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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal. Malar J 2024; 23:68. [PMID: 38443939 PMCID: PMC10916253 DOI: 10.1186/s12936-024-04897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. METHODS This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. RESULTS Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]). CONCLUSIONS When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Medoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Fatou Ba
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jessica Ribado
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua Suresh
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Albert Lee
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Katherine E Battle
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin A Bever
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
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2
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Rosenberg MC, Proctor JL, Steele KM. Quantifying changes in individual-specific template-based representations of center-of-mass dynamics during walking with ankle exoskeletons using Hybrid-SINDy. Sci Rep 2024; 14:1031. [PMID: 38200078 PMCID: PMC10781730 DOI: 10.1038/s41598-023-50999-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Ankle exoskeletons alter whole-body walking mechanics, energetics, and stability by altering center-of-mass (CoM) motion. Controlling the dynamics governing CoM motion is, therefore, critical for maintaining efficient and stable gait. However, how CoM dynamics change with ankle exoskeletons is unknown, and how to optimally model individual-specific CoM dynamics, especially in individuals with neurological injuries, remains a challenge. Here, we evaluated individual-specific changes in CoM dynamics in unimpaired adults and one individual with post-stroke hemiparesis while walking in shoes-only and with zero-stiffness and high-stiffness passive ankle exoskeletons. To identify optimal sets of physically interpretable mechanisms describing CoM dynamics, termed template signatures, we leveraged hybrid sparse identification of nonlinear dynamics (Hybrid-SINDy), an equation-free data-driven method for inferring sparse hybrid dynamics from a library of candidate functional forms. In unimpaired adults, Hybrid-SINDy automatically identified spring-loaded inverted pendulum-like template signatures, which did not change with exoskeletons (p > 0.16), except for small changes in leg resting length (p < 0.001). Conversely, post-stroke paretic-leg rotary stiffness mechanisms increased by 37-50% with zero-stiffness exoskeletons. While unimpaired CoM dynamics appear robust to passive ankle exoskeletons, how neurological injuries alter exoskeleton impacts on CoM dynamics merits further investigation. Our findings support Hybrid-SINDy's potential to discover mechanisms describing individual-specific CoM dynamics with assistive devices.
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Affiliation(s)
- Michael C Rosenberg
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Joshua L Proctor
- Department of Mechanical Engineering, University of Washington, Seattle, USA
- Department of Applied Mathematics, University of Washington, Seattle, USA
| | - Katherine M Steele
- Department of Mechanical Engineering, University of Washington, Seattle, USA
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3
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O'Brien ML, Zimmermann M, Eitmann L, Chao DL, Proctor JL. Contraceptive Adoption and Changes in Empowerment in Kenya, Nigeria, and Senegal. Stud Fam Plann 2023; 54:609-623. [PMID: 37531224 DOI: 10.1111/sifp.12250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Women's empowerment and contraceptive use are critical to achieving gender equality. The positive association between more empowered women and higher rates of contraceptive use has been well-established by cross-sectional research. However, there remains a gap in understanding the longitudinal relationship between contraceptive adoption and changes to women's empowerment. This study represents a novel approach to understanding the relationship between contraceptive adoption and women's empowerment longitudinally, at the individual level. To the authors' knowledge, this is the first attempt to measure the relationship between contraceptive adoption and women's empowerment using more than one wave of panel data. We leverage the longitudinal design of the Urban Reproductive Health Initiative data to code empowerment items by change over time (e.g., more empowered, no change, less empowered). We use sparse principal component analysis to establish empowerment change domains and calculate individual scores standardized by country-level averages. We estimate mixed effects models on these change domains, to investigate the link between contraceptive adoption and empowerment. We find common themes in empowerment across contexts-but contraceptive adoption has both positive and negative effects on those domains, and this varies across context. We discuss the need for cohort studies to examine this relationship.
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Schaffner SF, Badiane A, Khorgade A, Ndiop M, Gomis J, Wong W, Ndiaye YD, Diedhiou Y, Thwing J, Seck MC, Early A, Sy M, Deme A, Diallo MA, Sy N, Sene A, Ndiaye T, Sow D, Dieye B, Ndiaye IM, Gaye A, Ndiaye A, Battle KE, Proctor JL, Bever C, Fall FB, Diallo I, Gaye S, Sene D, Hartl DL, Wirth DF, MacInnis B, Ndiaye D, Volkman SK. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. Nat Commun 2023; 14:7268. [PMID: 37949851 PMCID: PMC10638404 DOI: 10.1038/s41467-023-43087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study's goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure.
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Affiliation(s)
- Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Aida Badiane
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Akanksha Khorgade
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Medoune Ndiop
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yaye Die Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Julie Thwing
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Angela Early
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Mouhamad Sy
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Awa Deme
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Aita Sene
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Tolla Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amy Gaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aliou Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Katherine E Battle
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin Bever
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Fatou Ba Fall
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Seynabou Gaye
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Sarah K Volkman
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
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5
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Mayor A, Ishengoma DS, Proctor JL, Verity R. Sampling for malaria molecular surveillance. Trends Parasitol 2023; 39:954-968. [PMID: 37730525 PMCID: PMC10580323 DOI: 10.1016/j.pt.2023.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided by public-health priorities. In this review we discuss sampling design practices for MMS and point out epidemiological, biological, and statistical factors that need to be considered. We present examples for different use cases, including detecting emergence and spread of rare variants, establishing transmission sources and inferring changes in malaria transmission intensity. This review will potentially guide the collection of samples and data, serve as a starting point for further methodological innovation, and enhance utilization of MMS to support malaria elimination.
