FB20: Medizin
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Research Data Open Access In vitro-in situ comparison study - Data set(Philipps-Universität Marburg) Jablonski-Momeni, AnahitaThis data set presents the data which were analysed for the following publication: A comparison between in vitro and randomized in situ models for remineralization of artificial enamel lesions Jablonski-Momeni A, Lentz J, Jablonski B, Kiesow A, Morawietz M. Sci Rep. 2024 Oct 25;14(1):25295. doi: 10.1038/s41598-024-76387-w. Abstract: The randomized study aimed to evaluate the comparability of in situ (iS) and in vitro (iV) study protocols regarding remineralization of artificial enamel lesions. Two toothpastes (group A: 1450 ppm sodium fluoride, group B: placebo 0 ppm F-), were investigated. IV, a pH-cycling model with toothpaste slurry treatment was applied for 10d. IS, remineralization was performed in 9 participants wearing splints with embedded enamel samples for 10 and 21d, randomly allocated to groups A and B. Samples were scanned by X-ray micro-computed tomography (μCT) and grayscale value line profiles corresponding to mineral density (rel.ΔZ) were analyzed. T-Test for dependent and independent data and analysis of variance (ANOVA) were used for further analyses (α = 0.05). Rel.ΔZ of fluoride treated samples (A) were iV = 40.2%, iS 10d = 11.5% and iS 21d = 46.1% (p > 0.05). Rel.ΔZ of placebo treated samples (B) were: iV = − 6.2%, iS 10d = 25.2% and iS 21d = 11.0% (p > 0.05). Remineralization potential of both toothpastes was significantly different regarding iV (p < 0.001) and iS after 21d (p = 0.034), while in case of iS 10d no significant difference was detected (p = 0.4). Despite different study protocols the μCT results after remineralization were comparable between iV and iS. The results suggest that selected studies can be carried out in faster, simplified iV studies using pH-cycling instead of iS studies.Research Data Open Access Human Uniprot Sequences FastafileBhagwat, Aditya M; Graumann, JohannesResearch Data Open Access Structural reflection data (.mtz) of soaked Sudan virus VP40 crystals(Philipps-Universität Marburg, Institut für Virologie) Werner, Anke-Dorothee; Becker, StephanThis repository contains structural data (.mtz) of Sudan virus VP40 crystals, soaked with small molecules. Files are ordered names correspond to internal lab crystal IDs (e.g. XDS_ASCII_AW61_scaled1.mtz, with "AWxxx" indicating the crystal ID). The resolution and data quality indicators for each dataset are provided in an accompanying metadata file. Users should refer to this file to select appropriate datasets for their analyses. Dimeric VP40 (approx. 7 mg/ml in 25 mM Tris, 300 mM NaCl, pH 8) was mixed 1:1 with crystallization buffer (100 mM HEPES, 40 mM MgCl2, 10% v/v PEG400). Crystals grew overnight at 18 °C using the hanging drop method. Fragments originating from the FragXtal Screen (Jena Biosciences) were dissolved in DMSO to 1 M and diluted 1:10 in crystallization buffer (with or without 20% ethylene glycol as a cryoprotectant) to a final concentration of 100 mM. Crystals were then placed in a drop of the diluted fragments and soaked for either only seconds, minutes, 1 h, or overnight. Crystals were then harvested, flash-frozen in liquid nitrogen and analyzed at the Swiss Light Source, Paul-Scherrer Institute, Villigen, Switzerland (SLS BEAMLINE X06SA, DECTRIS EIGER X 16M detector, single wavelength, data collection temperature 100 K). Datasets were collected and processed using XDS and scaled using the ccp4i suite Aimless. Mtz-files can be used for molecular replacement (using PDB-ID 8B3X or other structures of VP40 as template). To use these mtz files for molecular replacement: 1) Download the desired mtz file(s) and the accompanying metadata. 2) Initial Structure Solution: a. Use molecular replacement with programs such as Phaser or MOLREP from the CCP4 suite. b. Use PDB-ID 8B3X as the initial search model. Other VP40 structures may also be suitable. 3) Rapid Initial Model Building and Refinement: a. Use DIMPLE (Difference Map Pipeline) for quick initial refinement and map calculation. b. Run DIMPLE. c. This will produce refined models and maps for each dataset, suitable for initial analysis or as input for PanDDA. 4) Fragment Identification: a. For datasets suspected to contain bound fragments, use PanDDA (Pan-Dataset Density Analysis). b. Prepare input files as per PanDDA documentation, using DIMPLE output. c. Run PanDDA with appropriate parameters. d. Examine PanDDA event maps for evidence of bound fragments. 5) Model Building and Refinement: a. Build fragments into positive difference density or PanDDA event maps. b. Refine structures using programs like REFMAC5 or phenix.refine. Related datasets deposited to the Protein data bank (https://www.rcsb.org/) include 8B2U (Crystal structure of SUDV VP40 in complex with salicylic acid) and 8B1S (Co-crystal of SUDV VP40 with salicylic acid). This work was funded by the LOEWE Center DRUID (State of Hesse, Germany), project A1. For any questions regarding the use of these datasets or analysis methods, please contact the depositing authors Stephan Becker or Anke-Dorothee Werner at the insitutte for Virology, Marburg, Germany (https://www.uni-marburg.de/en/fb20/departments/ciii/virology).Research Data Restricted Prognostic impact of immunophenotypic variation in subcapsular sinus endothelium of sentinel lymph nodes in invasive breast carcinoma(Trafo, Institut für Pathologie, Philipps-Universität Marburg) Westhoff, Christina; Kalder, Matthias; Derben, JonasResearch Data Open Access Appendix-Demographic Mortality Measures as Indicators of Amenable or Avoidable Deaths in the 50 States of the United States of America. An Example of a Population-Based Health Care Quality Indicator - Applied to Chronic Obstructive Pulmonary Disease (COPD)(Yesser Falk) Falk, Yesser; Mueller, UlrichResearch Data Open Access Complement diagnostic algorithm(Ehinger & Pauly) Pauly, Diana; Ehinger, VeronikaResearch Data Open Access Complement associated diseases(Ehinger und Pauly) Pauly, Diana; Ehinger, VeronikaResearch Data Restricted Nodal lymphangiogenesis and immunophenotypic variations of sinus endothelium in sentinel and non-sentinel lymph nodes of invasive breast carcinomaWesthoff, Christina; Kalder, Matthias; Müller, Sabrina K.Research Data Open Access Collection