Agent-based modeling of malaria vectors: The importance of spatial simulation

Background: The modeling of malaria vector mosquito populations yields great insight into drivers of malaria transmission at the village scale. Simulation of individual mosquitoes as agents in a distributed, dynamic model domain may be greatly beneficial for simulation of spatial relationships of vectors and hosts. Methods. In this study, an agent-based model is used to simulate the life cycle and movement of individual malaria vector mosquitoes in a Niger Sahel village, with individual simulated mosquitoes interacting with their physical environment as well as humans. Various processes that are known to be epidemiologically important, such as the dependence of parity on flight distance between developmental habitat and blood meal hosts and therefore spatial relationships of pools and houses, are readily simulated using this modeling paradigm. Impacts of perturbations can be evaluated on the basis of vectorial capacity, because the interactions between individuals that make up the population- scale metric vectorial capacity can be easily tracked for simulated mosquitoes and human blood meal hosts, without the need to estimate vectorial capacity parameters. Results: As expected, model results show pronounced impacts of pool source reduction from larvicide application and draining, but with varying degrees of impact depending on the spatial relationship between pools and human habitation. Results highlight the importance of spatially-explicit simulation that can model individuals such as in an agent-based model. Conclusions: The impacts of perturbations on village scale malaria transmission depend on spatial locations of individual mosquitoes, as well as the tracking of relevant life cycle events and characteristics of individual mosquitoes. This study demonstrates advantages of using an agent-based approach for village-scale mosquito simulation to address questions in which spatial relationships are known to be important. © 2014 Bomblies; licensee BioMed Central Ltd

The changing risk of extreme event impacts on Vermont transportation infrastructure

Vermont is seeing significant increases in extreme precipitation, total precipitation, and precipitation persistence. These changes can affect the behavior of stream flows, resulting in changing magnitude of extreme flows such as the 100-year discharge. For hydraulic design of culverts and bridges, design flows are traditionally used based on assumptions of stationarity, resulting in a design that does not incorporate ongoing changes in streamflow behavior. This report describes a modeling study in the Mad River and the Missisquoi River that derives change factors for Vermont that can be applied to the magnitude of a design discharge (100- year, 50-year flow and 25-year discharge). The methodology is based on a stochastic Monte Carlo Markov Chain model that simulates the changing precipitation statistics and a hydrology model that translates climate inputs into stream discharge for the two test rivers based on climate-sensitive snowpack and soil moisture. The change factors for 100-year flows in 2050 for the Mad River (more flashy) and the Missisquoi River (less flashy) are 1.6 and 1.4, respectively. These results are based on the assumption that changes in the extreme value distributions continue in the same manner as during the observed period. The derived change factors can be applied based on a spatial map of changes of extreme precipitation. The differences in design flows from the nonstationary model, the stationary model, and downscaled climate model output are very large. This sensitivity of outcome to methodology presents a design challenge, and the results of this study can be applied to make conservative estimates of future extreme discharges

Field observations and mechanistic modeling of the malaria transmission response to environmental climatic variability

