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3,650 results for “antibody”
Data to accompany Structural prediction of chimeric immunogens to elicit targeted antibodies against betacoronaviruses
<p>This dataset contains predicted chimera structures, NanoDSF data on thermal stability of expressed chimeras on the surface of pseudoviruses, and immunofluorescence data on expressed chimeras on the surface of pseudoviruses as described in the manuscript.</p>
Dataset related to: Characterization of a Rat Model of Myeloperoxidase-Anti-Neutrophil Cytoplasmic Antibody-Associated Crescentic Glomerulonephritis
<p><strong>Background/aim: </strong> Necrotizing crescentic glomerulonephritis (GN) associated with anti-neutrophil cytoplasmic antibodies (ANCA) against myeloperoxidase (MPO) is a devastating disease that quickly progresses to kidney failure. Current therapies are broadly immunosuppressive and associated with adverse effects. We wanted to set up a model that could be suitable for testing narrowly targeted therapies.</p> <p><strong>Methods: </strong> The model was constructed in male Wistar Kyoto rats through injections of human MPO (hMPO) and pertussis toxin, followed by a sub-nephritogenic dose of sheep anti-rat glomerular basement membrane (GBM) serum to boost the disease. Rats were monitored for 35 days. Rats given hMPO alone, saline, or human serum albumin with or without anti-GBM serum were also studied.</p> <p><strong>Results: </strong> Rats receiving hMPO developed circulating anti-hMPO and anti-rat MPO antibodies. Challenging hMPO-immunized rats with the anti-GBM serum led to more glomerular neutrophil infiltration and MPO release, and severe haematuria, heavy proteinuria, and higher blood urea nitrogen than hMPO alone. Pauci-immune GN developed with crescents, affecting 25% of glomeruli. The majority of crescents were fibrocellular. Necrotizing lesions and Bowman capsule ruptures were detected. Cells double positive for claudin-1 (a marker of parietal epithelial cells [PECs]) and neural cell adhesion molecule (NCAM; progenitor PECs) were present in crescents. Double staining for NCAM and Ki-67 established proliferative status of progenitor PECs. Podocyte damage was associated with endothelial and GBM changes by electron microscopy. Monocyte/macrophages and CD4+ and CD8+ T cells accumulated in glomeruli and the surrounding area and in the tubulointerstitium. Lung haemorrhage also manifested.</p> <p><strong>Conclusion: </strong> This model reflects histological lesions of human ANCA-associated rapidly progressive GN and may be useful for investigating new therapies.</p>
Spermatocysts stained positively with anti-pHH3 antibody
<p>Males have the ability to compete for fertilizations through both pre-copulatory and post-copulatory intrasexual competition. Pre-copulatory competition has selected for large weapons and other adaptations to maximize access to females and mating opportunities while post-copulatory competition has resulted in ejaculate adaptations to maximize fertilization success. Negative associations between these strategies support the hypothesis that there is a trade-off between success at pre- and post-copulatory mating success. Recently, this trade-off has been demonstrated with experimental manipulation. Male leaf-footed cactus bugs, <i>Narnia femorata</i>. Males of this species can lose their hind limbs, their primary weapon in male-male competition, by autotomy during development. Weaponless males invest instead in large testes. While evolutionary outcomes of the trade-offs between pre- and post-copulatory strategies have been identified, less work has been done to identify proximate mechanisms by which the trade-off might occur, perhaps because the systems in which the trade-offs have been investigated are not ones that have the molecular tools required for exploring mechanism. Here we applied knowledge from a related model species for which we have developmental knowledge and molecular tools, the milkweed bug <i>Oncopeltus fasciatus</i>, to investigate the proximate mechanism by which autotomized <i>N. femorata</i> males developed larger testes. Autotomized males had evidence of a higher rate of transit amplification divisions in the spermatogonia, which would result more spermatocytes and thus in greater sperm numbers. Identification of mechanisms underlying a trade-off can help our understanding of the direction and constraints on evolutionary trajectories and thus the evolutionary potential under multiple forms of selection.</p>
Phosphoproteomics analysis of antibody-based stimulation of TCR in CD4+ T cells
<p>Code associated with the paper "LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN2 as a regulator of effector functions" published in Molecular Systems Biology in 2020.</p> <p>abstract: <br> T-cell receptor (TCR) ligation-mediated protein phosphorylation regulates the activation, cellular responses, and fates of T cells. Here, we used time-resolved high-resolution phosphoproteomics to identify, quantify, and characterize the phosphorylation dynamics of thousands of phosphorylation sites in primary T cells during the first 10 min after TCR stimulation. Bioinformatic analysis of the data revealed a coherent orchestration of biological processes underlying T-cell activation. In particular, functional modules associated with cytoskeletal remodeling, transcription, translation, and metabolic processes were mobilized within seconds after TCR engagement. Among proteins whose phosphorylation was regulated by TCR stimulation, we demonstrated, using a fast-track gene inactivation approach in primary lymphocytes, that the ITSN2 adaptor protein regulated T-cell effector functions. This resource, called LymphoAtlas, represents an integrated pipeline to further decipher the organization of the signaling network encoding T-cell activation. LymphoAtlas is accessible to the community at: <a href="https://bmm-lab.github.io/LymphoAtlas">https://bmm-lab.github.io/LymphoAtlas</a>.</p>
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
Open the record for dataset details and reuse information.
