scholarly journals SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces

2018 ◽  
Author(s):  
Jori Liesenborgs ◽  
Diana M Hendrickx ◽  
Elise Kuylen ◽  
David Niyukuri ◽  
Niel Hens ◽  
...  
Keyword(s):  
Open Source ◽  
Hiv Infections ◽  
Hiv Treatment ◽  
Model Parameters ◽  
Eligibility Criteria ◽  
Hiv Epidemiology ◽  
Treatment And Prevention ◽  
Individual Based Models ◽  
Prevention Programmes ◽  
The Impact

ABSTRACTSimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework.

scholarly journals SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jori Liesenborgs ◽  
Diana M. Hendrickx ◽  
Elise Kuylen ◽  
David Niyukuri ◽  
Niel Hens ◽  
...  
Keyword(s):  
Open Source ◽  
Hiv Infections ◽  
Hiv Treatment ◽  
Model Parameters ◽  
Eligibility Criteria ◽  
Hiv Epidemiology ◽  
Treatment And Prevention ◽  
Individual Based Models ◽  
Prevention Programmes ◽  
The Impact

AbstractSimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework.

Estimating the impact of the US President's Emergency Plan for AIDS Relief on HIV treatment and prevention programmes in Africa

2015 ◽  
Vol 91 (8) ◽  
pp. 615-620 ◽  
Author(s):  
Laura M Heaton ◽  
Paul D Bouey ◽  
Joe Fu ◽  
John Stover ◽  
Timothy B Fowler ◽  
...  
Keyword(s):  
Hiv Treatment ◽  
Emergency Plan ◽  
Treatment And Prevention ◽  
The Us ◽  
Prevention Programmes ◽  
The Impact

scholarly journals SWTICH DE ESQUEMAS ANTIRRETROVIRAIS DURANTE A PANDEMIA DE COVID-19 EM UM CENTRO DE REFERÊNCIA DA AMÉRICA LATINA

RAHIS ◽  
2021 ◽  
Vol 18 (4) ◽  
pp. 168-169
Author(s):  
Dirce Inês Silva ◽  
Isabela Estrela Santos ◽  
Jaqueline Xavier Oliveira
Keyword(s):  
Research Society ◽  
Hiv Treatment ◽  
Services Research ◽  
Prevention Services ◽  
Treatment And Prevention ◽  
The Social ◽  
America Latina ◽  
Terapia Antirretroviral ◽  
The Impact ◽  
Brazilian Journal

INTRODUÇÃO : O tratamento da infecção pelo vírus da imunodeficiência humana (HIV) é realizado por meio da terapia antirretroviral (TARV) e vem apresentando avanços importantes no decorrer dos anos. Ocorreu a introdução de novas drogas e classes que ampliaram de modo significativo as opções para o tratamento da infecção pelo HIV-1. Existem razões para a troca (Swtich) da TARV, são eles : manutenção da supressão viral, resistência, probabilidade de maior adesão ao tratamento, eventos adversos, interações medicamentosas (1). Durante a pandemia de Covid-19 que vivenciamos desde março de 2020 no Brasil muitas dificuldades ocorreram nos serviços de saúde, principalmente para as pessoas que vivem com HIV como : acesso aos serviços, diagnóstico, tratamento e acompanhamento (2.3). OBJETIVO: Avaliar a prevalência de trocas de esquemas em um centro de referência da América Latina no período de Janeiro de 2020 a 31 de Julho de 2021.METODOLOGIA : Realizamos um estudo transversal no período de 2020 a 2021 , utilizando o sistema de informação : Sistema de Controle Logístico de Medicamentos (SICLOM) do Ministério da Saúde . Os dados foram analisados no Statistical Package for the Social Science(SPSS® ) 22.RESULTADOS : No período do estudo foram detectadas 473 trocas. Em 2020 ocorreram 283 trocas, 83 em mulheres e 200 em homens. E 2021 até o dia 31/07/2021 foram detectadas 190 trocas, 76 ocorreram em mulheres e 114 em homens. As trocas ocorreram devido : resistência, reações adversas, gestação , tratamento concomitante da tuberculose e simplificação do tratamento ( Figura 1 e 2)).   Figura 1 – Ocorências de Swtich de esquemas antirretroviraisFigura 2- Razões de Trocas de Esquemas Antiretrovirais CONCLUSÃO : Swtich dos esquemas antirretrovirais em utilização pode ser uma estratégia de simplificação da TARV, melhoria da adesão, e em muitos casos a redução de eventos adversos. O arsenal terapêutico no contexto brasileiro é diversificado permitindo uma troca com segurança e sem risco de perda da eficácia virológica. Sendo uma estratégia para enfrentamento da infecção pelo HIV mesmo em tempos de pandemia do COVID19. REFERÊNCIAS:1-Brites, Carlos. Terapia antirretroviral atual: tendências e desafios. Estratégias de troca (switch) naterapia antirretroviral atual. Brazilian Journal of Infectious DiseaseVol 2 . Nº 1 . Fevereiro 20162- Moura, Maria Lucia Costa de. (2020). Coronavírus e COVID-19. Revista Saúde Coletiva, 53, 10.3- Parente, J. da S.; Azevedo, S. L. de .; Moreira, L. da F. A.; Abreu, L. M. .; Souza, L. V. de. The impact of social isolation on the COVID-19 pandemic on access to HIV treatment and prevention services. Research, Society and Development, [S. l.], v. 10, n. 1, p. e28110111692, 2021.  

