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1,257 results for “Human infections”
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>
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>
Zellige example dataset: primary culture of human bronchial cells infected by SARS-CoV-2
<p>A human bronchial epithelium was infected by SARS-CoV-2. The specimen was imaged four days post-infection. The z-stack image encompasses the very irregular epithelium surface. It was acquired with a point scanning microscope (Zeiss LSM700) equipped with Zeiss Plan-Apochromat 63x lens (NA=1.4). Pixel size 0.110µm, z step 0.4µm. This dataset contains both the ground-truth height map and the height map generated with Zellige. The Zellige parameters used are: <span class="math-tex">\(T_{A}=23, T_{otsu}=16, S_{min}=5, \sigma_{xy}=4, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.9, T_{OSE2}=0.1, R_{2}=5, C_{2}=0.8.\)</span>.</p> <p>Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map.</p> <p>See the related paper:<br> <a href="https://hal-pasteur.archives-ouvertes.fr/pasteur-03319522">https://hal-pasteur.archives-ouvertes.fr/pasteur-03319522</a></p> <p>See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: <a href="https://doi.org/10.1101/2022.04.05.485876">https://doi.org/10.1101/2022.04.05.485876</a></p> <p> </p>
HBV-only reads from cultured human hepatocytes infected with HBV used for testing HBVouroboros functionalities.
<p>The dataset consists of bulk-RNA reads extracted from cultured human hepatocytes infected with HBV. The data is used to test the performance of the HBVouroboros software (https://github.com/bedapub/HBVouroboros).</p> <p>Note that fastq files are comprised of reads that map to HBV genome, as such sample files for negative controls of HBV infection are empty files. We include these for the sake of completeness and to reflect the experimental design.</p>
Salmonella enterica serovar Derby isolated from eggs show genomic and phenotypic traits that may be linked to inability to produce human infection.
<p><em><span>Salmonella enterica</span></em><span> serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to <em>S</em>. Enteritidis from poultry, we conducted a large survey of commercially available eggs, where we isolated many <em>S.</em> Enteritidis strains but surprisingly also a much larger number (ratio 5:1) of <em>S</em>. Derby strains. No single case of <em>S</em>. Derby infection was detected in that period, suggesting that the <em>S</em>. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates, as well as fifteen isolates from pork or human infection that were isolated in Uruguay before and after that period, and all sequenced strains had the same sequence type <span>(ST40). Phylogenomic genomic analysis was conducted using more than 3500 genomes from the same sequence type (ST), revealing that Uruguayan isolates clustered into four distantly related lineages. Population structure analysis (BAPS) suggested the division of the analyzed genomes into nine different BAPS1 groups, with Uruguayan strains clustering within four of them. </span>All egg isolates clustered together as a monophyletic group and showed marked differences in gene content with the strains in the other clusters. <span>Differences included the absence of a C-terminal fragment of the <em>speF</em> gene, as well as variations in the composition of mobile genetic elements, such as plasmids, insertion sequences, transposons, and phages, between egg isolates and human/pork isolates.</span></span> <span>Egg isolates showed an acid susceptibility phenotype, reduced ability to reach the intestine after oral inoculation of mice, and reduced induction of SPI-2 <em>ssaG</em> gene, compared to human isolates from other monophyletic groups. Mice challenge experiments showed that mice infected intraperitoneally with human/pork isolates died between 1-7 days p.i., while all animals infected with the egg strain survived the challenge. Altogether, our results suggest that loss of gene functions and the absence of plasmids in egg isolates may explain why these <em>S</em>. Derby were not capable of producing human infection despite being at that time, the main serovar recovered from eggs countrywide.</span></p>
Evaluation of two 4th generation point-of-care assays for the detection of Human Immunodeficiency Virus infection.
