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Stochastic Modeling of Temporal Variability of HIV-1 Population [chapter]

Ilia Kiryukhin, Kirill Saskov, Alexander Boukhanovsky, Wilco Keulen, Charles Boucher, Peter M. A. Sloot
2003 Lecture Notes in Computer Science  
A multivariate stochastic model for describing the dynamics of complex non-numerical ensembles, such as observed in Human Immunodeficiency Virus (HIV) genome, is developed.  ...  The results indicate that we may use this model in short-term forecast of HIV evolution, for evaluation of HIV drug resistance and for testing and validation of diagnostic expert rules.  ...  Fig. 1 . 1 Fig. 1. General scheme for stochastic modeling of HIV population variability Fig. 2 . 2 Fig. 2.  ... 
doi:10.1007/3-540-44860-8_13 fatcat:tbmca4tx3rfw7kcvdcg3pmexvu

The effect of intrinsic stochasticity on transmitted HIV drug resistance patterns

Alison J. Marks, Deenan Pillay, Angela R. McLean
2010 Journal of Theoretical Biology  
MODELLING INTRINSIC STOCHASTICITY. Table 1 . 1 A Comparison of Two Types of Randomness or Stochasticity and Their Simulation.  ...  Our results indicate that stochastic temporal variability in transmitted drug- The role of stochasticity in influencing the transmission dynamics of drugresistant viral strains in infected populations  ... 
doi:10.1016/j.jtbi.2009.09.017 pmid:19766126 fatcat:diupky4u6rhqxdrzylmwu545dm

Numerical investigations of stochastic HIV/AIDS infection model

Zain Ul Abadin Zafar, Nigar Ali, Samina Younas, Sayed F. Abdelwahab, Kottakkaran Sooppy Nisar
2021 Alexandria Engineering Journal  
In this paper, a stochastic HIV/AIDS epidemic model has been studied numerically.  ...  If R 0 < 1 then disease is under control while the disease is out of control if R 0 > 1.  ...  [4] studied an HIV model by incorporating control variables denoting treatments and found the stability for their proposed model.  ... 
doi:10.1016/j.aej.2021.04.027 fatcat:ukm5rgyvcbgmfdn7eubvoui3tm

Interventions in Networks [article]

Steven K. Thompson
2015 arXiv   pre-print
These include a variety of link-tracing sampling designs in networks, a number of types of interventions, and a temporal spatial network model in which the intervention strategies are evaluated.  ...  Over time the effect of the intervention can have an effect on the population that goes beyond the sample units to which it is directly applied. This paper describes the methods used for this study.  ...  Acknowledgments This work is supported by the Natural Science and Engineering Research Council of Canada.  ... 
arXiv:1511.00323v1 fatcat:cm32bgvpu5fchhm7uwyjoslfj4

Deep Molecular Characterization of HIV-1 Dynamics under Suppressive HAART

Maria J. Buzón, Francisco M. Codoñer, Simon D. W. Frost, Christian Pou, Maria C. Puertas, Marta Massanella, Judith Dalmau, Josep M. Llibre, Mario Stevenson, Julià Blanco, Bonaventura Clotet, Roger Paredes (+2 others)
2011 PLoS Pathogens  
In order to design strategies for eradication of HIV-1 from infected individuals, detailed insight into the HIV-1 reservoirs that persist in patients on suppressive antiretroviral therapy (ART) is required  ...  Collectively, this suggests the presence of a chronic viral reservoir in which there is stochastic release of infectious virus and in which there are limited rounds of de novo infection.  ...  0.001 Table 2 . 2 Temporal population structure: AMOVA test for comparison between longitudinal episomal HIV-1 DNA.  ... 
doi:10.1371/journal.ppat.1002314 pmid:22046128 pmcid:PMC3203183 fatcat:xmqnajjavnewtf5nwwlwwcbmkm

Evidence synthesis for stochastic epidemic models [article]

Paul J Birrell, Daniela De Angelis, Anne M Presanis
2017 arXiv   pre-print
This review summarises the different types of stochastic epidemic models that use evidence synthesis and highlights current challenges.  ...  Models have become increasingly realistic and more complex, requiring the use of multiple data sources to estimate all quantities of interest.  ...  In common with the HIV models, the prevalence of HCV in hard-to-reach populations, such as people who inject drugs (PWID), requires simultaneous estimation of the proportion of the population who are PWID  ... 
arXiv:1706.02624v1 fatcat:l24ltecl2fbrzd6augwnjtcazm

A Stochastic Model for Early HIV-1 Population Dynamics

Henry C. Tuckwell, Emmanuelle Le Corfec
1998 Journal of Theoretical Biology  
A simple stochastic mathematical model is developed and investigated for early human immunodeficiency virus type-1 (HIV-1) population dynamics.  ...  In addition to modeling the intrinsic variability in HIV-1 growth, we have explored the effects of perturbations in the parameter values in order to assess the additional stochastic effects of between-patient  ...  A simple stochastic mathematical model is developed and investigated for early human immunodeficiency virus type-1 (HIV-1) population dynamics.  ... 
doi:10.1006/jtbi.1998.0806 pmid:9837702 fatcat:oxffuhqbxfhmlg2obfphoaf7o4