scholarly journals Stimulant Use Interventions May Strengthen ‘Getting to Zero’ Initiatives in Illinois: Insights from a Modeling Study

2021 ◽  
Author(s):  
Francis Lee ◽  
Daniel Sheeler ◽  
Anna Hotton ◽  
Natascha Del Vecchio ◽  
Rey Flores ◽  
...  
Keyword(s):  
Hiv Transmission ◽  
Crack Cocaine ◽  
Hiv Treatment ◽  
Annual Number ◽  
Hiv Incidence ◽  
Stimulant Use ◽  
Treatment And Prevention ◽  
Biomedical Intervention ◽  
The Impact ◽  
Modeling Study

AbstractObjective(s)Young Black men who have sex with men (YBMSM) are a key population identified in the Illinois Getting to Zero (GTZ) initiative who have experienced disproportionate HIV incidence. Rising stimulant use has been determined to impede the effectiveness of ART and pre-exposure prophylaxis for suppressing HIV transmission in populations. This modeling study explores the impact of stimulant use on HIV incidence among YBMSM – given the limited development of dedicated or culturally appropriate interventions for this population – and assesses the impact of these interventions on downstream HIV transmission in the context of achieving GTZ goals.MethodsA previously developed agent-based network model (ABNM), calibrated using data for YBMSM in Illinois, was extended to incorporate the impact of stimulant use (methamphetamines, crack/cocaine, and ecstasy) on sexual networks and engagement in HIV treatment and prevention continua. The model simulated the impact of a residential behavioral intervention (BI) for reducing stimulant dependency and an outpatient biomedical intervention (mirtazapine) for treating methamphetamine dependence on improved engagement in the HIV treatment and prevention continua. The downstream impact of these interventions on population-level HIV incidence was the primary intervention outcome.ResultsBaseline simulated annual HIV incidence in the ABNM was 6.9(95% CI: 6.83,7.04) per 100 person years (py) and 453 (95% CI: 445.9,461.2) new infections annually. A residential targeted to 25% of stimulant users yielded a 27.1% decline in the annual number of new infections. Initiating about 50% of methamphetamine users on mirtazapine reduced the overall HIV incidence by about 11%. A 25% increase in antiretroviral treatment (ART) and preexposure prophylaxis (PrEP) uptake in the non-stimulant using YBMSM population combined with a 25% uptake of BI for stimulant users produces an HIV incidence consistent with HIV elimination targets (about 200 infections/year) identified in the GTZ initiative.ConclusionsTargeted behavioral and biomedical interventions to treat stimulant dependency are likely to provide additive benefits to expanding ART and PrEP uptake for everyone in accomplishing GTZ initiatives for HIV elimination.

