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Horn S, Snoep JL, van Niekerk DD. Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study. BMC Bioinformatics 2021; 22:384. [PMID: 34303353 PMCID: PMC8305899 DOI: 10.1186/s12859-021-04289-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/11/2021] [Indexed: 12/04/2022] Open
Abstract
Background The fidelity and reliability of disease model predictions depend on accurate and precise descriptions of processes and determination of parameters. Various models exist to describe within-host dynamics during malaria infection but there is a shortage of clinical data that can be used to quantitatively validate them and establish confidence in their predictions. In addition, model parameters often contain a degree of uncertainty and show variations between individuals, potentially undermining the reliability of model predictions. In this study models were reproduced and analysed by means of robustness, uncertainty, local sensitivity and local sensitivity robustness analysis to establish confidence in their predictions. Results Components of the immune system are responsible for the most uncertainty in model outputs, while disease associated variables showed the greatest sensitivity for these components. All models showed a comparable degree of robustness but displayed different ranges in their predictions. In these different ranges, sensitivities were well-preserved in three of the four models. Conclusion Analyses of the effects of parameter variations in models can provide a comparative tool for the evaluation of model predictions. In addition, it can assist in uncovering model weak points and, in the case of disease models, be used to identify possible points for therapeutic intervention. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04289-z.
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Affiliation(s)
- Shade Horn
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, Stellenbosch, South Africa
| | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, Stellenbosch, South Africa.,Molecular Cell Physiology, Vrije Universiteit, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands
| | - David D van Niekerk
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, Stellenbosch, South Africa.
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Makenga G, Baraka V, Francis F, Nakato S, Gesase S, Mtove G, Madebe R, Kyaruzi E, Minja DT, Lusingu JP, Van geertruyden JP. Effectiveness and safety of intermittent preventive treatment for malaria using either dihydroartemisinin-piperaquine or artesunate-amodiaquine in reducing malaria related morbidities and improving cognitive ability in school-aged children in Tanzania: A study protocol for a controlled randomised trial. Contemp Clin Trials Commun 2020; 17:100546. [PMID: 32382685 PMCID: PMC7201189 DOI: 10.1016/j.conctc.2020.100546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND In high transmission settings, up to 70% of school-aged children harbour malaria parasites without showing any clinical symptoms. Thus, epidemiologically, school aged children act as a substantial reservoir for malaria transmission. Asymptomatic Plasmodium infections induce inflammation leading to iron deficiency anaemia. Consequently, anaemia retards child growth, predisposes children to other diseases and reduces cognitive potential that could lead to poor academic performance. School aged children become increasingly more vulnerable as compared to those aged less than five years due to delayed acquisition of protective immunity. None of the existing Intermittent Preventive Treatment (IPT) strategies is targeting school-aged children. Here, we describe the study protocol of a clinical trial conducted in north-eastern Tanzania to expand the IPT by assessing the effectiveness and safety of two antimalarial drugs, Dihydroartemisinin-Piperaquine (DP) and Artesunate-Amodiaquine (ASAQ) in preventing malaria related morbidities in school-aged children (IPTsc) living in a high endemic area. METHODS/DESIGN The trial is a phase IIIb, individual randomized, open label, controlled trial enrolling school children aged 5-15 years, who receive either DP or ASAQ or control (no drug), using a "balanced block design" with the "standard of care" arm as reference. The interventional treatments are given three times a year for the first year. A second non-interventional year will assess possible rebound effects. Sample size was estimated to 1602 school children (534 per group) from selected primary schools in an area with high malaria endemicity. Thick and thin blood smears (to measure malaria parasitaemia using microscope) were obtained prior to treatment at baseline, and will be obtained again at month 12 and 20 from all participants. Haemoglobin concentration using a haemoglobinometer (HemoCue AB, Sweden) will be measured four monthly. Finger-prick blood (dried bloodspot-DBS) prepared on Whatman 3 M filter paper, will be used for sub-microscopic malaria parasite detection usingPCR, detect markers of drug resistance (using next generation sequencing (NGS) technology), and malaria serological assays (using enzyme-linked immunosorbent assay, ELISA). To determine the benefit of IPTsc on cognitive and psychomotor ability test of everyday attention for children (TEA-Ch) and a '20 m Shuttle run' respectively, will be conducted at baseline, month 12 and 20. The primary endpoints are change in mean haemoglobin from baseline concentration and reduction in clinical malaria incidence at month 12 and 20 of follow up. Mixed design methods are used to assess the acceptability, cost-effectiveness and feasibility of IPTsc as part of a more comprehensive school children health package. Statistical analysis will be in the form of multilevel modelling, owing to repeated measurements and clustering effect of participants. DISCUSSION Malaria intervention using IPTsc strategy may be integrated in the existing national school health programme. However, there is limited systematic evidence to assess the effectiveness and operational feasibility of this approach. School-aged children are easily accessible in most endemic malaria settings. The evidence from this study will guide the implementation of the strategy to provide complementary approach to reduce malaria related morbidity, anaemia and contribute to the overall burden reduction. TRIAL REGISTRATION Clinicaltrials.gov: NCT03640403, registered on Aug 21, 2018, prospectively registered.Url https://www.clinicaltrials.gov/ct2/show/NCT03640403?term=NCT03640403&rank=1.
