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Optimization of HAART with genetic algorithms and agent-based models of HIV infection

F. Castiglione, F. Pappalardo, M. Bernaschi, S. Motta
2007 Bioinformatics  
In the present article we describe an application of genetic algorithms (GA) aimed at finding the optimal schedule for a HAART simulated with an agent-based model (ABM) of the immune system that reproduces  ...  To validate the efficacy of the therapy that the genetic algorithm indicates as optimal, we ran simulations of opportunistic diseases and found that the selected therapy shows the best survival curve among  ...  We thank the CINECA Super Computing Center for providing us with required computing time. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btm408 pmid:17942443 fatcat:z2csn3ciw5fkvgoxyjp4yiwqyy

Health, Risky Behaviour and the Value of Medical Innovation for Infectious Disease

Tat Y. Chan, Barton H. Hamilton, Nicholas W. Papageorge
2015 The Review of Economic Studies  
The model captures how, in lowering both the expected cost and likelihood of HIV infection, HAART reduced the implicit price of risky sex.  ...  Using the estimated model, we conduct counterfactual simulations to compute the value of HAART from the perspective of uninfected agents.  ...  Then, we integrate over the joint probability of X and h to obtain the probability of HAART usage conditional on health state h. 37 The model does not require infection with HIV for agents to die.  ... 
doi:10.1093/restud/rdv053 fatcat:v47s4hm46zagdctnwqd6zfymgi

Modeling the Genetic Control of HIV-1 Dynamics After Highly Active Antiretroviral Therapy

Chang-Xing Ma, Yao Li, Rongling Wu
2008 Current Genomics  
This detected major genetic determinant also affects several clinically important parameters, such as half-lives of infected cells and HIV eradication times.  ...  This model was employed to an HIV/AIDS trial, which led to the identification of a major genetic determinant that triggers an effect on HIV dynamics.  ...  The preparation of this manuscript is partially supported by NSF grant (No. 0540745).  ... 
doi:10.2174/138920208784340777 pmid:19440518 pmcid:PMC2679648 fatcat:ivupyyqgt5dzden6xzrd6zofva

Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization

Mattia C. F. Prosperi, Roberto D'Autilia, Francesca Incardona, Andrea De Luca, Maurizio Zazzi, Giovanni Ulivi
2008 Computer applications in the biosciences : CABIOS  
Motivation: Several mathematical models have been investigated for the description of viral dynamics in the human body: HIV-1 infection is a particular and interesting scenario, because the virus attacks  ...  For a set of widely used combination therapies, results were consistent with findings reported in literature and with estimates coming from analysis on a large retrospective data base (EuResist).  ...  While more recently in Castiglione et al. (2007) the authors presented a model for optimizing combination therapies based on genetic algorithms.  ... 
doi:10.1093/bioinformatics/btn568 pmid:18977781 fatcat:mozqofkkynd2jj3racxb5emsnu

State of the Science Conference

Steven K. Grinspoon, Carl Grunfeld, Donald P. Kotler, Judith S. Currier, Jens D. Lundgren, Michael P. Dubé, Steven E. Lipshultz, Priscilla Y. Hsue, Kathleen Squires, Morris Schambelan, Peter W.F. Wilson, Kevin E. Yarasheski (+3 others)
2008 Circulation  
Development of optimized screening, prediction, and treatment algorithms for cardiovascular disease in HIV-infected patients is of utmost importance.  ...  Hadigan, MD, MPH) As with non-HIV-infected patients, an important principle for HIV-infected patients is that risk-reducing interventions should be based on the level of CHD risk and whether the presence  ...  all members of the writing group are required to complete and submit.  ... 
doi:10.1161/circulationaha.107.189622 pmid:18566320 pmcid:PMC3642216 fatcat:5bgjn6mazzcfdm2sju7tkkjhuy

Broad-Spectrum and Personalized Guide RNAs for CRISPR/Cas9 HIV-1 Therapeutics

Will Dampier, Neil T. Sullivan, Joshua Chang Mell, Vanessa Pirrone, Garth D. Ehrlich, Cheng-Han Chung, Alexander G. Allen, Mathew DeSimone, Wen Zhong, Katherine Kercher, Shendra Passic, Jean W. Williams (+5 others)
2018 AIDS Research and Human Retroviruses  
In summary, these studies used an algorithmic design strategy to identify potential BS gRNAs to target a spectrum of HIV-1 long teriminal repeat (LTR) quasispecies for use with a small HIV-1-infected population  ...  for HIV-infected patients.  ...  the 48 samples to optimize cleavage efficiency in the face of LTR genetic diversity.  ... 
doi:10.1089/aid.2017.0274 pmid:29968495 pmcid:PMC6238604 fatcat:otftuorwhfczfclzsm6dghgozq

Current status and challenges of antiretroviral research and therapy

José A. Esté, Tomas Cihlar
2010 Antiviral Research  
Twenty-five years after the discovery of the therapeutic activity of azidothymidine (AZT), the first antiretroviral drug used in the clinic, infection with the human immunodeficiency virus (HIV) has become  ...  by leading experts of the efforts being made to meet the challenges of effective control of HIV infection.  ...  of antiretroviral drug discovery and development.  ... 
doi:10.1016/j.antiviral.2009.10.007 pmid:20018390 fatcat:weqwxmxtqzfoxf7i7srp4sdvle

Computational Study to Determine When to Initiate and Alternate Therapy in HIV Infection

