Browsing by Subject "Modelling"
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- ItemOpen AccessConcerning demographic limitations on the population growth rate of West Australian (breeding stock D) humpback whales(International Whaling Commission, 2011) Brandão, Anabela; Butterworth, Doug SThe upper bound of 0.126 on the maximum demographically possible annual growth rate for humpback whales that has standardly been imposed on recent applications of age-aggregated assessment models for this species in the IWC Scientific Committee, is based on an analysis that assumes steady age structure. It is conceivable that transient age-structure effects could admit greater population growth rates for short periods than suggested by such a bound. This possibility is addressed by developing an age-structured population model in which possible density dependent changes in pregnancy rate, age at first parturition and natural mortality are modelled explicitly, and allowance is made for the possibility of natural mortality increasing at older ages. The model is applied to the case of the west Australian humpback whale population (Breeding Stock D), for which breeding ground surveys over the 1982–1994 period provide a point estimate of 0.10 for the annual population growth rate. Results based upon the breeding population survey estimate of abundance of 10,032 in 1999 suggest that 0.12 is the maximum demographically feasible annual rate of increase for this stock over 1982–1994 if it is a closed population. This result is based on essentially the same parameter choices as led to the earlier r = 0.126 bound, i.e. that in the limit of low population size the age at first parturition approaches five years from above, the annual pregnancy rate 0.5 from below, and the annual natural mortality rate 0.01 from above. Transient effects do not appear able to reconcile the observed rate of increase with less extreme values of demographic parameters than led to the previously imposed upper bound of 0.126 on the maximum possible annual growth rate. Although use of extreme values reported for demographic parameters for Northern Hemisphere humpback whale populations, rather than those considered here, would reduce this suggested maximum rate of 0.12, the conclusion that transient effects have a very limited impact on observed population growth rates would be unlikely to change.
- ItemOpen AccessDesigning an optimal HIV programme for South Africa: Does the optimal package change when diminishing returns are considered?(2017) Chiu, Calvin; Johnson, Leigh F; Jamieson, Lise; Larson, Bruce A; Meyer-Rath, GesineAbstract Background South Africa has a large domestically funded HIV programme with highly saturated coverage levels for most prevention and treatment interventions. To further optimise its allocative efficiency, we designed a novel optimisation method and examined whether the optimal package of interventions changes when interaction and non-linear scale-up effects are incorporated into cost-effectiveness analysis. Methods The conventional league table method in cost-effectiveness analysis relies on the assumption of independence between interventions. We added methodology that allowed the simultaneous consideration of a large number of HIV interventions and their potentially diminishing marginal returns to scale. We analysed the incremental cost effectiveness ratio (ICER) of 16 HIV interventions based on a well-calibrated epidemiological model that accounted for interaction and non-linear scale-up effects, a custom cost model, and an optimisation routine that iteratively added the most cost-effective intervention onto a rolling baseline before evaluating all remaining options. We compared our results with those based on a league table. Results The rank order of interventions did not differ substantially between the two methods- in each, increasing condom availability and male medical circumcision were found to be most cost-effective, followed by anti-retroviral therapy at current guidelines. However, interventions were less cost-effective throughout when evaluated under the optimisation method, indicating substantial diminishing marginal returns, with ICERs being on average 437% higher under our optimisation routine. Conclusions Conventional league tables may exaggerate the cost-effectiveness of interventions when programmes are implemented at scale. Accounting for interaction and non-linear scale-up effects provides more realistic estimates in highly saturated real-world settings.
