cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34973/n8gb-yz69
title: Optimizing Pediatric Kidney Transplantation care, a regional, national and international perspective

description: Supplementary files of the thesis of Loes Oomen. 
Chapter 6 "International validation of a pre-transplant risk assessment tool for graft survival in pediatric kidney transplant recipients"
Chapter 7 "Pediatric kidney transplantation in Europe, a snapshot of clinical practice"
The files contain information about the participating registries, countries and data collected, additional analysis and supplementary results in the form of tables and figures
DOI: 10.34973/sy5h-zk11
title: Data values presented in the figures of the article 'Trained immunity is regulated by T cell-induced CD40-TRAF6 signaling'

description: This collection contains the data values that are presented in the figures and supplementary figures of the publication : 'Trained immunity is regulated by T cell-induced CD40-TRAF6 signaling' (Cell Reports, 2024, https://doi.org/10.1016/j.celrep.2024.114664). The files include the data values that are used to generate the figures and supplementary figures, the figure legends to explain what the data values represent and the figures themselves.


Abstract: Trained immunity is characterized by histone modifications and metabolic changes in innate immune cells following exposure to inflammatory signals, leading to heightened responsiveness to secondary stimuli. Although our understanding of the molecular regulation of trained immunity has increased, the role of adaptive immune cells herein remains largely unknown. Here, we show that T cells modulate trained immunity via CD40-TRAF6 signaling. CD40-TRAF6 inhibition modulates functional, transcriptomic and metabolic reprogramming, and modifies histone 3 lysine 4 trimethylation associated with trained immunity. Besides in vitro studies, we reveal that single nucleotide polymorphisms in the proximity of CD40 are linked to trained immunity responses in vivo, and that combining CD40-TRAF6 inhibition with CTLA4-Ig-mediated co-stimulatory blockade induces long-term graft acceptance in a murine heart transplantation model. Combined, our study reveals that trained immunity is modulated by CD40-TRAF6 signaling between myeloid and adaptive immune cells and that this can be leveraged for therapeutic purposes.
DOI: 10.34973/s07v-9e02
title: Assessing medical devices: a qualitative study from the validate perspective

description: In this collection you can find processed results of a study exploring procedures and methods used by Health Technology Assessment (HTA) agencies for assessing medical devices. An online survey was used to map the current landscape of assessing medical devices, and interviews with HTA practitioners were conducted to retrieve in-depth information about their views about appropriate methodology and the role of HTA.
DOI: 10.34973/qb8g-bb87
title: Cascaded dual-polarity plane wave velocity vector imaging data

description: Simulated and experimentally measured data of DOI: 10.1109/TUFFC.2024.3355712.
Article compares the velocity vector imaging performance of cascaded dual-polarity wave (CDW) imaging versus conventional plane wave imaging for different signal-to-noise ratio conditions. Data consists of simulated single scatterer motion, simulated and experimentally measured parabolic tube flow and simulated realistic carotid blood flow (based on 10.1109/TUFFC.2009.1071). All ultrafast ultrasound data uses a PRF of 8 kHz, with repeated steering angles of -20 and + 20 degrees. CDW imaging was performed using four pulses in a train.
DOI: 10.34973/c48g-kv10
title: Optical genome mapping enables accurate testing of large repeat expansions

description: Dataset belonging to the study entitled: "Optical genome mapping enables accurate testing of large repeat expansions".

This dataset contains for each of the 85 samples the local guided assembly as generated within the study. These .zip file can be imported into the Bionano Access software. Please refer to the readme.txt for more information.

