Browsing by Subject "Models, Biological"
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- ItemOpen AccessDevelopment and validation of a prognostic score during tuberculosis treatment(2017) Pefura-Yone, Eric Walter; Balkissou, Adamou Dodo; Poka-Mayap, Virginie; Fatime-Abaicho, Hadja Koté; Enono-Edende, Patrick Thierry; Kengne, André PascalBACKGROUND: Death under care is a major challenge for tuberculosis (TB) treatment programs. We derived and validated a simple score to predict mortality during tuberculosis treatment in high endemicity areas. METHODS: We used data for patients aged ≥15 years, diagnosed and treated for tuberculosis at the Yaounde Jamot Hospital between January 2012 and December 2013. Baseline characteristics associated with mortality were investigated using logistic regressions. A simple prognosis score (CABI) was constructed with regression coefficients for predictors in the final model. Internal validation used bootstrap resampling procedures. Models discrimination was assessed using c-statistics and calibration assessed via calibration plots and the Hosmer and Lemeshwow (H-L) statistics. The optimal score was based on the Youden's index. RESULTS: A total of 2250 patients (men 57.2%) with a mean age of 35.8 years were included; among whom 213 deaths (cumulative incidence 9.5%) were recorded. Clinical form of tuberculosis (C), age (A, years), adjusted body mass index (B, BMI, kg/m2) and status for HIV (Human immunodefiency virus) infection (I) were significant predictors in the final model (p < 0.0001) which was of the form Death risk = 1/(1 + e - (-1.3120 + 0.0474 ∗ age - 0.1866 ∗ BMI + 1.1637 (if smear negative TB) + 0.5418(if extra - pulmonary TB) + 1.3820(if HIV+))). The c-statistic was 0.812 in the derivation sample and 0.808 after correction for optimism. The calibration was good [H-Lχ2 = 6.44 (p = 0.60)]. The optimal absolute risk threshold was 4.8%, corresponding to a sensitivity of 81% and specificity of 67%. CONCLUSIONS: The preliminary promising findings from this study require confirmation through independent external validation studies. If confirmed, the model derived could facilitate the stratification of TB patients for mortality risk and implementation of additional monitoring and management measures in vulnerable patients.
- ItemOpen AccessInferring Process from Pattern in Plant Invasions: A Semimechanistic Model Incorporating Propagule Pressure and Environmental Factors(2003) Rouget, Mathieu; Richardson, David MAbstract: Propagule pressure is intuitively a key factor in biological invasions: increased availability of propagules increases the chances of establishment, persistence, naturalization, and invasion. The role of propagule pressure relative to disturbance and various environmental factors is, however, difficult to quantify. We explored the relative importance of factors driving invasions using detailed data on the distribution and percentage cover of alien tree species on South Africas Agulhas Plain (2,160 km2). Classification trees based on geology, climate, land use, and topography adequately explained distribution but not abundance (canopy cover) of three widespread invasive species (Acacia cyclops, Acacia saligna, and Pinus pinaster). A semimechanistic model was then developed to quantify the roles of propagule pressure and environmental heterogeneity in structuring invasion patterns. The intensity of propagule pressure (approximated by the distance from putative invasion foci) was a much better predictor of canopy cover than any environmental factor that was considered. The influence of environmental factors was then assessed on the residuals of the first model to determine how propagule pressure interacts with environmental factors. The mediating effect of environmental factors was species specific. Models combining propagule pressure and environmental factors successfully predicted more than 70% of the variation in canopy cover for each species.