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2009.Includes bibliographical references (leaves 205-222).A coupled HYDrology, Entomology and MAlaria Transmission Simulator (HYDREMATS) has been developed. The model simulates the hydrological and climatological determinants of malaria transmission mechanistically and at high spatialand temporal resolution, and is valid for semi-arid, desert fringe environments where the mosquito Anopheles gambiae s.l. is the dominant malaria vector. This includes much of the most malarious parts of Africa such as the Sahel. The model is validated with several years of field data collected from Banizoumbou village in southwestern Niger. Simulations of the 2005 and 2006 rain seasons in Banizoumbou using measured meteorological data successfully reproduce the observed interannual variability in malaria vector mosquito abundance. The distributed hydrology model operates at high spatial and temporal resolution, and incorporates remotely-sensed data for land cover and topography to simulate the formation and persistence of the small, temporary pools that constitute the breeding habitat of Anopheles gambiae s.l. mosquitoes. An agent-based mosquito population model is coupled to the distributed hydrology model, with aquatic stage and adult stage components. Aquatic stage mosquitoes are allowed to breed in any surface water, but the developing eggs, larvae and pupae die if the pool dries. The model structure maintains the spatial relationships of breeding pools, mosquitoes, and human habitation. For each individual adult mosquito, the model tracks the attributes relevant to population dynamics and malaria transmission, which are updated as mosquitoes interact with their environment, humans, and animals.(cont.) The model reproduces mosquito population variability at seasonal and interannual time scales, and highlights individual pool persistence as a dominant control of mosquito population dynamics. HYDREMATS is applied to study the impact of village-scale spatial variability in hydrologic conditions on malaria transmission. Zindarou is a village located only 30 km from Banizoumbou, but hydrologically it is very different from Banizoumbou. The groundwater table around Banizoumbou is about 25 meters below the surface, while the groundwater table around Zindarou is a few meters below the surface. HYDREMATS reproduces the much higher mosquito populations observed in Zindarou arising from the lush, wet conditions compared to drier Banizoumbou. This result exposes small scale spatial variability in surface and subsurface hydrology as a principal control of villagescale malaria transmission. Further experiments simulate the effect of climate shifts on Sahel malaria-transmitting mosquito abundance using HYDREMATS. Climate variability and climate change in West Africa often occur in the form of a shift from a wet regime to a dry regime or vice versa. Such a climate shift in the West African Sahel can greatly impact the intensity of regional malaria transmission. To investigate possible outcomes of such shifts, meteorological data from two different Sahel stations are used as alternate climatic forcings for the Banizoumbou model domain. The stations are located north and south of Banizoumbou in Agoufou, Mali, and in Djougou, Benin at 200 km and 400 km in the north-south direction from Banizoumbou, respectively.(cont.) These data series represent possible climate shift scenarios, based on the observation that a northward or southward translation of Sahelian climate conditions along the north-south gradient has accompanied past climate shifts. A series of simulations investigate individually the effects of precipitation frequency and ambient temperature on anopheles mosquito populations and vectorial capacity. The vectorial capacity with Djougou, Benin conditions exhibited a 25% increase compared to baseline Banizoumbou conditions, whereas the vectorial capacity decreased by 26% with the Agoufou, Mali meteorological conditions. Isolation of temperature contributions to these differences show that in a cooling scenario (to resemble Benin), elasticity of mosquito abundance is 1.3, compared to -8.9 for the shift to hotter conditions found in Agoufou, Mali. Mosquito mortality ultimately limits malaria transmission in shifts to warmer conditions, and parasite extrinsic incubation period (sporogony) becomes limiting at low temperatures. In all cases, changes in precipitation frequency can limit mosquito breeding due to small-scale hydrological processes influencing breeding pool persistence. Finally, a simple model of human immune response to malaria transmission is built into HYDREMATS. The HYDREMATS representation of acquired immunity acting in opposition to-yet depending on-malaria parasite in the bloodstream explains field observations of very similar malaria prevalence in Zindarou and Banizoumbou despite pronounced difference in vectorial capacity.(cont.) The results are consistent with various paradoxical observations in the literature of unexpectedly low prevalence with higher biting pressure. HYDREMATS represents acquired immunity as dependent on repeated inoculations of malaria, with a slow loss of immunity in the absence of infectious bites. Because climate variability determines variability in vectorial capacity, in an endemic environment acquired immunity level in a human population has a memory of past climate variability. Model experiments in Banizoumbou evaluating the impacts of climate shifts confirm this.by Arne Bomblies.Ph.D

The use of CMIP5 data to simulate climate change impacts on flow regime within the Lake Champlain Basin

Study region: Lake Champlain Basin, northwestern New England, USA. Study focus: Our study uses regional hydrologic analyses and modeling to examine alternative possibilities that might emerge in the Lake Champlain Basin streamflow regime for various climate scenarios. Climate data as well as spatial data were processed to calibrate the Regional Hydro-Ecological Simulation System (RHESSys) model runoff simulations. The 21st century runoff simulations were obtained by driving the RHESSys model with climate data from the Coupled Model Intercomparison Project phase 5 (CMIP5) for representative concentration pathways RCP 4.5 and 8.5. New hydrological insights for the region: Our analyses suggest that most of CMIP5 ensembles fail to capture both the trends and variability observed in historical precipitation when run in hindcast. This raises concerns of using such products in driving hydrologic models for the purpose of obtaining reliable runoff projections that can aid researchers in regional planning. A subset of five climate models among the CMIP5 ensembles have shown statistically significant trends in precipitation, but the magnitude of these trends is not adequately representative of those seen in observed annual precipitation. Adjusted precipitation forecasts project a streamflow regime described by an increase of about 30% in seven-day maximum flow, a four days increase in flooded days, a three orders of magnitude increase in base flow index, and a 60% increase in runoff predictability (Colwell index)