Organelles – understanding noise and heterogeneity in cell biology at an intermediate scale

Amy Y. Chang, Wallace F. Marshall
2017 Journal of Cell Science  
Many studies over the years have shown that non-genetic mechanisms for producing cell-to-cell variation can lead to highly variable behaviors across genetically identical populations of cells.  ...  studying organelle heterogeneity to develop a more comprehensive understanding of phenotypic heterogeneity.  ...  Acknowledgements We would like to acknowledge past and present members of the Marshall lab for guiding our thoughts about cellular heterogeneity.  ... 
doi:10.1242/jcs.181024 pmid:28183729 pmcid:PMC5358330 fatcat:qm3pdsi4gjb5jfldzyqibqguuq

Evidence Synthesis for Stochastic Epidemic Models

Paul J. Birrell, Daniela De Angelis, Anne M. Presanis
2018 Statistical Science  
This review summarises the different types of stochastic epidemic models that use evidence synthesis and highlights current challenges.  ...  Models have become increasingly realistic and more complex, requiring the use of multiple data sources to estimate all quantities of interest.  ...  FIG. 1 . 1 Directed acyclic graph (DAG) of a model with basic parameters, functional parameters and data. then L(θ; y) = N n=1 L n ψ n (θ ); y n , FIG. 2 . 2 (a) DAG of a HIV prevalence model with basic  ... 
doi:10.1214/17-sts631 pmid:31975746 pmcid:PMC6978147 fatcat:42tb5dgzgjbnxhz27ubhwfs7t4

A Grid-Based Hiv Expert System

Peter M. A. Sloot, Alexander V. Boukhanovsky, Wilco Keulen, Alfredo Tirado-Ramos, Charles A. Boucher
2005 Journal of clinical monitoring and computing  
The Dutch Virtual Laboratory on escience project supported parts of the research presented here: http://www.VL-e.nl.  ...  The authors gratefully acknowledge Fan Chen and Ferdinand Alimadhi for assistance in implementing the CA models and the roaming PDA access.  ...  In chapter 2 we give an overview of the two computational techniques we study to understand the temporal variability of HIV populations through stochastical modeling, the evolution of HIV infection and  ... 
doi:10.1007/s10877-005-0673-2 pmid:16328942 fatcat:rwr6gw3u7ngu5adbxsfnvremua

A grid-based HIV expert system

P.M.A. Sloot, A.V. Boukhanovsky, W. Keulen, C.A. Boucher
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
The Dutch Virtual Laboratory on escience project supported parts of the research presented here: http://www.VL-e.nl.  ...  The authors gratefully acknowledge Fan Chen and Ferdinand Alimadhi for assistance in implementing the CA models and the roaming PDA access.  ...  In chapter 2 we give an overview of the two computational techniques we study to understand the temporal variability of HIV populations through stochastical modeling, the evolution of HIV infection and  ... 
doi:10.1109/ccgrid.2005.1558592 dblp:conf/ccgrid/SlootBKB05 fatcat:2feckkzcpzgmlpqi24tmpgwq4i

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases

Denise Kühnert, Chieh-Hsi Wu, Alexei J. Drummond
2011 Infection, Genetics and Evolution  
processes and population dynamics of the infectious agent.  ...  Epidemic modeling of infectious diseases has a long history in both theoretical and empirical research.  ...  The first is environmental stochasticity and is often modeled by admitting temporal variation in the parameters of the population model.  ... 
doi:10.1016/j.meegid.2011.08.005 pmid:21906695 pmcid:PMC7106223 fatcat:yisqfpn3qzcl3hc4hy56eyfttq

Dynamic spatial and network sampling [article]

Steven K. Thompson
2013 arXiv   pre-print
For this purpose a dynamic spatial network model is developed based on simple stochastic processes.  ...  This paper considers some designs for sampling and interventions in dynamic networks and spatial temporal settings.  ...  ] (Supplement 1) modeled the individual variability of adherence over time for an individual as well as the variability between individuals.  ... 
arXiv:1306.0817v1 fatcat:ro6ox6zoeva3ljwrvhdyuktdd4

Eight challenges in phylodynamic inference

Simon D.W. Frost, Oliver G. Pybus, Julia R. Gog, Cecile Viboud, Sebastian Bonhoeffer, Trevor Bedford
2015 Epidemics  
population dynamics, host population structure, and different patterns at the within-host and between-host scales.  ...  Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place.  ...  sets (for HIV-1 and influenza A virus) consist of many thousands of whole genomes.  ... 
doi:10.1016/j.epidem.2014.09.001 pmid:25843391 pmcid:PMC4383806 fatcat:gtrobnfsgrh6pak5r2lrv2qhla

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

François Blanquart, Chris Wymant, Marion Cornelissen, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay (+19 others)
2017 PLoS Biology  
HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals  ...  To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable  ...  Acknowledgments We thank people living with HIV of all cohorts across Europe for contributing samples to respective biobanks, allowing this work, and physicians, study nurses, and the datacenters for the  ... 
doi:10.1371/journal.pbio.2001855 pmid:28604782 pmcid:PMC5467800 fatcat:suo5h5aopfbv7ekpksrwb7q5s4
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