KU Leuven Research Data Repository
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Replication Data for: Photoinduced Decarboxylation in Fluorescent Proteins: Charge-Transfer States and Structure-Function Relationship
No full textThis dataset forms the foundation of the publication associated with it titled: "Photoinduced Decarboxylation in Fluorescent Proteins: Charge-Transfer States and Structure-Function Relationship". In this study, the photoinduced decarboxylation of acidic amino acids near the chromophore of fluorescent proteins was investigated using computational methods on six variants to gain a deeper understanding of the reaction mechanism. This dataset provides all necessary files to replicate and validate the research. It includes: classical molecular dynamics parameter files, initial and optimized system structures, trajectory of 100 snapshots from QM/MM MD simulations of PA-GFP, and QM region coordinates with their corresponding embedding potentials
Contrast pairs in music instruction: on depiction and stance-taking
No full textThis dataset was analyzed as part of the dissertation project "Contrast pairs in music instruction: on depiction and stance-taking. The dataset contains video clips that served as examples in the dissertation. Next to that, dataset comprises exports from annotations made in video data that served as the basis for descriptive statistics and qualitative analysis. Datasets and scripts for an inter-coder agreement test are provided. The study investigates how instructors in musical settings (orchestra rehearsal, string quartet master class) use contrast pairs in the instructional process. During contrast pairs, instructors set up a contrast between two performance versions, one desired and one undesired. Contrast pairs are approached in this dissertation as a case study for composite and complex stance meanings. Across two video corpora, different sub-phenomena were analyzed: the multimodal and sequential structure of contrast pairs, simultaneous expressions of contrasts across speech and gesture, and mocking depictions during contrast pairs. As a whole, this dissertation contributes to the growing body of work on multimodal stance-taking
Supplementary materials for: "Scanning Electron Microscopy-based Automatic Defect Inspection for Semiconductor Manufacturing: A Systematic Review"
No full textThis dataset contains supplementary materials for: "Scanning Electron Microscopy-based Automatic Defect Inspection for Semiconductor Manufacturing: A Systematic Review". More specifically, it provides (i) a document containing the full search commands used to identify records/papers, (ii) a spreadsheet of the screening results, (iii) a spreadsheet of the selected papers and their categorization results, and (iv) a BibTeX document with citations for the selected papers
Replication data for: "The crystallization of language over time"
No full textThis repository contains the data and R script accompanying the paper "The crystallization of language over time" (under review). The datasets are stored in txt (tab-delimited) and rds format in the /data folder. The files ngrams_lemma.txt and ngrams_pos.txt contain lemma and part-of-speech trigrams and frequency information culled from the C-CLAMP corpus (1850-1999; Piersoul et al. 2021). These files are used to calculate the trigrams' association measures with the R code in 01_data_preparation.R. The file 02_analyses.R contains the R code used to model the trigrams' internal coherence through time using generalized linear and additive mixed models, and assess their distribution by means of Shannon's entropy and Kullback-Leibler Divergence
Full model script for Chapter 5 of the PhD Thesis: The tissue differentiation with regard to the central carbon metabolism in tomato fruit
No full textThis dataset contains the full mathematical model used in Chapter 5 of the PhD thesis "The tissue differentiation with regard to the central carbon metabolism in tomato fruit". The purpose of the model is to simulate changes in metabolite concentrations and ¹³C-label enrichment over time, in order to investigate oxygen-dependent metabolic fluxes in tomato fruit tissue.
The dataset includes a complete set of ordinary differential equations (ODEs) representing central carbon metabolism, structured across major subcellular compartments: the cytosol, mitochondria, plastids, and vacuole. Each equation reflects the carbon transitions in enzymatic reactions based on data from ¹³C-glucose labeling experiments.
This dataset contains only the mathematical structure of the model—ODEs, metabolite definitions, and reaction schemes—and does not include experimental data or simulation results. It is intended as a reusable resource for researchers working on kinetic modeling, plant metabolism, or systems biology
Replication Data for: Stretching the Limits: From Planar Biaxial Stress-Strain to Arterial Pressure-Diameter
No full textThis dataset is the supplementary materials for the research paper entitled "Stretching the Limits: From Planar Biaxial Stress-Strain to Arterial Pressure-Diameter".