- ItemOpen AccessDrivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study(2021-10-07) Riou, Julien; Dupont, Carole; Bertagnolio, Silvia; Gupta, Ravindra K.; Kouyos, Roger D.; Egger, Matthias; L. Althaus, ChristianIntroduction The rise of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI) threatens antiretroviral therapy's long-term success (ART). NNRTIs will remain an essential drug for the management of HIV-1 due to safety concerns associated with integrase inhibitors. We fitted a dynamic transmission model to historical data from 2000 to 2018 in nine countries of southern Africa to understand the mechanisms that have shaped the HIV-1 epidemic and the rise of pretreatment NNRTI resistance. Methods We included data on HIV-1 prevalence, ART coverage, HIV-related mortality, and survey data on pretreatment NNRTI resistance from nine southern Africa countries from a systematic review, UNAIDS and World Bank. Using a Bayesian hierarchical framework, we developed a dynamic transmission model linking data on the HIV-1 epidemic to survey data on NNRTI drug resistance in each country. We estimated the proportion of resistance attributable to unregulated, off-programme use of ART. We examined each national ART programme's vulnerability to NNRTI resistance by defining a fragility index: the ratio of the rate of NNRTI resistance emergence during first-line ART over the rate of switching to second-line ART. We explored associations between fragility and characteristics of the health system of each country. Results The model reliably described the dynamics of the HIV-1 epidemic and NNRTI resistance in each country. Predicted levels of resistance in 2018 ranged between 3.3% (95% credible interval 1.9–7.1) in Mozambique and 25.3% (17.9–33.8) in Eswatini. The proportion of pretreatment NNRTI resistance attributable to unregulated antiretroviral use ranged from 6% (2–14) in Eswatini to 64% (26–85) in Mozambique. The fragility index was low in Botswana (0.01; 0.0–0.11) but high in Namibia (0.48; 0.16–10.17), Eswatini (0.64; 0.23–11.8) and South Africa (1.21; 0.83–9.84). The combination of high fragility of ART programmes and high ART coverage levels was associated with a sharp increase in pretreatment NNRTI resistance. Conclusions This comparison of nine countries shows that pretreatment NNRTI resistance can be controlled despite high ART coverage levels. This was the case in Botswana, Mozambique, and Zambia, most likely because of better HIV care delivery, including rapid switching to second-line ART of patients failing first-line ART.
- ItemOpen AccessEstimating ionospheric currents by inversion from ground-based geomagnetic data and calculating geoelectric fields for studies of geomagnetically induced currents(2016) de Villiers, J S; Pirjola, R J; Cilliers, P JThis research focuses on the inversion of geomagnetic variation field measurements to obtain the source currents in the ionosphere and magnetosphere, and to determine the geoelectric fields at the Earth’s surface. During geomagnetic storms, the geoelectric fields create geomagnetically induced currents (GIC) in power networks. These GIC may disturb the operation of power systems, cause damage to power transformers, and even result in power blackouts. In this model, line currents running east–west along given latitudes are postulated to exist at a certain height above the Earth’s surface. This physical arrangement results in the fields on the ground being composed of a zero magnetic east component and a nonzero electric east component. The line current parameters are estimated by inverting Fourier integrals (over wavenumber) of elementary geomagnetic fields using the Levenberg–Marquardt technique. The output parameters of the model are the ionospheric current strength and the geoelectric east component at the Earth’s surface. A conductivity profile of the Earth is adapted from a shallow layered-Earth model for one observatory, together with a deep-layer model derived from satellite observations. This profile is used to obtain the ground surface impedance and therefore the reflection coefficient in the integrals. The inputs for the model are a spectrum of the geomagnetic data for 31 May 2013. The output parameters of the model are spectrums of the ionospheric current strength and of the surface geoelectric field. The inverse Fourier transforms of these spectra provide the time variations on the same day. The geoelectric field data can be used as a proxy for GIC in the prediction of GIC for power utilities. The current strength data can assist in the interpretation of upstream solar wind behaviour.
- ItemOpen AccessThe impact of blood transcriptomic biomarker targeted tuberculosis preventive therapy in people living with HIV: a mathematical modelling study(2021-10-29) Sumner, Tom; Mendelsohn, Simon C.; Scriba, Thomas J.; Hatherill, Mark; White, Richard G.Background Tuberculosis (TB) preventive therapy is recommended for all people living with HIV (PLHIV). Despite the elevated risk of TB amongst PLHIV, most of those eligible for preventive therapy would never develop TB. Tests which can identify individuals at greatest risk of disease would allow more efficient targeting of preventive therapy. Methods We used mathematical modelling to estimate the potential impact of using a blood transcriptomic biomarker (RISK11) to target preventive therapy amongst PLHIV. We compared universal treatment to RISK11 targeted treatment and explored the effect of repeat screening of the population with RISK11. Results Annual RISK11 screening, with preventive therapy provided to those testing positive, could avert 26% (95% CI 13–34) more cases over 10 years compared to one round of universal treatment. For the cost per case averted to be lower than universal treatment, the maximum cost of the RISK11 test was approximately 10% of the cost of preventive therapy. The benefit of RISK11 screening may be greatest amongst PLHIV on ART (compared to ART naïve individuals) due to the increased specificity of the test in this group. Conclusions Biomarker targeted preventive therapy may be more effective than universal treatment amongst PLHIV in high incidence settings but would require repeat screening.