scholarly journals Estimating the percentage of European MSM eligible for PrEP: insights from a bio-behavioural survey in thirteen cities

2021 ◽  
pp. sextrans-2020-054786
Author(s):  
Maddalena Cordioli ◽  
Lorenzo Gios ◽  
Jörg W Huber ◽  
Nigel Sherriff ◽  
Cinta Folch ◽  
...  
Keyword(s):  
Hiv Risk ◽  
Large Scale ◽  
Risk Index ◽  
Hiv Infections ◽  
Risk Scores ◽  
Eligibility Criteria ◽  
European Cities ◽  
Risk Indices ◽  
The Impact ◽  
Hiv Negative

ObjectivesThis paper aims to estimate the percentage of European men who have sex with men (MSM) who may benefit from pre-exposure prophylaxis (PrEP), applying the three most widely used HIV risk indices for MSM (MSM Risk Index, Menza score, San Diego Early Test (SDET) score) and drawing on a large-scale multisite bio-behavioural survey (Sialon II).MethodsThe Sialon II study was a bio-behavioural survey among MSM implemented in 13 European cities using either time-location sampling or respondent-driven sampling. Biological and behavioural data from 4901 MSM were collected. Only behavioural data of HIV-negative individuals were considered. Three widely used risk indices to assess HIV acquisition risk among MSM were used to estimate individual HIV risk scores and PrEP eligibility criteria.Results4219 HIV-negative MSM were considered. Regardless the HIV risk score used and the city, percentages of MSM eligible for PrEP were found to range between 5.19% and 73.84%. Overall, the MSM Risk Index and the Menza score yielded broadly similar percentages, whereas the SDET Index provided estimates constantly lower across all cities. Although all the three scores correlated positively (r>0.6), their concordance was highly variable (0.01<CCC<0.62).ConclusionOur findings showed the impact of different scoring systems on the estimation of the percentage of MSM who may benefit from PrEP in European cities. Although our primary aim was not to compare the performance of different HIV risk scores, data show that a considerable percentage of MSM in each city should be offered PrEP in order to reduce HIV infections. As PrEP is highly effective at preventing HIV among MSM, our findings provide useful, practical guidance for stakeholders in implementing PrEP at city level to tackle HIV infections in Europe.

scholarly journals Teaching hydrological modelling: Illustrating model structure uncertainty with a ready-to-use teaching module

2021 ◽  
Author(s):  
Wouter J. M. Knoben ◽  
Diana Spieler
Keyword(s):  
Open Source ◽  
Hydrological Modelling ◽  
Model Parameters ◽  
Model Structure ◽  
Teaching Module ◽  
Modelling Uncertainty ◽  
Time Investment ◽  
Model Structure Uncertainty ◽  
The Impact ◽  
Different Sources

Abstract. Estimating the impact of different sources of uncertainty along the modelling chain is an important skill graduates are expected to have. Broadly speaking, educators can cover uncertainty in hydrological modelling by differentiating uncertainty in data, model parameters and model structure. This provides students with insight on the impact of uncertainties on modelling results and thus on the usability of the acquired model simulations for decision making. A survey among teachers in the earth and environmental sciences showed that model structural uncertainty is the least represented uncertainty group in teaching. This paper introduces a teaching module that introduces students to the basics of model structure uncertainty through two ready-to-use exercises. The module is short and can easily be integrated into an existing hydrologic curriculum, limiting the time investment needed to teach this aspect of modelling uncertainty. A trial application at the Technische Universität Dresden (Germany) showed that the exercises can be completed in less than two afternoons and that the provided setup effectively transfers the intended insights about model structure uncertainty. The module requires either Matlab or Octave, and uses the open-source Modular Assessment of Rainfall-Runoff Models Toolbox (MARRMoT) and the open-source Catchment Attributes and Meteorology for Large-sample Studies (CAMELS) dataset.

scholarly journals Modeling HIV disease progression and transmission at population-level: The potential impact of modifying disease progression in HIV treatment programs