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Affiliation(s)
- Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique.
| | - Deus S Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania; Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, UK
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6
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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal. Res Sq 2023:rs.3.rs-3516287. [PMID: 37961451 PMCID: PMC10635402 DOI: 10.21203/rs.3.rs-3516287/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programs (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. Here, we examined parasites from 3,147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, we constructed a series of Poisson generalized linear mixed-effects models to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. We compared the model-predicted incidence with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (<10/1000/annual [‰]). When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence >10 ‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was <10 ‰, we found that many of the correlations between parasite genetics and incidence were reversed, which we hypothesize reflects the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
| | | | | | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic
| | | | - Fatou Ba
- Programme National de Lutte Contre le Paludisme
| | - Ibrahima Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Doudou Sene
- Programme National de Lutte Contre le Paludisme
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jessica Ribado
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Joshua Suresh
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Albert Lee
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Joshua L Proctor
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Caitlin A Bever
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
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7
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Schaffner SF, Badiane A, Khorgade A, Ndiop M, Gomis J, Wong W, Ndiaye YD, Diedhiou Y, Thwing J, Seck MC, Early A, Sy M, Deme A, Diallo MA, Sy N, Sene A, Ndiaye T, Sow D, Dieye B, Ndiaye IM, Gaye A, Ndiaye A, Battle KE, Proctor JL, Bever C, Fall FB, Diallo I, Gaye S, Sene D, Hartl DL, Wirth DF, MacInnis B, Ndiaye D, Volkman SK. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. medRxiv 2023:2023.04.11.23288401. [PMID: 37131838 PMCID: PMC10153316 DOI: 10.1101/2023.04.11.23288401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Parasite genetic surveillance has the potential to play an important role in malaria control. We describe here an analysis of data from the first year of an ongoing, nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal, intended to provide actionable information for malaria control efforts. Looking for a good proxy for local malaria incidence, we found that the best predictor was the proportion of polygenomic infections (those with multiple genetically distinct parasites), although that relationship broke down in very low incidence settings (r = 0.77 overall). The proportion of closely related parasites in a site was more weakly correlated ( r = -0.44) with incidence while the local genetic diversity was uninformative. Study of related parasites indicated their potential for discriminating local transmission patterns: two nearby study areas had similarly high fractions of relatives, but one area was dominated by clones and the other by outcrossed relatives. Throughout the country, 58% of related parasites proved to belong to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci as well as at one novel locus, reflective of ongoing selection pressure.
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8
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Bertozzi-Villa A, Bever CA, Gerardin J, Proctor JL, Wu M, Harding D, Hollingsworth TD, Bhatt S, Gething PW. An archetypes approach to malaria intervention impact mapping: a new framework and example application. Malar J 2023; 22:138. [PMID: 37101269 PMCID: PMC10131392 DOI: 10.1186/s12936-023-04535-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/15/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND As both mechanistic and geospatial malaria modeling methods become more integrated into malaria policy decisions, there is increasing demand for strategies that combine these two methods. This paper introduces a novel archetypes-based methodology for generating high-resolution intervention impact maps based on mechanistic model simulations. An example configuration of the framework is described and explored. METHODS First, dimensionality reduction and clustering techniques were applied to rasterized geospatial environmental and mosquito covariates to find archetypal malaria transmission patterns. Next, mechanistic models were run on a representative site from each archetype to assess intervention impact. Finally, these mechanistic results were reprojected onto each pixel to generate full maps of intervention impact. The example configuration used ERA5 and Malaria Atlas Project covariates, singular value decomposition, k-means clustering, and the Institute for Disease Modeling's EMOD model to explore a range of three-year malaria interventions primarily focused on vector control and case management. RESULTS Rainfall, temperature, and mosquito abundance layers were clustered into ten transmission archetypes with distinct properties. Example intervention impact curves and maps highlighted archetype-specific variation in efficacy of vector control interventions. A sensitivity analysis showed that the procedure for selecting representative sites to simulate worked well in all but one archetype. CONCLUSION This paper introduces a novel methodology which combines the richness of spatiotemporal mapping with the rigor of mechanistic modeling to create a multi-purpose infrastructure for answering a broad range of important questions in the malaria policy space. It is flexible and adaptable to a range of input covariates, mechanistic models, and mapping strategies and can be adapted to the modelers' setting of choice.
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Affiliation(s)
- Amelia Bertozzi-Villa
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, USA.
- Malaria Atlas Project, Telethon Kids Institute, Perth, Australia.
- Big Data Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK.
| | - Caitlin A Bever
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, USA
| | - Jaline Gerardin
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, USA
- Department of Preventive Medicine and Institute for Global Health, Northwestern University, Chicago, USA
| | - Joshua L Proctor
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, USA
| | - Meikang Wu
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, USA
| | - Dennis Harding
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, USA
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Peter W Gething
- Malaria Atlas Project, Telethon Kids Institute, Perth, Australia
- Curtin University, Perth, Australia
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9
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Mayor A, da Silva C, Rovira-Vallbona E, Roca-Feltrer A, Bonnington C, Wharton-Smith A, Greenhouse B, Bever C, Chidimatembue A, Guinovart C, Proctor JL, Rodrigues M, Canana N, Arnaldo P, Boene S, Aide P, Enosse S, Saute F, Candrinho B. Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol. BMJ Open 2022; 12:e063456. [PMID: 35820756 PMCID: PMC9274532 DOI: 10.1136/bmjopen-2022-063456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Genomic data constitute a valuable adjunct to routine surveillance that can guide programmatic decisions to reduce the burden of infectious diseases. However, genomic capacities remain low in Africa. This study aims to operationalise a functional malaria molecular surveillance system in Mozambique for guiding malaria control and elimination. METHODS AND ANALYSES This prospective surveillance study seeks to generate Plasmodium falciparum genetic data to (1) monitor molecular markers of drug resistance and deletions in rapid diagnostic test targets; (2) characterise transmission sources in low transmission settings and (3) quantify transmission levels and the effectiveness of antimalarial interventions. The study will take place across 19 districts in nine provinces (Maputo city, Maputo, Gaza, Inhambane, Niassa, Manica, Nampula, Zambézia and Sofala) which span a range of transmission strata, geographies and malaria intervention types. Dried blood spot samples and rapid diagnostic tests will be collected across the study districts in 2022 and 2023 through a combination of dense (all malaria clinical cases) and targeted (a selection of malaria clinical cases) sampling. Pregnant women attending their first antenatal care visit will also be included to assess their value for molecular surveillance. We will use a multiplex amplicon-based next-generation sequencing approach targeting informative single nucleotide polymorphisms, gene deletions and microhaplotypes. Genetic data will be incorporated into epidemiological and transmission models to identify the most informative relationship between genetic features, sources of malaria transmission and programmatic effectiveness of new malaria interventions. Strategic genomic information will be ultimately integrated into the national malaria information and surveillance system to improve the use of the genetic information for programmatic decision-making. ETHICS AND DISSEMINATION The protocol was reviewed and approved by the institutional (CISM) and national ethics committees of Mozambique (Comité Nacional de Bioética para Saúde) and Spain (Hospital Clinic of Barcelona). Project results will be presented to all stakeholders and published in open-access journals. TRIAL REGISTRATION NUMBER NCT05306067.