Matthias Haering, Andreas Hördt, Michael Meyer-Hermann, Esteban A. Hernandez-Vargas
2014 BioMed Research International  
We contribute to this discussion with predictions derived from a mathematical model of HIV dynamics.  ...  Current HIV treatment guidelines seem poorly supported as practitioners have not achieved a consensus on the optimal time to initiate and to switch antiretroviral treatments.  ...  Acknowledgments This work was supported by BMBF-GerontoSys initiative (GerontoShield), portfolio HGF (metabolic dysfunction), and BMBF e-Med project SYSIMIT. BioMed Research International  ... 
doi:10.1155/2014/472869 pmid:24900966 pmcid:PMC4037596 fatcat:4mzqantoivhxdk4sohspdxfddq

HIV Reservoirs and Immune Surveillance Evasion Cause the Failure of Structured Treatment Interruptions: A Computational Study

Emiliano Mancini, Filippo Castiglione, Massimo Bernaschi, Andrea de Luca, Peter M. A. Sloot, Vladimir Brusic
2012 PLoS ONE  
We validate our model with data from a clinical trial and show that it is possible to optimize the schedule of interruptions to perform as well as the continuous treatment in the absence of drug resistance  ...  Our computational model of the HIV infection dynamics in lymphoid tissue inside lymph nodes, demonstrates that HIV reservoirs and evasion from immune surveillance themselves are sufficient to cause the  ...  In this work we use a well-established and validated agent-based model (ABM) of HIV infection [32] [33] [34] [35] [36] . See File S1 for a brief description of the model used in this work.  ... 
doi:10.1371/journal.pone.0036108 pmid:22558348 pmcid:PMC3338637 fatcat:xd6otkc3hrfgfkae5usl4h45xy

The Global Status of Resistance to Antiretroviral Drugs

Stefano Vella, Lucia Palmisano
2005 Clinical Infectious Diseases  
This latter population represents potential transmitters of resistant viruses to newly infected persons.  ...  Since 1989, the emergence of resistant human immunodeficiency virus mutants has been documented for any new antiretroviral agent introduced in the clinical setting; it is a major cause of failure of antiretroviral  ...  Acknowledgments Potential conflicts of interest. S.V. and L.P.: no conflicts.  ... 
doi:10.1086/430784 pmid:16032559 fatcat:mvpicnqq5vhidmp3kuj34hv75m

Human Immunodeficiency Virus-Associated Dementia: An Evolving Disease

Justin C McArthur, Norman Haughey, Suzanne Gartner, Kathy Conant, Carlos Pardo, Avi Nath, Ned Sacktor
2003 Journal of Neurovirology  
This article reviews the changing epidemiology of HIV-associated dementia, current concepts of the different patterns of dementia under the influence of highly active antiretroviral therapy, and reviews  ...  Journal of NeuroVirology (2003) 9, 205-221.  ...  7 Model of different patterns of HIV dementia in era of HAART.  ... 
doi:10.1080/13550280390194109 pmid:12707851 fatcat:ilt7uyypovexrpbbotbbjsphmq

Optimal and MPC Switching Strategies for Mitigating Viral Mutation and Escape

Esteban A. Hernandez-Vargas, Richard H. Middleton, Patrizio Colaneri
2011 IFAC Proceedings Volumes  
This paper is motivated by the study of mutation in HIV infection.  ...  This technique is compared with an optimal control approach and with the strategy commonly used in clinical practice.  ...  This is based on the guidelines for the use of antiretrovirals agents in HIV-1 infected adults presented by the Department of Health [2009] .  ... 
doi:10.3182/20110828-6-it-1002.01137 fatcat:2zhm34opofaabiezym7r26u6ce

Sub-optimal switching with dwell time constraints for control of viral mutation

Esteban A. Hernandez-Vargas, Patrizio Colaneri, Richard H. Middleton
2012 2012 IEEE 51st IEEE Conference on Decision and Control (CDC)  
In this paper we extend previous work on suboptimal control of a simplified model of HIV infection with mutations.  ...  Regulation of mutant viri is important in many disease including HIV infection.  ...  As a simple motivating example of HIV mutation, we consider a model with 4 genetic variants, that is n = 4, and 2 possible drug therapies, D = 2.  ... 
doi:10.1109/cdc.2012.6426559 dblp:conf/cdc/Hernandez-VargasCM12 fatcat:mxiuatj65rd4bmsymmzgfqofki

Why medical innovation is valuable: Health, human capital, and the labor market

Nicholas W. Papageorge
2016 Quantitative Economics  
This allows me to model each HIV drug along two dimensions of quality-effectiveness and side effects.  ...  I use the framework to examine the treatment and employment decisions of human immunodeficiency virus (HIV) positive men before and after a medical breakthrough known as highly active anti-retroviral treatment  ...  Absent treatment, an individual newly infected with HIV lives an average of 11 years.  ... 
doi:10.3982/qe459 fatcat:csh73sgcrjfcnkbfjwou6tluby

Novel peptide-based HIV-1 immunotherapy

Maja A Sommerfelt, Jørgen Nyhus, Birger Sørensen
2004 Expert Opinion on Biological Therapy  
One problem with these animal models is the inability to establish a chronic HIV-1 infection.  ...  Conclusion Peptide-based HIV-1 immunotherapy in combination with HAART represents a new and promising approach to the long-term control of HIV infection that can minimise the long-term adverse effects  ... 
doi:10.1517/14712598.4.3.349 pmid:15006729 fatcat:a7tqejxqural7nv46ruql2a5ma
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