2016 ◽  
Author(s):  
Jennifer M. Ross ◽  
Roger Ying ◽  
Connie L. Celum ◽  
Jared M. Baeten ◽  
Katherine K. Thomas ◽  
...  
Keyword(s):  
Viral Load ◽  
Hiv Infection ◽  
Disease Progression ◽  
Hiv Transmission ◽  
Acute Infection ◽  
Hiv Infections ◽  
Hiv Treatment ◽  
Hiv Viral Load ◽  
Potential Impact ◽  
The Impact

AbstractIntroductionMathematical models of HIV transmission that incorporate the dynamics of disease progression can estimate the potential impact of adjunctive strategies to antiretroviral therapy (ART) for HIV treatment and prevention. Suppressive treatment of HIV-positive persons co-infected with herpes simplex virus-2 (HSV-2) with valacyclovir, a medication directed against HSV-2, can lower HIV viral load, but the impact of valacyclovir on population HIV transmission has not been estimated.MethodsWe applied data on CD4 and viral load progression in ART-naïve persons studied in two HIV clinical trials to a novel, discrete-time Markov model. We validated our disease progression estimates using data from a trial of home-based HIV counseling and testing in KwaZulu-Natal, South Africa. Finally, we applied our disease progression estimates to a dynamic transmission model estimating the impact of providing valacyclovir to ART-naïve individuals to reduce onward transmission of HIV in three scenarios of different ART and valacyclovir population coverage. We assumed that valacyclovir reduced HIV viral load by 1.23 log copies/μL, and that persons treated with valacyclovir initiated ART more rapidly when their CD4 fell below 500 due to improved retention in pre-ART care.ResultsThe average duration of HIV infection following acute infection was 9.5 years. The duration of disease after acute infection and before reaching CD4 200 cells/μL was 2.53 years longer for females than males. Relative to a baseline of community HIV testing and counseling and ART initiation at CD4 <=500 cells/μL, valacyclovir with increased linkage to care resulted in 166,000 fewer HIV infections over ten years, with an incremental cost-effectiveness ratio (ICER) of $4,696 per HIV infection averted. The Test and Treat scenario with 70% ART coverage and no valacyclovir resulted in 202,000 fewer HIV infections at an ICER of $6,579.ConclusionEven when compared with initiation of valacyclovir, a safe drug that reduces HIV viral load, universal treatment for HIV is the optimal strategy for averting new infections and increasing public health benefit. Universal HIV treatment should be pursued by all countries to most effectively and efficiently reduce the HIV burden.

scholarly journals The role of HIV viral load in mathematical models of HIV transmission and treatment: a review

2020 ◽  
Vol 5 (1) ◽  
pp. e001800 ◽  
Author(s):  
Tracy Glass ◽  
Landon Myer ◽  
Maia Lesosky
Keyword(s):  
Viral Load ◽  
Mathematical Models ◽  
Hiv Transmission ◽  
Simulation Models ◽  
Population Level ◽  
Hiv Treatment ◽  
Hiv Viral Load ◽  
Hiv Epidemiology ◽  
The Impact

IntroductionHIV viral load (VL) is accepted as a key biomarker in HIV transmission and pathogenesis. This paper presents a review of the role of VL testing in mathematical models for HIV prevention and treatment.MethodsA search for simulation models of HIV was conducted in PubMed, yielding a total of 1210 studies. Publications before the year 2000, studies involving animals and analyses that did not use mathematical simulations were excluded. The full text of eligible articles was sourced and information about the intervention and population being modelled, type of modelling approach and disease monitoring strategy was extracted.Results and discussionA total of 279 studies related to HIV simulation models were included in the review, though only 17 (6%) included consideration of VL or VL testing and were evaluated in detail. Within the studies that included assessment of VL, routine monitoring was the focus, and usually in comparison to alternate monitoring strategies such as clinical or CD4 count-based monitoring. The majority of remaining models focus on the impact or delivery of antiretroviral therapy (n=68; 27%), pre-exposure prophylaxis (n=28; 11%) and/or HIV testing (n=24; 9%) on population estimates of HIV epidemiology and exclude consideration of VL. Few studies investigate or compare alternate VL monitoring frequencies, and only a small number of studies overall (3%) include consideration of vulnerable population groups such as pregnant women or infants.ConclusionsThere are very few simulations of HIV treatment or prevention that include VL measures, despite VL being recognised as the key determinant of both transmission and treatment outcomes. With growing emphasis on VL monitoring as key tool for population-level HIV control, there is a clear need for simulations of HIV epidemiology based on VL.

