271 research outputs found
Host markers in Quantiferon supernatants differentiate active TB from latent TB infection: preliminary report
<p>Abstract</p> <p>Background</p> <p>Interferon gamma release assays, including the QuantiFERON<sup>® </sup>TB Gold In Tube (QFT) have been shown to be accurate in diagnosing <it>Mycobacterium tuberculosis </it>infection. These assays however, do not discriminate between latent TB infection (LTBI) and active TB disease.</p> <p>Methods</p> <p>We recruited twenty-three pulmonary TB patients and 34 household contacts from Cape Town, South Africa and performed the QFT test. To investigate the ability of new host markers to differentiate between LTBI and active TB, levels of 29 biomarkers in QFT supernatants were evaluated using a Luminex multiplex cytokine assay.</p> <p>Results</p> <p>Eight out of 29 biomarkers distinguished active TB from LTBI in a pilot study. Baseline levels of epidermal growth factor (EGF) soluble CD40 ligand (sCD40L), antigen stimulated levels of EGF, and the background corrected antigen stimulated levels of EGF and macrophage inflammatory protein (MIP)-1β were the most informative single markers for differentiation between TB disease and LTBI, with AUCs of 0.88, 0.84, 0.87, 0.90 and 0.79 respectively. The combination of EGF and MIP-1β predicted 96% of active TB cases and 92% of LTBIs. Combinations between EGF, sCD40L, VEGF, TGF-α and IL-1α also showed potential to differentiate between TB infection states. EGF, VEGF, TGF-α and sCD40L levels were higher in TB patients.</p> <p>Conclusion</p> <p>These preliminary data suggest that active TB may be accurately differentiated from LTBI utilizing adaptations of the commercial QFT test that includes measurement of EGF, sCD40L, MIP-1β, VEGF, TGF-α or IL-1α in supernatants from QFT assays. This approach holds promise for development as a rapid diagnostic test for active TB.</p
Accurate Charge-Dependent Nucleon-Nucleon Potential at Fourth Order of Chiral Perturbation Theory
We present the first nucleon-nucleon potential at
next-to-next-to-next-to-leading order (fourth order) of chiral perturbation
theory. Charge-dependence is included up to next-to-leading order of the
isospin-violation scheme. The accuracy for the reproduction of the NN data
below 290 MeV lab. energy is comparable to the one of phenomenological
high-precision potentials. Since NN potentials of order three and less are
known to be deficient in quantitative terms, the present work shows that the
fourth order is necessary and sufficient for a reliable NN potential derived
from chiral effective Lagrangians. The new potential provides a promising
starting point for exact few-body calculations and microscopic nuclear
structure theory (including chiral many-body forces derived on the same
footing).Comment: 4 pages Revtex including one figur
BMC Bioinformatics
Background: For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for homogeneous cell populations, e.g. by applying micro-dissection, fluorescence activated cell sorting, or in-silico deconfounding. We studied feasibility and validity of a non-negative matrix decomposition algorithm using experimental gene expression data for blood and sorted cells from the same donor samples. Our objective was to optimize the algorithm regarding detection of differentially expressed genes and to enable its use for classification in the difficult scenario of reversely regulated genes. This would be of importance for the identification of candidate biomarkers in heterogeneous tissues. Results: Experimental data and simulation studies involving noise parameters estimated from these data revealed that for valid detection of differential gene expression, quantile normalization and use of non-log data are optimal. We demonstrate the feasibility of predicting proportions of constituting cell types from gene expression data of single samples, as a prerequisite for a deconfounding-based classification approach. Classification cross-validation errors with and without using deconfounding results are reported as well as sample-size dependencies. Implementation of the algorithm, simulation and analysis scripts are available. Conclusions: The deconfounding algorithm without decorrelation using quantile normalization on non-log data is proposed for biomarkers that are difficult to detect, and for cases where confounding by varying proportions of cell types is the suspected reason. In this case, a deconfounding ranking approach can be used as a powerful alternative to, or complement of, other statistical learning approaches to define candidate biomarkers for molecular diagnosis and prediction in biomedicine, in realistically noisy conditions and with moderate sample sizes
Accuracy of diabetes screening methods used for people with tuberculosis, Indonesia, Peru, Romania, South Africa
Objective
To evaluate the performance of diagnostic tools for diabetes mellitus, including laboratory methods and clinical risk scores, in newly-diagnosed pulmonary tuberculosis patients from four middle-income countries.
