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12,799 results for “immunity”
Fig. 1 in Nasal vaccination of six squirrel monkeys (Saimiri sciureus): Improved immunization protocol against Toxoplasma gondii with a nanoparticle-born vaccine
Fig. 1. Schedule of the vaccinal protocol and of the immunological analysis performed on the 6 Saimiris.
Fig. 2. T in Nasal vaccination of six squirrel monkeys (Saimiri sciureus): Improved immunization protocol against Toxoplasma gondii with a nanoparticle-born vaccine
Fig. 2. T-cell immune response analyzed by IFN-γ ELISPOT on PBMC from 6 Saimiris. The results are presented as Spot Forming Units for 106 PBMC (left), before the immunization (T0), one month after the prime, 5 months after the 1st boost and 2 months after the 2nd boost. A representative picture of the ELISPOT plate after the 2nd boost is presented (right). Only 4 animals were analyzed by ELISPOT after the 2nd boost due to blood coagulation in the sampling tubes. Statistical analyses were made by KruskalWallis test, * p <0.05, ** p <0.01.
Fig. 3 in Nasal vaccination of six squirrel monkeys (Saimiri sciureus): Improved immunization protocol against Toxoplasma gondii with a nanoparticle-born vaccine
Fig. 3. Humoral immune response analyzed by ELISA on serum for each Saimiri. The results are presented as optical density (OD) before the immunization (T0), and 2 months after the 2nd boost. Serum from one seropositive and three seronegative humans were used as positive and negative controls, respectively. Cut-off was determined at each dilution, as the mean + 2.5xSD of the negative controls.
Immune repertoire profiling reveals its clinical application potential and triggers for Neuromyelitis Optica Spectrum Disorders
<p>This dataset, containing TCRbeta-chain sequcening data of Neuromyelitis Optica Spectrum Disorders patients and healthy, is the basis for the following publication: "Immune repertoire profiling reveals its clinical application potential and triggers for Neuromyelitis Optica Spectrum Disorders".</p>
Data for milk immune factors/nutrients and infection
<p><span>Data for milk immune factors/nutrients and infection</span></p> <p><span><span> </span></span></p> <p><span>Important</span><span> Information</span></p> <p><span>This file (Milk_immune_factors-nutrients&infection_data) contains the dataset used for the journal article manuscript entitled, "</span><span>Lactose in human milk is associated with lower rates of infection during a drought" </span><span>by Fujita and Wander.</span><span> This</span><span> manuscript is under review for publication as of August, 2024. The variables and data are found under the data tab, and the data coding information in the info & code tab. </span></p> <p> </p> <p><span>Please contact Masako Fujita (ORCID 0000-0001-9173-6678, E-mail masakof@msu.edu) for questions regarding the data.</span></p> <p> </p> <p><span>Condition for data use</span><span>: Please cite DOI: </span><span>10.5281/zenodo.13377353 </span><span>for this data file and the article, and acknowledge the support from the grant agencies listed below: </span></p> <p> </p> <p><span>Data source/article:</span></p> <ul> <li><span><span> </span>Fujita M</span><span>. 2024. Data for milk immune factors/nutrients and infection. DOI:<span> </span></span><span>10.5281/zenodo.13377353</span><span>.</span></li> <li><span><span> </span>Fujita M, Wander K</span><span>. [Year] </span><span>Lactose in human milk is associated with lower rates of infection during a drought. [Journal name, article DOI].</span></li> </ul> <p> </p> <p><span>Grant support:</span></p> <ul> <li><span>National Science Foundation (BCS-0622358, BCS-1638167) </span></li> <li><span>Wenner</span><span>-</span><span>Gren Foundation (Gr. 7460, Gr. 9278) </span></li> </ul>
Dataset - Targeted social immunity is associated with a pathogen-specific erosion of individual immune function in the black garden ant
<p>Datasets and code used to generate the figures. Files sorted by figure panel number. <a href="../api/records/12820609/draft/files/Videos_grooming_.zip/content" target="_blank" rel="noopener noreferrer">Videos_grooming_.zip</a> contains the original videos used for the grooming analysis. </p>
Hepatic transcriptomic analysis reveals differential regulation of metabolic and immune pathways in three strains of chickens with distinct growth rate exposed to mixed parasites infections
<p><span>This dataset was generated from the study investigating hepatic gene expression in three strains of chickens: Ross-308 (R), Lohmann Brown Plus (LB), and Lohmann Dual (LD), 2 weeks after either an experimental infection (n = 18) with both <em>A. galli</em> and <em>H. gallinarum or kept as uninfected control (n = 12)</em>. </span></p>
