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131 results for “P. falciparum”
Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites
We used a high density SNP array to genotype 75 P. falciparum isolates recently collected from Senegal and The Gambia in order to search for signals of selection in this malaria endemic region. We found little geographic or temporal stratification of the genetic diversity among the sampled parasites. Through application of the iHS and REHH haplotype-based tests for positive selection, we found evidence of recent selective sweeps at a known drug resistance locus, at several known antigenic loci, and at several genomic regions not previously identified as sites of recent selection. We discuss the value of deep population-specific genomic analyses for identifying selection signals within sampled endemic populations of parasites, which may correspond to local selection pressures such as distinctive therapeutic regimes or mosquito vectors.
Data from: Global database of matched Plasmodium falciparum and P. vivax incidence and prevalence records from 1985–2013
Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique incidence records were collected for the database: 1,187 for P. falciparum and 493 for P. vivax. These data were gathered to model the relationship between clinical incidence and prevalence of infection and can be used for a variety of modelling exercises including the assessment of change in disease burden in relation to age and control interventions. The subset of data that have been used for such modelling exercises are described and identified.
Code and data for maximum likelihood estimation (MLE) of P. falciparum age from RNA-seq data
<p>The original R code was written by Avi Feller and Jacob Lemieux and is described in this publication:</p> <p>Lemieux JE, Gomez-Escobar N, Feller A, Carret C, Amambua-Ngwa A, Pinches R, Day F, Kyes SA, Conway DJ, Holmes CC and Newbold CI (2009): Statistical estimation of cell-cycle progression and lineage commitment in <em>Plasmodium falciparum </em>reveals a homogeneous pattern of transcription in <em>ex vivo</em> culture. <em>Proc Natl Acad Sci U S A</em> 106(18), 7559-7564 doi: 10.1073/pnas.0811829106 <a href="https://www.pnas.org/doi/full/10.1073/pnas.0811829106">https://www.pnas.org/doi/full/10.1073/pnas.0811829106</a></p> <p>In this deposition, the original R script is adapted for command-line use. For usage instructions, see file "README.md".</p> <p>Furthermore, this deposition contains RNA-seq data for <em>P. falciparum</em> 3D7 cultured with blood from individuals with high, normal or low iron status (experiment 1) or with blood from a healthy donor in the presence vs. absence of 0.7 µM hepcidin (experiment 2) at 6 – 9 and 26 – 29 hours post erythrocyte invasion (hpi). For more details see publication:</p> <p>Iron transport pathways in the human malaria parasite <em>Plasmodium falciparum</em> revealed by RNA-sequencing, Wunderlich et al. (<a href="https://www.biorxiv.org/content/10.1101/2024.04.18.590068v1" target="_blank" rel="noopener">biorxiv</a>).</p> <p>Finally, this deposition contains a variety of pre-processed datasets obtained from the following references:</p> <p>Bártfai R, Hoeijmakers WA, Salcedo-Amaya AM, Smits AH, Janssen-Megens E, Kaan A, Treeck M, Gilberger TW, Françoijs KJ and Stunnenberg HG (2010): H2A.Z demarcates intergenic regions of the <em>Plasmodium falciparum</em> epigenome that are dynamically marked by H3K9ac and H3K4me3. <em>PLoS Pathog</em> 6(12), e1001223 doi: 10.1371/journal.ppat.1001223</p> <p>Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL and Sabeti PC (2015): Strand-specific RNA sequencing in <em>Plasmodium falciparum</em> malaria identifies developmentally regulated long non-coding RNA and circular RNA. <em>BMC Genomics</em> 16(1), 454 doi: 10.1186/s12864-015-1603-4</p> <p>López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K and Su X-z (2011): Directional gene expression and antisense transcripts in sexual and asexual stages of <em>Plasmodium falciparum</em>. <em>BMC Genomics</em> 12(1), 587 doi: 10.1186/1471-2164-12-587</p> <p>Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C and Llinás M (2010): New insights into the blood-stage transcriptome of <em>Plasmodium falciparum</em> using RNA-Seq. <em>Mol Microbiol</em> 76(1), 12-24 doi: 10.1111/j.1365-2958.2009.07026.x</p> <p>Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppée JY and Scherf A (2014): Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in <em>Plasmodium falciparum</em>. <em>BMC Genomics</em> 15(1), 150 doi: 10.1186/1471-2164-15-150</p> <p>Wichers JS, Scholz JAM, Strauss J, Witt S, Lill A, Ehnold LI, Neupert N, Liffner B, Lühken R, Petter M, Lorenzen S, Wilson DW, Löw C, Lavazec C, Bruchhaus I, Tannich E, Gilberger TW and Bachmann A (2019): Dissecting the gene expression, localization, membrane topology, and function of the <em>Plasmodium falciparum</em> STEVOR protein family. <em>mBio</em> 10(4), doi: 10.1128/mBio.01500-19</p>
Re-exposure of Human Volunteers to a Heterologous Strain of P. Falciparum Sporozoites
ClinicalTrials.gov study NCT01660854. IPD Sharing: Not stated. Countries: 1. Publications: 2.