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Affiliation(s)
- Geofrey Makenga
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Vito Baraka
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Swabra Nakato
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Samwel Gesase
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - George Mtove
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Rashid Madebe
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Edna Kyaruzi
- College of Education (DUCE), University of Dar Es Salaam, Dar Es Salaam, Tanzania
| | - Daniel T.R. Minja
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - John P.A. Lusingu
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
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Rugani JN, Quaresma PF, Gontijo CF, Soares RP, Monte-Neto RL. Intraspecies susceptibility of Leishmania (Viannia) braziliensis to antileishmanial drugs: Antimony resistance in human isolates from atypical lesions. Biomed Pharmacother 2018; 108:1170-1180. [PMID: 30372818 DOI: 10.1016/j.biopha.2018.09.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/21/2018] [Accepted: 09/26/2018] [Indexed: 02/07/2023] Open
Abstract
Leishmania (Viannia) braziliensis is the most common etiological agent of cutaneous and mucocutaneous leishmaniasis (MCL) in Latin America. An interesting aspect of the disease outcome caused by this species is the appearance of non-ulcerated atypical cutaneous leishmaniasis. Atypical (AT) lesions are often associated with therapeutic failure when treated with antimony(Sb)-based drugs. Refractory cases are not necessarily due to intrinsic parasite drug resistance. The status of in vitro drug susceptibility from L. braziliensis field isolates is less assessed than patient treatment outcome. In this work, L. braziliensis isolated from typical CL (6), MCL (1) and AT (3) lesions and vector (1) were tested for their susceptibility to amphotericin B (AmB), miltefosine (MIL), glucantime (GLU) and non-comercial meglumine antimoniate (MA). Overall, intracellular amastigotes of all isolates were sensitive to the tested antileishmanial drugs except AT lesions-derived strains 316, 330 and 340 that presented in vitro resistance against SbV-based drugs. Although susceptible to miltefosine - based on phenotypic screening - intramacrophagic quiescent amastigotes could restore infection. L. braziliensis promastigotes isolated from AT lesions also displayed 29% reduced capacity to infect human monocyte-derived macrophages when compared with parasites obtained from patients with typical lesions, MCL or from sand-fly. These data indicate differences in drug susceptibility and infectiveness among L. braziliensis isolated from patients exhibiting different types of lesions and highlight the importance of its characterization for drug response prediction outcome in clinical practice.
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Affiliation(s)
- Jeronimo N Rugani
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-009, Belo Horizonte, MG, Brazil.
| | - Patrícia F Quaresma
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-009, Belo Horizonte, MG, Brazil.
| | - Célia F Gontijo
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-009, Belo Horizonte, MG, Brazil.
| | - Rodrigo P Soares
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-009, Belo Horizonte, MG, Brazil.
| | - Rubens L Monte-Neto
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-009, Belo Horizonte, MG, Brazil.
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Gurarie D, Karl S, Zimmerman PA, King CH, St. Pierre TG, Davis TME. Mathematical modeling of malaria infection with innate and adaptive immunity in individuals and agent-based communities. PLoS One 2012; 7:e34040. [PMID: 22470511 PMCID: PMC3314696 DOI: 10.1371/journal.pone.0034040] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 02/21/2012] [Indexed: 11/26/2022] Open
Abstract
Background Agent-based modeling of Plasmodium falciparum infection offers an attractive alternative to the conventional Ross-Macdonald methodology, as it allows simulation of heterogeneous communities subjected to realistic transmission (inoculation patterns). Methodology/Principal Findings We developed a new, agent based model that accounts for the essential in-host processes: parasite replication and its regulation by innate and adaptive immunity. The model also incorporates a simplified version of antigenic variation by Plasmodium falciparum. We calibrated the model using data from malaria-therapy (MT) studies, and developed a novel calibration procedure that accounts for a deterministic and a pseudo-random component in the observed parasite density patterns. Using the parasite density patterns of 122 MT patients, we generated a large number of calibrated parameters. The resulting data set served as a basis for constructing and simulating heterogeneous agent-based (AB) communities of MT-like hosts. We conducted several numerical experiments subjecting AB communities to realistic inoculation patterns reported from previous field studies, and compared the model output to the observed malaria prevalence in the field. There was overall consistency, supporting the potential of this agent-based methodology to represent transmission in realistic communities. Conclusions/Significance Our approach represents a novel, convenient and versatile method to model Plasmodium falciparum infection.
