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3,650 results for “antibody”
Seroprevalence of immunoglobulin G antibodies against SARS-CoV-2 in Cyprus
<p>Four vaccines that have been authorized in the European Union offer different levels of protection against SARS-CoV-2 by generating immune responses against the spike receptor-binding domain (RBD) of the virus. Monitoring the levels of IgG antibodies against the SARS-CoV-2 is important during the coronavirus disease 2019 (COVID-19) pandemic to plan an adequate and evidence-based public health response. We compared the levels of serum IgG antibodies against SARS-CoV-2 spike protein in three groups: i) individuals without evidence of prior infection with SARS-CoV-2 who received one or two doses of either an mRNA-based (Comirnaty BNT162b2/Pfizer-BioNTech or Spikevax mRNA-1273/Moderna) or an adenoviral-based vaccine (Vaxzervia ChAdOx1 nCoV-19 /Oxford-Astra Zeneca) (n=227), ii) unvaccinated individuals with evidence of prior infection with SARS-CoV-2 (n=109), and iii) individuals with evidence of prior infection with SARS-CoV-2 who received at least one dose of a vaccine (n=30). Unvaccinated individuals without evidence of prior infection with SARS-CoV-2 were used as a control group (n=211). Our results indicate that vaccine-induced responses lead to higher levels of IgG antibodies compared to those produced following infection with the virus. In agreement with previous studies, our results suggest that among individuals previously infected with SARS-CoV-2, even a single dose of a vaccine is adequate to elicit high levels of humoral immunity.</p>
Corticosteroid therapy in patients with COVID-19 has little effect on the production of specific antibodies
<p>This excel data includes our research, ”Corticosteroid therapy in patients with COVID-19 has little effect on the production of specific antibodies."</p>
Data from: SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals
<p class="MsoNormal"><span>The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Here we tested monthly blood donation samples for IgG antibodies from March 2020 to March 2021 in eight of Brazil's most populous cities. The inferred attack rate of SARS-CoV-2 adjusted for seroreversion in December 2020, before the Gamma VOC was dominant, ranged from 19.3% (95% CrI 17.5% - 21.2%) in Curitiba to 75.0% (95% CrI 70.8% - 80.3%) in Manaus. Seroprevalence was consistently smaller in women and donors older than 55 years. The age-specific infection fatality rate (IFR) differed between cities and consistently increased with age. The infection hospitalisation rate (IHR) increased significantly during the Gamma-dominated second wave in Manaus, suggesting increased morbidity of the Gamma VOC compared to previous variants circulating in Manaus. The higher disease penetrance associated with the health system's collapse increased the overall IFR by a minimum factor of 2.91 (95% CrI 2.43 – 3.53). These results highlight the utility of blood donor serosurveillance to track epidemic maturity and demonstrate demographic and spatial heterogeneity in SARS-CoV-2 spread.</span></p>
Genome and gene annotation for yeast strain SK1 used in "Deciphering the "m6A Code" via Antibody-Independent Quantitative Profiling"
<p>Genome and gene annotation used in "Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling" provided by Schraga Schwartz from his time at the Broad Institute.</p>
Migraine monoclonal antibodies against CGRP change brain activity depending on ligand or receptor target – an fMRI study
<p>Background: Monoclonal antibodies (mAbs) against calcitonin gene-related peptides (CGRP) are novel treatments for migraine prevention. Based on a previous functional imaging study which investigated the CGRP receptor mAb (erenumab), we hypothesized that (i) the CGRP ligand mAb galcanezumab would alter central trigeminal pain processing; (ii) responders to galcanezumab treatment would show specific hypothalamic modulation in contrast to non-responders; and (iii) the ligand and the receptor antibody differ in brain responses.</p> <p>Methods: Using an established trigeminal nociceptive functional magnetic imaging paradigm, 26 migraine patients were subsequently scanned twice: before and 2–3 weeks after administration of galcanezumab.</p> <p>Results: We found that galcanezumab decreases hypothalamic activation in all patients and that the reduction was stronger in responders than in non-responders. Contrasting erenumab and galcanezumab showed that both antibodies activate a distinct network. We also found that pre-treatment activity of the spinal trigeminal nucleus (STN) and coupling between the STN and the hypothalamus covariates with the response to galcanezumab.</p> <p>Conclusions: These data suggest that despite relative impermeability of the blood-brain barrier for CGRP mAb, mAb treatment induces certain and highly specific brain effects which may be part of the mechanism of their efficacy in migraine treatment.</p> <p>Funding: This work was supported by the German Ministry of Education and Research (BMBF) of ERA-Net Neuron under the project code BIOMIGA (01EW2002 to AM) and by the German Research Foundation (SFB936-178316478-A5 to AM). The funding sources did not influence study conduction in any way. </p> <p>Clinical trial number: The basic science study was preregistered in the Open Science Framework (https://osf.io/m2rc6).</p>
In vivo characterization of antibodies directed against TREAT-AD target proteins in mouse model of AD pathology
<p><em>In vivo </em>characterization of antibodies directed against TREAT-AD target proteins (Moesin, CD44, Midkine, and SFRP1) in the 5xFAD mouse model</p>
Supplementary figure: No evidence of any wild animal samples positive for SARS-CoV-2 RNA or antibodies were found in China.