The study has the following abstract:
Short tandem repeats (STRs) are common variations in human genomes that frequently expand or contract, causing genetic disorders, mainly when expanded. Traditional diagnostic methods for identifying these expansions, such as repeat-primed PCR and Southern blotting, are often labor-intensive, locus-specific, and are unable to precisely determine long repeat expansions. Sequencing-based methods, though capable of genome-wide detection, are limited by inaccuracy (short-read technologies) and high associated costs (long-read technologies).
This study evaluated optical genome mapping (OGM) as an efficient, accurate approach for measuring STR lengths and assessing somatic stability in 85 samples with known pathogenic repeat expansions in DMPK, CNBP, and RFC1, causing myotonic dystrophy types 1 and 2 and cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), respectively. Three workflows—manual de novo assembly, local guided assembly (local-GA), and a molecule distance script—were applied, of which the latter two were developed as part of this study to assess the repeat sizes and somatic repeat stability.
OGM successfully identified 84/85 (98.8%) of the pathogenic expansions, distinguishing between wild-type and expanded alleles or between two expanded alleles in recessive cases, with greater accuracy than standard of care (SOC) for long repeats and no apparent upper size limit. Notably, OGM detected somatic instability in a subset of DMPK, CNBP, and RFC1 samples. These findings suggest OGM could advance diagnostic accuracy for large repeat expansions, providing a more comprehensive genome-wide assay for repeat expansion disorders by measuring exact repeat lengths and somatic instability across multiple loci simultaneously.
DOI: 10.34973/wb7z-8q19
title: Lessons Learned: Long-Term Impacts of COVID-19 on the Homeless Population

description: In this study, research was conducted on the experiences of experts by experience with homelessness, staff of shelters, street care personnel, and municipal policy officials regarding the long-term consequences of COVID-19 on homeless individuals and their views on the current state of pandemic preparedness concerning homelessness.

Data for this study was collected through a short questionnaire and in-depth interviews.
The collection contains data summarized in small reports in Dutch.
These reports are a follow-up to a previous study: doi:10.17026/dans-2c7-wksz

Factsheet 11: Pandemic preparedness of street care personnel
Factsheet 12: Pandemic preparedness of shelters for homeless individuals; according to shelter staff and experts by experience
Factsheet 13: Pandemic preparedness of municipalities for homeless individuals
DOI: 10.34973/55g7-4936
title: Nijmegen Exercise Study: a longitudinal data collection on lifestyle characteristics and chronic diseases in a population-based cohort including highly physically active individuals.

description: This Data Sharing Collection (DSC) contains datasets based on the Nijmegen Exercise Study (NES).

The NES provides a comprehensive, longitudinal data collection on lifestyle characteristics and chronic diseases in a population-based cohort including highly physically active individuals. Physical activity is known to reduce the risk of many non-communicable diseases (e.g. cardiovascular diseases, cancer, and dementia). In addition, exercise is an effective therapy in the treatment of a wide range of chronic diseases. Previous research on physical activity often has limitations, such as single measurements or an underrepresentation of highly active individuals. The Nijmegen Exercise Study (NES) provides a comprehensive, longitudinal collection of data on lifestyle characteristics and chronic diseases in a population-based cohort including highly physically active individuals.
DOI: 10.34973/7wze-g513
title: Mapping the Catalytic Cycle of Ru-Catalyzed Ammonia Oxidation

description: This study presents a complete mechanistic picture of ammonia oxidation catalyzed by [RuII(NH3)][PF6]2 (Ru = Ru(tpy)(dmabpy)) complexes. All intermediates, including the elusive [RuIII(NH2)]2+ and [RuIV(NH)]2+, were detected, with several intermediates characterized spectroscopically. The catalytic cycle follows multiple reaction pathways branching at the key intermediates [RuIII(NH2)]2+ and [RuII(N2H4)]2+. The competition between the pathways is influenced by ammonia concentration and the local proton concentration generated during electrooxidation at the anode. In the N–N bond-forming steps, dimerization of [RuIII(NH2)]2+ and nucleophilic attack of [RuIV(NH)]2+ by ammonia compete, while in the subsequent [RuII(N2H4)]2+ oxidation, direct oxidation competes with proton-catalyzed disproportionation. These findings provide molecular-level insights into the catalytic cycle and offer guidance for developing more efficient ruthenium-based ammonia oxidation catalysts. In this collection, you can find the original experimental and computational data for the paper and SI.
DOI: 10.34973/trwh-bz50
title: Het gebruik van uitkomstinformatie in de spreekkamer

description: This study employed a mixed-methods design. Using a grounded theory approach, we interviewed healthcare professionals (HCPs) (n=11) about the use of outcome data in patient consultations. Patients with prostate cancer, lung cancer, and inflammatory bowel disease (IBD) completed questionnaires (n=283) to identify important outcomes.