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Affiliation(s)
- David Gurarie
- Department of Mathematics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Stephan Karl
- School of Physics, The University of Western Australia, Crawley, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Fremantle Hospital, Fremantle, Western Australia, Australia
- * E-mail:
| | - Peter A. Zimmerman
- The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Charles H. King
- The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Timothy G. St. Pierre
- School of Physics, The University of Western Australia, Crawley, Western Australia, Australia
| | - Timothy M. E. Davis
- School of Medicine and Pharmacology, The University of Western Australia, Fremantle Hospital, Fremantle, Western Australia, Australia
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Thibodeaux JJ, Schlittenhardt TP. Optimal Treatment Strategies for Malaria Infection. Bull Math Biol 2011; 73:2791-808. [DOI: 10.1007/s11538-011-9650-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 03/07/2011] [Indexed: 10/18/2022]
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Chang H, Astolfi A, Shim H. A control theoretic approach to venom immunotherapy with state jumps. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2010:742-5. [PMID: 21095900 DOI: 10.1109/iembs.2010.5626304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigate a model-based control method to boost the immune response. We apply this control method to select the appropriate immune response between the Th1 and Th2 responses. The idea of state jump is discussed using hybrid models notation. To implement the control idea we propose physically available methods.
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Affiliation(s)
- H Chang
- Department of Electrical and Electronic Engineering, Imperial College London, SW7 2AZ, UK.
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Chaves LF, Kaneko A, Pascual M. Random, top-down, or bottom-up coexistence of parasites: malaria population dynamics in multi-parasitic settings. Ecology 2009; 90:2414-25. [PMID: 19769120 DOI: 10.1890/08-1022.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Epidemiological models concerned with the control of malaria using interventions such as bed nets and vaccines increasingly incorporate realistic aspects of malaria biology. The increasing complexity of these models limits their ability to abstract ecological processes and to address questions on the regulation of population dynamics using time-series data, particularly in regards to interactions between different pathogens and the regulatory role of innate (bottom-up) and acquired (top-down) immunity. We use a theoretical framework to test hypotheses on the importance of population-level immunity and parasite abundance in regulating the population dynamics of malaria. We use qualitative loop analyses to examine the sign of the interaction between Plasmodium falciparum and P. vivax at the population level, and we discuss implications of this sign for the within-host regulation of parasites. Our analyses of monthly malaria time-series data from the island of Espirito Santo, Vanuatu (1983-1997), show that the dynamics of P. falciparum are not sensitive to P. vivax, whereas infections by the latter increase in response to those of the former. These results support a differential use of resources inside the hosts, a resource-consumer interaction between hosts and their immune system, and within-host regulation of parasites. Finally, our results emphasize the need to better understand factors regulating malaria dynamics before developing control strategies and call for the use of control strategies directed at the interruption of transmission, such as vector control and the use of bed nets.
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Affiliation(s)
- Luis Fernando Chaves
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan 48109-1048, USA.
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Gurarie D, McKenzie FE. A stochastic model of immune-modulated malaria infection and disease in children. Math Biosci 2007; 210:576-97. [PMID: 17709118 PMCID: PMC2173879 DOI: 10.1016/j.mbs.2007.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 06/28/2007] [Accepted: 07/03/2007] [Indexed: 11/23/2022]
Abstract
We develop a simple three-state stochastic description of individual malaria infections that relates dynamics of disease and immune status to age and previous exposure, under different intensities of transmission. We apply the resulting individual-based community models to examine the effects of drug treatment and vaccination on the frequency and severity of disease in ensembles of children. The several broad qualitative similarities between our results and field observations include potential rebound effects following intervals of drug treatment.
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Affiliation(s)
- David Gurarie
- Department of Mathematics, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Corresponding author. Tel: 216-368-2857; Fax: 216-368-5163
| | - F. Ellis McKenzie
- Fogarty International Center, Room 306, Building 16, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
Oscillations are surprisingly common in the immune system, both in its healthy state and in disease. The most famous example is that of periodic fevers caused by the malaria parasite. A number of hereditary disorders, which also cause periodic fevers, have also been known for a long time. Various reports of oscillations in cytokine concentrations following antigen challenge have been published over at least the past three decades. Oscillations can also occur at the intracellular level. Calcium oscillations following T-cell activation are familiar to all immunologists, and metabolic and reactive oxygen species oscillations in neutrophils have been well documented. More recently, oscillations in nuclear factor kappaB activity following stimulation by tumor necrosis factor alpha have received considerable publicity. However, despite all of these examples, oscillations in the immune system still tend to be considered mainly as pathological aberrations, and their causes and significance remained largely unknown. This is partly because of a lack of awareness within the immunological community of the appropriate theoretical frameworks for describing and analyzing such behavior. We provide an introduction to these frameworks and give a survey of the currently known oscillations that occur within the immune system.
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Affiliation(s)
- Jaroslav Stark
- Department of Mathematics, Imperial College London, London, UK.
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