- ItemRestrictedMeasurement and modelling of organic fouling deposition in ultrafiltration by ultrasonic transfer signals and reflections.(Elsevier, 2002) Li, Jianxin; Sanderson, R; Hallbauer, D; Hallbauer-Zadorozhnaya, V YThe development of a non-destructive, real-time observation technique to detect and monitor fouling during liquid separation processes is of great importance to the development of strategies to improve operating conditions. In this study ultrasonic time-domain reflectometry (UTDR) was used to measure organic fouling, in real time, during ultrafiltration (UF) with polysulfone (PS) membranes. The feed solution was a paper-mill effluent, which contains breakdown products of lignin or lignosulphonate, from a wastewater treatment plant. An asymmetric, composite PS membrane can be detected by UTDR. Experimental results showed that the ultrasonic signal response can be used to monitor fouling-layer formation and growth on the membrane in real-time. Traditional flux measurements and analysis of the membrane surface by microscopy corroborated the UTDR results. Further, the differential signal developed indicate the state and progress of the fouling layer and gives warning of advanced fouling during operation. Moreover, a predictive modelling program — ultrasonic reflection (USRF) was developed to model the fouling deposits. This contributed to a better understanding of the fouling layer formation and its recognition during ultrasonic testing. This modelling was applied to model the density and thickness of a fouling layer on a membrane surface so as to predict the fouling behavior. The modelling results were in a good agreement with the actual observations.
- ItemRestrictedModelling of bioleach processes: connection between science and engineering(Elsevier, 2010) Petersen, JThis paper gives a brief introduction to the modelling of bioleach processes, developed from a careful analysis of the fundamental process steps at the gas–liquid, biological and mineral interfaces, and how these interact in a given reactor environment (tanks and heaps). The insights gained from such modelling work can guide both engineers in the optimisation of processes and scientist in directing their research at areas not yet well understood. From this perspective, some future directions of the bioleaching field are discussed.
- ItemRestrictedModelling zinc heap bioleaching(Elsevier, 2007) Petersen, J; Dixon, D GA comprehensive modelling study of the HydroZinc™ heap bioleach process, using the HeapSim modelling tool, is described. The model was calibrated on the basis of a small number of column leach experiments and compared against pilot heap test results. The model calibration thus confirmed, a detailed sensitivity study was conducted in order to establish the key parameters that determine the overall rate of Zn extraction. In the present case these were found to be oxygen gas–liquid mass transfer, various factors affecting the delivery of acid into the heap, and factors affecting the temperature distribution within the heap. A set of improved design parameters are proposed that would almost double the zinc conversion rate measured in the pilot plant – from 83% in 740 days to 78% in 383 days – and increase zinc production rate from 1.77 to 4.35 kg/m2/day. However, this improvement must be evaluated in the context of various implications for the downstream process.