Improving antibody language models with native pairing
<p><strong>Motivation.</strong> Existing large language models designed to predict antibody structure and function have been trained exclusively with unpaired antibody sequences. This is a substantial drawback, as each antibody represents a unique pairing of heavy and light chains that both contribute to antigen recognition. The cost of generating large datasets of natively paired antibody sequences is orders of magnitude higher than the cost of unpaired sequences, and the paucity of available paired antibody sequence datasets precludes training a state-of-the-art language model using only paired training data. Here, we sought to determine whether and to what extent natively paired training data improves model performance.</p> <p><strong>Results.</strong> Using a unique and recently reported dataset of approximately 1.6 x 10<sup>6</sup> natively paired human antibody sequences, we trained two baseline antibody language model (BALM) variants: BALM-paired and BALM-unpaired. We quantify the superiority of BALM-paired over BALM-unpaired, and we show that BALM-paired's improved performance can be attributed at least in part to its ability to learn cross-chain features that span natively paired heavy and light chains. Additionally, we fine-tuned the general protein language model ESM-2 using these paired antibody sequences and report that the fine-tuned model, but not base ESM-2, demonstrates a similar understanding of cross-chain features.</p> <p><strong>Files.</strong> The following files are included in this repository:</p> <ul> <li><em><strong>BALM-paired.tar.gz</strong></em>: Model weights for the BALM-paired model.</li> <li><em><strong>BALM-shuffled.tar.gz</strong></em>: Model weights for the BALM-shuffled model.</li> <li><em><strong>BALM-unpaired.tar.gz</strong></em>: Model weights for the BALM-unpaired model.</li> <li><em><strong>ESM2-650M_paired-fine-tuned.tar.gz</strong></em>: Model weights for the 650M-parameter ESM-2 model after fine-tuning with natively paired antibody sequences.</li> <li><em><strong>jaffe-paired-dataset_airr-annotation.tar.gz</strong></em>: All natively paired antibody sequences from the <a href="https://www.nature.com/articles/s41586-022-05371-z">Jaffe dataset</a> were annotated with <a href="https://github.com/briney/abstar">abstar</a> and subsequently filtered to remove duplicates or unproductive sequences. The annotated sequences are provided in an <a href="https://docs.airr-community.org/en/stable/datarep/rearrangements.html">AIRR-compliant format</a>.</li> <li><em><strong>test-dataset_annotated.tar.gz</strong></em>: Two csv files, both with sequences annotated in an <a href="https://docs.airr-community.org/en/stable/datarep/rearrangements.html">AIRR-compliant format</a>. <em>lc-coherence_test-unique_annotated.csv</em> contains all sequences from the test dataset and <em>fig3-20kembeddings_annotated.csv</em> contains the 20k sequences from the test used for the Figure 2 UMAP embeddings. For both datasets, the sequences can be paired together based on their pair_id.</li> <li><em><strong>train-test-eval_paired.tar.gz</strong></em>: Datasets used to train, test, and evaluate the BALM-paired model. Compressed folder containing three files: <em>train.txt</em>,<em> test.txt</em>, and <em>eval.txt</em>. Each file has one input sequence per line. This dataset was also used to fine-tune the 650M-parameter ESM-2 variant.</li> <li><em><strong>train-test-eval_shuffled.tar.gz</strong></em>: Datasets used to train, test, and evaluate the BALM-shuffled model. Compressed folder containing three csv files, with two columns for the heavy and light chains.</li> <li><em><strong>train-test-eval_unpaired.tar.gz</strong></em>: Datasets used to train, test, and evaluate the BALM-unpaired model. Compressed folder containing three files: <em>train.txt</em>, <em>test.txt</em>, and <em>eval.txt</em>. Each file has one input sequence per line.</li> <li><em><strong>classification-datasets.tar.gz</strong></em>: Three classification datasets used to train classification models in Figure 5. The datasets are: <em>flu-0_cov-1.csv</em>, <em>hd-0_cov-1.csv</em>, and <em>hd-0_flu-1_cov-2.csv</em>. CoV antibody sequences were obtained from <a href="https://doi.org/10.1093/bioinformatics/btaa739">CoV-AbDab</a>, Flu antibody sequences were obtained from <a href="https://doi.org/10.1101/2023.09.11.557288">Wang et al.</a>, and healthy donor antibody sequences were obtained from <a href="https://doi.org/10.1016/j.celrep.2024.114307">Hurtado et al</a>.</li> </ul> <p><strong>Code:</strong> All code used for model training, testing, and figure generation is available under the MIT license on <a href="https://www.github.com/briney/BALM-paper">GitHub</a>. An archived version of the GitHub repository (from the time of manuscript publication) is included here as <em><strong>code-archive.zip</strong></em>.</p> <p> </p>
Database of Study SARS-CoV-2 Antibody Level after Homologous and Heterologous Booster Vaccines an 18-month Longitudinal Observational Cohort Study in Indonesia (Ardyanto et el., 2024)
Open the record for dataset details and reuse information.