1. HCPs from the Santeon hospitals were invited for an interview. Santeon is a collaboration of seven non-academic teaching hospitals that collectively strive to improve their care following the principles of value based healthcare. The inclusion criterion was: medical specialists and nurses who were part of a VI team and thus had experience with using outcome data for quality improvement and benchmarking. The exclusion criteria were: 1) HCPs from recently started VI teams with limited experience in outcome data collection and 2) HCPs who participated in the SHOUT study, as their perspectives might be influenced by their role in the study. Interview data is archived at St. Antonius hospital. 

2. Patients with one of the following three health conditions, i.e., prostate cancer, lung cancer, and inflammatory bowel disease (IBD), were recruited via Dutch patient organizations and online forums (Crohn & Colitis NL, kanker.nl, Prostaatkanker Stichting, Longkanker NL, foundation DUOS). Patients were asked to rate the importance of aggregated outcomes on a 5-point Likert-scale. They were also asked whether they preferred merely being informed about the outcome or desired a discussion with their HCP about that outcome. The questionnaires incorporated outcomes that were collected by VI teams for quality improvement of the corresponding health condition. To check whether we had reached an inclusive group of patients with regard to health literacy, the three health literacy questions were added to the questionnaire. Data is available from repository upon reasonable request.
DOI: 10.34973/dy13-h870
title: Improving patient participation in VBHC

description: Insight is needed in how to overcome barriers in patient participation and how to improve patient participation within Value Based Health Care (VBHC). As multidisciplinary project teams around medical conditions are most commonly used by hospitals; this study mainly focused on improving patient participation within such teams. To this end, an action research approach was used, with the ultimate goal to develop a practical guide for patient participation based on the lessons learned. 

This study was conducted in seven Dutch Santeon hospitals from March 2023 to November 2024. Seven multidisciplinary project teams were selected to participate in the cyclical action research steps. These included the following patient groups: prostate cancer, vulnerable elderly, breast cancer, diabetes, maternity care, colorectal cancer, and chronic kidney disease. Qualitative observations and minutes of meetings with the intervention teams were collected. The Public and Patient Engagement Evaluation Tool (PPEET) was completed by multiple members of the intervention (n=7) and control teams (n=94) at three time points (T1=6 months, T2=12 months, T3=end of study).

Notes were made during 106 meetings with the VI teams as part of the action research study. On average, each team had 15 meetings (ranging from 5-75 minutes) where 1-12 VI team members attended the meetings. The observation tool was completed 42 times. Furthermore, throughout the action research process, 302 PPEET questionnaires were completed by intervention and control team members. 

The data is archived at St. Antonius hospital and not available for reuse due to privacy restrictions.
DOI: 10.34973/xm23-zc14
title: Evaluating patient participation in VBHC

description: We conducted a multi-center mixed-methods study between February 2022 and January 2023 in a consortium of seven Dutch hospitals (Santeon hospitals) that collaborate in implementing VBHC by actively measuring, benchmarking, and improving value of care for fifteen medical conditions. Multidisciplinary Value improvment (VI) teams per medical condition have been set up in each of the seven hospitals, with a few exceptions when the hospital does not provide care for that condition. These VI teams consist of healthcare professionals, project leaders, managers, and data-analysts who work together to achieve value improvements.

 A questionnaire on patient participation (the public and patient engagement evaluation tool) was tailored to the study’s context, completed by value improvment team members (n=147 from 76 different VI teams). In addition, 30 semi-structured interviews were held with VI team members, and analyzed through thematic analysis. 

Data is archived at St. Antonius Hospital and not available due to privacy restrictions. Aggregated questionnaire data is available as appendix to the published open acces article.
DOI: 10.34973/zdtw-df87
title: MetroMapping blaaskanker

description: Patient journeys are structured overviews that allow healthcare professionals and researchers to follow and understand a patient's path through the healthcare system. Different methodologies for designing patient journeys focus on specific aspects of care, such as Metro Mapping.  In this study, we investigate how Metro Mapping can be used by Value Improvement (VI) teams to improve care based on insights from patient experiences.

This study has a mixed-methods case study design. The development of a Metro Map for the St. Antonius Hospital’s bladder cancer VI team was used as a case. Patients (n=20) and their partners were interviewed about their experiences with care for bladder cancer. Based on the insights of the interviews, a questionnaire was selected to validate the qualitative insights with a larger group of patients (n=57). The results of the interviews and questionnaire together form the ‘patient experience’ layer of the Metro Map. 

