Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
18,535
datasets available to search
ShareScore release 0.9.0
Dataset results
18,535 results for “Infections”
Metabolic alterations in Strongyloidiasis stool samples unveil potential biomarkers of infection_dataset
<p>Strongyloidiasis, a parasitosis caused by <em>Strongyloides stercoralis</em> in humans, is a very prevalent infection in tropical or subtropical areas. Gaps on public health strategies corroborates to the high global incidence of strongyloidiasis especially due to challenges involved on its diagnosis. Based on the lack of a gold-standard diagnostic tool, we aimed to present a metabolomic study for the assessment of stool metabolic alterations. Stool samples were collected from 25 patients segregated into positive for strongyloidiasis (n = 10) and negative control (n = 15) and prepared for direct injection high-resolution mass spectrometry analysis. Using metabolomics workflow, 18 metabolites were annotated increased or decreased in strongyloidiasis condition, from which a group of 5 biomarkers comprising caprylic acid, mannitol, glucose, lysophosphatidylinositol and hydroxy-dodecanoic acid demonstrated accuracy over 89% to be explored as potential markers. The observed metabolic alteration in stool samples indicates involvement of microbiota remodeling, parasite constitution, and host response during <em>S. stercoralis</em> infection.</p>
Supplementary Figures. "In silico research of new therapeutics rotenoids derivatives against Leishmania amazonensis infection"
<p>Supplementary figures corresponding to the submitted manuscript entitled "In silico research of new therapeutics rotenoids derivatives against Leishmania amazonensis infection"</p>
Data for: Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its Daphnia host
<p>This dataset supports the findings of the study 'Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its <em>Daphnia</em> host', published in Hydrobiologia (https://doi.org/10.1007/s10750-022-04889-7)</p>
Data and code for 'Age structure of amphibian populations with endemic chytridiomycosis, across climatic regions with markedly different infection risk'
<p>This repository provides all data and R code from the analysis presented in the following paper:</p> <p>Turner, A., Heard, G., Hall, A., Wassens, S. (in review). Age structure of amphibian populations with endemic chytridiomycosis, across climatic regions with markedly different infection risk.</p> <p>The data are provided as a series of .csv files, R script and two zip folders of R packages (Surv_mod and VB_mod)</p> <p>1. <strong>Skeleto_dat_ready_Jan2021.csv</strong> Data from frog surveys conducted by Anna Turner</p> <p>2. <strong>Geoffs_data.csv</strong> Data from frog surveys conducted by Geoff Heard</p> <p>3. <strong>Environmental_variables_skeleto.csv</strong> Environmental data collected during surveys </p> <p>4. <strong>sk.dat_July21.csv</strong> Collated data from Anna and Geoff - created by 'Data_collation_for_analysis_2.R' ready for analysis</p> <p>5. <strong>Variables_that_are_highly_correlated_with_each_other_season_wide.csv</strong> Testing for correlation</p> <p>6. <strong>Model_structure_skeleto_2.csv </strong>creates model structure for analysis</p> <p>7. <strong>Model_selection_statistics_June_21.csv </strong>Output from model</p> <p>R code is provided seperately for each of the following components:</p> <p>1. <strong>Data_collation_for_analysis_2.R</strong> Collating data from Anna and Geoffs datasets</p> <p>2. <strong>Skeleto_analysis_5.R - </strong>First uses regression modelling to explore factors correlated with variation in age</p> <p> - Following Scheele et al. (2016) regression models with a poisson distribution</p> <p> - Use bayesian non-linear regression to fit the Von Bertalanffy growth model to size-at-age data</p> <p> - Plots male and female growth curves</p> <p> - Uses catch curve approach to estimate survival from best fitting regression model following Scroggie (2012) but with bayesian implementation</p>
Diet and SARS-Cov-2 Infection Risk: A Retrospective Observational Study
<p>Dataset, Analysis, Regression and Description.</p> <p>From mid-summer 2020 to January 2022, based on phase 2 to 3 of a self-reported questionnaire survey, we asked 15851 families across Iran about their diet and their COVID-19 disease. The results showed that some diets increased the risk of SARS-Cov-2 Apparent Infection Risk and some reduced it.</p> <p>The results show that the risk of reporting SARS-CoV-2 apparent infection in the second group was 12 times higher than the Third group. <strong>The two-tailed P value is less than 0.0001</strong>. Also, the risk of reporting SARS-CoV-2 apparent infection in the first group was 9 times higher than the Third group. <strong>The two-tailed P value is less than 0.0001</strong>. By conventional criteria, these differences are considered to be extremely statistically significant.</p>
The repurposing of tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug resistant Shigella spp.
