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3,650 results for “antibody”
Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding
<p>Data for non-regenerative bivalent analyte binding interaction between CH505 transmitted founder gp120 and CH31 monoclonal antibody, an HIV-1 mAb with CD4-binding site specificity.</p> <p>This data set is submitted as part of the manuscript titled "Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding"</p>
Accurate profiling of full length Fv in highly homologous antibody libraries using UMI tagged short reads
<p>Data consists of raw Illumina MiSeq 2x250bp reads from the Fab mini library Mix9A, and Illumina MiSeq 2x300bp reads from the Fab mini library Mix14 at 8 attomole as described in the journal publication "Accurate profiling of full length Fv in highly homologous antibody libraries using UMI tagged short reads".</p>
Datasets generated for KA-Search: rapid and exhaustive sequence identity search of known antibodies
<p>Datasets generated for testing KA-Search in the paper "KA-Search: rapid and exhaustive sequence identity search of known antibodies".</p> <p>Includes OAS-test and the 100 randomly selected non-redundant heavy chains of therapeutics.</p>
A antibody-based array reveals a serum protein signature as biomarker for adolescent idiopathic scoliosis patients
<p>Evident adolescent idiopathic scoliosis (AIS) incurs high treatment costs, low quality of life, and many complications. Early screening of AIS is essential to avoid progressing to an evident stage. However, there is no valid serum biomarker for AIS for early screening. Antibody-based array is a large-scale study of proteins, which is expected to reveal a serum protein signature as biomarker for AIS. There are two segments of the research, including biomarkers screening and validation. In the biomarkers screening group, a total of 16 volunteers participated in this study, and we carried out differentially expressed proteins screening via protein array assay between No-AIS group and the AIS group.</p>
Modeling the Sequence Dependence of Differential Antibody Binding in the Immune Response to Infectious Disease
<p>Raw peptide microarray data of fluorescence intensities representing relative binding of antibodies in sera samples collected from different cohorts of patients diagnosed with a number of viral infections. Healthy controls are also included.</p> <p>Columns:</p> <p>Sequence - peptide sequence</p> <p>HCV - Hepatitis Virus C</p> <p>Dengue - Dengue virus</p> <p>WNV - West Nile Virus</p> <p>HBV - Hepatitis Virus B</p> <p>Chagas - Chagas disease</p> <p>ND - negative/healthy donor</p> <p>LowCV - low coefficient of variation</p> <p>HighCV - high coefficient of variation</p>
Dataset for the CHCHD10 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the CHCHD10 protein, encoded by the CHCHD10 gene. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.5259992">https://doi.org/10.5281/zenodo.5259992</a>).</em></p>
mit-ll/AlphaSeq_Antibody_Dataset: AlphaSeq Antibody Datasets 1 & 2
<p>This release contains a major release that includes a restructuring of the repository for dataset 1, and includes the release of dataset 2 and associated documentation.</p>
Data from: Genome-wide epitope mapping reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection
<p><em>Coxiella burnetii</em> is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of infection. Vaccination is a key control measure and two commercial vaccines based on formalin-inactivated<em> C. burnetii </em>bacterins are currently available. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to <em>C. burnetii </em>antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on <em>C. burnetii</em> bacterin preparations. Subunit vaccines based on recombinant proteins offer significant advantages, as they can be designed to reduce reactogenicity and can be co-designed with defined antigen serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to <em>C. burnetii </em>vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 ORFs in the <em>C. burnetii</em> genome. We found significant diversity in the antibody responses within and between species and across different <em>C. burnetii</em> exposure statuses. However, <em>C. burnetii</em> exposure did result in more uniform seroreactivity across species. Through the implementation of three different vaccine candidate methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic, out of which 65 have been previously described. This is the first study to investigate seroreactivity against the entire <em>C. burnetii </em>genome presented as overlapping linear peptides and provides the basis for selection of antigen targets for next generation Q fever vaccines and diagnostic tests.</p>
Data for: Evaluation of antibody kinetics and durability in health individuals vaccinated with inactivated COVID-19 vaccine (CoronaVac): a cross-sectional and cohort study in Zhejiang, China