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Affiliation(s)
- Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Clemente da Silva
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Eduard Rovira-Vallbona
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Caitlin Bever
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Caterina Guinovart
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | - Simone Boene
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
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10
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Noori N, Proctor JL, Efevbera Y, Oron AP. Effect of adolescent pregnancy on child mortality in 46 countries. BMJ Glob Health 2022; 7:bmjgh-2021-007681. [PMID: 35504693 PMCID: PMC9066488 DOI: 10.1136/bmjgh-2021-007681] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/27/2022] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION Adolescent pregnancy is a known health risk to mother and child. Statements and reports of health outcomes typically group mothers under 20 years old together. Few studies examined this risk at a finer age resolution, none of them comprehensively, and with differing results. METHODS We analysed Demographic and Health Surveys data from 2004 to 2018 in sub-Saharan Africa (SSA) and South Asia, on firstborn children of mothers 25 years old or younger. We examined the association between maternal age and stillbirths, and neonatal mortality rate (NNMR), infant mortality rate (IMR) and under-5 mortality rate (U5MR), using mixed-effects logistic regression adjusting for major demographic variables and exploring the impact of maternal health-seeking. RESULTS In both regions and across all endpoints, mortality rates of children born to mothers aged <16 years, 16-17 years and 18-19 years at first birth were about 2-4 times, 1.5-2 times and 1.2-1.5 times higher, respectively, than among firstborn children of mothers aged 23-25. Absolute mortality rates declined over time, but the age gradient remained similar across time periods and regions. Adjusting for rural/urban residence and maternal education, in SSA in 2014-2018 having a <16-year-old mother was associated with ORs of 3.71 (95% CI: 2.50 to 5.51) for stillbirth, 1.92 (1.60-2.30) for NNMR, 2.13 (1.85-2.46) for IMR and 2.39 (2.13-2.68) for U5MR, compared with having a mother aged 23-25. In South Asia, in 2014-2018 ORs were 5.12 (2.85-9.20) for stillbirth, 2.46 (2.03-2.97) for NNMR, 2.62 (2.22-3.08) for IMR and 2.59 (2.22-3.03) for U5MR. Part of the effect on NNMR and IMR may be mediated by a lower maternal health-seeking rate. CONCLUSIONS Adolescent pregnancy is associated with dramatically worse child survival and mitigated by health-seeking behaviour, likely reflecting a combination of biological and social factors. Refining maternal age reporting will avoid masking the increased risk to children born to very young adolescent mothers. Collection of additional biological and social data may better reveal mediators of this relationship. Targeted intervention strategies to reduce unintended pregnancy at earlier ages may also improve child survival.
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Affiliation(s)
- Navideh Noori
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Joshua L Proctor
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Yvette Efevbera
- Gender Equality Division, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Assaf P Oron
- University of Washington, Institute for Health Metrics and Evaluation, Seattle, Washington, USA
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11
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Levin R, Chao DL, Wenger EA, Proctor JL. Insights into population behavior during the COVID-19 pandemic from cell phone mobility data and manifold learning. Nat Comput Sci 2021; 1:588-597. [PMID: 38217135 PMCID: PMC10766515 DOI: 10.1038/s43588-021-00125-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/09/2021] [Indexed: 01/15/2024]
Abstract
Understanding the complex interplay between human behavior, disease transmission and non-pharmaceutical interventions during the COVID-19 pandemic could provide valuable insights with which to focus future public health efforts. Cell phone mobility data offer a modern measurement instrument to investigate human mobility and behavior at an unprecedented scale. We investigate aggregated and anonymized mobility data, which measure how populations at the census-block-group geographic scale stayed at home in California, Georgia, Texas and Washington from the beginning of the pandemic. Using manifold learning techniques, we show that a low-dimensional embedding enables the identification of patterns of mobility behavior that align with stay-at-home orders, correlate with socioeconomic factors, cluster geographically, reveal subpopulations that probably migrated out of urban areas and, importantly, link to COVID-19 case counts. The analysis and approach provide local epidemiologists a framework for interpreting mobility data and behavior to inform policy makers' decision-making aimed at curbing the spread of COVID-19.
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Affiliation(s)
- Roman Levin
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Dennis L Chao
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Edward A Wenger
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA.
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12
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Van Gordon MM, McCarthy KA, Proctor JL, Hagedorn BL. Evaluating COVID-19 reporting data in the context of testing strategies across 31 low- and middle-income countries. Int J Infect Dis 2021; 110:341-352. [PMID: 34303843 PMCID: PMC8299143 DOI: 10.1016/j.ijid.2021.07.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The case count for coronavirus disease 2019 (COVID-19) is the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to interpret COVID-19 case counts consistently in the context of other surveillance data is needed, especially for data-limited settings in low- and middle-income countries (LMICs). METHODS Statistical analyses were used to detect changes in COVID-19 surveillance data. The pruned exact linear time change detection method was applied for COVID-19 case counts, number of tests, and test positivity rate over time. With this information, change points were categorized as likely driven by epidemiological dynamics or non-epidemiological influences, such as noise. FINDINGS Higher rates of epidemiological change detection are more associated with open testing policies than with higher testing rates. This study quantified alignment of non-pharmaceutical interventions with epidemiological changes. LMICs have the testing capacity to measure prevalence with precision if they use randomized testing. Rwanda stands out as a country with an efficient COVID-19 surveillance system. Subnational data reveal heterogeneity in epidemiological dynamics and surveillance. INTERPRETATION Relying solely on case counts to interpret pandemic dynamics has important limitations. Normalizing counts by testing rate mitigates some of these limitations, and an open testing policy is key to efficient surveillance. The study findings can be leveraged by public health officials to strengthen COVID-19 surveillance and support programmatic decision-making.