VAC063C: A Study to Assess Repeat Blood-stage P. Falciparum Infection
ClinicalTrials.gov study NCT03906474. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
P. Falciparum Infection Dynamics and Transmission to Inform Elimination (INDIE-1a)
ClinicalTrials.gov study NCT03705624. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Multi-Centre Trial Comparing Three Artemisinin-Based Combination Treatments on P. Falciparum Malaria
ClinicalTrials.gov study NCT00484900. IPD Sharing: Not stated. Countries: 4. Publications: 1.
Evaluation of Safety and Efficacy of Artemether-Lumefantrine Tablets in African Infants and Children With Uncomplicated P. Falciparum Malaria
ClinicalTrials.gov study NCT00709969. IPD Sharing: Not stated. Countries: 3. Publications: 1.
ICC-1132 - Candidate Vaccine Against P Falciparum Malaria
ClinicalTrials.gov study NCT00587249. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Azithromycin Plus Chloroquine Versus Mefloquine In the Treatment of Uncomplicated P. Falciparum Malaria.
ClinicalTrials.gov study NCT00367653. IPD Sharing: Not stated. Countries: 6. Publications: 1.
Antimalarial Treatments for Clearing Low Density P. Falciparum and Its Impact on Malaria Transmission
ClinicalTrials.gov study NCT00646126. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy and Safety of the Pediatric Formulation of Artemether- Lumefantrine in Children With Uncomplicated P. Falciparum Malaria.
ClinicalTrials.gov study NCT00386763. IPD Sharing: Not stated. Countries: 5. Publications: 2.
Controlled Human Malaria Infection After Bites From Mosquitoes Infected With Two Novel P. Falciparum Strains
ClinicalTrials.gov study NCT02149550. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy, Safety and Pharmacokinetic of ArtequinTM P. Falciparum Malaria
ClinicalTrials.gov study NCT00243737. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pyramax in Asymptomatic Carriers of P. Falciparum Monoinfections
ClinicalTrials.gov study NCT03814616. IPD Sharing: UNDECIDED. Countries: 2. Publications: 1.
Optimization of Controlled Human Malarial Infection by Injection of P. Falciparum Sporozoites in Non-Immune Adults
ClinicalTrials.gov study NCT01771848. IPD Sharing: Not stated. Countries: 1. Publications: 5.
A Study to Assess Safety, Immunogenicity and Parasite Growth Inhibition of an Asexual Blood Stage Vaccine for P. Falciparum Malaria
ClinicalTrials.gov study NCT00984763. IPD Sharing: Not stated. Countries: 1. Publications: 1.
P. Falciparum Resistance to Artemisinin in Vietnam
ClinicalTrials.gov study NCT02604966. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Pyronaridine-artesunate With Low Dose Primaquine for Preventing P. Falciparum Transmission
ClinicalTrials.gov study NCT04049916. IPD Sharing: NO. Countries: 2. Publications: 1.
Randomised Efficacy Study of Two Artemether-Lumefantrine Oral Formulations for the Treatment of Uncomplicated P. Falciparum Malaria
ClinicalTrials.gov study NCT00529867. IPD Sharing: Not stated. Countries: 1. Publications: 2.
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.