There is a renewed effort to develop novel malaria control strategies as even well-implemented existing malaria control tools may fail to block transmission in some regions. Currently, transgenic ...implementations of the sterile insect technique (SIT) such as the release of insects with a dominant lethal, homing endonuclease genes, or flightless mosquitoes are in development. These implementations involve the release of transgenic male mosquitoes whose matings with wild females produce either no viable offspring or no female offspring. As these technologies are all in their infancy, little is known about the relative efficiencies of the various implementations.
This paper describes agent-based modelling of emerging and theoretical implementations of transgenic SIT in Anopheles gambiae for the control of malaria. It reports on female suppression as it is affected by the SIT implementation, the number of released males, and competitiveness of released males.
The simulation experiments suggest that a late-acting bisex lethal gene is the most efficient of the four implementations we simulated. They demonstrate 1) the relative impact of release size on a campaign's effectiveness 2) late-acting genes are preferred because of their ability to exploit density dependent larval mortality 3) late-acting bisex lethal genes achieve elimination before their female-killing counterparts.
Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. They have the ability to move and replicate within a genome, often influencing genome evolution and gene ...expression. The identification of TEs is an important part of every genome project. The number of sequenced genomes is rapidly rising, and the need to identify TEs within them is also growing. The ability to do this automatically and effectively in a manner similar to the methods used for genes is of increasing importance. There exist many difficulties in identifying TEs, including their tendency to degrade over time and that many do not adhere to a conserved structure. In this work, we describe a homology-based approach for the automatic identification of high-quality consensus TEs, aimed for use in the analysis of newly sequenced genomes.
We describe a homology-based approach for the automatic identification of TEs in genomes. Our modular approach is dependent on a thorough and high-quality library of representative TEs. The implementation of the approach, named TESeeker, is BLAST-based, but also makes use of the CAP3 assembly program and the ClustalW2 multiple sequence alignment tool, as well as numerous BioPerl scripts. We apply our approach to newly sequenced genomes and successfully identify consensus TEs that are up to 99% identical to manually annotated TEs.
While TEs are known to be a major force in the evolution of genomes, the automatic identification of TEs in genomes is far from mature. In particular, there is a lack of automated homology-based approaches that produce high-quality TEs. Our approach is able to generate high-quality consensus TE sequences automatically, requiring the user to only provide a few basic parameters. This approach is intentionally modular, allowing researchers to use components separately or iteratively. Our approach is most effective for TEs with intact reading frames. The implementation, TESeeker, is available for download as a virtual appliance, while the library of representative TEs is available as a separate download.
Agent-based models (ABMs) have been used to model the behaviour of individual mosquitoes and other aspects of malaria. In this paper, a conceptual entomological model of the population dynamics of ...Anopheles gambiae and the agent-based implementations derived from it are described. Hypothetical vector control interventions (HVCIs) are implemented to target specific activities in the mosquito life cycle, and their impacts are evaluated.
The core model is described in terms of the complete An. gambiae mosquito life cycle. Primary features include the development and mortality rates in different aquatic and adult stages, the aquatic habitats and oviposition. The density- and age-dependent larval and adult mortality rates (vector senescence) allow the model to capture the age-dependent aspects of the mosquito biology. Details of hypothetical interventions are also described.
Results show that with varying coverage and temperature ranges, the hypothetical interventions targeting the gonotrophic cycle stages produce higher impacts than the rest in reducing the potentially infectious female (PIF) mosquito populations, due to their multi-hour mortality impacts and their applicability at multiple gonotrophic cycles. Thus, these stages may be the most effective points of target for newly developed and novel interventions. A combined HVCI with low coverage can produce additive synergistic impacts and can be more effective than isolated HVCIs with comparatively higher coverages. It is emphasized that although the model described in this paper is designed specifically around the mosquito An. gambiae, it could effectively apply to many other major malaria vectors in the world (including the three most efficient nominal anopheline species An. gambiae, Anopheles coluzzii and Anopheles arabiensis) by incorporating a variety of factors (seasonality cycles, rainfall, humidity, etc.). Thus, the model can essentially be treated as a generic Anopheles model, offering an excellent framework for such extensions. The utility of the core model has also been demonstrated by several other applications, each of which investigates well-defined biological research questions across a variety of dimensions (including spatial models, insecticide resistance, and sterile insect techniques).