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Affiliation(s)
- Mollie M Van Gordon
- Institute for Disease Modeling at the Bill & Melinda Gates Foundation, Seattle, WA, USA.
| | - Kevin A McCarthy
- Institute for Disease Modeling at the Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling at the Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Brittany L Hagedorn
- Institute for Disease Modeling at the Bill & Melinda Gates Foundation, Seattle, WA, USA
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13
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Ribado JV, Li NJ, Thiele E, Lyons H, Cotton JA, Weiss A, Tchindebet Ouakou P, Moundai T, Zirimwabagabo H, Guagliardo SAJ, Chabot-Couture G, Proctor JL. Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad. PLoS Negl Trop Dis 2021; 15:e0009609. [PMID: 34310598 PMCID: PMC8341693 DOI: 10.1371/journal.pntd.0009609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 08/05/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022] Open
Abstract
Background Guinea worm (Dracunculus medinensis) was detected in Chad in 2010 after a supposed ten-year absence, posing a challenge to the global eradication effort. Initiation of a village-based surveillance system in 2012 revealed a substantial number of dogs infected with Guinea worm, raising questions about paratenic hosts and cross-species transmission. Methodology/principal findings We coupled genomic and surveillance case data from 2012-2018 to investigate the modes of transmission between dog and human hosts and the geographic connectivity of worms. Eighty-six variants across four genes in the mitochondrial genome identified 41 genetically distinct worm genotypes. Spatiotemporal modeling revealed worms with the same genotype (‘genetically identical’) were within a median range of 18.6 kilometers of each other, but largely within approximately 50 kilometers. Genetically identical worms varied in their degree of spatial clustering, suggesting there may be different factors that favor or constrain transmission. Each worm was surrounded by five to ten genetically distinct worms within a 50 kilometer radius. As expected, we observed a change in the genetic similarity distribution between pairs of worms using variants across the complete mitochondrial genome in an independent population. Conclusions/significance In the largest study linking genetic and surveillance data to date of Guinea worm cases in Chad, we show genetic identity and modeling can facilitate the understanding of local transmission. The co-occurrence of genetically non-identical worms in quantitatively identified transmission ranges highlights the necessity for genomic tools to link cases. The improved discrimination between pairs of worms from variants identified across the complete mitochondrial genome suggests that expanding the number of genomic markers could link cases at a finer scale. These results suggest that scaling up genomic surveillance for Guinea worm may provide additional value for programmatic decision-making critical for monitoring cases and intervention efficacy to achieve elimination. The global eradication effort for Guinea worm disease has dramatically decreased the global burden of the disease and enabled 187 countries to be certified by the World Health Organization to be free of endemic transmission. Despite this progress, several countries continue to have endemic transmission. In Chad, a long absence of reported cases was interrupted with the identification of new Guinea worm cases, prompting a substantial scale up of surveillance and intervention efforts. Here, we study the value of increasing genomic surveillance as a tool for programmatic evaluation of surveillance and intervention efforts in Chad. Linking surveillance and genomic samples, parsimonious spatial models help reveal a consistent geographic clustering of similar genetic sequences across Chad. We also demonstrate that expanding the sequencing can offer better resolution for distinguishing Guinea worm samples. In this retrospective study, we found evidence that scaling up genomic surveillance can be an important monitoring and evaluation tool for the eradication program in Chad.
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Affiliation(s)
- Jessica V. Ribado
- Institute for Disease Modeling, Global Health Division of the Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Nancy J. Li
- Institute for Disease Modeling, Global Health Division of the Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Elizabeth Thiele
- Vassar College, Poughkeepsie, New York, United States of America
| | - Hil Lyons
- Institute for Disease Modeling, Global Health Division of the Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - James A. Cotton
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Adam Weiss
- The Carter Center, Atlanta, Georgia, United States of America
| | | | - Tchonfienet Moundai
- National Guinea Worm Eradication Program, Ministry of Public Health, N’Djamena, Chad
| | | | - Sarah Anne J. Guagliardo
- The Carter Center, Atlanta, Georgia, United States of America
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Guillaume Chabot-Couture
- Institute for Disease Modeling, Global Health Division of the Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Joshua L. Proctor
- Institute for Disease Modeling, Global Health Division of the Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
- * E-mail:
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14
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Brintz BJ, Haaland B, Howard J, Chao DL, Proctor JL, Khan AI, Ahmed SM, Keegan LT, Greene T, Keita AM, Kotloff KL, Platts-Mills JA, Nelson EJ, Levine AC, Pavia AT, Leung DT. A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea. eLife 2021; 10:63009. [PMID: 33527894 PMCID: PMC7853717 DOI: 10.7554/elife.63009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/17/2021] [Indexed: 11/13/2022] Open
Abstract
Traditional clinical prediction models focus on parameters of the individual patient. For infectious diseases, sources external to the patient, including characteristics of prior patients and seasonal factors, may improve predictive performance. We describe the development of a predictive model that integrates multiple sources of data in a principled statistical framework using a post-test odds formulation. Our method enables electronic real-time updating and flexibility, such that components can be included or excluded according to data availability. We apply this method to the prediction of etiology of pediatric diarrhea, where 'pre-test’ epidemiologic data may be highly informative. Diarrhea has a high burden in low-resource settings, and antibiotics are often over-prescribed. We demonstrate that our integrative method outperforms traditional prediction in accurately identifying cases with a viral etiology, and show that its clinical application, especially when used with an additional diagnostic test, could result in a 61% reduction in inappropriately prescribed antibiotics.
