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376 results for “human papillomavirus”
Human papillomavirus (HPV) detection in vaginal self-samples: evaluation of eNat® as an alternative suspension medium to ThinPrep®PreservCyt® for vaginal swabs
<p>Dataset 1: HPV positivity on cervical and vaginal self-samples with different HPV real-time PCR assays</p> <p>Dataset 2: hrHPV viral load in cervical and vaginal self-samples</p> <p>Datakey 1: HPV positivity on cervical and vaginal self-samples with different HPV real-time PCR assays</p> <p>Datakey 2: hrHPV viral load in cervical and vaginal self-samples</p>
HDX-MS dataset for: "Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility"
<p>Hydrogen/deuterium exchange mass spectrometry dataset used in: <strong>Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility.</strong> Yuzhen Feng*, Dominik van Bodegraven*, Alan Kádek*, Ignacio L.B. Munguira, Laura Soria-Martinez, Sarah Nentwich, Sreedeepa Saha, Florian Chardon, Daniel Kavan, Charlotte Uetrecht#, Mario Schelhaas#, Wouter H. Roos#. <em>Nature Communications</em> 10076 (2024). doi: 10.1038/s41467-024-54373-0</p> <p>* - authors contributing equally</p> <p># - corresponding authors</p> <p><strong>Description:</strong></p> <p>Hydrogen/deuterium exchange mass spectrometry (HXMS) analysis of the effect of heparin on the conformational dynamics of human papillomavirus 16 pseudovirus (PsV).</p> <p><strong>Sample processing:</strong></p> <p>HPV16 PsV were prepared according to (Buck & Thompson: Current Protocols in Cell Biology 2007). In short, p16Shell and pClneo-EGFP were transfected into HEK293TT cells. After 48 h, cells were harvested and lysed followed by maturation of the virus particles for 24 h. For purification, the particles were purified using a CsCl step gradient (27 % w/V and 38.8 % w/V CsCl in 10 mM Tris-HCl pH 7.4, 207570 x g, 3 h 50 min, 4 °C) followed by dialysis in Float-A-Lyzer devices (1 mL, Spectra/Por) against a total of 3 L HPV virion buffer (1x PBS, 635 mM NaCl, 0.9 mM CaCl2, 0.5 mM MgCl2, 2.1 mM KCl, pH 7.4).</p> <p>PsV were pre-incubated for 1 h either with or without heparin (H4784, Sigma-Aldrich) at room temperature. To initiate deuterium labelling the samples were 6-fold diluted with the virion buffer they were obtained in, only made of 99.9% D2O (150 mM NaCl, 4.8 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, 0.9 mM CaCl2, 0.5 mM MgCl2, pD 7.2). This resulted in a final concentration of 0.5 µM L1 monomer in the form of PsV with or without 1 mg/ml heparin during deuterium labelling. The exchange reaction was left to proceed at room temperature until aliquots of 45 µl were removed at predetermined time points (1 min, 5 min, 15 min, 1 h and 4 h). In the aliquots, the exchange was immediately stopped by twofold dilution with ice-cold quench buffer (0.25 M glycine, 100 mM TCEP, 8 M urea, indicated pH 2.7), resulting in final pH 2.5. For samples with heparin, the quench buffer additionally contained 1 mg/ml protamine sulphate (P4020, Sigma-Aldrich). After 30 s incubation on ice, the samples were centrifuged at 10.000 x g for 1 min at 0 °C. Each supernatant was transferred to a fresh tube and flash frozen in liquid nitrogen. Low binding microtubes and low binding pipette tips (both Axygen) were used throughout for all handling of viral particles.</p> <p>The frozen samples were quickly thawed and injected into a refrigerated (1°C) HPLC system (Infinity 1260, Agilent Technologies), through a porcine pepsin column (≥ 3200 units/mg, Sigma-Aldrich) in-house immobilized onto POROS-20AL perfusion resin (Thermo Scientific) as described previously (Wang et al.: Molecular & Cellular Proteomics 2002), which was kept at 4°C. Pepsin digestion was performed at isocratic 200 µl/min flow rate (0.4 % formic acid in water). After the digestion, peptides were online desalted for 3 min on a peptide microtrap (OPTI-TRAP, Optimize Technologies) and then eluted on a reversed-phase analytical column (ZORBAX 300SB-C18, 0.5 x 35 mm, 3.5 µm, 300Å, Agilent Technologies). There LC separation proceeded at 25 µl/min flow rate through an 8 min gradient of 8–30% solvent B, followed by a 3 min gradient of 