Authors:
Thibault Vervenne (KU Leuven), Nic Vermeeren (KU Leuven), Nele Demeersseman (KU Leuven), Heleen Fehervary (KU Leuven), Mathias Peirlinck (TU Delft), Ellen Kuhl (Stanford) and Nele Famaey (KU Leuven)
Affiliations:
Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
FIBEr - KU Leuven Core Facility for Biomechanical Experimentation, Leuven, Belgium
Department of BioMechanical Engineering, TU Delft, Delft, The Netherlands
Department of Mechanical Engineering, Stanford University, Stanford, CA, United States
All data files and MATLAB/Python codes are included for:
- Preparation and processing of planar biaxial data (both modeled and experimental).
- Reproducing pressure-diameter results (modeled and experimental), including optimizations and extension-inflation data.
- Ring-opening experiments data.
- Constitutive Artificial Neural Network (CANN) code
***Please consider the readme.txt first**
Data for paper: Patient-Centered Communication in A Diverse General Practice Setting: A Multi-Perspective Case Study
No full textThis is the dataset used for the paper Patient-Centered Communication in A Diverse General Practice Setting: A Multi-Perspective Case Study. The dataset consists of the transcriptions of the two discussed cases in the paper and the open recall interviews with the treating doctor and the intercultural mediator. These data aren't made publicly available because of their sensitive content and ethical regulations. Acces can be requested through the author, after explicit approval of EC Research UZ/KU Leuven
Replication Data for: Capabilities of the High-Order Spectral - Numerical Wave Tank to Model Wave Inhomogeneities due to Limited Wavemaker Length
No full textThis dataset contains the numerical results and experimental measurements used in the paper titled 'Capabilities of the High-Order Spectral - Numerical Wave Tank to
Model Wave Inhomogeneities due to Limited Wavemaker Length'. Numerical simulations are done using an adjusted version of the High-Order Spectral - Numerical Wave Tank. The source code is provided, as well as the compiled version of the code that was run for each test with MPI parallelization, the corresponding input files for the simulations, and the resulting free surface elevation (both at numerical probe locations, and over the full domain). Experimental data were collected in the Coastal & Ocean Basin (COB) within the Flanders Maritime Laboratory in Ostend, Belgium. The experimental setup for the different tests are described in detail in the paper. The coordinates of the probes present during the different tests are provided in the dataset, together with the measurements of these probes and the realized paddle displacements of the wavemakers
Understanding the Endo- and Exo-mechanisms Involved in the Enzymatic Hydrolysis of Levan and Inulin Polymers
No full textSupporting Data and File Instructions for the paper: Understanding the Endo- and Exo-mechanisms Involved in the Enzymatic Hydrolysis of Levan and Inulin Polymer.
Published in Journal of Agriculture and Food Chemistry.
This dataset and accompanying documentation provide all necessary files and instructions to reproduce the molecular dynamics simulations, structure analyses, and phylogenetic comparisons described in the article "Understanding the Endo- and Exo-mechanisms Involved in the Enzymatic Hydrolysis of Levan and Inulin Polymers."
Researchers are encouraged to use these resources to explore enzyme-substrate interactions, replicate the computational workflows, or extend the analyses to related GH32 enzymes used in this study. For questions or further details, please refer to the original publication or contact the corresponding authors
Interviews with European Researchers on Open Science and Reproducibility in Research, 2023-2024
No full textCollection of transcripts of interviews with sixty European researchers on the topic of reproducibility. These semi-structured interviews were conducted to understand what reproducibility means in different research disciplines and contexts and how researchers personally view it; what researchers do in practice to make their research reproducible; the underlying drivers and barriers to reproducibility and what motivates researchers towards reproducible research. When the term reproducibility was unfamiliar or ambiguous, we focused the interview on related concepts such as reliability, validity, trustworthiness, and how researchers aim to increase confidence in their work.
Sixty researchers, representing various career stages, disciplines, and institutions across Europe, were interviewed online using Microsoft Teams or in person between December 2023 and 2024. Each interview lasted approximately 60 minutes. Interviews were audio/video recorded, transcribed, translated to English where needed, anonymised and reviewed by interviewees. All transcripts are in English.
This data collections forms part of the Horizon Europe OSIRIS project (Open Science to Increase the Reproducibility of Science)