18,709 research outputs found
Combination interventions for Hepatitis C and Cirrhosis reduction among people who inject drugs: An agent-based, networked population simulation experiment
Hepatitis C virus (HCV) infection is endemic in people who inject drugs
(PWID), with prevalence estimates above 60 percent for PWID in the United
States. Previous modeling studies suggest that direct acting antiviral (DAA)
treatment can lower overall prevalence in this population, but treatment is
often delayed until the onset of advanced liver disease (fibrosis stage 3 or
later) due to cost. Lower cost interventions featuring syringe access (SA) and
medically assisted treatment (MAT) for addiction are known to be less costly,
but have shown mixed results in lowering HCV rates below current levels. Little
is known about the potential synergistic effects of combining DAA and MAT
treatment, and large-scale tests of combined interventions are rare. While
simulation experiments can reveal likely long-term effects, most prior
simulations have been performed on closed populations of model agents--a
scenario quite different from the open, mobile populations known to most health
agencies. This paper uses data from the Centers for Disease Control's National
HIV Behavioral Surveillance project, IDU round 3, collected in New York City in
2012 by the New York City Department of Health and Mental Hygiene to
parameterize simulations of open populations. Our results show that, in an open
population, SA/MAT by itself has only small effects on HCV prevalence, while
DAA treatment by itself can significantly lower both HCV and HCV-related
advanced liver disease prevalence. More importantly, the simulation experiments
suggest that cost effective synergistic combinations of the two strategies can
dramatically reduce HCV incidence. We conclude that adopting SA/MAT
implementations alongside DAA interventions can play a critical role in
reducing the long-term consequences of ongoing infection
An Agent-Based Spatially Explicit Epidemiological Model in MASON
This paper outlines the design and implementation of an agent-based epidemiological simulation system. The system was implemented in the MASON toolkit, a set of Java-based agent-simulation libraries. This epidemiological simulation system is robust and extensible for multiple applications, including classroom demonstrations of many types of epidemics and detailed numerical experimentation on a particular disease. The application has been made available as an applet on the MASON web site, and as source code on the author\'s web site.Epidemiology, Social Networks, Agent-Based Simulation, MASON Toolkit
Equation-Free Multiscale Computational Analysis of Individual-Based Epidemic Dynamics on Networks
The surveillance, analysis and ultimately the efficient long-term prediction
and control of epidemic dynamics appear to be one of the major challenges
nowadays. Detailed atomistic mathematical models play an important role towards
this aim. In this work it is shown how one can exploit the Equation Free
approach and optimization methods such as Simulated Annealing to bridge
detailed individual-based epidemic simulation with coarse-grained,
systems-level, analysis. The methodology provides a systematic approach for
analyzing the parametric behavior of complex/ multi-scale epidemic simulators
much more efficiently than simply simulating forward in time. It is shown how
steady state and (if required) time-dependent computations, stability
computations, as well as continuation and numerical bifurcation analysis can be
performed in a straightforward manner. The approach is illustrated through a
simple individual-based epidemic model deploying on a random regular connected
graph. Using the individual-based microscopic simulator as a black box
coarse-grained timestepper and with the aid of Simulated Annealing I compute
the coarse-grained equilibrium bifurcation diagram and analyze the stability of
the stationary states sidestepping the necessity of obtaining explicit closures
at the macroscopic level under a pairwise representation perspective
Some Remarks about the Complexity of Epidemics Management
Recent outbreaks of Ebola, H1N1 and other infectious diseases have shown that
the assumptions underlying the established theory of epidemics management are
too idealistic. For an improvement of procedures and organizations involved in
fighting epidemics, extended models of epidemics management are required. The
necessary extensions consist in a representation of the management loop and the
potential frictions influencing the loop. The effects of the non-deterministic
frictions can be taken into account by including the measures of robustness and
risk in the assessment of management options. Thus, besides of the increased
structural complexity resulting from the model extensions, the computational
complexity of the task of epidemics management - interpreted as an optimization
problem - is increased as well. This is a serious obstacle for analyzing the
model and may require an additional pre-processing enabling a simplification of
the analysis process. The paper closes with an outlook discussing some
forthcoming problems
Innovative in silico approaches to address avian flu using grid technology
The recent years have seen the emergence of diseases which have spread very
quickly all around the world either through human travels like SARS or animal
migration like avian flu. Among the biggest challenges raised by infectious
emerging diseases, one is related to the constant mutation of the viruses which
turns them into continuously moving targets for drug and vaccine discovery.