<p><strong>dataset for The repurposing of tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug resistant <em>Shigella</em> spp.</strong></p> <p>Elena Fernández Alvaro <sup>1*</sup>, Phat Voong Vinh <sup>2</sup>, Cristina de Cozar <sup>1</sup>, David Wille <sup>1</sup>, Beatriz Urones <sup>1</sup>,</p> <p>Alan Price <sup>1</sup>, Nhu Tran Do Hoang <sup>2</sup>, Tuyen Ha Thanh <sup>2</sup>, Molly McCloskey <sup>3</sup>, Shareef Shaheen<sup> 3</sup>, Denise Dayao<sup> 4</sup>, Jaime de Mercado <sup>1</sup>, Pablo Castañeda <sup>1</sup>, Adolfo García-Perez <sup>1</sup>, Benson Singa <sup>5</sup>, Patricia Pavlinac <sup>6</sup>,</p> <p>Judd Walson<sup>3</sup>, Maria Santos Martínez-Martínez <sup>1</sup>, Samuel L.M. Arnold <sup>3</sup>, Tzipori Saul <sup>4</sup>, Lluis Ballell <sup>1#</sup>,</p> <p>and Stephen Baker <sup>7,8*</sup></p> <p> </p>
A Niclosamide-releasing hot-melt extruded catheter prevents Staphylococcus aureus experimental biomaterial-associated infection
<p>Biomaterial-associated infections are a major healthcare challenge as they are responsible for high disease burden in critically ill patients. In this study, we have developed drug-eluting antibacterial catheters to prevent catheter-related infections. Niclosamide (NIC), originally an antiparasitic drug, was incorporated into the polymeric matrix of thermoplastic polyurethane (TPU) via solvent casting, and catheters were fabricated using hot-melt extrusion technology. The mechanical and physicochemical properties of TPU polymers loaded with NIC were studied. NIC was released in a sustained manner from the catheters and exhibited <em>in vitro</em> antibacterial activity against <em>Staphylococcus aureus</em> and <em>Staphylococcus epidermidis</em>. Moreover, the antibacterial efficacy of NIC-loaded catheters was validated in an <em>in vivo</em> biomaterial-associated infection mouse model using a methicillin-susceptible and methicillin-resistant strain of <em>S. aureus. </em>The released NIC from the produced catheters reduced bacterial colonization of the catheter as well as of the surrounding tissue. In summary, the NIC-releasing hot-melt extruded catheters prevented implant colonization and reduced the bacterial colonization of peri-catheter tissue by methicillin sensitive as well as resistant <em>S. aureus</em> in a biomaterial-associated infection mouse model and has good prospects for preclinical development.</p>
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>
data set to bioRxiv preprint 'Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation
<p>This is supporting data and software code for the following preprint in bioRxiv</p> <p><strong>Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation</strong></p> <p>https://www.biorxiv.org/content/10.1101/2022.04.18.488629v1</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>
Data for: Polystyrene nanoplastics differentially influence the outcome of infection by two microparasites of the host Daphnia magna
<p>This dataset supports the findings of the study 'Polystyrene nanoplastics differentially influence the outcome of infection by two microparasites of the host <em>Daphnia magna</em>', published in Philosophical Transactions of the Royal Society B (https://doi.org/10.1098/rstb.2022.0013).</p>
Supplementary dataset to publication: "Neuroglia Infection by Rabies Virus after Anterograde Virus Spread in Peripheral Neurons"
<p>Supplementary data to the publication: Potratz M., Zaeck L.M., Weigel C., Klein A., Freuling C.M., Müller T., <strong>Finke S.</strong> <strong>2020. </strong>Neuroglia Infection by Rabies Virus after Anterograde Virus Spread in Peripheral Neurons. <strong>Acta Neuropathologica Communications. </strong>8:199. doi.org/10.1186/s40478-020-01074-6.</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>