Spatial Tumor-Immune Analysis: Insights from Pathology Slides and Breast Cancer Survival
<p>Cancer is the second leading cause of death in the US. Among the various forms of cancer, breast cancer and lung cancer are particularly significant due to their prevalence and impact. Breast cancer in particular contributing to around 30\% of all new female cases each year, while also having some of the highest mortality rates. Scientists and doctors rely on pathology slides to aid in the discovery of a cure, diagnose patients, and provide treatment. These slides play a crucial role in examining samples and identifying any abnormalities. The primary goal of this project was to analyze pathology slides from 873 cancer patients in The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA). We developed STAIN (Spatial Tumor and Immune Analysis for Novel insights) with the hypothesize that quantitative analysis of cell type specific clusters in the spatial context can lead to novel insights on patient survival. First, we identified tumor and immune cells using a HD-Yolo algorithm. Then we identify tumor clusters and immune cell clusters. Next, descriptive statistics such as Jaccard distance, Hausdorff distance, Wasserstein distance, tumor density, and immune cell density were derived and correlated with the patients survival while adjusting for clinical attributes such as patient age and tumor stage using Cox proportional Hazard models. The results discover spatial attributes and known clinical risk features associated with survival. </p>
Data used in analyses of Danaher et al. 2024 "Childhood-onset lupus nephritis is characterized by complex interactions between kidney stroma and infiltrating immune cells"
<p>CosMx 1000-plex data and R code from childhood-onset lupus nephris samples, generated for the article Danaher et al. 2024 "Childhood-onset lupus nephritis is characterized by complex interactions between kidney stroma and infiltrating immune cells".</p>
The influence of the gut microbiome on BCG-induced trained immunity
<p>This repository contains the code to reproduce the analysis in the study investigating the effects of gut microbiota on Bacillus Calmette-Guerin (BCG) vaccination of 321 healthy Dutch individuals. The results are presented in the paper</p> <p><em>The influence of the gut microbiome on BCG-induced trained immunity</em></p> <p>by</p> <p>Martin Stražar, Vera P. Mourits, Valerie A.C.M. Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A.B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier</p> <p>(2021)</p> <p> </p> <p>The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high interindividual variation in specific and nonspecific (trained) immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. </p> <p>Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling two weeks and three months afterwards. Metagenomics based on de novo genome assembly revealed 43 immunomodulatory taxa. The nonspecific, trained immune response was detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlated with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, was associated positively with Ruminococcus and Eggerthella lenta. The immunomodulatory taxa identified also had the strongest effects on circulating metabolites, with Roseburia predominantly affecting phenylalanine metabolism. This was corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. </p> <p><br> Variability in cytokine production after BCG vaccination was associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia was found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.</p> <p>The analysis and dataset details are further described in README.md and <a href="https://gitlab.com/xavier-lab-computation/public/bcg300">https://gitlab.com/xavier-lab-computation/public/bcg300</a> .</p>
Longitudinal structural MRI and behavioural data for mice prenatally exposed to maternal immune activation either early or late in gestation
