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796 results for “Plasmodium”
Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies
<p>AIRR Community-compliant information comprising all antibodies described in EMBO Mol Med 15:e17454 [DOI:10.15252/emmm.202317454].</p>
A dataset of human and Plasmodium falciparum genotypes in severe malaria cases from The Gambia and Kenya
<p>This data release contains human and <em>Plasmodium falciparum</em> malaria genotypes from the article:</p> <p><strong>Malaria protection due to sickle haemoglobin depends on parasite genotype</strong></p> <p>Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne<br> M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy<br> Nguyen, Sónia Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto<br> Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin<br> Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor10, David J.<br> Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski</p> <p>Nature (2021) doi: <a href="https://doi.org/10.1038/s41586-021-04288-3">10.1038/s41586-021-04288-3</a> <strong>bioRxiv link</strong>: <a href="http://doi.org/10.1101/2021.03.30.437659">doi.org/10.1101/2021.03.30.437659</a>.</p> <p>The release contains genotypes from human and <em>Plasmodium falciparum</em> genetic variants, genotyped using blood samples from 4,171 children ascertained with severe symptoms of malaria at the Royal Victoria Teaching Hospital (now the Edward Francis Small Teaching Hospital), The Gambia, and from the Kilifi District Hospital (now Kilifi County Hospital), Kenya in the period 1995-2009.</p> <p>An accompanying set of association test summary statistics has also been released on Zenodo (doi: <a href="https://doi.org/10.5281/zenodo.5722497">10.5281/zenodo.5722497</a>). Please see <a href="http://www.malariagen.net/resource/32">www.malariagen.net/resource/32</a> for full details of other resources associated with the above manuscript.</p> <p> </p>
Data files: Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets
<p>Scripts, preprocessed count matrices, and single-cell data objects generated in <strong>“Single-cell RNA profiling of <em>Plasmodium vivax</em><em>-</em>infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets” </strong></p>
Validation data for a Microwave Exposure Prototype for In Vitro Growth Inhibition of Plasmodium falciparum
<p>The dataset presented in this article revolves around the validation of an innovative irradiation device designed for <em>in vitro</em> malaria tests. The motivation stems from the escalating need for new malaria treatments due to the high mortality rates, the absence of an effective vaccine, and rising antimalarial drug resistance. The theoretical background for generating this data is based on prior studies indicating that microwave exposure can non-thermally kill malaria parasites by interacting with hemozoin crystals within infected erythrocytes, a process in which healthy cells remain unaffected, probably due to the absence of these crystals. This dataset aims to provide a thorough validation of the device's biological and electrical efficacy, by providing models to simulate various parameters such as the magnetic and electric field strength, and experimentally validate the biological effects on parasite viability under controlled microwave exposure. This contribution is pivotal for advancing research in electromagnetic therapy as a potential treatment for malaria, providing a foundational dataset for future experimental and theoretical work.</p>
Application of optical tweezer technology reveals that PfEBA and PfRH ligands, not PfMSP1, play a central role in Plasmodium-falciparum merozoite-erythrocyte attachment, Supporting Information
<p>This repository contains the dataset and analysis scripts associated with the upcoming publication titled <em>Application of optical tweezer technology reveals that PfEBA and PfRH ligands, not PfMSP1, play a central role in Plasmodium-falciparum merozoite-erythrocyte attachment</em>. The repository includes a comprehensive collection of data and scripts related to optical tweezer experiments, growth assays, qPCR data, and supplementary information. It is organized into several sections, each detailing different aspects of the study:</p> <ul> <li><strong>Growth Assays:</strong> Includes raw and processed data on parasitemia levels, invasion rates, and growth rate assays, along with corresponding Jupyter notebooks and Python scripts for data visualization (e.g., <code>GrowthAssayPlotlib.py</code>, <code>Plot GA1.ipynb</code>, and <code>GA2_df_melted.json</code>).</li> <li><strong>qPCR Data:</strong> Contains results from multiple qPCR runs, including quantification data for various samples, as well as analysis scripts and plotted results (<code>qpcr_plotbench.ipynb</code>, <code>qPCR_plotting.py</code>, etc.). Data files such as <code>.xlsx</code> and <code>.json</code> contain gene expression data and fold changes to NF54.