The emergence of Accountable Care Organizations (ACOs) in the landscape of the U.S. healthcare system marks a paradigm shift in healthcare operations. The potential impact of ACOs has been a topic of ...intense debate. Traditional analytical approaches do not lend themselves to examining the complex phenomenon of the emergence and growth of ACOs in the healthcare network. We adopt a complex adaptive system lens to examine the growth of ACOs among physician groups and explore factors that influence this growth. We also discuss the impact of ACOs on the profit of physician groups. An agent-based model was built to simulate physician groups' ACO entrance and exit based on a set of simple rules and their complex interactions with other agents. Based on the simulation results, we derive patterns of ACO expansion and contraction, following four stages of wait-and-see, rollercoaster, fast growth, and stabilizing. Findings suggest that the growth of ACOs is sensitive to the initial state of ACO membership. When the initial size of ACO membership increases, it helps to eliminate the rollercoaster stage. In addition, the growth of the ACO varies depending on the cost–quality tradeoff. When both cost and quality objectives can be met simultaneously, the growth of ACO membership follows wait-and-see and fast growth stages followed by a different stage that we term sticky state. The impact of ACOs on physician groups’ cumulative profit varies by the service quality level of the physician group. Physician groups affiliated with insurance companies charging the lowest or the highest level of health insurance premiums are worse off with the ACO option. However, the ACO benefits physician groups affiliated with an insurance company charging a moderate level of premiums.
A landscape epidemiology modeling framework is presented which integrates the simulation outputs from an established spatial agent-based model (ABM) of malaria with a geographic information system ...(GIS). For a study area in Kenya, five landscape scenarios are constructed with varying coverage levels of two mosquito-control interventions. For each scenario, maps are presented to show the average distributions of three output indices obtained from the results of 750 simulation runs. Hot spot analysis is performed to detect statistically significant hot spots and cold spots. Additional spatial analysis is conducted using ordinary kriging with circular semivariograms for all scenarios. The integration of epidemiological simulation-based results with spatial analyses techniques within a single modeling framework can be a valuable tool for conducting a variety of disease control activities such as exploring new biological insights, monitoring epidemiological landscape changes, and guiding resource allocation for further investigation.
Agent-based models (ABMs) have been used to estimate the effects of malaria-control interventions. Early studies have shown the efficacy of larval source management (LSM) and insecticide-treated nets ...(ITNs) as vector-control interventions, applied both in isolation and in combination. However, the robustness of results can be affected by several important modelling assumptions, including the type of boundary used for landscapes, and the number of replicated simulation runs reported in results. Selection of the ITN coverage definition may also affect the predictive findings. Hence, by replication, independent verification of prior findings of published models bears special importance.
A spatially-explicit entomological ABM of Anopheles gambiae is used to simulate the resource-seeking process of mosquitoes in grid-based landscapes. To explore LSM and replicate results of an earlier LSM study, the original landscapes and scenarios are replicated by using a landscape generator tool, and 1,800 replicated simulations are run using absorbing and non-absorbing boundaries. To explore ITNs and evaluate the relative impacts of the different ITN coverage schemes, the settings of an earlier ITN study are replicated, the coverage schemes are defined and simulated, and 9,000 replicated simulations for three ITN parameters (coverage, repellence and mortality) are run. To evaluate LSM and ITNs in combination, landscapes with varying densities of houses and human populations are generated, and 12,000 simulations are run.