Methods
In a multicentre, prospective study, we recruited 2185 patients with pulmonary tuberculosis from sites in Indonesia, Peru, Romania and South Africa from January 2014 to September 2016. Using laboratory-measured glycated haemoglobin (HbA1c) as the gold standard, we measured the diagnostic accuracy of random plasma glucose, point-of-care HbA1c, fasting blood glucose, urine dipstick, published and newly derived diabetes mellitus risk scores and anthropometric measurements. We also analysed combinations of tests, including a two-step test using point-of-care HbA1cwhen initial random plasma glucose was ≥ 6.1 mmol/L.
Findings
The overall crude prevalence of diabetes mellitus among newly diagnosed tuberculosis patients was 283/2185 (13.0%; 95% confidence interval, CI: 11.6–14.4). The marker with the best diagnostic accuracy was point-of-care HbA1c (area under receiver operating characteristic curve: 0.81; 95% CI: 0.75–0.86). A risk score derived using age, point-of-care HbA1c and random plasma glucose had the best overall diagnostic accuracy (area under curve: 0.85; 95% CI: 0.81–0.90). There was substantial heterogeneity between sites for all markers, but the two-step combination test performed well in Indonesia and Peru.
Conclusion
Random plasma glucose followed by point-of-care HbA1c testing can accurately diagnose diabetes in tuberculosis patients, particularly those with substantial hyperglycaemia, while reducing the need for more expensive point-of-care HbA1c testing. Risk scores with or without biochemical data may be useful but require validation
Effect of four plant species on soil 15N-access and herbage yield in temporary agricultural grasslands
Positive plant diversity-productivity relationships have been reported for experimental semi-natural grasslands (Cardinale et al. 2006; Hector et al. 1999; Tilman et al. 1996) as well as temporary agricultural grasslands (Frankow-Lindberg et al. 2009; Kirwan et al. 2007; Nyfeler et al. 2009; Picasso et al. 2008). Generally, these relationships are explained, on the one hand, by niche differentiation and facilitation (Hector et al. 2002; Tilman et al. 2002) and, on the other hand, by greater probability of including a highly productive plant species in high diversity plots (Huston 1997). Both explanations accept that diversity is significant because species differ in characteristics, such as root architecture, nutrient acquisition and water use efficiency, to name a few, resulting in composition and diversity being important for improved productivity and resource use (Naeem et al. 1994; Tilman et al. 2002). Plant diversity is generally low in temporary agricultural grasslands grown for ruminant fodder production. Grass in pure stands is common, but requires high nitrogen (N) inputs. In terms of N input, two-species grass-legume mixtures are more sustainable than grass in pure stands and consequently dominate low N input grasslands (Crews and Peoples 2004; Nyfeler et al. 2009; Nyfeler et al. 2011).
In temperate grasslands, N is often the limiting factor for productivity (Whitehead 1995). Plant available soil N is generally concentrated in the upper soil layers, but may leach to deeper layers, especially in grasslands that include legumes (Scherer-Lorenzen et al. 2003) and under conditions with surplus precipitation (Thorup-Kristensen 2006). To improve soil N use efficiency in temporary grasslands, we propose the addition of deep-rooting plant species to a mixture of perennial ryegrass and white clover, which are the most widespread forage plant species in temporary grasslands in a temperate climate (Moore 2003). Perennial ryegrass and white clover possess relatively shallow root systems (Kutschera and Lichtenegger 1982; Kutschera and Lichtenegger 1992) with effective rooting depths of <0.7 m on a silt loamy site (Pollock and Mead 2008). Grassland species, such as lucerne and chicory, grow their tap-roots into deep soil layers and exploit soil nutrients and water in soil layers that the commonly grown shallow-rooting grassland species cannot reach (Braun et al. 2010; Skinner 2008). Chicory grown as a catch crop after barley reduced the inorganic soil N down to 2.5 m depth during the growing season, while perennial ryegrass affected the inorganic soil N only down to 1 m depth (Thorup-Kristensen 2006). Further, on a Wakanui silt loam in New Zealand chicory extracted water down to 1.9 m and lucerne down to 2.3 m soil depth, which resulted in greater herbage yields compared with a perennial ryegrass-white clover mixture, especially for dryland plots (Brown et al. 2005).