</li> <li><strong>Optical Tweezer Experiments:</strong> Includes detailed results and plots from optical tweezer measurements of attachment forces, time dependence, and multiple merozoite attachments. Notebooks (<code>tweezer_plots.ipynb</code>, <code>Antibody_binding_assay_plots.ipynb</code>) and data files support these analyses.</li> <li><strong>Optical Tweezer Images</strong>: Includes images that were used to measure RBC diameters for deformation and force measurements in <code>.tiff</code> format.</li> <li><strong>Supplementary Information (SI):</strong> Provides additional data and visualizations, such as scatter plots of two stretched RBCs, time post-egress vs. detachment force, and antibody GIA flow data. The accompanying figures (e.g., <code>SupFig1d_egress time vs force_3D7.svg</code>, <code>SupFig5a_GIA.svg</code>) are provided as <code>.svg</code> files.</li> </ul> <p>This repository offers all necessary resources to replicate the findings, including the complete codebase, raw data, and graphical representations of results. Researchers are encouraged to explore the included notebooks and datasets for detailed insights.</p>
Plasmodium falciparum infection in febrile Congolese children: prevalence of clinical malaria ten years after introduction of Artemisinin-combination therapies
<p>dataset used in the paper.</p>
Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya
<p>This dataset contains summary statistics for association tests between human and<br> <em>Plasmodium falciparum</em> malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya. These results underlie the analysis described in our paper:</p> <p><strong>"Malaria protection due to sickle haemoglobin depends on parasite genotype"</strong></p> <p>Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia M. Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski</p> <p>Nature (2021) doi: <a href="https://doi.org/10.1038/s41586-021-04288-3">10.1038/s41586-021-04288-3</a> <strong>bioRxiv link</strong>:: <a href="https://doi.org/10.1101/2021.03.30.437659">doi.org/10.1101/2021.03.30.437659</a><br> <br> The genotype data underlying these summary statistics has also been deposited on Zenodo<br> (<a href="https://zenodo.org/record/4973477">doi:10.5281/zenodo.4973477</a>). The <a href="https://www.well.ox.ac.uk/~gav/hptest)">HPTEST software</a> used to generate these results has also been deposited (<a href="https://doi.org/10.5281/zenodo.5685580">doi:10.5281/zenodo.5685580</a>). Please see the <a href="https://www.malariagen.net/resource/32">MalariaGEN website</a> for a full list of datasets which have been released with this manuscript.</p> <p><strong>Data contents.</strong></p> <p>The dataset consists of a single <a href="http://sqlite.org">sqlite database file</a> containing the results, and an accompanying README file in markdown and html format. Please see the README file for full details of the data contents.</p> <p> </p>
Data files: Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures
<p>Scripts, preprocessed count matrices, single-cell data objects, and generated data (tables and .rds files) from the scRNA-seq analyses performed in <strong>“Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures".</strong></p> <p> </p>
Figure 4 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 4. Prevalence of six different sub-allele types of Pvmsp-3β (A1-A3, B1-B2 and C1) based on PCR-RFLP.
Figure 2 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 2. Prevalence of nine different sub-allele types of Pvmsp- 3α(A1-A4), (B1-B3), C1 and D are the nine different alleles from PCR-RFLP.
Tutorial DAPCy: the Plasmodium falciparum (Pf7) genotype dataset from MalariaGEN
Open the record for dataset details and reuse information.
Fig. 3. Minimum spanning network for Haemoproteus and Plasmodium mitochondrial DNA cytochrome b in Spatial, temporal, molecular, and intraspecific differences of haemoparasite infection and relevant selected physiological parameters of wild birds in Georgia, USA
Fig. 3. Minimum spanning network for Haemoproteus and Plasmodium mitochondrial DNA cytochrome b haplotypes detected in four species of passerines from Georgia (USA). Circles are drawn proportional to the frequency at which haplotypes were observed. Color represents the host species from which haplotypes originated: red for Northern Cardinal (Cardinalis cardinalis), blue for Indigo Bunting (Passerina cyanea), yellow for White-throated Sparrow (Zonotrichia albicollis), and grey for Tufted Titmouse (Baeolophus bicolor). A single mutation separates nodes unless explicitly indicated by number. Letters within each node refer to Table 8 which indicates the haplotype name, sampling location, and other factors associated with hosts.