<p>A compilation of results of wildlife sampling from the Huanan market and from China showing no evidence of positive animal for SARS-CoV-2 in China</p>
Supplementary Data and Figures for "Myomedin replicas of gp120 V3 loop glycan epitopes of PGT121 and PGT126 antibodies as non-cognate antigens for HIV-1 broadly neutralizing antibodies"
<p>Supplementary pymol sessions for "Myomedin replicas of gp120 V3 loop glycan epitopes of PGT121 and PGT126 antibodies as non-cognate antigens for HIV-1 broadly neutralizing antibodies". Pymol sessions contain the source data for Figure 3, panels A-K.</p>
Data from: A Nonadjuvanted Whole-Inactivated Pneumococcal Vaccine Induces Multiserotype Opsonophagocytic Responses Mediated by Noncapsule-Specific Antibodies
<p><em>Streptococcus pneumoniae</em> (Spn) remains a major cause of global mortality, with extensive antigenic diversity between capsular serotypes that poses an ongoing challenge for vaccine development. Widespread use of pneumococcal conjugate vaccines (PCVs) targeting Spn capsules has greatly reduced infections by vaccine-included serotypes, but has led to increased infections by non-included serotypes. To date, high cost of PCVs has also limited their usefulness in low-income regions where disease burdens are highest. To overcome these limitations, serotype-independent vaccines are being actively researched. We have developed a whole-cell gamma-irradiated Spn vaccine (termed Gamma-PN) providing serotype-independent protection. We demonstrate that Gamma-PN immunization via the clinically relevant intramuscular route induces protein-specific antibodies able to bind numerous non-vaccine encapsulated serotypes, which mediate opsonophagocytic killing and protection against lethal challenges. Gamma-PN induced comparable or superior OPKA responses to serotypes found in the licensed Prevnar13 (PCV13), and a superior response to non-included serotypes, including emergent 22F and 35B. Additionally, despite a lower observed reactogenicity, administration of Gamma-PN without adjuvant resulted in higher OPKA responses and improved protection compared to adjuvanted Gamma-PN. To our knowledge, this has never been demonstrated for a whole-inactivated Spn vaccine. Eliminating the requirement for adjuvant comes with numerous benefits for clinical applications of this vaccine, and poses interesting questions for the inclusion of adjuvant in similar vaccines in development.</p>
T cell deficiency precipitates antibody evasion and emergence of neurovirulent polyomavirus
<p>JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy (PML), a life-threatening brain disease in immunocompromised patients. Inherited and acquired T cell deficiencies are associated with PML. The incidence of PML is increasing with the introduction of new immunomodulatory agents, several of which target T cells or B cells. PML patients often carry mutations in the JCPyV VP1 capsid protein, which confer resistance to neutralizing VP1 antibodies (Ab). Polyomaviruses (PyV) are tightly species-specific; the absence of tractable animal models has handicapped understanding of PyV pathogenesis. Using mouse polyomavirus (MuPyV), we found that T cell deficiency during persistent infection, in the setting of monospecific VP1 Ab, was required for outgrowth of VP1 Ab-escape viral variants. CD4 T cells were primarily responsible for limiting polyomavirus infection in the kidney, a major reservoir of persistent infection by both JCPyV and MuPyV, and checking emergence of these mutant viruses. T cells also provided a second line of defense by controlling the outgrowth of VP1 mutant viruses that evaded Ab neutralization. A virus with two capsid mutations, one conferring Ab-escape yet impaired infectivity and a second compensatory mutation, yielded a highly neurovirulent variant. These findings link T cell deficiency and evolution of Ab-escape polyomavirus VP1 variants with neuropathogenicity.</p>
