A Simulation Model for Intra-Urban Movements.
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ABSTRACT:
SUBMITTER: Serok N
PROVIDER: S-EPMC4498912 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:MotivationSimulations of cancer evolution are highly useful to study the effects of selection and mutation rates on cellular fitness. However, most methods are either lattice-based and cannot simulate realistically sized tumours, or they omit spatial constraints and lack the clonal dynamics of real-world tumours.ResultsStochastic model of intra-tumour heterogeneity (SMITH) is an efficient and explainable model of cancer evolution that combines a branching process with a new confinement mechanism limiting clonal growth based on the size of the individual clones as well as the overall tumour population. We demonstrate how confinement is sufficient to induce the rich clonal dynamics observed in spatial models and cancer samples across tumour types, while allowing for a clear geometric interpretation and simulation of 1 billion cells within a few minutes on a desktop PC.Availability and implementationSMITH is implemented in C# and freely available at https://bitbucket.org/schwarzlab/smith. For visualizations, we provide the accompanying Python package PyFish at https://bitbucket.org/schwarzlab/pyfish.Supplementary informationSupplementary data are available at Bioinformatics online.
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Project description:BackgroundThe World Health Organization estimates that the global number of dengue infections range between 80-100 million per year, with some studies estimating approximately three times higher numbers. Furthermore, the geographic range of dengue virus transmission is extending with the disease now occurring more frequently in areas such as southern Europe. Ae. aegypti, one of the most prominent dengue vectors, is endemic to the far north-east of Australia and the city of Cairns frequently experiences dengue outbreaks which sometimes lead to large epidemics.MethodA spatially-explicit, individual-based mathematical model that accounts for the spread of dengue infection as a result of human movement and mosquito dispersion is presented. The model closely couples the four key sub-models necessary for representing the overall dynamics of the physical system, namely those describing mosquito population dynamics, human movement, virus transmission and vector control. Important features are the use of high quality outbreak data and mosquito trapping data for calibration and validation and a strategy to derive local mosquito abundance based on vegetation coverage and census data.ResultsThe model has been calibrated using detailed 2003 dengue outbreak data from Cairns, together with census and mosquito trapping data, and is shown to realistically reproduce a further dengue outbreak. The simulation results replicating the 2008/2009 Cairns epidemic support several hypotheses (formulated previously) aimed at explaining the large-scale epidemic which occurred in 2008/2009; specifically, while warmer weather and increased human movement had only a small effect on the spread of the virus, a shorter virus strain-specific extrinsic incubation time can explain the observed explosive outbreak of 2008/2009.ConclusionThe proof-of-concept simulation model described in this study has potential as a tool for understanding factors contributing to dengue spread as well as planning and optimizing dengue control, including reducing the Ae. aegypti vector population and for estimating the effectiveness and cost-effectiveness of future vaccination programmes. This model could also be applied to other vector borne viral diseases such as chikungunya, also spread by Ae. aegypti and, by re-parameterisation of the vector sub-model, to dengue and chikungunya viruses spread by Aedes albopictus.
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Project description:Urban floods caused by expanding impervious areas due to urban development and short-term heavy precipitation adversely affect many coastal cities. Notably, Seoul, one of the coastal cities that experiences acute urban floods, suffers annually from urban floods during the rainfall season. Consequently, to mitigate the impacts of urban floods in Seoul, we established flood-vulnerable areas as target areas where green infrastructure planning was applied using the Stormwater Runoff Reduction Module (SRRM). We selected the Gangdong, Gangbuk, and Dobong districts in Seoul, Korea, all of which demonstrate high flood vulnerability. Analyses in reducing the runoff amount and peak time delay effect were estimated by model simulation using the SRRM. The reduction in peak discharge for the whole area occurred in the following order: Gangdong district, then Gangbuk district, and lastly Dobong district. In contrast, the reduction in peak discharge per unit area was most prominent in Gangbuk district, followed by Dobong and Gangdong districts. However, the delay effect was almost identical in all target areas. Based on the simulation results in this study, we planned green infrastructure, including green roofs, infiltration storage facilities, and porous pavement. We believe that the results of this study can significantly enhance the efficiency of urban flood restoration and green infrastructure planning in coastal cities.Supplementary informationThe online version contains supplementary material available at 10.1007/s11069-022-05477-7.
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Project description:Migratory birds often move significantly within their non-breeding range before returning to breed. It remains unresolved under which circumstances individuals relocate, whether movement patterns are consistent between populations and to what degree the individuals benefit from the intra-tropical movement (ITM). We tracked adult great reed warblers Acrocephalus arundinaceus from a central and a southeastern European breeding population, which either stay at a single non-breeding site, or show ITM, i.e. move to a second site. We related ITM to the normalized difference vegetation index (NDVI) describing vegetation conditions and probably reflecting food abundance for these insectivorous birds. Three-quarters of birds showed ITM across the non-breeding range. We found no difference in range values and mean values of NDVI between the single non-breeding sites of stationary birds and the two sites of moving birds. The vegetation conditions were better at the second sites compared to the first sites during the period which moving birds spent at the first sites. Vegetation conditions further deteriorated at the first sites during the period the moving birds resided at their second sites. Our study provides evidence that birds probably benefit from improved conditions after ITM compared to the conditions at the sites from where they departed.
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Project description:A yearlong air monitoring campaign was conducted to assess the impact of local temperature, relative humidity, and wind speed on the temporal and spatial variability of PM2.5 in El Paso, Texas. Monitoring was conducted at four sites purposely selected to capture the local traffic variability. Effects of meteorological events on seasonal PM2.5 variability were identified. For instance, in winter low-wind and low-temperature conditions were associated with high PM2.5 events that contributed to elevated seasonal PM2.5 levels. Similarly, in spring, high PM2.5 events were associated with high-wind and low-relative humidity conditions. Correlation coefficients between meteorological variables and PM2.5 fluctuated drastically across seasons. Specifically, it was observed that for most sites correlations between PM2.5 and meteorological variables either changed from positive to negative or dissolved depending on the season. Overall, the results suggest that mixed effects analysis with season and site as fixed factors and meteorological variables as covariates could increase the explanatory value of LUR models for PM2.5.
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Project description:AimsChildren's health is affected by the environment in which they live and grow. Within Sweden's urban areas, several city districts can be classified as socio-economically disadvantaged. This article describes the creation of a child health index to visualise disparities within and between Sweden's three major cities, and how these relate to indicators of demography and socio-economic status.MethodsData were collected for seven child health indicators and seven socio-economic and demographic indicators from the Swedish Pregnancy Register, Child Health Services and Statistics Sweden. An index was created from the health indicators using principal component analysis, generating weights for each indicator. Correlations between index outcomes and socio-economic and demographic indicators were analysed using linear regression.ResultsThe largest variance in index values could be seen in Stockholm followed by Malmö, and the poorest mean index outcome was seen in Malmö followed by Gothenburg. The largest intra-urban percentage range in health indicators could be seen for tobacco exposure at 0-4 weeks (0.8-33.9%, standard deviation (SD)=8.8%) and, for the socio-economic and demographic indicators, foreign background (19.9-88.5%, SD=19.8%). In the multivariate analysis, index outcomes correlated most strongly with foreign background (R2=0.364, p=0.001).ConclusionsChildren's health follows a social gradient and a pattern of ethnic segregation in Swedish cities, where it can be visualised using an index of child health. The resulting map highlights the geographical distribution of these disparities, and displays in which city districts child health interventions may be most needed.
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