<p>Prenatal maternal immune activation (MIA) is a risk factor for neurodevelopmental disorders. How the gestational timing of MIA-exposure differentially impacts downstream development remains unclear. The data presented here includes longitudinal structural magnetic resonance imaging (MRI) data from weaning to adulthood, and behavioural testing in adolescence and adulthood on C57BL/6 mice exposed to MIA induced by the viral mimetic, polyinosinic:polycytidylic acid (poly I:C) either early (gestational day [GD]9) or late (GD17) in gestation. </p> <p>The data published here was collected and analyzed for the following publication, where more details can be found (Guma et al., 2021 https://doi.org/10.1016/j.biopsych.2021.03.017). Briefly, we found that early MIA-exposure was associated with accelerated brain volume increases in adolescence/early-adulthood that normalized in later adulthood, in regions including the striatum, hippocampus, and cingulate cortex. Similarly, alterations in anxiety-like, stereotypic, and sensorimotor gating behaviours observed in adolescence normalized in adulthood. In contrast, MIA-exposure in late gestation had less impact on anatomical and behavioural profiles. </p> <p>In addition to the univariate analyses described above, we also undertook a multivariate analysis (partial least squares) to relate imaging and behavioural variables for the time of greatest alteration, i.e. adolescence/early adulthood. We further explored the molecular underpinnings of region-specific alterations in early MIA-exposed mice in adolescence using RNA sequencing (data for differentially expressed genes in the anterior cingulate cortex, dorsal hippocampus, and ventral hippocampus are available via the original publication https://doi.org/10.1016/j.biopsych.2021.03.017 for a separate cohort of adolescent mice prenatally exposed to MIA or vehicle at GD9). </p> <p>In this dataset, you will find a total of <strong>376 preprocessed structural MRIs</strong> (in MINC format) acquired at postnatal day ~21, ~38, ~60, and ~90 in mice exposed to poly I:C or vehicle control (0.9% sterile saline) at GD9 or 17. These are T1-weighted, manganese enhanced (50mg/kg 24 hours pre-scan), structural images at 100 micron isotropic resolution acquired on a 7 Tesla Bruker Biospec 70/30; matrix size of 180 x 160 x 90; 14.5 minutes, 2 averages, using 5% isoflurane for induction, 1.5% for maintenance of anesthesia during the scan. T1-weighted scans were preprocessed by stripping native coordinates, flipping left-right to maintain fidelity, denoising, correcting inhomogeneities in the bias field using the N4 algorithm, and registering in LSQ6 alignment (i.e. 6 degrees of freedom are allowed for imagine alignment: translations and rotations along x, y, and z dimensions). The demographics information for each animal is included in the <strong>demographics.csv</strong> file. </p> <p>Behavioural tests were performed following the postnatal day 38 and 90 scans in all animals with a 2 day rest period. These include: open field test, marble burying test, three chambered social approach, and prepulse inhibition. The attentional set shifting task was also performed following the final behavioural test in the postnatal day 90 wave of behaviours. The data for all of these tests is presented in its own individual .csv spreadsheet and includes data for both the timepoints evaluated.</p> <p>Included in this data set are the structural MRIs in MINC format, the behavioural .csv data, and a <strong>readme.txt</strong> file providing further detail on the data structure and content, and on how to interpret the data column titles. DICOMS are also available for the structural MRI data, as are the raw (not-preprocessed) MINC files, available upon request to the authors. </p> <p>Finally, the authors would like to acknowledge the funding bodies that supported the completion of this work including the Canadian Institute for Health Research, the Fonds de Recherche du Québec en Santé, and the Healthy Brains for Healthy Lives at McGill University.</p>
Immune challenges increase network centrality in a queenless ant
<p>Social animals display a wide range of behavioural defences against infectious diseases, some of which inherently increase social contacts with infectious individuals (e.g., mutual grooming), while others decrease them (e.g., social exclusion). These defences often rely on the detection of infectious individuals, but this can be achieved in several ways that are difficult to differentiate. Here, we combine non-pathogenic immune challenges with automated tracking in colonies of the clonal raider ant to ask whether ants can detect the immune status of their social partners and to quantify their behavioural responses to this perceived infection risk. We first show that a key behavioural response elicited by live pathogens (allogrooming) can be qualitatively recapitulated by immune challenges alone. Automated scoring of interactions between all colony members reveals that this behavioural response increases the network centrality of immune-challenged individuals through a general increase in physical contacts. These results show that ants can detect the immune status of their nestmates and respond with a general "caring" strategy, rather than avoidance, towards social partners that are perceived to be infectious. Finally, we find no evidence that changes in cuticular hydrocarbon profiles drive these behavioural effects.</p>
