic phlegm mediated the association between high gases/fumes exposure and long-term SA. Two of 11 SNPs investigated had a positive interaction with exposure on SA and one SNP negatively interacted with exposure on SA. Exposure to metals and gases/fumes showed a clear dose–response relationship with a higher prevalence of long-term SA; contrary, exposure to pesticides and biological/mineral dust showed a protective effect on any SA. Respiratory symptoms mediated the association between occupational exposures and SA. Moreover, gene-by-exposure interactions exist

Interleukin-10 and soluble tumor necrosis factor receptor II are potential biomarkers of Plasmodium falciparum infections in pregnant women: a case-control study from Nanoro, Burkina Faso.

BACKGROUND: Diagnosis of malaria in pregnancy is problematic due to the low sensitivity of conventional diagnostic tests (rapid diagnostic test and microscopy), which is exacerbated due to low peripheral parasite densities, and lack of clinical symptoms. In this study, six potential biomarkers to support malaria diagnosis in pregnancy were evaluated. METHODS: Blood samples were collected from pregnant women at antenatal clinic visits and at delivery. Microscopy and real-time PCR were performed for malaria diagnosis and biomarker analyses were performed by ELISA (interleukin 10, IL-10; tumor necrosis factor-α, TNF-α; soluble tumor necrosis factor receptor II, sTNF-RII; soluble fms-like tyrosine kinase 1, sFlt-1; leptin and apolipoprotein B, Apo-B). A placental biopsy was collected at delivery to determine placental malaria. RESULTS: IL-10 and sTNF-RII were significantly higher at all time-points in malaria-infected women (p < 0.001). Both markers were also positively associated with parasite density (p < 0.001 and p = 0.003 for IL-10 and sTNF-RII respectively). IL-10 levels at delivery, but not during pregnancy, were negatively associated with birth weight. A prediction model was created using IL-10 and sTNF-RII cut-off points. For primigravidae the model had a sensitivity of 88.9% (95%CI 45.7-98.7%) and specificity of 83.3% (95% CI 57.1-94.9%) for diagnosing malaria during pregnancy. For secundi- and multigravidae the sensitivity (81.8% and 56.5% respectively) was lower, while specificity (100.0% and 94.3% respectively) was relatively high. Sub-microscopic infections were detected in 2 out of 3 secundi- and 5 out of 12 multigravidae. CONCLUSIONS: The combination of biomarkers IL-10 and sTNF-RII have the potential to support malaria diagnosis in pregnancy. Additional markers may be needed to increase sensitivity and specificity, this is of particular importance in populations with sub-microscopic infections or in whom other inflammatory diseases are prevalent

Oseltamivir resistance during treatment of influenza A (H5N1) infection

Influenza A (H5N1) virus with an amino acid substitution in neuraminidase conferring high-level resistance to oseltamivir was isolated from two of eight Vietnamese patients during oseltamivir treatment. Both patients died of influenza A (H5N1) virus infection, despite early initiation of treatment in one patient. Surviving patients had rapid declines in the viral load to undetectable levels during treatment. These observations suggest that resistance can emerge during the currently recommended regimen of oseltamivir therapy and may be associated with clinical deterioration and that the strategy for the treatment of influenza A (H5N1) virus infection should include additional antiviral agents. Copyright © 2005 Massachusetts Medical Society.published_or_final_versio