30-90 % solvent B (solvent A: 0.4 % formic acid in water, solvent B: 0.4 % formic acid in acetonitrile). The outlet of the HPLC system was connected to an electrospray ionization (ESI) source of an Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Scientific). The instrument was operated in positive ESI MS-only mode for deuterated samples, scan range 300-2000 m/z, using 4 microscans at resolving power setting 120,000. In a separate measurement on non-deuterated sample, the instrument was used in positive data-dependent ESI MS/MS mode with 30% HCD dissociation, 1 microscan and 240,000 resolving power setting for the identification of all peptides produced by non-specific pepsin cleavage.</p> <p>In total 22 pmol and 50 pmol L1 protein were injected per MS and MS/MS analysis, respectively. To minimize sample carry-over on the protease column, two washing solutions were always injected between sample injections modified from Majumdar et al. 69 (wash solution 1: 5% acetonitrile, 5% isopropanol, 20% acetic acid; wash solution 2: 4 M Urea, 1 M glycine, pH 2.5). All HDX samples were analysed in technical triplicates, except for the 15 min time point for PsV without heparin, which was measured in duplicate.</p> <p><br><strong>Data processing:</strong></p> <p>Peptides were identified from the MS/MS data by the Andromeda search algorithm implemented in MaxQuant (version 1.6.5.0) using a custom protein database containing the sequences of HPV16 L1 and L2 proteins. Deuterium uptake for the identified peptides was calculated with DeutEx (in-house developed), manually inspected and the statistical significance of the observed differences in deuteration was evaluated by applying an unpaired two-tailed Student’s T-test with single pooled variance evaluated with alpha ≤ 0.05 using the Holm-Šidák correction for multiple comparisons in Prism 8.0.1 (GraphPad Software). The processed data were visualized using MSTools (https://peterslab.org/MSTools/, Kavan & Man: International Journal of Mass Spectrometry 2011) and open-source PyMol 2.6.0a0 (Schrödinger, Inc).</p> <p>For ZENODO the datafiles were deposited as native Thermo .raw files (including instrumental parameters metadata) while all peaks in the spectra were additionally exported into plain m/z vs intensity .txt files per each scan in the LC-MS analysis as also used for the DeutEx HDX-MS processing.</p>
Immunogenicity and Safety of Dengue Tetravalent Vaccine (TDV) and Recombinant 9-valent Human Papillomavirus Vaccine (9vHPV) in Participants Aged ≥9 to <15 Years
ClinicalTrials.gov study NCT04313244. IPD Sharing: YES. Countries: 1. Publications: 3.
Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV)
<p>R-loop-triggered collateral single-stranded DNA (ssDNA) nuclease activity within Class 1 Type I CRISPR-Cas systems holds immense potential for nucleic acid detection. However, the hyperactive ssDNase activity of Cas3 introduces unwanted noise and false-positive results. In this study, we identified a novel Type I-A Cas3 variant derived from <em>Thermococcus siculi</em>, which remains in an auto-inhibited state until it is triggered by Cascade complex and R-loop formation. This Type I-A CRISPR-Cas3 system not only exhibits an expanded protospacer adjacent motif (PAM) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. Furthermore, it exhibits dual activation modes—responding to both DNA and RNA targets. The culmination of our research efforts has led to the development of the Hyper-Active-Verification Establishment (HAVE, 惠父). This innovation enables swift and precise <em>human papillomavirus</em> (HPV) diagnosis in clinical samples, providing a robust molecular diagnostic tool based on the Type I-A CRISPR-Cas3 system. Our findings contribute to understanding type I-A CRISPR-Cas3 system regulation and facilitate the creation of advanced diagnostic solutions with broad clinical applicability.</p>
Anti-PD-L1/TGF-beta Trap (M7824) Alone and in Combination With TriAd Vaccine and N-803 for Resectable Head and Neck Squamous Cell Carcinoma Not Associated With Human Papillomavirus Infection
ClinicalTrials.gov study NCT04247282. IPD Sharing: YES. Countries: 1. Publications: 3.