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Affiliation(s)
- Ben J Brintz
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | - Benjamin Haaland
- Population Health Sciences, University of Utah, Salt Lake City, United States
| | - Joel Howard
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City, United States
| | - Dennis L Chao
- Institute of Disease Modeling, Bill and Melinda Gates Foundation, Seattle, United States
| | - Joshua L Proctor
- Institute of Disease Modeling, Bill and Melinda Gates Foundation, Seattle, United States
| | - Ashraful I Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Sharia M Ahmed
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | - Lindsay T Keegan
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | - Tom Greene
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | | | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, University of Maryland, Baltimore, United States
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, United States
| | - Eric J Nelson
- Departments of Pediatrics, University of Florida, Gainesville, United States.,Departments of Environmental and Global Health, University of Florida, Gainesville, United States
| | - Adam C Levine
- Department of Emergency Medicine, Brown University, Providence, United States
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City, United States
| | - Daniel T Leung
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, United States.,Division of Microbiology and Immunology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
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15
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Routledge I, Lai S, Battle KE, Ghani AC, Gomez-Rodriguez M, Gustafson KB, Mishra S, Unwin J, Proctor JL, Tatem AJ, Li Z, Bhatt S. Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach. PLoS Comput Biol 2020; 16:e1007707. [PMID: 32203520 PMCID: PMC7117777 DOI: 10.1371/journal.pcbi.1007707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/02/2020] [Accepted: 02/03/2020] [Indexed: 01/02/2023] Open
Abstract
In order to monitor progress towards malaria elimination, it is crucial to be able to measure changes in spatio-temporal transmission. However, common metrics of malaria transmission such as parasite prevalence are under powered in elimination contexts. China has achieved major reductions in malaria incidence and is on track to eliminate, having reporting zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we introduce a novel Bayesian framework to model a latent diffusion process and estimate the joint likelihood of transmission between cases and the number of cases with unobserved sources of infection. This is used to estimate the case reproduction number, Rc. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. We estimate the mean Rc between 2011 and 2016 to be 0.171 (95% CI = 0.165, 0.178) for P. vivax cases and 0.089 (95% CI = 0.076, 0.103) for P. falciparum cases. From 2014 onwards, no cases were estimated to have a Rc value above one. An unobserved source of infection was estimated to be moderately likely (p>0.5) for 19/ 611 cases and high (p>0.8) for 2 cases, suggesting very high levels of case ascertainment. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean of 0.005 projected up to 2020, locally-acquired cases are possible due to high levels of importation.
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Affiliation(s)
| | - Shengjie Lai
- University of Southampton, Southampton, United Kingdom
| | | | | | | | - Kyle B. Gustafson
- Institute for Disease Modelling, Bellevue, Washington, United States of America
| | | | | | - Joshua L. Proctor
- Institute for Disease Modelling, Bellevue, Washington, United States of America
| | | | - Zhongjie Li
- Chinese Centers for Disease Control and Prevention, Beijing, China
| | - Samir Bhatt
- Imperial College London, London, United Kingom
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16
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Mercer LD, Lu F, Proctor JL. Sub-national levels and trends in contraceptive prevalence, unmet need, and demand for family planning in Nigeria with survey uncertainty. BMC Public Health 2019; 19:1752. [PMID: 31888577 PMCID: PMC6937659 DOI: 10.1186/s12889-019-8043-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/04/2019] [Indexed: 11/24/2022] Open
Abstract
Background Ambitious global goals have been established to provide universal access to affordable modern contraceptive methods. To measure progress toward such goals in populous countries like Nigeria, it’s essential to characterize the current levels and trends of family planning (FP) indicators such as unmet need and modern contraceptive prevalence rates (mCPR). Moreover, the substantial heterogeneity across Nigeria and scale of programmatic implementation requires a sub-national resolution of these FP indicators. The aim of this study is to estimate the levels and trends of FP indicators at a subnational scale in Nigeria utilizing all available data and accounting for survey design and uncertainty. Methods We utilized all available cross-sectional survey data from Nigeria including the Demographic and Health Surveys, Multiple Indicator Cluster Surveys, National Nutrition and Health Surveys, and Performance, Monitoring, and Accountability 2020. We developed a hierarchical Bayesian model that incorporates all of the individual level data from each survey instrument, accounts for survey uncertainty, leverages spatio-temporal smoothing, and produces probabilistic estimates with uncertainty intervals. Results We estimate that overall rates and trends of mCPR and unmet need have remained low in Nigeria: the average annual rate of change for mCPR by state is 0.5% (0.4%,0.6%) from 2012-2017. Unmet need by age-parity demographic groups varied significantly across Nigeria; parous women express much higher rates of unmet need than nulliparous women. Conclusions Understanding the estimates and trends of FP indicators at a subnational resolution in Nigeria is integral to inform programmatic decision-making. We identify age-parity-state subgroups with large rates of unmet need. We also find conflicting trends by survey instrument across a number of states. Our model-based estimates highlight these inconsistencies, attempt to reconcile the direct survey estimates, and provide uncertainty intervals to enable interpretation of model and survey estimates for decision-making.
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Affiliation(s)
- Laina D Mercer
- Institute for Disease Modeling, Bellevue, Washington, USA
| | - Fred Lu
- Institute for Disease Modeling, Bellevue, Washington, USA
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17
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Chao DL, Roose A, Roh M, Kotloff KL, Proctor JL. The seasonality of diarrheal pathogens: A retrospective study of seven sites over three years. PLoS Negl Trop Dis 2019; 13:e0007211. [PMID: 31415558 PMCID: PMC6711541 DOI: 10.1371/journal.pntd.0007211] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 08/27/2019] [Accepted: 07/26/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Pediatric diarrhea can be caused by a wide variety of pathogens, from bacteria to viruses to protozoa. Pathogen prevalence is often described as seasonal, peaking annually and associated with specific weather conditions. Although many studies have described the seasonality of diarrheal disease, these studies have occurred predominantly in temperate regions. In tropical and resource-constrained settings, where nearly all diarrhea-associated mortality occurs, the seasonality of many diarrheal pathogens has not been well characterized. As a retrospective study, we analyze the seasonal prevalence of diarrheal pathogens among children with moderate-to-severe diarrhea (MSD) over three years from the seven sites of the Global Enteric Multicenter Study (GEMS), a case-control study. Using data from this expansive study on diarrheal disease, we characterize the seasonality of different pathogens, their association with site-specific weather patterns, and consistency across study sites. METHODOLOGY/PRINCIPAL FINDINGS Using traditional methodologies from signal processing, we found that certain pathogens peaked at the same time every year, but not at all sites. We also found associations between pathogen prevalence and weather or "seasons," which are defined by applying modern machine-learning methodologies to site-specific weather data. In general, rotavirus was most prevalent during the drier "winter" months and out of phase with bacterial pathogens, which peaked during hotter and rainier times of year corresponding to "monsoon," "rainy," or "summer" seasons. CONCLUSIONS/SIGNIFICANCE Identifying the seasonally-dependent prevalence for diarrheal pathogens helps characterize the local epidemiology and inform the clinical diagnosis of symptomatic children. Our multi-site, multi-continent study indicates a complex epidemiology of pathogens that does not reveal an easy generalization that is consistent across all sites. Instead, our study indicates the necessity of local data to characterizing the epidemiology of diarrheal disease. Recognition of the local associations between weather conditions and pathogen prevalence suggests transmission pathways and could inform control strategies in these settings.