Variation in symbiont density is linked to changes in constitutive immunity in the facultatively symbiotic coral, Astrangia poculata
<p>Scleractinian corals are essential ecosystem engineers, forming the basis of coral reef ecosystems. However, these organisms are in decline globally, in part due to rising disease prevalence. Most corals are dependent on symbiotic interactions with single-celled algae from the family Symbiodiniaceae to meet their nutritional needs, however suppression of host immunity may be essential to this relationship. To explore immunological consequences of algal symbioses in scleractinian corals, we investigated constitutive immune activity in the facultatively symbiotic coral, <em>Astrangia poculata</em>. We compared immune metrics (melanin synthesis, antioxidant production, and antibacterial activity) between coral colonies of varying symbiont density. Symbiont density was positively correlated to both antioxidant activity and melanin concentration. Our results suggest that the relationship between algal symbiosis and host immunity may be more complex than originally hypothesized and highlight the need for nuanced approaches when considering these relationships.</p>
Immune checkpoint molecule TIGIT regulates kidney T cell functions and mediates acute kidney injury
<p>This dataset includes the single cell RNA-seq data associated with the publication listed in the title (abstract below).<br> <br> CellRanger.zip contains the raw transcript counts as produced by CellRanger. There is one folder per sample. The samples are indicated by the folder name (e.g. KO_Ctrl). <br> <br> We have also included .h5ad files that contain of cells that passed quality control, as described in the manuscript.<br> <br> adTIGIT_raw_031422.h5ad contains all passing cells and the raw counts, as well as cell annotations ('celltype')<br> <br> adTIGIT_Tonly_091421.h5ad contains only T cells, .X contains the normalized data and T-cell sub-type ('cluster').<br> <br> Abstract: T cells mediate pathologic and reparative processes during acute kidney injury (AKI) but exact mechanisms regulating kidney T cell functions are unclear. This study identified upregulation of the novel immune checkpoint molecule, TIGIT, on mouse and human kidney T cells following AKI. TIGIT-expressing kidney T cells produced proinflammatory cytokines and had effector and central memory phenotype. Kidney Tregs were predominantly TIGIT+ and reduced after ischemia reperfusion (IR) injury. TIGIT deficient mice had protection from both ischemic and nephrotoxic AKI. Single cell RNA sequencing led to discovery of possible downstream targets of TIGIT. TIGIT mediates AKI pathophysiology, is a promising target for developing AKI therapy, and is being increasingly studied in human cancer therapy trials.</p>
Effects of exogenous elevation of corticosterone on immunity and the skin microbiome of Eastern Newts (Notophthalmus viridescens): Data & R scripts
<p>The amphibian chytrid fungus, <em>Batrachochytrium</em> <em>salamandrivorans</em> (<em>Bsal</em>) threatens salamander biodiversity. The factors underlying <em>Bsal</em> susceptibility may include glucocorticoid hormones (GCs). The effects of GCs on immunity and disease susceptibility are well studied in mammals, but less is known in other groups, including salamanders. We used <em>Notophthalmus</em> <em>viridescens</em> (Eastern Newts) to test the hypothesis that GCs modulate salamander immunity. We first determined the dose required to elevate corticosterone (CORT; primary GC in amphibians) to physiologically relevant levels. We then measured immunity (neutrophil-lymphocyte ratios, plasma bacterial killing ability [BKA], skin microbiome, splenocytes, melanomacrophage centers [MMCs]) and overall health in newts following treatment with CORT or an oil vehicle control. Treatments were repeated for a short (2 treatments over 5 days) or long (18 treatments over 26 days) time period. Contrary to our predictions, most immune and health parameters were similar for CORT and oil-treated newts. Surprisingly, differences in BKA, skin microbiome, and MMCs were observed between newts subjected to short and long-term treatments, regardless of treatment type (CORT, oil vehicle). Taken together, CORT does not appear to be a major factor contributing to immunity in Eastern Newts, although more studies examining additional immune factors are necessary.</p>