Detecting Features of Antibody Structure through their Mediator-Accessible Redox Activities
<p>There are the compiled csv data per figure. </p>
Antiviral Tfh response by "immunotolerant" virus carriers drives antibody-mediated control of congenital infection
<p>Analysed and annotated SingleCellExperiment object </p>
Data from: Glutamate receptor delta2 serum antibodies in paediatric opsoclonus myoclonus ataxia syndrome
Objective: To identify neuronal surface antibodies in opsoclonus myoclonus ataxia syndrome (OMAS) usingcontemporary antigen discovery methodology. Methods: OMAS patient serum IgG immunohistochemistry using age-equivalent rat cerebellar tissue was followed by immunoprecipitation, gel electrophoresis and mass spectrometry. Data are available via ProteomeXchange (identifier PXD009578). This generated a list of potential neuronal surface cerebellar autoantigens. Live cell-based assays (CBA) were used to confirm membrane-surface antigens and adsorb antigen-specific IgGs. The serological results were compared to the clinical data. Results: Four of the six OMAS sera tested bound rat cerebellar sections. Two of these sera with similar immunoreactivities were used in immunoprecipitation experiments using cerebellum from postnatal rat pups (P18). Mass spectrometry identified 12 cell-surface proteins, of which glutamate receptor delta 2 (GluD2), a predominately cerebellar-expressed protein, was found at a threefold higher concentration than the other 11 proteins. Antibodies to GluD2 were identified in 14/16 (87%) OMAS samples, compared with 5/139 (5%) pediatric and 1/38 (2.6%) adult serum controls (p<0.0001), and in 2/4 sera from patients with neuroblastoma without neurological features. Adsorption of positive OMAS sera against GluD2-transfected cells substantially reduced but did not eliminate, reactivity towards cerebellar sections. Conclusion: Autoantibodies to GluD2 are frequent in patients with OMAS, bind to surface determinants and are potentially pathogenic.
Protective efficacy of anti-Hyr1p monoclonal antibody against systemic candidiasis due to multi-drug resistant Candida auris
<p>Supplementary data set </p>
Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX
<p>Representative dataset using OMAP-13: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.0. See https://humanatlas.io/omap.</p>
Dataset for the Tyrosine-protein kinase SYK antibody screening study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for Tyrosine-protein kinase SYK. The study is available on Zenodo (https://doi.org/10.5281/zenodo.6566940).</p>
Dataset for the SPARC-related modular calcium-binding protein 1(SMOC-1) antibody screening study
<p>This project contains the following underlying data included in a study which characterized seven commercially-available antibodies for SMOC-1. The study is also available on Zenodo<strong> </strong>(https://doi.org/10.5281/zenodo.8277962).</p>
Fig. 1 in Triterpene glycosides from Blighia welwitschii and evaluation of their antibody recognition capacity in multiple sclerosis
Fig. 1. Structures of new triterpene saponins 1–7 isolated from the fruits of B. welwitschii.
Anti-Hep B Antibodies at Age 9 to 10 Years After Hep B Vaccine at Birth and DTaP-IPV-Hep B-PRP-T Hexavalent Vaccine.
ClinicalTrials.gov study NCT02697474. IPD Sharing: YES. Countries: 1. Publications: 0.
ANTIBODY-LEVEL BASED ANALYSIS OF COVID-19 CONVALESCENT SERUM (ABACCuS)
ClinicalTrials.gov study NCT04432272. IPD Sharing: NO. Countries: 1. Publications: 0.
Generation of Anti-HCV Antibodies From Bone Marrow: Defining the Repertoire of Immune Response to HCV Quasispecies
ClinicalTrials.gov study NCT00004851. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Clinical Usefulness of Cortisol, Antinuclear Antibodies and High-sensitivity C-reactive Protein in Acute Pancreatitis
ClinicalTrials.gov study NCT03830060. IPD Sharing: Not stated. Countries: 0. Publications: 4.
Sirolimus Monotherapy in the Treatment of Antiphospholipid Antibody Related Thrombocytopenia
ClinicalTrials.gov study NCT06722586. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
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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.