Fig. 2 in Plasmodium (Novyella) nucleophilum from an Egyptian Goose in São Paulo Zoo, Brazil: microscopic confirmation and molecular characterization
Fig. 2. Bayesian phylogeny of cytochrome b gene lineages of species of avian haemosporidian parasites. A lineage recorded in the Egyptian Goose Alopochen aegyptiacus is provided underlined. Names of the lineages are given after the species names of parasites. GenBank accession numbers of the lineages are provided before the parasite species names. Nodal support values (in percentage) indicate posterior clade probabilities. Plasmodium species from Novyella subgenus are boxed.
Fig. 1 in Plasmodium (Novyella) nucleophilum from an Egyptian Goose in São Paulo Zoo, Brazil: microscopic confirmation and molecular characterization
Fig. 1. Photomicrographs of Plasmodium parasites visualized from thin blood smears obtained from an Egyptian Goose (Alopochen aegyptiacus) in São Paulo Zoo, Brazil. Characteristic of Plasmodium (Novyella) nucleophilum (lineage EG01, GenBank JX467689) the trophozoite (a), meronts (b–c), macrogametocytes (d, e), and microgametocyte (f) are appressed to erythrocyte nuclei (nucleophilic features). Plasmodium (Haemamoeba) sp. (g–i) lacks nucleophilic blood stages and possesses large roundish trophozoites, each with a prominent centrally located vacuole; pigment granules are gathered around the vacuoles. Note that early Plasmodium (H.) sp. trophozoites markedly displace erythrocyte nuclei (g). Arrows, pigment granules. Scale bar = 10 µm.
Fig. 2 in Hemoparasites in a wild primate: Infection patterns suggest interaction of Plasmodium and Babesia in a lemur species
Fig. 2. Age-dependence of Babesia sp. infections (grey) and Plasmodium sp. infections (black). The lines represent the predicted values according to the two different GLMMs.
Fig. 1 in Hemoparasites in a wild primate: Infection patterns suggest interaction of Plasmodium and Babesia in a lemur species
Fig. 1. Maximum likelihood tree of malaria parasite cytochrome b sequences (P. = Plasmodium). The clade formed by lemur malaria parasites is blue. The two sequences detected in this study are highlighted with grey rectangles. Bootstrap values are reported above branches when>50. The scale is in substitution per site.
Fig. 1 in Apparent effect of chronic Plasmodium infections on disease severity caused by experimental infections with Mycoplasma gallisepticum in house finches
Fig. 1. Mean severity of eye lesions ± SE (circles), and M. gallisepticum-load (log (qPCR+1)) (triangles) of birds infected through horizontal transmission with the CA2015 strain of M. gallisepticum. Birds in which Plasmodium was detected by PCR (grey symbols) developed more severe disease than birds in which Plasmodium was not found (white symbol). As there is no significant interaction between M. gallisepticum ‾strain and Plasmodium infection (Table 2) the results for the other M. gallisepticum strains are qualitatively similar and therefore not shown.
Fig. 3 in Close relationship of Plasmodium sequences detected from South American pampas deer (Ozotoceros bezoarticus) to Plasmodium spp. in North American white-tailed deer
Fig. 3. Phylogenetic relationship of Plasmodium sequences from Brazilian pampas deer within ungulate Plasmodium spp. The tree was constructed using concatenated partial nucleotide sequences of cytb and cox1 by maximum likelihood (ML) method based on the GTR + I + G model. Bootstrap values (BV) for ML with 1000 replicates of ultrafast bootstrap analysis and Bayesian posterior probability (BPP) are indicated for each internal branch. The compositions of collapsed clades are described in Fig. 2 legend. The length for the substitutions/site (0.07) is indicated.