A regional model for malaria vector developmental habitats evaluated using explicit, pond-resolving surface hydrology simulations

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Dynamical malaria models can relate precipitation to the availability of vector breeding sites using simple models of surface hydrology. Here, a revised scheme is developed for the VECTRI malaria model, which is evaluated alongside the default scheme using a two year simulation by HYDREMATS, a 10 metre resolution, village-scale model that explicitly simulates individual ponds. Despite the simplicity of the two VECTRI surface hydrology parametrization schemes, they can reproduce the sub-seasonal evolution of fractional water coverage. Calibration of the model parameters is required to simulate the mean pond fraction correctly. The default VECTRI model tended to overestimate water fraction in periods subject to light rainfall events and underestimate it during periods of intense rainfall. This systematic error was improved in the revised scheme by including the a parametrization for surface run-off, such that light rainfall below the initial abstraction threshold does not contribute to ponds. After calibration of the pond model, the VECTRI model was able to simulate vector densities that compared well to the detailed agent based model contained in HYDREMATS without further parameter adjustment. Substituting local rain-gauge data with satellite-retrieved precipitation gave a reasonable approximation, raising the prospects for regional malaria simulations even in data sparse regions. However, further improvements could be made if a method can be derived to calibrate the key hydrology parameters of the pond model in each grid cell location, possibly also incorporating slope and soil texture. Copyright

Characterization of increased persistence and intensity of precipitation in the northeastern United States

We present evidence of increasing persistence in daily precipitation in the northeastern United States that suggests that global circulation changes are affecting regional precipitation patterns. Meteorological data from 222 stations in 10 northeastern states are analyzed using Markov chain parameter estimates to demonstrate that a significant mode of precipitation variability is the persistence of precipitation events. We find that the largest region‐wide trend in wet persistence (i.e., the probability of precipitation in 1 day and given precipitation in the preceding day) occurs in June (+0.9% probability per decade over all stations). We also find that the study region is experiencing an increase in the magnitude of high‐intensity precipitation events. The largest increases in the 95th percentile of daily precipitation occurred in April with a trend of +0.7 mm/d/decade. We discuss the implications of the observed precipitation signals for watershed hydrology and flood risk

Evaluation of daily precipitation from the era5 global reanalysis against ghcn observations in the northeastern united states

Licensee MDPI, Basel, Switzerland. Precipitation is a primary input for hydrologic, agricultural, and engineering models, so making accurate estimates of it across the landscape is critically important. While the distribution of in-situ measurements of precipitation can lead to challenges in spatial interpolation, gridded precipitation information is designed to produce a full coverage product. In this study, we compare daily precipitation accumulations from the ERA5 Global Reanalysis (hereafter ERA5) and the US Global Historical Climate Network (hereafter GHCN) across the northeastern United States. We find that both the distance from the Atlantic Coast and elevation difference between ERA5 estimates and GHCN observations affect precipitation relationships between the two datasets. ERA5 has less precipitation along the coast than GHCN observations but more precipitation inland. Elevation differences between ERA5 and GHCN observations are positively correlated with precipitation differences. Isolated GHCN stations on mountain peaks, with elevations well above the ERA5 model grid elevation, have much higher precipitation. Summer months (June, July, and August) have slightly less precipitation in ERA5 than GHCN observations, perhaps due to the ERA5 convective parameterization scheme. The heavy precipitation accumulation above the 90th, 95th, and 99th percentile thresholds are very similar for ERA5 and the GHCN. We find that daily precipitation in the ERA5 dataset is comparable to GHCN observations in the northeastern United States and its gridded spatial continuity has advantages over in-situ point precipitation measurements for regional modeling applications

