Modelling optimal use of tests for monitoring disease progression and recurrence

Background: Monitoring to identify disease recurrence or progression is common, often with limited evidence to support the tests used, subsequent decisions, frequency and duration of monitoring. Aims: To develop methods for designing evidence-based monitoring strategies and estimating measurement error, a key consideration in selecting monitoring tests. Methods: To investigate studies of measurement error: frameworks were identified; design, analysis and reporting of studies were reviewed; a case study was analysed; and, simulation studies were performed to evaluate varying sample size and outlier detection methods. To develop methods for designing monitoring strategies the methods literature was reviewed and simulation models were developed and validated. Results: Biological variability studies are often poorly designed and reported. Studies are frequently small and may not produce valid results; the required precision of estimates can inform the sample size. Outlier detection can negatively bias variability estimates; methods should be used with caution, with interpretation allowing for potential bias. Modelling monitoring data requires knowledge of the natural history of disease, test performance and measurement error; such evaluation enables selection of evidence-based monitoring strategies prior to full-scale investigation. Conclusions: Poor monitoring tests can be identified early using small-scale studies and monitoring strategies should be optimised prior to full evaluation

Photoconductivity in conjugated polymers

This thesis reports the results of photoconductivity experiments on films of the conjugated polymers poly(2-methoxy-5- (2'ethylhexyloxy)-l,4-phenylene vinylene) (MEH-PPV), poly(2,5-pyridinediyl) (PPY) and poly(9,9-bis(2-ethyl hexyl)fluorene-2,7-diyl) (PF2/6) sandwiched between gold and indium tin oxide on a glass substrate. The methods used to fabricate the sandwich structures, the photoconductivity methods used and the procedures used to normalise the data are described. Results indicate that, at photon energies appropriate to the fundamental absorption of the particular polymer, the absorption of photons leads to the formation of excitons. These excitons can be extrinsically dissociated at an electrode to give free charge carriers. These free charge carriers then give rise to a photocurrent. At photon energies above the fundamental absorption of the conjugated polymer, free charge carriers are intrinsically generated in the bulk polymer. The polymer film thickness and the relative mobilities of electrons and holes in the conjugated polymers influence the spectral response of the photocurrent In MEH-PPV, the hole mobility is one order of magnitude greater than the electron mobility. The effects of charge carrier mobility explain the temperature dependence of the photocurrent spectra for MEH-PPV samples. The charge carrier generation mechanism explains the electric field dependence of the photocurrent spectra for MEH-PPV samples. The electron mobility is greater than the hole mobility in PPY and this is confirmed by photoconductivity experiments. A comparison of the spectra obtained from photoconductivity experiments in PF2/6 and PPY suggest that excitations involving the nitrogen atom in the PPY molecule occur producing additional features in the photocurrent spectr

Incorporating Natural Vegetation into the LUC Project Framework

A detailed description of the incorporation of natural vegetation within the larger LUC model framework is given. The approach focuses on first adapting and then coupling three existing vegetation models: BIOME3 (Haxeltine et al., 1996), BIOMEl (Prentice I.C. et al., 1992) and the CBM (Kurz W.A. et al., 1992). Section 1 concentrates on a description of the adaptations made to BIOME3 and BIOMEl and a comparison of the results obtained from a present climate run for Russia, Mongolia and China with the existing LUC natural vegetation data set. The three way model coupling methodology and usage within the larger LUC model framework is given in Section 2

Unit of analysis issues in laboratory-based research

Many studies in the biomedical research literature report analyses that fail to recognise important data dependencies from multilevel or complex experimental designs. Statistical inferences resulting from such analyses are unlikely to be valid and are often potentially highly misleading. Failure to recognise this as a problem is often referred to in the statistical literature as a unit of analysis (UoA) issue. Here, by analysing two example datasets in a simulation study, we demonstrate the impact of UoA issues on study efficiency and estimation bias, and highlight where errors in analysis can occur. We also provide code (written in R) as a resource to help researchers undertake their own statistical analyses

Technical note: A simple theoretical model framework to describe plant stomatal "sluggishness" in response to elevated ozone concentrations