Fig. 2 in Close relationship of Plasmodium sequences detected from South American pampas deer (Ozotoceros bezoarticus) to Plasmodium spp. in North American white-tailed deer
Fig. 2. Phylogenetic relationships of Plasmodium sequences from Brazilian pampas deer within Haemosporidia. The tree was constructed using ∼3.4 kb of partial mitochondrial nucleotide sequences by the maximum likelihood (ML) method based on the GTR + I + G model. Bootstrap values (BV) for ML with 1000 replicates of ultrafast bootstrap analysis and Bayesian posterior probability (BPP) are indicated for each internal branch. The compositions of collapsed clades are Leucocytozoon (L. fringillinarium, L. majoris, and L. sabrasezi); Haemoproteus and Parahaemoproteus (Haemoproteus sp. jb1.JA27, Haemoproteus sp. jb2.SEW5141, and Parahaemoproteus vireonis); and bird, lizard and non-ungulate mammalian Plasmodium (P. gallinaceum, P. relictum, P. juxtinucleare, P. lutzi, P. floridense, P. mexicanum, P. falciparum, P. vivax, P. malariae, P. ovale, P. coatneyi, P. cynomolgi, P. fieldi, P. gonderi, P. inui, P. knowlesi, P. fragile, P. simiovale, P. simium, P. hylobati, P. reichenowi, P. billicollinsi, P. billbrayi, P. berghei, P. chabaudi, P. vinckei, and P. yoelii). Mitochondrial DNA sequences (including cytb and cox1) used in this study were listed in the Supplementary Table S1 of Templeton et al. (2016a). Nucleotide sequences of Plasmodium sp. in the North American white-tailed deer was based on Table S4 of Martinsen et al. (2016). Nucleotide positions containing indels or undetermined nucleotides, or those where the alignment was not clearly made were excluded. Nucleotide positions corresponding to the P. falciparum mtDNA (NC_002375.1) 974–1502, 1509–1576, 1578–1628, 1637–1678, 1698–1760, 1762–1769, 1774–1800, 1806–1831, 1834–1867, 1870–1909, 1914–2031, 2050–3474, and 3486–4444 were used. The length for the substitutions/site (0.04) is indicated.
Experiments for detection of Plasmodium berghei infected Anopheles stephensi mosquitoes using near-infrared spectroscopy
<p> </p> <p><strong>Experiments for detection of <em>Plasmodium berghei</em> infected <em>Anopheles stephensi</em> mosquitoes using near-infrared spectroscopy</strong></p> <p>This dataset contains near-infrared spectroscopy (NIRS) measurements on <em>Plasmodium berghei</em> infected <em>Anopheles stephensi</em> mosquitoes reared in the lab together with either oocyst counts or sporozoite counts, correponding to the two experiments undertaken:</p> <ul> <li>Experiment 1 (oocysts), file "NIRSdata2017_Lab_AnSteph_PlasmBerg_oocysts.txt"</li> <li>Experiment 2 (sporozoites), file "NIRSdata2017_Lab_AnSteph_PlasmBerg_sporozoites.txt"</li> </ul> <p>For further details on the experimental setup see: P.M. Esperança, A.M. Blagborough, D.F. Da, F.E. Dowell, T.S. Churcher (2018) "Detection of <em>Plasmodium berghei</em> infected <em>Anopheles stephensi</em> using near-infrared spectroscopy". <em>Parasites and Vector</em>, <strong>11</strong>:377. <a href="https://doi.org/10.1186/s13071-018-2960-z">https://doi.org/10.1186/s13071-018-2960-z</a>.</p> <p>The structure of the data files is as follows:</p> <ul> <li>column 1 (<strong>Scan_ID</strong>): scan identifier</li> <li>column 2 (<strong>Mosquito_ID</strong>): mosquito identifier</li> <li>column 3 (<strong>Replication</strong>): replication identifier</li> <li>column 4 (<strong>Oocysts</strong> or <strong>Sporozoites</strong>): response variable <ul> <li>for the Experiment 1, the oocyst count<em> </em>on a level-scale</li> <li>for the Experiment 2, the sporozoite count on a log-scale: 0 (no sporozoites), 1 (1–10), 2 (11–100), 3 (101–1000), 4 (>1000)</li> </ul> </li> <li>columns 5 to 2155 (<strong>x350</strong> to <strong>x2500</strong>): NIRS absorbance measurements for wavelengths in the range 350 to 2500 nanometers</li> </ul> <p> </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.