<p><strong>Background</strong>: Although inactivated COVID-19 vaccines are proven to be safe and effective in the general population, the dynamic response and duration of antibodies after vaccination in the real world should be further assessed.</p> <p><strong>Methods</strong>: We enrolled 1067 volunteers who had been vaccinated with one or two doses of CoronaVac in Zhejiang Province, China. Another 90 healthy adults without previous vaccinations were recruited and vaccinated with three doses of CoronaVac, 28 days and 6 months apart. Serum samples were collected from multiple timepoints and analyzed for specific IgM/IgG and neutralizing antibodies (NAbs) for immunogenicity evaluation. Antibody responses to the Delta and Omicron variants were measured by pseudovirus-based neutralization tests.</p> <p><strong>Results</strong>: Our results revealed that binding antibody IgM peaked 14–28 days after one dose of CoronaVac, while IgG and NAbs peaked approximately 1 month after the second dose and then declined slightly over time. Antibody responses had waned by month 6 after vaccination and became undetectable in the majority of individuals at 12 months. Levels of NAbs to live SARS-CoV-2 were correlated with anti-SARS-CoV-2 IgG and NAbs to pseudovirus, but not IgM. Homologous booster around 6 months after primary vaccination activated anamnestic immunity and raised NAbs 25.5-fold. The neutralized fraction subsequently rose to 36.0% for Delta (p=0.03) and 4.3% for Omicron (p=0.004), and the response rate for Omicron rose from 7.9% (7/89) to 17.8% (16/90).</p> <p><strong>Conclusions</strong>: Two doses of CoronaVac vaccine resulted in limited protection over a short duration. The inactivated vaccine booster can reverse the decrease of antibody levels to prime strain, but it does not elicit potent neutralization against Omicron; therefore, the optimization of booster procedures is vital.</p>
Validation of a SARS-CoV-2 surrogate neutralization test detecting neutralizing antibodies against the major variants of concern
<p>SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) as well as VOC Delta, Omicron BA.1, BA.2 and BA.5. Performances were compared to the reference virus neutralization test (VNT) against the respective VOC using three different cohorts collected during the COVID waves. Pre-COVID samples confirmed 100% specificity of the sVNT. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman’s r=0.7081 for BA.1, r=0.7205 for BA.2 and r=0.6042 for BA.5), and for WT (r=0.8458) and Delta-sVNT (r=0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD commercial kits “Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit” and “Genscript cPass kit” revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity resulting in a Youden Index of 78.24. This midway trend was further confirmed on 100 double-vaccinated individuals. The BA.2-sVNT performance was similar to that of the Genscript test. Finally, sVNT ability to assess neutralizing antibodies against Omicron BA.5 was validated on a double-vaccinated cohort (n=100) and an Omicron-breakthrough infection cohort (n=91). Correlation analysis revealed a strong association (r=0.8583) between BA.5-sVNT and VNT. Accurate classification was confirmed by receiving operating characteristic (ROC) analysis reporting an area under the curve (AUC) of 0.9543. In conclusion, the sVNT allows for efficient prediction of immune protection against the various VOCs.</p>
Reduced Graphene Oxide Electrolyte-Gated Transistor Immunosensor with Highly Selective Multiparametric Detection of Anti-Drug Antibodies
<p>Dataset for the publication: </p> <p>Sensi, M., de Oliveira, R. F., Berto, M., Palmieri, M., Ruini, E., Livio, P. A., Conti, A., Pinti, M., Salvarani, C., Cossarizza, A., Cabot, J. M., Ricart, J., Casalini, S., González-García, M. B., Fanjul-Bolado, P., Bortolotti, C. A., Samorì, P., Biscarini, F., Reduced Graphene Oxide Electrolyte-Gated Transistor Immunosensor with Highly Selective Multiparametric Detection of Anti-Drug Antibodies. <em>Adv. Mater.</em> 2023, 2211352. <a href="https://doi.org/10.1002/adma.202211352">https://doi.org/10.1002/adma.202211352</a></p> <p>Transfer curves measured with different analytes (used for Figure 3 in the results and discussion section of the publication). In every file are reported the gate-source voltages (V<sub>GS</sub>) and the average drain-source currents (I<sub>DS</sub>) after exposure of the gate to ATI (Transfer_ATI-dataset), ATI+TNFa(Transfer_ATI+TNFa-dataset), TNFa(Transfer_TNFa-dataset) at specific concentration. Transfer_control is the dataset for the control experiments, without the probe on gate.</p> <p>EIS (EIS-functionalization-dataset) dataset has been used for the functionalization in figure 2b. In the the file are reported the frequency, the real and the imaginary impedance for each functionalization step (in specific tabs Au, SAM, IFX+ETA). Transfer (Transfer-functionalization-dataset) dataset used for the functionalization in figure 2c. In the the file are reported the V<sub>GS</sub> and the I<sub>DS </sub>for each functionalization step (in specific tabs Au, SAM, IFX+ETA).</p>
Inverse folding for antibody sequence design using deep learning