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Affiliation(s)
- Dennis L. Chao
- Institute for Disease Modeling, Bellevue, Washington, United States of America
- * E-mail:
| | - Anna Roose
- Center for Vaccine Development and Global Health, University of Maryland, Baltimore, Maryland, United States of America
| | - Min Roh
- Institute for Disease Modeling, Bellevue, Washington, United States of America
| | - Karen L. Kotloff
- Center for Vaccine Development and Global Health, University of Maryland, Baltimore, Maryland, United States of America
| | - Joshua L. Proctor
- Institute for Disease Modeling, Bellevue, Washington, United States of America
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18
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Mangan NM, Askham T, Brunton SL, Kutz JN, Proctor JL. Model selection for hybrid dynamical systems via sparse regression. Proc Math Phys Eng Sci 2019; 475:20180534. [PMID: 31007544 PMCID: PMC6451978 DOI: 10.1098/rspa.2018.0534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
Hybrid systems are traditionally difficult to identify and analyse using classical dynamical systems theory. Moreover, recently developed model identification methodologies largely focus on identifying a single set of governing equations solely from measurement data. In this article, we develop a new methodology, Hybrid-Sparse Identification of Nonlinear Dynamics, which identifies separate nonlinear dynamical regimes, employs information theory to manage uncertainty and characterizes switching behaviour. Specifically, we use the nonlinear geometry of data collected from a complex system to construct a set of coordinates based on measurement data and augmented variables. Clustering the data in these measurement-based coordinates enables the identification of nonlinear hybrid systems. This methodology broadly empowers nonlinear system identification without constraining the data locally in time and has direct connections to hybrid systems theory. We demonstrate the success of this method on numerical examples including a mass–spring hopping model and an infectious disease model. Characterizing complex systems that switch between dynamic behaviours is integral to overcoming modern challenges such as eradication of infectious diseases, the design of efficient legged robots and the protection of cyber infrastructures.
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Affiliation(s)
- N M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| | - T Askham
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
| | - S L Brunton
- Institute for Disease Modeling, Bellevue, WA 98005, USA
| | - J N Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
| | - J L Proctor
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
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Proctor JL, Holmes P. The effects of feedback on stability and maneuverability of a phase-reduced model for cockroach locomotion. Biol Cybern 2018; 112:387-401. [PMID: 29948143 DOI: 10.1007/s00422-018-0762-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
In previous work, we built a neuromechanical model for insect locomotion in the horizontal plane, containing a central pattern generator, motoneurons, muscles actuating jointed legs, and rudimentary proprioceptive feedback. This was subsequently simplified to a set of 24 phase oscillators describing motoneuronal activation of agonist-antagonist muscle pairs, which facilitates analyses and enables simulations over multi-dimensional parameter spaces. Here we use the phase-reduced model to study dynamics and stability over the typical speed range of the cockroach Blaberus discoidalis, the effects of feedback on response to perturbations, strategies for turning, and a trade-off between stability and maneuverability. We also compare model behavior with experiments on lateral perturbations, changes in body mass and moment of inertia, and climbing dynamics, and we present a simple control strategy for steering using exteroceptive feedback.
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Affiliation(s)
- J L Proctor
- Institute for Disease Modeling, 3150, 139th Ave SE, Bellevue, WA, 98005, USA
| | - P Holmes
- Department of Mechanical and Aerospace Engineering, Program in Applied and Computational Mathematics and Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA.
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Gustafson KB, Proctor JL. Identifying spatio-temporal dynamics of Ebola in Sierra Leone using virus genomes. J R Soc Interface 2018; 14:rsif.2017.0583. [PMID: 29187639 PMCID: PMC5721162 DOI: 10.1098/rsif.2017.0583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/02/2017] [Indexed: 01/19/2023] Open
Abstract
Containing the recent West African outbreak of Ebola virus (EBOV) required the deployment of substantial global resources. Despite recent progress in analysing and modelling EBOV epidemiological data, a complete characterization of the spatio-temporal spread of Ebola cases remains a challenge. In this work, we offer a novel perspective on the EBOV epidemic in Sierra Leone that uses individual virus genome sequences to inform population-level, spatial models. Calibrated to phylogenetic linkages of virus genomes, these spatial models provide unique insight into the disease mobility of EBOV in Sierra Leone without the need for human mobility data. Consistent with other investigations, our results show that the spread of EBOV during the beginning and middle portions of the epidemic strongly depended on the size of and distance between populations. Our phylodynamic analysis also revealed a change in model preference towards a spatial model with power-law characteristics in the latter portion of the epidemic, correlated with the timing of major intervention campaigns. More generally, we believe this framework, pairing molecular diagnostics with a dynamic model selection procedure, has the potential to be a powerful forecasting tool along with offering operationally relevant guidance for surveillance and sampling strategies during an epidemic.