Data: Fate of intravenously administered umbilical cord mesenchymal stromal cells and interactions with the host's immune system
<p>This data set includes all the raw data collected for the following article: "Fate of intravenously administered umbilical cord mesenchymal stromal cells and interactions with the host's immune system".</p>
INSPIRE-seq simultaneously selects nanobodies for immune epitopes in the complex tumor microenvironment
<p>scRNAseq of CD45 magnetic microbeads enriched cells were isolated form Py8119 bearing mice (three mice per pool/group) two hours after injection of either PBS, insertless phage display, CD45, DCs, or CD8 specific VHHs phage display libraries. </p>
Datset related to article "DUPLICATION OF EXONS 15 AND 16 IN MATRIN-3: A PHENOTYPE BRIDGING AMYOTROPHIC LATERAL SCLEROSIS AND IMMUNE-MEDIATED DISORDERS"
<p><strong>NGS analysis performed at Fondazione Besta carried out as part of the study reported at title </strong></p>
Age, but not an immune challenge, triggers terminal investment in the Pacific field cricket
<p>The terminal investment hypothesis proposes that, when individuals are faced with a threat to survival, they will increase investment in current reproduction. The level of the threat necessary to elicit terminal investment (the dynamic terminal investment threshold) may vary based on other factors that also influence future reproduction. Here, we tested whether there is an interactive effect of age and an immune challenge on the dynamic terminal investment threshold in the Pacific field cricket, <em>Teleogryllus</em> <em>oceanicus</em>. We measured the courtship call, mating attractiveness, ejaculate size and offspring production of <em>T. oceanicus</em> males. We found only limited support for the dynamic terminal investment threshold: there was no consistent evidence of a positive interaction between male age and immune challenge intensity. However, we found evidence for age-related terminal investment: older males produced a larger spermatophore than younger males. Older males also had a slower calling rate compared to younger males, suggesting a potential trade-off between these two pre- and post-copulatory traits. As some, but not, all reproductive traits responded plastically to cues for terminal investment, our research highlights the importance of considering a broad range of pre-and post-copulatory traits when exploring the potential for terminal investment to occur.</p>
Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease
<p><strong>Background </strong></p> <p>Individuals with cystic fibrosis have an elevated lifetime risk of colonization, infection, and disease caused by nontuberculous mycobacteria. A prior study involving non-cystic fibrosis individuals reported a gene expression signature associated with susceptibility to nontuberculous mycobacteria pulmonary disease (NTM-PD). In this study, we determined whether people living with cystic fibrosis who progress to NTM-PD have a gene expression pattern similar to the one seen in the non-cystic fibrosis population. <strong> </strong></p> <p><strong>Methods</strong></p> <p>We evaluated whole blood transcriptomics using bulk RNA-seq in a cohort of cystic fibrosis patients with samples collected closest in timing to the first isolation of nontuberculous mycobacteria. The study population included patients who did (n = 12) and did not (n = 30) develop NTM-PD following the first mycobacterial growth. Progression to NTM-PD was defined by a consensus of two expert clinicians based on reviewing clinical, microbiological, and radiological information. Differential gene expression was determined by DESeq2.</p> <p><strong>Results</strong></p> <p>No differences in demographics or composition of white blood cell populations between groups were identified at baseline. Out of 213 genes associated with NTM-PD in the non-CF population, only two were significantly different in our cystic fibrosis NTM-PD cohort. Gene set enrichment analysis of the differential expression results showed that CF individuals who developed NTM-PD had higher expression levels of genes involved in the interferon (α and γ), tumor necrosis factor, and IL6-STAT3-JAK pathways. <strong> </strong></p> <p><strong>Conclusion</strong></p> <p>In contrast to the non-cystic fibrosis population, the gene expression signature of patients with cystic fibrosis who develop NTM-PD is characterized by increased innate immune responses.</p>
ScienceDex guides
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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.