scholarly journals Comparison of two simulators for individual based models in HIV epidemiology in a population with HSV 2 in Yaoundé (Cameroon)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Diana M. Hendrickx ◽  
João Dinis Sousa ◽  
Pieter J. K. Libin ◽  
Wim Delva ◽  
Jori Liesenborgs ◽  
...  
Keyword(s):  
Model Complexity ◽  
Policy Makers ◽  
Basic Model ◽  
Hiv Epidemiology ◽  
Hiv Epidemic ◽  
Individual Based Models ◽  
Simplex Virus ◽  
Evidence For Policy ◽  
The Impact

AbstractModel comparisons have been widely used to guide intervention strategies to control infectious diseases. Agreement between different models is crucial for providing robust evidence for policy-makers because differences in model properties can influence their predictions. In this study, we compared models implemented by two individual-based model simulators for HIV epidemiology in a heterosexual population with Herpes simplex virus type-2 (HSV-2). For each model simulator, we constructed four models, starting from a simplified basic model and stepwise including more model complexity. For the resulting eight models, the predictions of the impact of behavioural interventions on the HIV epidemic in Yaoundé-Cameroon were compared. The results show that differences in model assumptions and model complexity can influence the size of the predicted impact of the intervention, as well as the predicted qualitative behaviour of the HIV epidemic after the intervention. These differences in predictions of an intervention were also observed for two models that agreed in their predictions of the HIV epidemic in the absence of that intervention. Without additional data, it is impossible to determine which of these two models is the most reliable. These findings highlight the importance of making more data available for the calibration and validation of epidemiological models.

Evaluation of direct-to-angiography suite (DTAS) and conventional clinical pathways in stroke care: a simulation study

2021 ◽  
pp. neurintsurg-2021-018253
Author(s):  
Mehrad Bastani ◽  
Timothy G White ◽  
Gabriela Martinez ◽  
Joseph Ohara ◽  
Kinpritma Sangha ◽  
...  
Keyword(s):  
Care Pathway ◽  
Clinical Pathways ◽  
Stroke Care ◽  
Sensitivity Analyses ◽  
Model Parameters ◽  
Eligibility Criteria ◽  
Angiography Suite ◽  
Time Savings ◽  
Conventional Ct ◽  
The Impact

BackgroundRapid time to reperfusion is essential to minimize morbidity and mortality in acute ischemic stroke due to large vessel occlusion (LVO). We aimed to evaluate the workflow times when utilizing a direct-to-angiography suite (DTAS) pathway for patients with suspected stroke presenting at a comprehensive stroke center compared with a conventional CT pathway.MethodsWe developed a discrete-event simulation (DES) model to evaluate DTAS workflow timelines compared with a conventional CT pathway, varying the admission NIHSS score treatment eligibility criteria. Model parameters were estimated based on 2 year observational data from our institution. Sensitivity analyses of simulation parameters were performed to assess the impact of patient volume and baseline utilization of angiography suites on workflow times utilizing DTAS.ResultsSimulation modeling of stroke patients (SimStroke) demonstrated door-to-reperfusion time savings of 0.2–3.5 min (p=0.05) for a range of DTAS eligibility criteria (ie, last known well to arrival <6 hours and National Institutes of Health Stroke Scale ≥6–11), when compared with the conventional stroke care pathway. Sensitivity analyses revealed that DTAS time savings is highly dependent on baseline utilization of angiography suites.ConclusionsThe results of the SimStroke model showed comparable time intervals for door-to-reperfusion for DTAS compared with a conventional stroke care pathway. However, the DTAS pathway was very sensitive to baseline angiography suite utilization, with even a 10% increase eliminating the advantages of DTAS compared with the conventional pathway. Given the minimal time savings modeled here, further investigation of implementing the DTAS pathway in clinical care is warranted.

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