Introducing the COVID-19 YouTube (COVYT) speech dataset featuring the same speakers with and without infection
<p>The COVYT dataset contains speech samples from individuals who self-reported their COVID-19 infection on public social media platforms (YouTube, Xiaohongshu). These videos, as well as accompanying videos of the same people prior to infection, were mined in an attempt to gather publicly-available data for COVID-19 research. This release includes the links to the original videos along with the accompanying manual segmentation and diarisation that identifies the utterances of the target individuals. We are additionally releasing features derived from the segmented utterances. Finally, the dataset includes partitioning information according to 4 different cross-validation schemes. See the arxiv pre-print for more details: https://arxiv.org/abs/2206.11045</p>
Infection increases activity via Toll dependent and independent mechanisms in Drosophila melanogaster - ethoscope dataset
<p>Ethoscope dataset for Vicent et al 2022, PLoS Pathogens</p> <p>Original preprint available at: https://www.biorxiv.org/content/10.1101/2021.08.24.457493v1</p> <p> </p>
direct RNA seq data, triplicate of RSV - strain A2 in Calu-3 cells at 48 hours post infection
<p>Raw fastq data from Calue-3 cells infected with RSV strain A2</p>
Coswara: A respiratory sounds and symptoms dataset for remote screening of SARS-CoV-2 infection
<p>Coswara is a dataset containing diverse set of respiratory sounds and rich meta-data from COVID-19 positive and Non-COVID subjects.</p>
Altered infective proficiency of the gut microbiome following COVID-19
<p><strong>The effects of SARS-CoV-2 infections comprise of many heterogeneous symptoms including several involving the human gastrointestinal tract. We assess the effects of COVID-19 on the host microbiome</strong></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>
Dataset of "Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells"
<p><strong>Detailed quantitative analysis of GFP expression in SAHA and TCR-treated cells & Computational analysis of bulk and single-cell RNA-Seq data.</strong></p> <p> </p> <p><em><strong>Detailed quantitative analysis of GFP expression in SAHA and TCR-treated cells.</strong></em></p> <p>Cells were prepared for single cell analysis at the Genome Technology Facility (GTF) of the University of Lausanne. Cells were loaded on Fluidigm C1 IFC plates (5-10 μm), with run ID smart33, smart34 and smart35, corresponding to untreated, SAHA- and TCR-treated conditions respectively. After single cell capture on the Fluidigm C1 IFC plate, each chamber was inspected visually by microscopy and pictures were captured with a Zeiss Axiovert 200 M fluorescence microscope equipped with a Roper Scientific CoolSnap HQ camera using a Plan-Neofluar 10X lens (smart34 run) or 20X lens (for smart35 run). For each capture chamber, pictures in bright field and FITC channel were taken with the MetaMorph 6.3 software. Picture analysis was then performed using ImageJ 1.50b software (open access software: website). Brightness and contrast were adjusted for qualitative assessment of the pictures.</p> <p><em><strong>Computational analysis of bulk and single-cell RNA-Seq data.</strong></em></p> <p>Upon bulk or single cell isolation, RNA extraction and library preparation was performed according to Illumina protocols. Bulk and single-cell RNA-Seq data analysis are detailed here.</p> <p> </p> <p>Linked to the paper published in Cell Reports (doi:10.1016/j.celrep.2018.03.102): </p> <p><strong>Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells</strong></p> <p>Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle towards HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression.</p> <p> </p> <p> </p>
ScienceDex guides
Understand access before you commit
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.