Novel trehalose-based excipients for stabilizing nebulized anti-SARS-CoV-2 antibody
<p>Raw data associated to the study entitled "Novel trehalose-based excipients for stabilizing nebulized anti-SARS-CoV-2 antibody", including:</p> <p>- Synthesis development: experimental procedures and characterization</p> <p>- DLS data for CxxTreSuc excipients</p> <p>- Cytotoxicity</p>
Data and model weights for a series of antibody language models
<p>This repo contains the sequence dataset for finetuning and model weights including pre-trained meta model and a series of finetuned antibody language models.</p> <p>The antibody language models were used in the paper "<em>Physics-driven structural docking and protein language models accelerate antibody screening and design for broad-spectrum antiviral therapy"</em> for antibody sequence embedding.</p>
Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"
<p>Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"</p>
Supplemental Figures - Detection of SARS-CoV-2-Specific Secretory IgA and Neutralizing Antibodies in the Nasal Secretions of Exposed Seronegative Individuals
<p>Figure S1: Flow diagram of exposed seronegative cohort.</p> <p>Figure S2: SARS-CoV-2-specific neutralization activity at Days 1 and 8 relative to enrollment in exposed seronegative nasal SIgA positive and infected participants. NPS SARS-CoV-2-specific neutralization activity is shown for exposed seronegative and infected participants with normalized OD490 at Day 1 and Day 8, respectively. Sample sizes (N) are indicated in parentheses. Wilcoxon signed-rank tests were used to determine if the median SARS-CoV-2 nasal SIgA neutralization activity differed significantly. A two-tailed p < 0.05 was considered significant.</p>
Somatic hypermutation-mediated paratope flexibility improves the cross-reactivity of human malaria antibodies -- Molecular Dynamics dataset
<p>4493 Manuscript Data<br>====================</p> <p>author: Anton Hanke<br>size of uncompressed folder: ~19Gb.<br>DOI: 10.5281/zenodo.11470585</p> <p># Standard MD simulation data</p> <p>Standard Simulations were generated with gromacs 2021.5 using the charmm36m forcefield Juli 2021 release tarball (https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2021.ff.tgz).<br>Post processed (PBC) simulations are structured as follows:<br>Mature generally refers to the wildtype 4493 antibody.</p> <p>- simulations/standardMD<br> |<br> |- prod.mdp example production mdp file used to run all production simulations.<br> |<br> |- mature Mature simulation set. (folder and file naming the same in all simulation directories)<br> | |- {peptide}_{replicate}_prod.gro {peptide} = peptide; {replicate} = standard MD replicate<br> | |- {peptide}_{replicate}_prod.tpr<br> | `- {peptide}_{replicate}_prod_align_noPBC.xtc (10Frames/ns)<br> |<br> |- mature_rerun Additional set of replicates with the wildtype 4493.<br> |- matureCapped Set of simulations with termini capped peptides<br> |- mature_nanpv2 Set of simulations with NPDP similar positioning of NANP<br> |- wo_pep Set of simulations without peptides for germline and mature<br> `- germline Set of germline simulations.</p> <p><br># RAMD simulation data</p> <p>RAMD simulations were generated with gromacs_2020.5 patched with RAMDv2 modified to account for the connected multiple ligand groups.<br>(Source code provided as tar file ./sw/gromacs_ramd_patchv2.tar.gz)</p> <p>Not all trajectories contain an unbinding event (gromacs CUDA bug.). <br>These trajectories were not considered in the analysis of simulations. </p> <p>- simulations/ramd<br> |<br> |- prod.mdp Exemplary production mdp file with RAMD settings, these were used in all trajectories w/<br> | differing RAMD random seed.<br> |<br> |- mature_2.625kcalmolA_4.0_3.0<br> | |- {peptide}_{replicate}_prod_{startFrame}.gro {peptide} = peptide; {replicate} = standard MD replicate; {startFrame} = Frame in standard MD used to start simulation.