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18,535 results for “Infections”
A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations (Vancouver Island 2023, University of Wisconsin Madison Laboratory colony 2024)
Helminth infections represent a significant challenge to human, livestock, and wildlife health, yet they remain relatively under-studied, especially in terms of their ecological impacts. Better understanding of how these parasites spread in wildlife populations could improve our ability to predict and manage disease transmission across various species. Traditional detection methods, such as visually identifying parasites in environmental samples or infected hosts, often fall short, especially during the early stages of infection when parasite loads are minimal. In this study, we introduce a highly sensitive and precise droplet digital PCR (ddPCR) assay that quantifies helminth DNA in aquatic habitats, focusing on the 18S rRNA gene as a marker. These data utilize the model host-parasite system between the tapeworm Schistocephalus solidus, and its cyclopoid copepod host, Acanthocyclops robustus. The molecular assays are built around creating an infection standard in the lab, where copepods were singly infected with a single tapeworm parasite. We extracted DNA from 100 infected adults and used this as a standard to translate gene copy numbers from the ddPCR reactions to actual animal values. After creating a known lab standard, we then use the generated probes and primers to detect (and quantify!) infection burdens in field samples, which include both water filter samples (eDNA) and zooplankton tows from several lakes around Vancouver Island, B.C. The data presented here include well-specific data from ddPCR runs (amplitude of individual level oil droplets in the reaction) as well as each ddPCR analysis in its entirety. In order to prove the specificity of probes and probe-primers, we include here ddPCR runs of closely related helminth species, Schistocephalus cotti and Schistocephalus pungitii. We also consider the binding to another genera of copepod, the calanoid Eurytomora. All of the data wrangling, analysis, and data visualization are included as .Rmd files in th
Soil Carbon in a Hemlock Stand Infected by Hemlock Woolly Adelgid at Harvard Forest since 2015
The main objective of this research is to study changes in soil carbon stocks (soil C, root biomass) and fluxes (soil respiration) in a hemlock stand that is currently infested by the hemlock woolly adelgid, and where trees are declining in vigor and dying off. Soil respiration is measured throughout the growing season using an automated system, which produces a long-term, high-temporal-resolution series of soil respiration over multiple locations. Soil carbon stocks and root biomass are estimated by sampling soil in multiple locations throughout the hemlock stand following the sampling design used by Serita Frey at Harvard Farm (“Conant plots”). The large number of samples will be used to determine how many should be resampled in the future to be able to determine if any difference in soil C content or root biomass is statistically significant. Soil and roots will be sampled every 5 to 10 years to evaluate the trends in soil carbon stocks during and after the decline of hemlock caused by the hemlock woolly adelgid infestation.
Selecting for infectivity across metapopulations can increase virulence in the social microbe Bacillus thuringiensis:data set.
<p>Passage experiments that sequentially infect hosts with parasites have long been used to manipulate virulence. However, for many invertebrate pathogens passage has been applied naively without a full theoretical understanding of how best to select for increased virulence and this has led to very mixed results. Understanding the evolution of virulence is complex because selection on parasites occurs across multiple spatial scales with potentially different conflicts operating on parasites with different life-histories. For example, in social microbes, strong selection on replication rate within hosts can lead to cheating and loss of virulence, because investment in public goods virulence reduces replication rate. </p> <p>In this study<em> </em>we tested how varying mutation supply and selection for infectivity or pathogen yield (population size in hosts) affected evolution of virulence against resistant hosts in the specialist insect pathogen <em>Bacillus thuringiensis</em>, aiming to optimize methods for strain improvement against a difficult to kill insect target. We show that selection for infectivity using competition between sub-populations in a metapopulation prevents social cheating, acts to retain key virulence plasmids and facilitates increased virulence. Increased virulence was associated with reduced efficiency of sporulation, and possible loss of function in putative regulatory genes but not with altered expression of the primary virulence factors. Selection in a metapopulation provides a broadly applicable tool for improving the efficacy of biocontrol agents. Moreover, a structured host population can facilitate artificial selection on infectivity, while selection on life history traits such as faster replication or larger population sizes can reduce virulence in social microbes.</p>
Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection [Primary data]
<p>Primary data underlying journal article titled "<strong>Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection</strong>"</p>
Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention
<p>Single cell RNA seq datasets used for analysis in the Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention</p>
Dynamics of macrophage polarization in Salmonella infection : Raw data
<p>Experimental raw data of the paper "Dynamics of macrophage polarization support <em>Salmonella</em> persistence in a whole living organism", Leiba et al.</p>
dual scRNA-seq analysis of P. vivax infected hepatocytes
<p>Malaria-causing <em>Plasmodium vivax</em> parasites can linger in the human liver for weeks to years, and then reactivate to cause recurrent blood-stage infection. While an important target for malaria eradication, little is known about the molecular features of the replicative and non-replicative states of intracellular <em>P. vivax</em> parasites, or their human host-cell dependencies and the host responses to them. Here, we leverage a bioengineered human microliver platform to culture patient-derived <em>P. vivax</em> parasites in primary human hepatocytes and conduct transcriptional profiling. By coupling enrichment strategies with bulk and single-cell analyses, we captured both parasite and host transcripts in individual hepatocytes throughout the infection course. We define host- and state-dependent transcriptional signatures and identify previously unappreciated populations of replicative and non-replicative parasites, sharing features with sexual transmissive forms. We find that infection suppresses transcription of key hepatocyte function genes, and that <em>P. vivax</em> elicits an innate immune response that can be manipulated to control infection. Our work provides an extendible framework and resource for understanding host-parasite interactions and reveals new insights into the biology of <em>P. vivax</em> dormancy and transmission.</p>
Dataset of 'HIV infection is associated with compromised tumor microenvironment adaptive immune reactivity in Hodgkin Lymphoma'
<p><span><span>§<span> </span></span></span><strong><span>:</span></strong><span>The data were generated using the i) GeoMx Digital Spatial Profiler (DSP) platform developed by Nanostring Technologies. GeoMx analysis utilizes <em>in situ </em>RNA hybridization with Whole Atlas Transcriptome probe (Nanostring) and ii) HTG platform (Immune Response kit) Our dataset comprises samples from donors categorized as HLposHIVnegEBVneg, HLposHIVposEBVpos, or HLposHIVnegEBVpos (HL: Hodgkin Lymphoma). Regions of interest (ROI) were spatially profiled to capture distinct molecular signatures associated with these donor categories.</span></p>
Infection Inspection: Classifications and images of ciprofloxacin-treated Escherichia coli clinical isolates
<p>This dataset includes a .csv file with the image metadata and a folder of RGB images of <i>E. coli</i> grown from clinical isolates with varying concentrations of the antibiotic ciprofloxacin and varying minimum inhibitory concentrations. The <i>E. coli</i> cell membranes are stained with Nile Red and the DNA is stained with DAPI. The details of the image data collection are included in: https://doi.org/10.1038/s42003-023-05524-4. The classification data come from a Zooniverse citizen science project, Infection Inspection. (https://www.zooniverse.org/projects/conor-feehily/infection-inspection) Volunteers learned how to interpret ciprofloxacin response phenotypes as antibiotic-sensitive or antibiotic-resistant, and their classifications are included in the Metadata.csv file.</p><p>This dataset could be used for further analysis into the volunteer classifications, or the image data could be used for further image feature analysis of the ciprofloxacin response phenotypes.</p>