- ItemOpen AccessNon-optimal apparent temperature and cardiovascular mortality: the association in Puducherry, India between 2011 and 2020(2023-02-08) Shrikhande, Shreya S; Pedder, Hugo; Röösli, Martin; Dalvie, Mohammad A; Lakshmanasamy, Ravivarman; Gasparrini, Antonio; Utzinger, Jürg; Cissé, GuéladioBackground Cardiovascular diseases (CVDs), the leading cause of death worldwide, are sensitive to temperature. In light of the reported climate change trends, it is important to understand the burden of CVDs attributable to temperature, both hot and cold. The association between CVDs and temperature is region-specific, with relatively few studies focusing on low-and middle-income countries. This study investigates this association in Puducherry, a district in southern India lying on the Bay of Bengal, for the first time. Methods Using in-hospital CVD mortality data and climate data from the Indian Meteorological Department, we analyzed the association between apparent temperature (Tapp) and in-hospital CVD mortalities in Puducherry between 2011 and 2020. We used a case-crossover model with a binomial likelihood distribution combined with a distributed lag non-linear model to capture the delayed and non-linear trends over a 21-day lag period to identify the optimal temperature range for Puducherry. The results are expressed as the fraction of CVD mortalities attributable to heat and cold, defined relative to the optimal temperature. We also performed stratified analyses to explore the associations between Tapp and age-and-sex, grouped and considered together, and different types of CVDs. Sensitivity analyses were performed, including using a quasi-Poisson time-series approach. Results We found that the optimal temperature range for Puducherry is between 30°C and 36°C with respect to CVDs. Both cold and hot non-optimal Tapp were associated with an increased risk of overall in-hospital CVD mortalities, resulting in a U-shaped association curve. Cumulatively, up to 17% of the CVD deaths could be attributable to non-optimal temperatures, with a slightly higher burden attributable to heat (9.1%) than cold (8.3%). We also found that males were more vulnerable to colder temperature; females above 60 years were more vulnerable to heat while females below 60 years were affected by both heat and cold. Mortality with cerebrovascular accidents was associated more with heat compared to cold, while ischemic heart diseases did not seem to be affected by temperature. Conclusion Both heat and cold contribute to the burden of CVDs attributable to non-optimal temperatures in the tropical Puducherry. Our study also identified the age-and-sex and CVD type differences in temperature attributable CVD mortalities. Further studies from India could identify regional associations, inform our understanding of the health implications of climate change in India and enhance the development of regional and contextual climate-health action-plans.
- ItemRestrictedA review of rate equations proposed for microbial ferrous-iron oxidation with a view to application to heap bioleaching(Elsevier, 2006) Ojumu, T V; Petersen, J; Searby, G E; Hansford, G SIn view of the fact that the microbial oxidation of ferrous iron to the ferric form is an essential sub-process in the bioleaching of sulphide minerals, the development of a comprehensive rate equation for this sub-process is critical. Such a rate equation is necessary for the design and modelling of both tank and heap bioleach systems. Most of the rate equations presented in the literature define the specific microbial growth rate using a Monod-type form for ferrous substrate limitation, with further terms added to account for ferric product inhibition, ferrous substrate limitation and inhibition. A few of the published rate equations describe the specific substrate utilization rate in terms of a modified Michaelis–Menten equation and include the maximum yield constant and cell maintenance via the Pirt equation. Other rate equations are based on chemiosmotic theory or an analogy with an electrochemical cell. In the present paper a selection of rate equations are compared against each other by calibrating them against the same set of data and comparing the fits. It was found that none fits the data particularly well and that some of the underlying assumptions need to be questioned. In particular, it appears that ferric inhibition is perhaps not as significant a factor than previously assumed and that rate control by the availability of ferrous is more significant. Some rate equations include terms to account for the effects of temperature, pH, biomass concentration, ionic strength as well as inhibition due to arsenic. In general these effects have been studied in isolation and in ranges not too far off the optimum. Few rate equations combine more than 2 effects and there is no clarity on how a comprehensive model to account for all effects should be constructed. Rate equations have been applied to tank bioleach systems, which usually operate under controlled conditions near the optimum. Heap bioleach systems, on the other hand, often operate far from optimum conditions with respect to temperature, pH, solution conditions, etc., at the same time. The kinetics of such sub-optimal systems are still poorly understood. Future studies should be directed towards the development of a comprehensive rate equation useful for describing the kinetics of heap bioleaching over a wide range of conditions.
- ItemOpen AccessThermophilic Heap Leaching of a Chalcopyrite Concentrate(Elsevier, 2002) Petersen, J; Dixon, D GThermophiles have been shown to be the only micro-organisms to leach chalcopyrite successfully. Heap leaching may be a feasible alternative to conventional bio-reactors, providing a high temperature environment can be maintained within the heap without external heating. In the present study thermophilic heap leaching of a chalcopyrite concentrate coated onto inert support rocks (the GEOCOAT™ process) was studied in sets of small heated columns. The temperature was gradually increased to 70 °C, while successively introducing various mesophile and thermophile cultures. Individual columns were dismantled after progressively longer leach periods and the residual concentrates analysed. Copper extractions in excess of 90% were achieved within 100 days. On the basis of head and residue analyses the rate of reaction heat generated was calculated. A comprehensive heap heat conservation model was used to determine whether the experimental temperatures can be achieved and maintained in a full scale heap. Results indicate that operating hot heaps successfully is possible within a certain range of process parameters.