<br> | |- {peptide}_{replicate}_prod_{startFrame}.tpr<br> | |- {peptide}_{replicate}_prod_{startFrame}.ndx<br> | |- {peptide}_{replicate}_prod_{startFrame}_align_noPBC.xtc (100Frames/ns) Files omited due to size -- available on request.<br> | `- {peptide}_{replicate}_prod_{startFrame}_lastframe.pdb Last frame of the processed RAMD trajectory.<br> `- gl_2.625kcalmolA_4.0_3.0</p> <p><br># Analysis</p> <p>- analysis<br> |<br> |- entropie Quasi harmonic entropy estimation.<br> | |- inp Concatenated & Bootstrapped, coarse-grained and aligned trajectories of all systems<br> | |- out CPPTRAJ runs to calculate QHE on the bootstrapped trajectories<br> | |- run_complex.sh Script running analysis.<br> | |- ana.py Script to calculte average and std of QHE for each system. (generates *.out *.tsv *.png)<br> | |- cg.py Script used to bootstrap, coarse-grain align and build average structure with.<br> | `- delta_entropies.ods Excel file used to calculate Tab 1. in Main text of paper from entropies.out.<br> |<br> |- mmpbsa MMPBSA calculations (MM + SolvEnergy) with gmx_MMPBSA<br> | |- inp Input trajectories and topologies processed for MMPBSA<br> | |- out/gmx_mmpbsa Output directories in which gmx_MMPBSA was run.<br> | | ` *.dat Output files containing calculated energy terms from gmx_MMPBSA.<br> | |- mmpbsa.in MMPBSA input file used to run analysis.<br> | |- plot_results.py Python script to plot correlation of MMPBSA output with experimental data<br> | |- pca_eig_extr.py Script to reduce simulations to regions of high probability density within trajectory (not used in the present analysis)<br> | |- slurm-91315023.out Log file of the analysis run<br> | `- run_mmpbsa.sh Shell script to run the MMPBSA analysis (generates input and output file trees).<br> |<br> `- ramd RAMD analysation.<br> |- run.sh Shell script to run the analysis<br> |- run_ramd_ana.py Python script called by `run.sh` to run the analysis using `ramdAnalysis.py`<br> |- contact_clusters.py Python script to generate plots based on output of the analysis.<br> |- ramdAnalysis.py Python module containing analysis classes called/used within `run_ramd_ana.py`<br> | Based on tauRAMD & Fingerprint analysis by Dr. Daria Khokh (https://doi.org/10.1021%2Facs.jctc.8b00230; https://doi.org/10.1063%2F5.0019088)<br> |- abrun.* Log files from the present run<br> |- *.svg; *.png Analysis output files.<br> |- tramd_patchv2/ Output PDB structures from the analysis (excluded due to size, available on request)<br> `- representatives.pse Pymol session of cluster representatives along unbinding for germline and wildtype with contact probabilities within the<br> cluster mapped as b-factor.</p> <p># Figures</p> <p>- figure_pdbs PDB files (and pymol sessions) used to generate figures in the papers main text.</p>
Antibody dataset Kd
<p>A dataset of ~500 antibodies with binding affinity: antibody sequence, antigen sequence, Kd. Obtained from SAbDab via Therapeutic Data Commons</p> <p>Python code (get_antibody_affinity_data.py) and dataset (antibody_affinity_protein_sabdab.csv) </p>
anti-phospho-SMAD1/5 antibody can recognize formaldehyde-fixed epitope
<p>Determining whether anti-phospho-SMAD1-5 and anti-phospho-SMAD2 antibodies can recognize formaldehyde-fixed epitopes</p>
Finding an antibody to detect EZH1 protein expression – Part 2
<p>Follow up to previous post of trying to find an antibody to determine EZH1 expression in AML patient cells.</p>
Screen of Pr20 TCR mimic antibody against a library of HLA-A*02:01 MHC-I peptides
<p>Minigene sequencing of T2 cells sorted for high and low binding to the TCR mimic antibody "Pr20."</p>
Finding an antibody to detect EZH1 protein expression – Part 3
<p>Follow up to previous post of trying to find an antibody to determine EZH1 expression in AML patient cells.</p>
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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.
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.