There is little information on both the ability of deep- and shallow-rooting grassland species to access soil N from different vertical soil layers and the relation of soil N-access and herbage yield in temporary agricultural grasslands. Therefore, the objective of the present work was to test the hypotheses 1) that a mixture comprising both shallow- and deep-rooting plant species has greater herbage yields than a shallow-rooting binary mixture and pure stands, 2) that deep-rooting plant species (chicory and lucerne) are superior in accessing soil N from 1.2 m soil depth compared with shallow-rooting plant species, 3) that shallow-rooting plant species (perennial ryegrass and white clover) are superior in accessing soil N from 0.4 m soil depth compared with deep-rooting plant species, 4) that a mixture of deep- and shallow-rooting plant species has greater access to soil N from three soil layers compared with a shallow-rooting two-species mixture and that 5) the leguminous grassland plants, lucerne and white clover, have a strong impact on grassland N acquisition, because of their ability to derive N from the soil and the atmosphere
Elastic e-d Scattering Data and the Deuteron Wave Function
What range of momentum components in the deuteron wave function are available
e d elastic scattering data sensitive to ? This question is addressed within
the context of a model calculation of the deuteron form factors, based on
realistic interactions and currents. It is shown that the data on the ,
, and observables at fm essentially probe
momentum components up to .Comment: 5 figure
Lattice calculations for A=3,4,6,12 nuclei using chiral effective field theory
We present lattice calculations for the ground state energies of tritium,
helium-3, helium-4, lithium-6, and carbon-12 nuclei. Our results were
previously summarized in a letter publication. This paper provides full details
of the calculations. We include isospin-breaking, Coulomb effects, and
interactions up to next-to-next-to-leading order in chiral effective field
theory.Comment: 38 pages, 11 figures, final publication versio
Tuberculosis research in South Africa over the past 30 years: From bench to bedside
The South African Medical Research Council Centre for Tuberculosis Research has a rich history of high-impact research that has influenced our understating of this hyper-epidemic which is further exacerbated by the emergence and spread of drug-resistant forms of the disease. This review aims to summarise the past 30 years of research conducted in the Centre which has influenced the way that tuberculosis (TB) is diagnosed and treated. The review includes the development of new technologies for rapid screening of people with probable TB and the repurposing of human diagnostics for wildlife conservation
Deuteron form factors in chiral effective theory: regulator-independent results and the role of two-pion exchange
We evaluate the deuteron charge, quadrupole, and magnetic form factors using
wave functions obtained from chiral effective theory (ET) when the
potential includes one-pion exchange, chiral two-pion exchange, and genuine
contact interactions. We study the manner in which the results for form factors
behave as the regulator is removed from the ET calculation, and compare
co-ordinate- and momentum-space approaches. We show that, for both the LO and
NNLO chiral potential, results obtained by imposing boundary conditions in
co-ordinate space at are equivalent to the limit of
momentum-space calculations. The regulator-independent predictions for deuteron
form factors that result from taking the limit using the
LO ET potential are in reasonable agreement with data up to momentum
transfers of order 600 MeV, provided that phenomenological information for
nucleon structure is employed. In this range the use of the NNLO ET
potential results in only small changes to the LO predictions, and it improves
the description of the zero of the charge form factor
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