General agreement with an earlier LSM study is observed when an absorbing boundary is used. However, using a non-absorbing boundary produces significantly different results, which may be attributed to the unrealistic killing effect of an absorbing boundary. Abundance cannot be completely suppressed by removing aquatic habitats within 300 m of houses. Also, with density-dependent oviposition, removal of insufficient number of aquatic habitats may prove counter-productive. The importance of performing large number of simulation runs is also demonstrated. For ITNs, the choice of coverage scheme has important implications, and too high repellence yields detrimental effects. When LSM and ITNs are applied in combination, ITNs' mortality can play more important roles with higher densities of houses. With partial mortality, increasing ITN coverage is more effective than increasing LSM coverage, and integrating both interventions yields more synergy as the densities of houses increase.
Using a non-absorbing boundary and reporting average results from sufficiently large number of simulation runs are strongly recommended for malaria ABMs. Several guidelines (code and data sharing, relevant documentation, and standardized models) for future modellers are also recommended.
Small Unmanned Aircraft Systems (sUAS) are an emerging application area for many industries including surveillance, agriculture monitoring, and vector-borne disease control. With drastically lower ...costs and increasing performance and autonomy, future application evolution will more than likely include the use of sUAS swarms. Several largely successful experiments in recent years, using off the shelf sUAS, have been conducted to address the long standing challenge of controlling and monitoring vector-borne diseases. In this paper we build on lessons learned from these prior efforts, and discuss ways in which swarms of sUAS could be deployed to place and monitor Autocidal Gravid Ovitraps for reducing the mosquito population.
In recent years, Unmanned Aerial Vehicles (UAV), have been increasingly utilized by both military and civilian organizations because they are less expensive, provide greater flexibilities and remove ...the need for on-board pilot support. Largely due to their utility and increased capabilities, in the near future, swarms of UAVs will replace single UAV use. Efficient control of swarms opens a set of new challenges, such as automatic UAV coordination, efficient swarm monitoring and dynamic mission planning. In this paper, we investigate the problem of dynamic mission planning for a UAV swarm. A centralized-distributed hybrid control framework is proposed for mission assignment and scheduling. The Dynamic Data Driven Application System (DDDAS) principles are applied to the framework so that it can adapt to the changing nature of the environment and the missions. A prototype simulation program is implemented as a proof-of- concept of the framework. Experimentation with the framework suggests the effectiveness of swarm control for several mission planning mechanisms.
BACKGROUND: Landscape complexity can mitigate or facilitate host dispersal, influencing patterns of pathogen transmission. Spatial transmission of pathogens through landscapes, therefore, presents an ...important but not fully elucidated aspect of transmission dynamics. Using an agent-based model (LiNK) that incorporates GIS data, we examined the effects of landscape information on the spatial patterns of host movement and pathogen transmission in a system of long-tailed macaques and their gut parasites. We first examined the role of the landscape to identify any individual or additive effects on host movement. We then compared modeled dispersal distance to patterns of actual macaque gene flow to both confirm our model’s predictions and to understand the role of individual land uses on dispersal. Finally, we compared the rate and the spread of two gastrointestinal parasites, Entamoeba histolytica and E. dispar, to understand how landscape complexity influences spatial patterns of pathogen transmission. RESULTS: LiNK captured emergent properties of the landscape, finding that interaction effects between landscape layers could mitigate the rate of infection in a non-additive way. We also found that the inclusion of landscape information facilitated an accurate prediction of macaque dispersal patterns across a complex landscape, as confirmed by Mantel tests comparing genetic and simulated dispersed distances. Finally, we demonstrated that landscape heterogeneity proved a significant barrier for a highly virulent pathogen, limiting the dispersal ability of hosts and thus its own transmission into distant populations. CONCLUSIONS: Landscape complexity plays a significant role in determining the path of host dispersal and patterns of pathogen transmission. Incorporating landscape heterogeneity and host behavior into disease management decisions can be important in targeting response efforts, identifying cryptic transmission opportunities, and reducing or understanding potential for unintended ecological and evolutionary consequences. The inclusion of these data into models of pathogen transmission patterns improves our understanding of these dynamics, ultimately proving beneficial for sound public health policy.
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