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Mangan NM, Kutz JN, Brunton SL, Proctor JL. Model selection for dynamical systems via sparse regression and information criteria. Proc Math Phys Eng Sci 2017; 473:20170009. [PMID: 28878554 PMCID: PMC5582175 DOI: 10.1098/rspa.2017.0009] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/26/2017] [Indexed: 11/13/2022] Open
Abstract
We develop an algorithm for model selection which allows for the consideration of a combinatorially large number of candidate models governing a dynamical system. The innovation circumvents a disadvantage of standard model selection which typically limits the number of candidate models considered due to the intractability of computing information criteria. Using a recently developed sparse identification of nonlinear dynamics algorithm, the sub-selection of candidate models near the Pareto frontier allows feasible computation of Akaike information criteria (AIC) or Bayes information criteria scores for the remaining candidate models. The information criteria hierarchically ranks the most informative models, enabling the automatic and principled selection of the model with the strongest support in relation to the time-series data. Specifically, we show that AIC scores place each candidate model in the strong support, weak support or no support category. The method correctly recovers several canonical dynamical systems, including a susceptible-exposed-infectious-recovered disease model, Burgers’ equation and the Lorenz equations, identifying the correct dynamical system as the only candidate model with strong support.
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Affiliation(s)
- N M Mangan
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA.,Institute for Disease Modeling, Bellevue, WA 98005, USA
| | - J N Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
| | - S L Brunton
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
| | - J L Proctor
- Institute for Disease Modeling, Bellevue, WA 98005, USA
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Abstract
Understanding the interplay of order and disorder in chaos is a central challenge in modern quantitative science. Approximate linear representations of nonlinear dynamics have long been sought, driving considerable interest in Koopman theory. We present a universal, data-driven decomposition of chaos as an intermittently forced linear system. This work combines delay embedding and Koopman theory to decompose chaotic dynamics into a linear model in the leading delay coordinates with forcing by low-energy delay coordinates; this is called the Hankel alternative view of Koopman (HAVOK) analysis. This analysis is applied to the Lorenz system and real-world examples including Earth’s magnetic field reversal and measles outbreaks. In each case, forcing statistics are non-Gaussian, with long tails corresponding to rare intermittent forcing that precedes switching and bursting phenomena. The forcing activity demarcates coherent phase space regions where the dynamics are approximately linear from those that are strongly nonlinear. The huge amount of data generated in fields like neuroscience or finance calls for effective strategies that mine data to reveal underlying dynamics. Here Brunton et al.develop a data-driven technique to analyze chaotic systems and predict their dynamics in terms of a forced linear model.
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Affiliation(s)
- Steven L Brunton
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Bingni W Brunton
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | | | - Eurika Kaiser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - J Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA, 98195, USA
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Rudy SH, Brunton SL, Proctor JL, Kutz JN. Data-driven discovery of partial differential equations. Sci Adv 2017; 3:e1602614. [PMID: 28508044 PMCID: PMC5406137 DOI: 10.1126/sciadv.1602614] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/11/2017] [Indexed: 05/18/2023]
Abstract
We propose a sparse regression method capable of discovering the governing partial differential equation(s) of a given system by time series measurements in the spatial domain. The regression framework relies on sparsity-promoting techniques to select the nonlinear and partial derivative terms of the governing equations that most accurately represent the data, bypassing a combinatorially large search through all possible candidate models. The method balances model complexity and regression accuracy by selecting a parsimonious model via Pareto analysis. Time series measurements can be made in an Eulerian framework, where the sensors are fixed spatially, or in a Lagrangian framework, where the sensors move with the dynamics. The method is computationally efficient, robust, and demonstrated to work on a variety of canonical problems spanning a number of scientific domains including Navier-Stokes, the quantum harmonic oscillator, and the diffusion equation. Moreover, the method is capable of disambiguating between potentially nonunique dynamical terms by using multiple time series taken with different initial data. Thus, for a traveling wave, the method can distinguish between a linear wave equation and the Korteweg-de Vries equation, for instance. The method provides a promising new technique for discovering governing equations and physical laws in parameterized spatiotemporal systems, where first-principles derivations are intractable.
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Affiliation(s)
- Samuel H. Rudy
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
- Corresponding author.
| | - Steven L. Brunton
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Joshua L. Proctor
- Institute for Disease Modeling, 3150 139th Avenue Southeast, Bellevue, WA 98005, USA
| | - J. Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
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Kunert JM, Proctor JL, Brunton SL, Kutz JN. Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion. PLoS Comput Biol 2017; 13:e1005303. [PMID: 28076347 PMCID: PMC5226684 DOI: 10.1371/journal.pcbi.1005303] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 12/12/2016] [Indexed: 01/19/2023] Open
Abstract
Using a computational model of the Caenorhabditis elegans connectome dynamics, we show that proprioceptive feedback is necessary for sustained dynamic responses to external input. This is consistent with the lack of biophysical evidence for a central pattern generator, and recent experimental evidence that proprioception drives locomotion. The low-dimensional functional response of the Caenorhabditis elegans network of neurons to proprioception-like feedback is optimized by input of specific spatial wavelengths which correspond to the spatial scale of real body shape dynamics. Furthermore, we find that the motor subcircuit of the network is responsible for regulating this response, in agreement with experimental expectations. To explore how the connectomic dynamics produces the observed two-mode, oscillatory limit cycle behavior from a static fixed point, we probe the fixed point's low-dimensional structure using Dynamic Mode Decomposition. This reveals that the nonlinear network dynamics encode six clusters of dynamic modes, with timescales spanning three orders of magnitude. Two of these six dynamic mode clusters correspond to previously-discovered behavioral modes related to locomotion. These dynamic modes and their timescales are encoded by the network's degree distribution and specific connectivity. This suggests that behavioral dynamics are partially encoded within the connectome itself, the connectivity of which facilitates proprioceptive control.