<p>Model weights of the <a href="https://arxiv.org/abs/2310.19513">AbMPNN model (arXiv:2310.19513)</a> presented at the <a href="https://icml-compbio.github.io/">2023 ICML Workshop on Computational Biology</a>, and csv files with the split between train, test and validation across the <a href="https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/">SAbDab</a> and <a href="https://zenodo.org/record/7258553">ImmuneBuilder</a> datasets.</p><p>This model is based on <a href="https://www.biorxiv.org/content/10.1101/2022.06.03.494563v1">ProteinMPNN</a> and can be run using the corresponding code: <a href="https://github.com/dauparas/ProteinMPNN">https://github.com/dauparas/ProteinMPNN</a>.</p>
Dataset Associated with "Biochemical and biophysical characterization of natural polyreactivity in antibodies"
<p>Processed data for recreating figures and statistical analysis from Borowska & Boughter et al. <em>Cell Reports</em> 2023. Scripts for creating the figures and analysis from these data, as well as the scripts used to generate these datasets, can be found on the GitHub page (https://github.com/ctboughter/manuscript_md_analysis)</p>
Defining neutralization and allostery by antibodies against COVID-19 variants
<p>The changing landscape of mutations in the SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. A major factor that contributes to the functional activity of neutralizing antibodies are the intrinsic quaternary changes that occur as a result of antibody-Spike trimer interactions. In this study, we reveal the conformational dynamics and allosteric perturbations linked to binding of human monoclonal antibodies and the viral Spike protein. We identify epitope hotspots of known and novel antibodies, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants of concern (VoCs) on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Our comparative analyses of the antibody-footprints on Spike variants reveal how antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects. These differences have important implications for neutralization efficacy and for developing new antibodies targeting emerging variants. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19, and provide a foundation for the design of effective antiviral strategies.</p>
Data for: A cell surface-binding antibody atlas nominates a MUC18-directed antibody-drug conjugate for targeting melanoma
<p><span>Recent advances in targeted therapy and immunotherapy have substantially improved the treatment of melanoma. However, therapeutic strategies are still needed for unresponsive or treatment-relapsed melanoma patients. To discover antibody-drug conjugate (ADC)-tractable cell surface targets for melanoma, we developed an atlas of melanoma cell surface binding antibodies (pAbs) using a proteome-scale antibody array platform (PETAL). Target identification of pAbs led to development of melanoma cell killing ADCs against LGR6, TRPM1, ASAP1, and MUC18, among others. MUC18 was overexpressed in both tumor cells and tumor-infiltrating blood vessels across major melanoma subtypes, making it a potential dual-compartment and universal melanoma therapeutic target. AMT-253, an MUC18-directed ADC based on topoisomerase I inhibitor exatecan and a self-immolative T moiety, had a higher therapeutic index compared to its microtubule inhibitor-based counterpart and favorable pharmacokinetics and tolerability in monkeys. AMT-253 exhibited MUC18-specific cytotoxicity through DNA damage and apoptosis and a strong bystander killing effect, leading to potent antitumor activities against melanoma cell line and patient-derived xenograft models. Tumor vasculature-targeting by a mouse MUC18-specific antibody-T1000-exatecan conjugate inhibited tumor growth in human melanoma xenografts. Combination therapy of AMT-253 with an anti-angiogenic agent generated higher efficacy than single agent in a mucosal melanoma model. Beyond melanoma, AMT-253 was also efficacious in a wide range of MUC18-expressing solid tumors. Efficient target/antibody discovery in combination with the T moiety-exatecan linker-payload exemplified here may facilitate discovery of new ADC to improve cancer treatment</span><span>.</span></p>
A candidate antibody drug for prevention of malaria.
<p>Plasmablast human antibody repertoire sequences from volunteers in a malaria vaccine (RTS,S) clinical trial with sequence and donor annotations</p>
Trial Evaluating PCSK9 Antibody in Subjects With LDL Receptor Abnormalities
ClinicalTrials.gov study NCT01588496. IPD Sharing: Not stated. Countries: 12. Publications: 3.
Phase I Study to Evaluate a Human Monoclonal Antibody (MAb) 10E8VLS Administered Alone or Concurrently With MAb VRC07-523LS Via Subcutaneous Injection in Healthy Adults
ClinicalTrials.gov study NCT03565315. IPD Sharing: NO. Countries: 1. Publications: 3.
A Study to Investigate the Efficacy and Safety of Two Doses of GSK2857916 in Participants With Multiple Myeloma Who Have Failed Prior Treatment With an Anti-CD38 Antibody
ClinicalTrials.gov study NCT03525678. IPD Sharing: YES. Countries: 8. Publications: 8.
Anti-SARS-CoV-2 Monoclonal Antibodies for Long COVID (COVID-19)
ClinicalTrials.gov study NCT05877508. IPD Sharing: NO. Countries: 1. Publications: 1.
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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.
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DANDI Archive for NWB datasets
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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.