Impacts of projected climate change over the Lake Champlain basin in Vermont

The Lake Champlain basin is a critical ecological and socioeconomic resource of the northeastern United States and southern Quebec, Canada. While general circulation models (GCMs) provide an overview of climate change in the region, they lack the spatial and temporal resolution necessary to fully anticipate the effects of rising global temperatures associated with increasing greenhouse gas concentrations. Observed trends in precipitation and temperature were assessed across the Lake Champlain basin to bridge the gap between global climate change and local impacts. Future shifts in precipitation and temperature were evaluated as well as derived indices, including maple syrup production, days above 32.2°C (90°F), and snowfall, relevant to managing the natural and human environments in the region. Four statistically downscaled, biascorrected GCM simulations were evaluated from the Coupled Model Intercomparison Project phase 5 (CMIP5) forced by two representative concentration pathways (RCPs) to sample the uncertainty in future climate simulations. Precipitation is projected to increase by between 9.1 and 12.8mmyr-1 decade-1 during the twenty-first century while daily temperatures are projected to increase between 0.43° and 0.49°C decade-1. Annual snowfall at six major ski resorts in the region is projected to decrease between 46.9%and 52.4%by the late twenty-first century. In the month of July, the number of days above 32.2°C in Burlington, Vermont, is projected to increase by over 10 days during the twenty-first century. © 2014 American Meteorological Society

Evaluating Effectiveness of Floodplain Sites along the Lamoille Valley Rail Trail: A Blueprint for Future Rail-River Projects

Floodplains perform many functions of value to society, including conveyance and storage of floodwaters for reduced downstream impacts, sediment and nutrient deposition to support soil formation, and maintenance of pulsed overbank flows to support diverse habitats. When constructed along Vermont’s river valleys in the mid-to-late 1800s, railroads often isolated large areas of natural floodplain, leading to decreased flood and sediment storage, and increased downstream flood stages, sediment and nutrient delivery. Where rail lines have been federally-banked and converted to recreational trails, floodplain reconnection could be achieved by modifying the rail embankment through lowering or installing cross culverts or bridges. With the Lamoille Valley Rail Trail (LVRT) in the Lamoille and Missisquoi River basins as a focal study area, this research has generated tools and planning frameworks for transportation and river managers to identify and prioritize candidate reconnection sites, and to holistically evaluate the benefits of these projects alongside potential impacts to adjacent infrastructure or land uses. Effectiveness of completed and proposed floodplain reconnection sites along the LVRT was evaluated at various spatial scales using a suite of tools. At the watershed and reach scales, a screening protocol was developed, leveraging stream geomorphic assessment data to prioritize potential floodplain reconnection sites for further vetting through field inspection. Ten out of twelve floodplain reconnection sites completed along the LVRT in 2006-2008 were predicted as a priority in a retrospective application of this screening protocol. Low-complexity (Height Above Nearest Drainage) hydraulic modeling results confirmed that most completed projects provided significant increases in the floodplain capacity for floods of 2- to 500-year recurrence intervals. Event-scale monitoring conducted at selected sites has confirmed accumulation of fine sediment and phosphorus. A conservative estimate of a half-ton of phosphorus deposited during one storm on 57 acres highlights the water quality benefits of restoring floodplains. Reconnection alternatives were evaluated in more detail using two-dimensional hydraulic modeling (2D HEC-RAS) at a demonstration reach of the Black Creek near East Fairfield spanning two completed reconnection sites and one proposed site on the LVRT. Modeled reconnection alternatives resulted in modest changes in flooding parameters due to an unexpected, existing degree of cross connection between floodplains of the Black Creek and Elm Brook tributary. Nevertheless, this research project has created a framework for more holistic analysis of floodplain reconnection opportunities at similar sites across Vermont and beyond. The hydraulic modeling products and scenarios developed for this project are being adapted to support analysis and modeling of fine sediment and phosphorus attenuation as the Vermont Agency of Transportation continues to collaborate with the Vermont Agency of Natural Resources and other stakeholders to develop a phosphorus-crediting framework for floodplain reconnection projects

From the Habit of Control to Institutional Enablement: Re-envisioning the Governance of Social-Ecological Systems from the Perspective of Complexity Sciences

Due to the inherent uncertainty in predicting the evolution of phase-spaces in social-ecological systems (SESs), these systems cannot be “optimally” managed through top-down, command and control type of governance designs. Instead, generalized autocatalytic set theory, a type of network and complexity theory with foundations in mathematical graph theory, may be used as a bottom-up, emergent and co-evolutionary framework to design the governance regimes of SESs. Under this theoretical re-conceptualization, the policy and institutional interventions can at best “enable” the policy-makers to nudge SESs towards socially desirable yet ecologically feasible phase-spaces, which in turn are continually revamped as new elements in phase-spaces emerge