- ItemOpen AccessNonlinear mixed effects modeling of gametocyte carriage in patients with uncomplicated malaria(BioMed Central Ltd, 2010) Distiller, Greg; Little, Francesca; Barnes, KarenBACKGROUND:Gametocytes are the sexual form of the malaria parasite and the main agents of transmission. While there are several factors that influence host infectivity, the density of gametocytes appears to be the best single measure that is related to the human host's infectivity to mosquitoes. Despite the obviously important role that gametocytes play in the transmission of malaria and spread of anti-malarial resistance, it is common to estimate gametocyte carriage indirectly based on asexual parasite measurements. The objective of this research was to directly model observed gametocyte densities over time, during the primary infection. METHODS: Of 447 patients enrolled in sulphadoxine-pyrimethamine therapeutic efficacy studies in South Africa and Mozambique, a subset of 103 patients who had no gametocytes pre-treatment and who had at least three non-zero gametocyte densities over the 42-day follow up period were included in this analysis. RESULTS: A variety of different functions were examined. A modified version of the critical exponential function was selected for the final model given its robustness across different datasets and its flexibility in assuming a variety of different shapes. Age, site, initial asexual parasite density (logged to the base 10), and an empirical patient category were the co-variates that were found to improve the model. CONCLUSIONS: A population nonlinear modeling approach seems promising and produced a flexible function whose estimates were stable across various different datasets. Surprisingly, dihydrofolate reductase and dihydropteroate synthetase mutation prevalence did not enter the model. This is probably related to a lack of power (quintuple mutations n = 12), and informative censoring; treatment failures were withdrawn from the study and given rescue treatment, usually prior to completion of follow up.
- ItemOpen AccessPhotographic measurement of upper-body sitting posture of high school students: A reliability and validity study(BioMed Central Ltd, 2008) van Niekerk, Sjan-Mari; Louw, Quinette; Vaughan, Christopher; Grimmer-Somers, Karen; Schreve, KristiaanBACKGROUND: All the reported measures of sitting posture, as well as photographs, have one flaw, as these measures are external to the body. These measures use calculations from external bony landmarks to estimate spinal posture, on the understanding that what is being measured externally reflects the shape, health and performance of structures of the underlying spine. Without a comparative measure of the relative position of the structures of the spine, the validity of any external spinal posture measure cannot be established. This paper reports on a study which tests the validity of photographs to measure adolescent sitting posture. METHODS: The study was conducted in a laboratory at the Department of Human Biology, University of Cape Town. A random sample of 40 adolescents were recruited from the Cape metropolitan schools, to detect differences of three degrees or more between the repeated measures of upright, normal or slouched posture (photographs) and between the posture photographs and LODOX measures. Eligible participants were healthy male and female subjects aged 15 or 16 years old, in Grade 10, and who were undertaking Computer or Computype studies at their schools. Two posture measurement tools were used in the study, namely: Photographs were taken using the Photographic Posture Analysis Method (PPAM) and Radiographs were taken using the LODOX (LODOX (Pty) Ltd) system. Subjects' posture was assessed in simulated computer workstations. The following angles were measured: the sagittal head angle, cervical angle, protraction/retraction angle, arm angle and the thoracic angle. RESULTS: Data from 39 subjects (19 males, 20 females) was used for analysis (17 15-year-olds (7 boys and 10 girls), 22 16-year-olds (12 boys and 10 girls)). All but one photographic angle showed moderate to good correlation with the LODOX angles (Pearson r values 0.67-0.95) with the exception being the shoulder protraction/retraction angle Pearson r values. Bland Altman limits of agreement illustrated a slight bias for all angles. The reliability study findings from repeated photographs demonstrated moderate to good correlation of all angles (ICC values 0.78-0.99). CONCLUSION: The findings of this study suggest that photographs provide valid and reliable indicators of the position of the underlying spine in sitting. Clinically it is important to know whether a patient is showing true progression in relation to a postural intervention. Based on the results of this study, the PPAM can be used in practice as a valid measure of sitting posture.
- ItemOpen AccessPurely competitive evolutionary dynamics for games(2012) Veller, Carl; Rajpaul, VineshWe introduce and analyze a purely competitive dynamics for the evolution of an infinite population subject to a 3-strategy game. We argue that this dynamics represents a characterization of how certain systems, both natural and artificial, are governed. In each period, the population is randomly sorted into pairs, which engage in a once-off play of the game; the probability that a member propagates its type to its offspring is proportional only to its payoff within the pair. We show that if a type is dominant (obtains higher payoffs in games with both other types), its 'pure' population state, comprising only members of that type, is globally attracting. If there is no dominant type, there is an unstable 'mixed' fixed point; the population state eventually oscillates between the three near-pure states. We then allow for mutations, where offspring have a non-zero probability of randomly changing their type. In this case, the existence of a dominant type renders a point near its pure state globally attracting. If no dominant type exists, a supercritical Hopf bifurcation occurs at the unique mixed fixed point, and above a critical (typically low) mutation rate, this fixed point becomes globally attracting: the implication is that even very low mutation rates can stabilize a system that would, in the absence of mutations, be unstable.