A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices

by James A. Watson, Aimee R. Taylor, Elizabeth A. Ashley, Arjen Dondorp, Caroline O. Buckee, Nicholas J. White, Chris C. Holmes Genetic surveillance of malaria parasites supports malaria control programmes, treatment guidelines and elimination strategies. Surveillance studies often pose questions about malaria parasite ancestry (e.g. how antimalarial resistance has spread) and employ statistical methods that characterise p arasite population structure. Many of the methods used to characterise structure are unsupervised machine learning algorithms which depend on a genetic distance matrix, notably principal coordinates analysis (PCoA) and hierarchical agglomerative clustering (HAC). PCoA and HAC are sensitive to both t he definition of genetic distance and algorithmic specification. Importantly, neither algorithm infers malaria parasite ancestry. As such, PCoA and HAC can inform (e.g. via exploratory data visualisation and hypothesis generation), but not answer comprehensively, key questions about malaria parasite ancestry. We illustrate the sensitivity of PCoA and HAC using 393Plasmodium falciparum whole genome sequences collected from Cambodia and neighbouring regions (where antimalarial resistance has emerged and spread recently) and we provide tentative guidance for the use and interpretation of PCoA and HAC in malaria parasite genetic epidemiology. This guidance includes a call for fully transparent and reproducible analysis pipelines that feature (i) a clearly outlined ...
Source: PLoS Genetics - Category: Genetics & Stem Cells Authors: Source Type: research

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Publication date: Available online 10 October 2020Source: Journal of Genetics and GenomicsAuthor(s): Chengqi Wang, Justin Gibbons, Swamy R. Adapa, Jenna Oberstaller, Xiangyun Liao, Min Zhang, John H. Adams, Rays H.Y. Jiang
Source: Journal of Genetics and Genomics - Category: Genetics & Stem Cells Source Type: research
Conclusion: This study demonstrates that the crude extract of A. hispidum DC, one of the plants used traditionally to treat malaria, inhibits the growth of P. falciparum in vitro and could be a potential source of antimalarial drug. The report has highlighted genotoxic and cytotoxic effects of the selected plant extracts on human leukocytes as well. PMID: 33029160 [PubMed]
Source: Evidence-based Complementary and Alternative Medicine - Category: Complementary Medicine Tags: Evid Based Complement Alternat Med Source Type: research
Conclusions: The low prevalence of asymptomatic malaria parasite carriage by the children living in the Cape Coast Metropolis suggests that the malaria control interventions in place in CCMA are highly effective and that additional malaria control interventions are required for the KEEA district to reduce the prevalence of asymptomatic malaria parasite carriers. No molecular evidence of P. ovale and P. vivax was identified in the afebrile children sampled from the selected schools. PMID: 33029151 [PubMed]
Source: Journal of Tropical Medicine - Category: Tropical Medicine Tags: J Trop Med Source Type: research
(New York University) A team of researchers at NYU Abu Dhabi (NYUAD) has found that the Plasmodium parasite, which transmits malaria to humans through infected mosquitos, triggers changes in human genes that alter the body's adaptive immune response to malarial infections.
Source: EurekAlert! - Medicine and Health - Category: International Medicine & Public Health Source Type: news
Org. Biomol. Chem., 2020, Accepted Manuscript DOI: 10.1039/D0OB01730B, PaperConstance Mawunyo Korkor, Larnelle Faye Garnie, Leah Amod, Timothy J Egan, Kelly Chibale The intrinsic fluorescence properties of two related pyrido[1,2-a]benzimidazole antimalarial compounds suitable for cellular imaging of the human malaria parasite Plasmodium falciparum without the need to attach extrinsic fluorophores are described.... The content of this RSS Feed (c) The Royal Society of Chemistry
Source: RSC - Organic and Biomolecular Chemistry - Category: Molecular Biology Authors: Source Type: research
AbstractThe declining effectiveness of the available antimalarial drugs due to drug resistance requires a continued effort to develop new therapeutic approaches. In this context, combination therapies hold a great promise for developing effective first ‐line antimalarial treatments for reducing malaria mortality. The present study explores the antimalarial efficacy of nanotized formulation of curcumin in combination with benzothiophene compound 6 (3‐bromo‐N‐(4‐fluorobenzyl)‐benzo[b]thiophene‐2‐carboxamide) with a view to achieve better efficacy at a very low dose in comparison to that accomplished with mono...
Source: IUBMB Life - Category: Research Authors: Tags: RESEARCH COMMUNICATION Source Type: research
Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved ...
Source: Malaria Journal - Category: Infectious Diseases Authors: Tags: Methodology Source Type: research
(PLOS) A new computational model suggests that certain mutations that block infection by the most dangerous species of malaria have not become widespread in people because of the parasite's effects on the immune system. Bridget Penman of the University of Warwick, U.K., and Sylvain Gandon of the CNRS and Montpellier University, France, present these findings in the open-access journal PLOS Computational Biology.
Source: EurekAlert! - Infectious and Emerging Diseases - Category: Infectious Diseases Source Type: news
by Tsukushi Kamiya, Megan A. Greischar, David S. Schneider, Nicole Mideo To understand why some hosts get sicker than others from the same type of infection, it is essential to explain how key processes, such as host responses to infection and parasite growth, are influenced by various biotic and abiotic factors. In many disease systems, the initial infection dose impa cts host morbidity and mortality. To explore drivers of dose-dependence and individual variation in infection outcomes, we devised a mathematical model of malaria infection that allowed host and parasite traits to be linear functions (reaction norms) of the...
Source: PLoS Computational Biology - Category: Biology Authors: Source Type: research
The pathogenesis of Plasmodium falciparum malaria is related to the ability of parasite ‑infected erythrocytes (IEs) to adhere to the vascular endothelium (cytoadhesion/sequestration) or to surrounding uninfected ...
Source: Malaria Journal - Category: Infectious Diseases Authors: Tags: Research Source Type: research
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