Associating Land Cover Changes with Climate Sensitive Infection in Fennoscandia, as part of the CLINF project: Example on Tick-Borne Diseases
<p>The data was used as part of the IJERPH article below. The GeoJSON and shapefile ZIP archive are two versions of the same geometries to represent geographically the districts whole of Fennoscandia and the Russian districts of Leningrad, St Petersburg, Vologda, Arkhangelsk, Nenetsia, Murmansk, Karelia, and Komi, making up 69 districts used for the analysis.</p> <p>Leibovici DG, Bylund H, Björkman C, Tokarevich N, Thierfelder T, Evengård B, Quegan S (2021). Associating Land Cover Changes with Patterns of Incidences of Climate Sensitive Infections: An Example on Tick-Borne Diseases in the Nordic Area. <strong><em>International Journal of Environmental Research and Public Health, 18(20):10963. <a href="https://doi.org/10.3390/ijerph182010963">doi:10.3390/ijerph182010963</a></em></strong></p> <p>Special Issue: <a href="https://www.mdpi.com/journal/ijerph/special_issues/Climate-Change_Effects">https://www.mdpi.com/journal/ijerph/special_issues/Climate-Change_Effects</a></p> <p> </p>
Database of infection control and surveillance program, 2011-2020
<p>A full anonymized data set was collected as a part of the ICU infection control and surveillance program; 01/01/2011-12/31/2020</p> <p>File "Zenodo_DB_v4<a href="https://zenodo.org/api/files/6d089d03-7a43-4513-b476-92f438837941/VAE_Data_Main_0821_1338.csv">.csv</a>" contains daily data (one row is one day) on infection surveillance ordered by date.</p> <p>File "<a href="https://zenodo.org/api/files/6d089d03-7a43-4513-b476-92f438837941/Data_Dictionary_MainDB.csv">Data_Dictionary_MainDB_2021.csv</a>" contains the description of all variables from the data set.</p> <p> </p>
Dataset on UAV RGB videos acquired over a vineyard property of Bodegas Terras Gauda at an early stage of Botrytis cinerea infection in 2021
<p>The videos were collected in a vineyard owned by Bodegas Terras Gauda, in June 2021. The videos were collected with a DJI Matrice 210 RTK UAV, which had a DJI Zenmuse X5S sensor onboard. A total of 4 rows were recorded with side videos. The flights were carried out on a sunny day with wind velocity lower than 0.5 m/s. Annotations of the grape clusters in the MOTS style are provided. </p>
Weekly CoMix contact matrices for UKHSA COVID-19 dashboard and ONS COVID-19 infection survey age-groups
<p>Weekly contact matrices calculated from data collected as part of the UK arm of the CoMix survey. All contact matrices were calculated over two survey rounds (SR) of data to account for alternating panels (the indicated SR and the previous SR). Full details of composition can be found in Munday et. al. [1]. Contact matrices are provided for age-groups consistent with publicly available case data from the UKHSA COVID-19 dashboard <strong> (0-9, 10-19, 20-29, 30-39, 40-49, 50-59, 60-69, 70+) </strong>and publicly available aggregates of infection and antibody prevalence from the ONS COVID-19 infection survey <strong>(2-10, 11-15, 16-24, 25-34, 35-49, 49-69 and 70+)</strong>. The data is provided in qs files as 1000 bootstrapped samples of each contact matrix for weekly 'survey rounds' between 19 and 94 (see directory "survey_round_dates.csv"). The files that begin with UKHSA contain the contact matrices for the age stratification of the UKHSA COVID-19 dashboard case data. The files that begin with ONS contain the contact matrices for the age stratification of the ONS COVID-19 infection survey. </p> <p>Ethics: The study and method of informed consent were approved by the ethics committee of the London School of Hygiene & Tropical Medicine (LSHTM; reference number 21795).</p> <p>1. Munday, J.D., Jarvis, C.I., Gimma, A. <em>et al.</em> Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data. <em>BMC Med</em> <strong>19</strong>, 233 (2021). https://doi.org/10.1186/s12916-021-02107-0</p>
Neutrophil and emergency granulopoietic drivers of sepsis immune suppression and an extreme response to infection