This is the final version. Available from European Geosciences Union (EGU) via the DOI in this record.Elevated levels of tropospheric ozone, O3, cause damage to terrestrial vegetation, affecting leaf stomatal functioning and reducing photosynthesis. Climatic impacts under future raised atmospheric greenhouse gas (GHG) concentrations will also impact on the net primary productivity (NPP) of vegetation, which might for instance alter viability of some crops. Together, ozone damage and climate change may adjust the current ability of terrestrial vegetation to offset a significant fraction of carbon dioxide (CO2) emissions. Climate impacts on the land surface are well studied, but arguably large-scale modelling of raised surface level O3effects is less advanced. To date most models representing ozone damage use either O3concentration or, more recently, flux-uptake-related reduction of stomatal opening, estimating suppressed land-atmosphere water and CO2fluxes. However there is evidence that, for some species, O3damage can also cause an inertial sluggishness of stomatal response to changing surface meteorological conditions. In some circumstances (e.g. droughts), this loss of stomata control can cause them to be more open than without ozone interference. To both aid model development and provide empiricists with a system on to which measurements can be mapped, we present a parameter-sparse framework specifically designed to capture sluggishness. This contains a single time-delay parameter τO3, characterizing the timescale for stomata to catch up with the level of opening they would have without damage. The larger the value of this parameter, the more sluggish the modelled stomatal response. Through variation of τO3, we find it is possible to have qualitatively similar responses to factorial experiments with and without raised O3, when comparing to reported measurement time series presented in the literature. This low-parameter approach lends itself to the inclusion of ozone-induced inertial effects being incorporated in the terrestrial vegetation component of Earth system models (ESMs).NERC-CEH National Capability FundNatural Environment Research Counci

Conversion from forests to pastures in the Colombian Amazon leads to contrasting soil carbon dynamics depending on land management practices

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordStrategies to mitigate climate change by reducing deforestation and forest degradation (e.g. REDD+) require country- or region-specific information on temporal changes in forest carbon (C) pools to develop accurate emission factors. The soil C pool is one of the most important C reservoirs, but is rarely included in national forest reference emission levels due to a lack of data. Here, we present the soil organic C (SOC) dynamics along 20 years of forest-to-pasture conversion in two subregions with different management practices during pasture establishment in the Colombian Amazon: high-grazing intensity (HG) and low-grazing intensity (LG) subregions. We determined the pattern of SOC change resulting from the conversion from forest (C3 plants) to pasture (C4 plants) by analysing total SOC stocks and the natural abundance of the stable isotopes (13) C along two 20-year chronosequences identified in each subregion. We also analysed soil N stocks and the natural abundance of (15) N during pasture establishment. In general, total SOC stocks at 30 cm depth in the forest were similar for both subregions, with an average of 47.1 ± 1.8 Mg C ha(-1) in HG and 48.7 ± 3.1 Mg C ha(-1) in LG. However, 20 years after forest-to-pasture conversion SOC in HG decreased by 20%, whereas in LG SOC increased by 41%. This net SOC decrease in HG was due to a larger reduction in C3-derived input and to a comparatively smaller increase in C4-derived C input. In LG both C3- and C4-derived C input increased along the chronosequence. N stocks were generally similar in both subregions and soil N stock changes during pasture establishment were correlated with SOC changes. These results emphasize the importance of management practices involving low-grazing intensity in cattle activities to preserve SOC stocks and to reduce C emissions after land-cover change from forest to pasture in the Colombian Amazon.This study was funded by AXA Research Fund (2012‐Doc‐University‐of‐Exeter‐NAVARRETE‐D)

Hadron Spectrum in a Two-Colour Baryon-Rich Medium

The hadron spectrum of SU(2) lattice gauge theory with two flavours of Wilson quark is studied on an 8^3x16 lattice using all-to-all propagators, with particular emphasis on the dependence on quark chemical potential mu. As mu is increased from zero the diquark states with non-zero baryon number B respond as expected, while states with B=0 remain unaffected until the onset of non-zero baryon density at mu=m_pi/2. Post onset the pi-meson mass increases in accordance with chiral perturbation theory while the rho becomes lighter. In the diquark sector a Goldstone state associated with a superfluid ground state can be identified. A further consequence of superfluidity is an approximate degeneracy between mesons and baryons with the same spacetime and isospin quantum numbers. Finally we find tentative evidence for the binding of states with kaon quantum numbers within the baryonic medium.Comment: 14 pages, 5 figure