<p>Background. Fourth generation assays detect simultaneously antibodies for HIV and the p24 antigen, identifying HIV infection earlier than previous generation tests. Previous studies have shown that the Alere Determine HIV-1/2 Combo has lower than anticipated performance in detecting antibodies for HIV and the p24 antigen. Furthermore, there are currently very few studies evaluating the performance of Standard Diagnostics BIOLINE HIV Ag/Ab Combo.</p> <p>Objective: To evaluate the performance of the Alere Determine HIV-1/2 Combo and the Standard Diagnostics BIOLINE HIV Ag/Ab Combo in a panel of frozen serum samples.</p> <p>Study Design: The testing panel included 133 previously frozen serum specimens from the UCLA Clinical Microbiology & Immunoserology laboratory. Reference testing included testing for HIV antibodies by a 3<sup>rd</sup> generation enzyme immunoassay followed by HIV RNA detection. Antibody negative and RNA positive sera were also tested by a laboratory 4<sup>th</sup> generation HIV Ab/Ag enzyme immunoassay.</p> <p>Results: Reference testing yielded 97 positives for HIV infection and 36 negative samples. Sensitivity of the Alere test was 95% (88-98%), while the SD Bioline sensitivity was 91% (83-96%). Both assays showed 100% (90-100%) specificity. No indeterminate or invalid results were recorded. Among 13 samples with acute infection (HIV RNA positive, HIV antibody negative), 12 were found positive by the first assay and 8 by the second. The antigen component of the Alere assay detected 10 acute samples, while the SD Bioline assay detected only one.</p> <p>Conclusions: Both rapid assays showed very good overall performance in detecting HIV infection in frozen serum samples, but further improvements are required to improve the performance in acute infection.</p>
Data for Variation of human milk lactoferrin in relation to maternal-infant infection status among dyads from northern Kenya
<p><strong>Information about</strong><strong> Data</strong></p> <p> </p> <p>DOI: 10.5281/zenodo.6581038</p> <p>September 8, 2022</p> <p> </p> <p>Hello, and thanks for your interest in this data set.</p> <p> </p> <p>This file contains the data utilized for a journal manuscript, "Variation of human milk lactoferrin in relation to maternal-infant infection status among dyads from northern Kenya" by Nerli Paredes Ruvalcaba, Amelia N Odo, and Masako Fujita, under review for publication. Data are found under the Data tab, and the variable coding information under the Code tab.</p> <p> </p> <p>The data are for the concentrations of lactoferrin in mothers' milk and reported illnesses among 83 mother-infant dyads in Ariaal communities of northern Kenya. This is a subset of data on milk lactoferrin, characterized in the Biomarker Laboratory for Anthropological Research at Michigan State University in 2019, using cryogenically archived milk specimens. The milk specimens and other data on maternal and infant characteristics, including illness recalls, were originally collected in research among 241 mother-infant dyads by Masako Fujita in 2006 in collaboration with the Center for Public Health Research of Kenya Medical Research Institute (KEMRI) under approvals by the institutional review boards of the University of Washington and KEMRI.</p> <p> </p> <p>Please contact Fujita (masakof@msu.edu) for questions regarding the data.</p> <p> </p> <p>If you decide to use the data, please cite this file's DOI 10.5281/zenodo.6581038 and the above-mentioned manuscript upon publication, and acknowledge the following parties for grant support:</p> <p>National Science Foundation (BCS-0622358, BCS-1638167);</p> <p>Wenner-Gren Foundation (Gr. 7460, Gr. 9278);</p> <p>Provost Undergraduate Research Initiative Grant, Michigan State University; and </p> <p>African Futures Research Leadership Program of the Alliances for African Partnership, Michigan State University</p> <p> </p> <p>Thanks,</p> <p>Masako Fujita</p> <p> </p> <p>Masako Fujita, Associate Professor of Anthropology</p> <p>Michigan State University</p> <p>ORCID: 0000-0001-9173-6678</p> <p>Emaiil: masakof@msu.edu</p>
The Supplementary Material for the article entitled "Comparative analysis of global transcriptomes in nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after infecting human intestinal epithelium in vitro"
<p>The Supplementary Material (Additional files 1-5, including Table S1-S4 and Figure S1) for this article.</p> <p> </p> <p><strong>Table S1.</strong> Upregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S2.</strong> Downregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S3. </strong>The enriched GO terms in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S4. </strong>The enriched KEGG pathways in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Figure S1. </strong>The enriched GO terms and KEGG pathways in Group B relative to Group A. Bar charts show the enriched GO terms (A) and the enriched KEGG pathways (B) by significance power. Color of bars indicate power of significance and length in x axes of bar indicate number of annotated genes in the particular term of pathway. Cnetplots show the relationship between GO term (C) and KEGG pathways (D). Dot size representing GO terms and KEGG pathways indicates number of significantly changed and its annotated genes. The GO terms or KEGG pathways connected through their common and annotated genes. </p>
