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.
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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.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
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.
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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).
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We describe a prototype emergency response system. This dynamic data driven application system (DDDAS) uses wireless call data, including call volume, who calls whom, call duration, services in use, ...and cell phone location information. Since all cell phones (that are powered on) maintain contact with one or more local cell towers, location data about each phone is updated periodically and available throughout the cellular phone network. This permits the cell phones of a city to serve as an ad hoc mobile sensor net, measuring the movement and calling patterns of the population. Social network theory and statistical analysis on normal call activity and call locations establish a baseline. A detection and alert system monitors streaming summary cell phone call data. Abnormal call patterns or population movements trigger a simulation and prediction system. Hypotheses about the anomaly are generated by a rule-based system, each initiating an agent-based simulation. Automated dynamic validation of the simulations against incoming streaming data is used to test each hypothesis. A validated simulation is used to predict the evolution of the anomaly and made available to an emergency response decision support system.
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FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Workflow management, which is concerned with the coordination and control of business processes using information technology, has grown from its origins in document routing to include the automation ...of process logic in business process reengineering. Workflow also has a strong temporal aspect; activity sequencing, deadlines, routing conditions, and scheduling all involve the element of time. Temporal expert systems, which use knowledge-based constructs to represent and reason about time, can be used to enhance the capabilities of workflow software. This paper presents a temporal expert system workflow component for tracking engineering design changes. The authors use Allen's theory of temporal intervals in their model to enhance the decision-making, timing, and routing activities in a workflow application. They test the model using information from a "real-world" engineering design situation and suggest further research opportunities.
We have measured the parity-violating electroweak asymmetry in the elastic scattering of polarized electrons from the proton. The kinematic point (theta_lab = 12.3 degrees and Q^2=0.48 (GeV/c)^2) is ...chosen to provide sensitivity, at a level that is of theoretical interest, to the strange electric form factor G_E^s. The result, A=-14.5 +- 2.2 ppm, is consistent with the electroweak Standard Model and no additional contributions from strange quarks. In particular, the measurement implies G_E^s + 0.39G_M^s = 0.023 +- 0.034 (stat) +- 0.022 (syst) +- 0.026 (delta G_E^n), where the last uncertainty arises from the estimated uncertainty in the neutron electric form factor.
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