A Post Marketing Surveillance (PMS) Study to Monitor the Safety of GlaxoSmithKline (GSK) Biologicals' Human Papillomavirus (HPV) Vaccine in Female Chinese Subjects
ClinicalTrials.gov study NCT03438006. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Evaluation of Immunogenicity and Safety of Two 2-dose Human Papillomavirus (HPV) Vaccine Schedules in 9-14 Year Old Girls
ClinicalTrials.gov study NCT01381575. IPD Sharing: YES. Countries: 5. Publications: 4.
Cryotherapy for Human Papillomavirus Clearance in Biopsy-confirmed Cervical Low-grade Squamous Intraepithelial Lesions
ClinicalTrials.gov study NCT00566579. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Post-marketing Surveillance Study to Assess the Safety of Cervarix (GlaxoSmithKline [GSK] Biologicals' Human Papillomavirus [HPV] -16/18 Vaccine), When Administered According to the Approved Prescri
ClinicalTrials.gov study NCT03671369. IPD Sharing: NO. Countries: 1. Publications: 1.
A Study of ADXS11-001 or MEDI4736 Alone or Combination In Cervical or Human Papillomavirus (HPV)+ Head & Neck Cancer
ClinicalTrials.gov study NCT02291055. IPD Sharing: NO. Countries: 1. Publications: 0.
Evaluation of Long-term Immunogenicity and Safety of a Human Papillomavirus (HPV) Vaccine in Healthy Female Subjects
ClinicalTrials.gov study NCT00947115. IPD Sharing: YES. Countries: 2. Publications: 1.
Post Operative Adjuvant Therapy De-intensification Trial for Human Papillomavirus-related, p16+ Oropharynx Cancer
ClinicalTrials.gov study NCT01687413. IPD Sharing: NO. Countries: 1. Publications: 1.
Study to Evaluate the Efficacy of the Human Papillomavirus Vaccine in Healthy Adult Women of 26 Years of Age and Older
ClinicalTrials.gov study NCT00294047. IPD Sharing: YES. Countries: 12. Publications: 9.
Healthcare Provider Human Papillomavirus Education and Professional Skills Intervention
ClinicalTrials.gov study NCT05120869. IPD Sharing: YES. Countries: 1. Publications: 4.
Safety of and Immune Response to the Human Papillomavirus (HPV) Vaccine in HIV-Infected Women
ClinicalTrials.gov study NCT00604175. IPD Sharing: Not stated. Countries: 4. Publications: 8.
Innovative Tool to Increase Completion of Human Papillomavirus (HPV) Vaccine Series
ClinicalTrials.gov study NCT01343485. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Vaccine Therapy in Preventing Human Papillomavirus Infection in Younger Cancer Survivors
ClinicalTrials.gov study NCT01492582. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Immunogenicity and Safety Study of GSK Biologicals' Human Papillomavirus 580299 Vaccine in Healthy Female Subjects
ClinicalTrials.gov study NCT00996125. IPD Sharing: YES. Countries: 1. Publications: 2.
Vaccine Therapy in Preventing Human Papillomavirus Infection in Young HIV-Positive Male Patients Who Have Sex With Males
ClinicalTrials.gov study NCT01209325. IPD Sharing: NO. Countries: 2. Publications: 1.
Evaluation of Long-term Immunogenicity and Safety of a Human Papillomavirus (HPV) Vaccine in Healthy Female Subjects.
ClinicalTrials.gov study NCT00877877. IPD Sharing: YES. Countries: 5. Publications: 2.
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International Brain Laboratory public data
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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.