Another challenge is related to the early detection and surveillance of the
diseases as new cases can appear just anywhere due to the globalization of
exchanges and the circulation of people and animals around the earth, as
recently demonstrated by the avian flu epidemics. For 3 years now, a
collaboration of teams in Europe and Asia has been exploring some innovative in
silico approaches to better tackle avian flu taking advantage of the very large
computing resources available on international grid infrastructures. Grids were
used to study the impact of mutations on the effectiveness of existing drugs
against H5N1 and to find potentially new leads active on mutated strains. Grids
allow also the integration of distributed data in a completely secured way. The
paper presents how we are currently exploring how to integrate the existing
data sources towards a global surveillance network for molecular epidemiology.Comment: 7 pages, submitted to Infectious Disorders - Drug Target
Mobility traces and spreading of COVID-19
We use human mobility models, for which we are experts, and attach a virus infection dynamics to it, for which we are not experts but have taken it from the literature, including recent publications. This results in a virus spreading dynamics model. The results should be verified, but because of the current time pressure, we publish them in their current state. Recommendations for improvement are welcome. We come to the following conclusions:
1. Complete lockdown works. About 10 days after lockdown, the infection dynamics dies down. This assumes that lockdown is complete, which can be guaranteed in the simulation, but not in reality. Still, it gives strong support to the argument that it is never too late for complete lockdown.
2. As a rule of thumb, we would suggest complete lockdown no later than once 10% of hospital capacities available for COVID-19 are in use, and possibly much earlier. This is based on the following insights:
a. Even after lockdown, the infection dynamics continues at home, leading to another tripling of the cases before the dynamics is slowed.
b. There will be many critical cases coming from people who were infected before lockdown. Because of the exponential growth dynamics, their number will be large.
c. Researchers with more detailed disease progression models should improve upon these statements.
3. Our simulations say that complete removal of infections at child care, primary schools, workplaces and during leisure activities will not be enough to sufficiently slow down the infection dynamics. It would have been better, but still not sufficient, if initiated earlier.
4. Infections in public transport play an important role. In the simulations shown later, removing infections in the public transport system reduces the infection speed and the height of the peak by approximately 20%. Evidently, this depends on the infection parameters, which are not well known. – This does not point to reducing public transport capacities as a reaction to the reduced demand, but rather use it for lower densities of passengers and thus reduced infection rates.
5. In our simulations, removal of infections at child care, primary schools, workplaces, leisure activities, and in public transport may barely have been sufficient to control the infection dynamics if implemented early on. Now according to our simulations it is too late for this, and (even) harsher measures will have to be initiated until possibly a return to such a restrictive, but still somewhat functional regime will again be possible.
Evidently, all of these results have to be taken with care. They are based on preliminary infection parameters taken from the literature, used inside a model that has more transport/movement details than all others that we are aware of but still not enough to describe all aspects of reality, and suffer from having to write computer code under time pressure. Optimally, they should be confirmed independently. Short of that, given current knowledge we believe that they provide justification for “complete lockdown” at the latest when about 10% of available hospital capacities for COVID-19 are in use (and possibly earlier; we are no experts of hospital capabilities).
What was not investigated in detail in our simulations was contact tracing, i.e. tracking down the infection chains and moving all people along infection chains into quarantine. The case of Singapore has so far shown that this may be successful. Preliminary simulation of that tactic shows that it is difficult to implement for COVID-19, since the incubation time is rather long, people are contagious before they feel sick, or maybe never feel sufficiently sick at all. We will investigate in future work if and how contact tracing can be used together with a restrictive, but not totally locked down regime.
When opening up after lockdown, it would be important to know the true fraction of people who are already immune, since that would slow down the infection dynamics by itself. For Wuhan, the currently available numbers report that only about 0.1% of the population was infected, which would be very far away from “herd immunity”. However, there have been and still may be many unknown infections (Frankfurter Allgemeine Zeitung GmbH 2020)
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