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Affiliation(s)
- James M. Kunert
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Joshua L. Proctor
- Institute for Disease Modeling, Bellevue, Washington, United States of America
| | - Steven L. Brunton
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - J. Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
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Brunton SL, Proctor JL, Kutz JN. Sparse Identification of Nonlinear Dynamics with Control (SINDYc)**SLB acknowledges support from the U.S. Air Force Center of Excellence on Nature Inspired Flight Technologies and Ideas (FA9550-14-1-0398). JLP thanks Bill and Melinda Gates for their active support of the Institute of Disease Modeling and their sponsorship through the Global Good Fund. JNK acknowledges support from the U.S. Air Force Office of Scientific Research (FA9550-09-0174). ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ifacol.2016.10.249] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
BACKGROUND The development and application of quantitative methods to understand disease dynamics and plan interventions is becoming increasingly important in the push toward eradication of human infectious diseases, exemplified by the ongoing effort to stop the spread of poliomyelitis. METHODS Dynamic mode decomposition (DMD) is a recently developed method focused on discovering coherent spatial-temporal modes in high-dimensional data collected from complex systems with time dynamics. The algorithm has a number of advantages including a rigorous connection to the analysis of nonlinear systems, an equation-free architecture, and the ability to efficiently handle high-dimensional data. RESULTS We demonstrate the method on three different infectious disease sets including Google Flu Trends data, pre-vaccination measles in the UK, and paralytic poliomyelitis wild type-1 cases in Nigeria. For each case, we describe the utility of the method for surveillance and resource allocation. CONCLUSIONS We demonstrate how DMD can aid in the analysis of spatial-temporal disease data. DMD is poised to be an effective and efficient computational analysis tool for the study of infectious disease.
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Delahunt C, Horning MP, Wilson BK, Proctor JL, Hegg MC. Limitations of haemozoin-based diagnosis of Plasmodium falciparum using dark-field microscopy. Malar J 2014; 13:147. [PMID: 24739286 PMCID: PMC4021049 DOI: 10.1186/1475-2875-13-147] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/12/2014] [Indexed: 11/13/2022] Open
Abstract
Background The haemozoin crystal continues to be investigated extensively for its potential as a biomarker for malaria diagnostics. In order for haemozoin to be a valuable biomarker, it must be present in detectable quantities in the peripheral blood and distinguishable from false positives. Here, dark-field microscopy coupled with sophisticated image processing algorithms is used to characterize the abundance of detectable haemozoin within infected erythrocytes from field samples in order to determine the window of detection in peripheral blood. Methods Thin smears from Plasmodium falciparum-infected and uninfected patients were imaged in both dark field (DF) unstained and bright field (BF) Giemsa-stained modes. The images were co-registered such that each parasite had thumbnails in both BF and DF modes, providing an accurate map between parasites and DF objects. This map was used to find the abundance of haemozoin as a function of parasite stage through careful parasite staging and correlation with DF objects. An automated image-processing and classification algorithm classified the bright spots in the DF images as either haemozoin or non-haemozoin objects. Results The algorithm distinguishes haemozoin from non-haemozoin objects in DF images with an object-level sensitivity of 95% and specificity of 97%. Ring stages older than about 6 hours begin to show detectable haemozoin, and rings between 10–16 hours reliably contain detectable haemozoin. However, DF microscopy coupled with the image-processing algorithm detect no haemozoin in rings younger than six hours. Discussion Although this method demonstrates the most sensitive detection of haemozoin in field samples reported to date, it does not detect haemozoin in ring-stage parasites younger than six hours. Thus, haemozoin is a poor biomarker for field samples primarily composed of young ring-stage parasites because the crystal is not present in detectable quantities by the methods described here. Based on these results, the implications for patient-level diagnosis and recommendations for future work are discussed.
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Proctor JL, Kutz JN. Passive mode-locking by use of waveguide arrays. Opt Lett 2005; 30:2013-5. [PMID: 16092250 DOI: 10.1364/ol.30.002013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A novel mode-locking technique is presented in which the intensity-dependent spatial coupling dynamics of a waveguide array is used to achieve temporal mode-locking in a passive optical fiber laser. By use of the discrete, nearest-neighbor spatial coupling of the waveguide array, low-intensity light can be transferred to the neighboring waveguides and ejected (attenuated) from the laser cavity. In contrast, higher-intensity light is self-focused in the waveguide and remains largely unaffected. Numerical studies of this pulse shaping mechanism (intensity discrimination) show that using current waveguide arrays and standard optical fiber technology produces stable and robust mode-locked soliton-like pulses.
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Affiliation(s)
- Joshua L Proctor
- Department of Applied Mathematics, University of Washington, Seattle, Washington 98195-2420, USA
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Dolan SA, Proctor JL, Alling DW, Okubo Y, Wellems TE, Miller LH. Glycophorin B as an EBA-175 independent Plasmodium falciparum receptor of human erythrocytes. Mol Biochem Parasitol 1994; 64:55-63. [PMID: 8078523 DOI: 10.1016/0166-6851(94)90134-1] [Citation(s) in RCA: 159] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Invasion of erythrocytes by malaria parasites involves multiple receptor-ligand interactions. To elucidate these pathways, we made use of four parasite clones with differing specificities for invasion, erythrocytes that are mutant for either glycophorin A or B, and enzyme modification of the erythrocyte surface with neuraminidase and trypsin. Neuraminidase alone abolishes invasion of two parasite clones (Dd2, FCR3/A2); these invade after trypsin treatment alone. A third clone (7G8) is unable to invade trypsin-treated erythrocytes. The fourth clone (HB3) can invade after either neuraminidase or trypsin treatment. The receptor for invasion of trypsin-treated erythrocytes was explored in two ways: treatment of trypsin-treated normal cells with neuraminidase, and trypsin treatment of glycophorin B-deficient cells. Both treatments eliminated invasion by all clones, indicating that the trypsin-independent pathway uses sialic acid and glycophorin B. To identify parasite proteins involved in the different pathways, erythrocyte binding assays were performed with soluble parasite proteins from each clone. Based on binding assays using erythrocytes that lack glycophorin A, the parasite protein known as EBA-175 appears to bind predominantly to glycophorin A. In contrast, the glycophorin B pathway does not appear to involve EBA-175, as binding of EBA-175 was similarly reduced to trypsin-treated normal and trypsin-treated glycophorin B-deficient erythrocytes. Thus, the glycophorin B-dependent, sialic acid-dependent invasion of trypsin-treated normal erythrocytes uses a different parasite ligand, indicating two or more sialic-dependent pathways for invasion. Clone 7G8, which cannot invade trypsin-treated erythrocytes, may be missing the ligand for invasion via glycophorin B.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S A Dolan
- Laboratory of Malaria Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
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