Genome-wide expression profile of AAV2-infected normal human fibroblasts
<p>Datasets containing the genome-wide expression profile of AAV2-infected normal human fibroblasts.</p> <p>Raw data: results--A1--over--M1-3.txt</p> <p>p<0.01, reads>40: A1_M1_p0.01_r40_fc not restricted.txt</p>
Fig. 2 in Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA
Fig. 2 Phylogenetic tree demonstrating the relative position of Leishmania sp. strain 218-L139 based on a concatenated sequence comprising several nuclear loci. Phylogenetic tree demonstrating the relative position of Leishmania strain 218-L139 (brown star) based on alignment of a concatenated sequence comprising the 18S rDNA, 28S rDNA, CKIIα, GAPDH, and RPOIILS nuclear sequences. The alignment contains 6577 positions from 33 taxa. The tree was built using maximum likelihood (1000 bootstrap replicates) and Bayesian
Fig. 1 in Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA
Fig. 1 Morphology of Leishmania strain 218-L139 promastigotes and amastigotes. Cultured Leishmania strain 218-L139 promastigotes as observed under DIC microscopy following growth in complete RPMI culture medium without gentamicin (A). Giemsa-stained touch preparation made from a cutaneous lesion, showing Leishmania strain 218-L139 amastigotes inside a mononuclear phagocyte in addition to free amastigotes (B). Giemsastained smear of cultured promastigotes of Leishmania strain 218-L139 grown in gentamicin-free complete RPMI medium (C)
Fig. 3 in Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA
Fig. 3 Phylogenetic tree demonstrating the relative position of Leishmania strain 218-L139 based on partial maxicircle genome sequences. Phylogenetic tree demonstrating the relative position of Leishmania strain 218-L139 (brown star) based on alignment of partial maxicircle genome sequences. The alignment contains 9471 positions from 67 taxa. The tree was built using maximum likelihood (1000 bootstrap replicates) and the TVM + F + I + G4 model, and Bayesian inference using the GTR + I + G model where the proportion of invariable sites was set to 0.1. Posterior probability values and bootstrap support are reported for each node (pp/bs). The tree was rooted with the Strigomonas/Blechomonas/Herpetomonas clade. The relative position of each Leishmania subgenus is shown to the right of the corresponding clades (Leishmania, Sauroleishmania, Viannia, Mundinia). The scale bar represents the number of substitutions per site
Fig. 1 in Epidemiology of Trichinella infection in wild boar from Spain and its impact on human health during the period 2006-2019
Fig. 1. Prevalence of Trichinella infection in wild boar from several Spanish autonomous communities.
Fig. 4 in Epidemiology of Trichinella infection in wild boar from Spain and its impact on human health during the period 2006-2019
Fig. 4. Box-plot and post hoc pairwise comparison via Dunn's test of the incidence. Box-plot with different letters indicate a statistically significant difference.
Fig. 3 in Epidemiology of Trichinella infection in wild boar from Spain and its impact on human health during the period 2006-2019
Fig. 3. Three-dimensional plots for the interaction effects of the total number of wild boars hunted and the prevalence of the Trichinella infection in wild boar on incidence of trichinellosis in humans.
Fig. 2. A in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran
Fig. 2. A GIS map of IgM seroprevalence of Toxoplasma gondii (Nicolle et Manceaux, 1908) in different provinces of Iran, during 2015–2020 (ND – no data).
Fig. 3. A in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran
Fig. 3. A GIS map of IgG seroprevalence of Toxoplasma gondii (Nicolle et Manceaux, 1908) in different provinces of Iran, during 2015–2020.
Fig. 1 in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran
Fig. 1. The seroprevalence plot of Toxoplasma gondii (Nicolle et Manceaux, 1908) in Iran in different age groups (m-month; y-year).
Malaria drives unique regulatory responses across multiple immune cells during human infection
<p>To investigate malaria driven transcriptional changes in specific immune cell subsets, we sorted live PBMCs from 6 malaria infected donors (day 0), and two subsequent time points after drug treatment (day 7 and 28), along with PBMCs from 2 healthy controls. We performed scRNAseq of these cells, and used clustering and sub-clustering to identify specific immune cell subsets. Differential gene analysis between day 0 and day 28 was performed for each cell cluster and sub-cluster. Key transcriptional changes were confirmed at the protein level with additional donor samples.</p>
Human memory CD4+ T cells recognize <em>Mycobacterium tuberculosis</em>-infected macrophages amid broader pathogen-specific responses
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