<p>The dysregulated host response to infection leading to organ dysfunction is highly heterogeneous. It is currently poorly delineated by sepsis as a clinical syndromic classification, thus confounding immunotherapy trials. Here we establish the pathophysiology and potential therapeutic targets of a specific extreme response to infection state (sepsis response signature SRS1), characterised by immune compromise and poor outcome. We first derive a whole blood single-cell multi-omic atlas of the sepsis response (2727,993 cells, n=39), finding an increase in IL1R2+ immature neutrophils in SRS1, which we confirmed by CyTOF and RNA-sequencing (n=53). We next uncovered high activity of neutrophil STAT3 gene expression programs in SRS1, which were shared across multiple infectioius disease settings (n=1044) irrespective of the clinical definition of the patient cohorts. We observed elevated plasma G-CSF and IL-6 in SRS1, suggesting heightened emergency granulopoiesis (EG). We therefore characterised patient and healthy control hematopoietic stem cells (HSCs) using single-cell RNA/chromatin accessibility multi-omics (29,366 cells, n=27), identifying SRS1-specific EG transcriptional skewing, together with STAT3 and EG master regulator CEBPB epigenetic signatures. Our findings establish a common cellular axis present across extreme responses to infection, reveal its hematopoietic origin, and nominate G-CSF and IL-6 as potential therapeutic targets for the SRS1 state.</p> <p> </p> <p>The present data deposit includes processed and quality-controlled data tables for:</p> <p>1. Whole blood leukocytes profiled with the BD Rhapsody platform in a cohort of 39 sepsis patients (RNA and protein count matrices, as well as their accompanying metadata table)</p> <p>2. Circulating HSCs in blood profiled with the 10X multiomics platform in a cohort of 27 sepsis patients (RNA and ATAC-seq count matrices, as well as their accompanying metadata tables)</p>
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection
<p>Processed TCRbeta and TCRalpha repertoires after mild COVID-19 (Version 2.0: day 85 timepoints added) infection, see preprint: <a href="https://www.biorxiv.org/content/10.1101/2020.05.18.100545v3">https://www.biorxiv.org/content/10.1101/2020.05.18.100545v3</a></p> <p>and GitHub repository: <a href="https://github.com/pogorely/Minervina_COVID">https://github.com/pogorely/Minervina_COVID</a></p> <p>Two donors (M and W), two biological replicates of PBMC (F1 and F2), CD4+, CD8+, and Memory subpopulations for each post-infection time points (day 15, 30, 37, 45, 85 post-infection), and pre-infection PBMC repertoires sampled in 2019 and 2018. </p>
Supplementary Data - MORTALITY RATE DUE TO PULMONERY FIBROSIS ASSOCIATED WITH SARS- COV-2 INFECTION: SCOPE OF BEST FIT REGRESSION
<p>The dataset contains number of infected pateints - Death Frquencies - Mortality rate globally due to pulmonary fibrosis associated with SARS-COV-2 infection with effect from 21st Jan to 28 th April ,2020 . Data analysis report by best fit regression software Curve Expert V.1.4 supported with Spreadsheet ( Excel , Office 2007 ) are included for computation of statistical significance .</p>
Public dataset for Antibiotic Prophylaxis for Surgical Site Infections as a Risk Factor for Infection with Clostridium difficile
<p>This is the minimal publicly available dataset for the manuscript titled "Antibiotic Prophylaxis for Surgical Site Infections as a Risk Factor for Infection with Clostridium difficile". We have also included the data dictionary. </p>
Type III interferons may suppress viral infections by triggering cell death -- Imaging Dataset
<p>This dataset accompanies the article "Type III interferons may suppress viral infections by triggering cell death". Earlier version is available as a preprint, <a href="https://doi.org/10.1101/2024.09.09.612051" target="_blank" rel="noopener">https://doi.org/10.1101/2024.09.09.612051</a>. The updated dataset includes quantifications for Figure 7C and Figure 7D.</p>
Time-lapse 3D confocal microscopy videos of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains
<div>The dataset consists of time-lapse, 3D confocal images of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains. Images were captured at 60X magnification in an environmental chamber at 35°C for live-cell imaging. Host cell mitochondria were labeled with red fluorescent protein (RFP) and infected with both wildtype (wt) and ESAT-6 operon knockout mutant labeled with green fluorescent protein (GFP) at MOI of 100 for 24 hours at 35°C. Infected cells were identified and analyzed to explore the effect of pathogenic mycobacteria on mitochondrial morphology over time.</div> <div> </div> <div>More details available in this preprint: <a href="https://doi.org/10.48550/arXiv.2411.06035">https://doi.org/10.48550/arXiv.2411.06035</a></div>
Latent infection of an active giant endogenous virus in a unicellular green alga
<p>Additional data for Latent infection of an active giant endogenous virus in a unicellular green alga.</p>
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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.
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