The results of the interviews were presented in two co-creation session with the VI team, including two patient representatives. Observations were made by the researcher during these co-creation sessios. Finally, the VI team evaluated their experiences with and added value of the Metro Map in a focus group session.

The qualitative data is archived at the St. Antonius hospital and not available for reuse due to privacy restrictions. The anonymized quantitative data is added to the repository and available upon reasonable request.
DOI: 10.34973/f550-9765
title: Disorder to order: how halide mixing in MAPbI3-xBrx perovskites restricts MA dynamics

description: Mixed-halide lead perovskites are of particular interest for the design of tandem solar cells currently reaching record efficiencies. While halide phase segregation upon illumination of mixed perovskites is extensively studied, the effect of halide disorder on A cation dynamics is not well understood, despite its importance for charge carrier diffusion and lifetime. Here, we study the methylammonium (MA) reorientational dynamics in mixed halide MAPbI3−xBrx perovskites by a combined approach of
experimental solid-state NMR spectroscopy and molecular dynamics (MD) simulations based on
machine-learning force-fields (MLFF). 207Pb NMR spectra indicate the halides are randomly distributed over their lattice positions, whereas PXRD measurements show that all mixed MAPbI3−xBrx samples are cubic. The experimental 14N spectra and 1H double-quantum (DQ) NMR data reveal anisotropic MA
reorientations depending on the halide composition and thus associated disorder in the inorganic
sublattice. MD calculations allow us to correlate these experimental results to restrictions of MA
dynamics due to preferred MA orientations in their local Pb8I12−nBrn “cages”. Based on the experimental and simulated results, we develop a phenomenological model that correlates the 1
H dipolar coupling and thus the MA dynamics with the local composition and reproduces the experimental data over the whole composition range. We show that the dominant interaction between the MA cations and the Pb–X lattice that influences the cation dynamics is the local electrostatic potential being inhomogeneous in mixed halide systems. As such, we generate a fundamental understanding of the predominant interaction between the MA cations and the inorganic sublattice, as well as MA dynamics in asymmetric halide coordinations.
This repository includes the NMR (1H, 14N and 207Pb) and XRD data collected for the samples.
DOI: 10.34973/hn9r-3r37
title: Swatches On Suit project: semi controlled real-scale fire experiments

description: Data and code realted to the Thesis chapter:The applicability of the Swatch technology on real-life simulated fires
DOI: 10.34973/vf0v-8s11
title: Dataset Quantification of biomolecular condensate volume reveals network swelling and dissolution regimes during phase transition

description: Accurate determination of biomolecular condensate volume reveals that destabilization of condensates can lead to either swelling or shrinking of condensates, giving fundamental insights into regulation of the volume of cellular condensates. Determination of the volume of biomolecular condensates and coacervate protocells is essential to investigate their precise composition and impact on (bio)chemical reactions that are localized inside the condensates. It is not a straightforward task, as condensates have tiny volumes, are highly viscous and prone to wetting. Here we examine different strategies to determine condensate volume, and introduce two new methods, with which condensate volumes of 1 μL or less (volume fraction 0.4%) can be determined with a standard deviation of 0.03 μL. Using these methods we show that the swelling or shrinking of condensates depends on the degree of physical crosslinking. These observations are supported by Flory-Huggins theory and can have profound effects on condensates in cell biology. 
In this collection, you can find the data underlying this study.
DOI: 10.34973/az9q-em97
title: Dataset Shape transformations in peptide-DNA coacervates driven by  enzyme-catalyzed deacetylation

description: Biomolecular condensates formed by liquid-liquid phase separation (LLPS) are important organizers of biochemistry in living cells. Condensate formation can be dynamically regulated, for example by protein binding or enzymatic processes. However, how enzymatic reactions can influence condensate shape and control shape transformations is less well understood. Here, we design a model condensate that can be formed by the enzymatic deacetylation of a small peptide by sirtuin-3 in the presence of DNA. Interestingly, upon nucleation condensates initially form gel-like aggregates that gradually transform into spherical droplets, displaying fusion and wetting. This process is governed by sirtuin-3 concentration, as more enzyme resulted in a faster aggregate-to-viscous liquid transformation of the condensates. We show that the aggregate-like nature of the early-stage condensates is linked to the presence of short, double-stranded DNA. The counterintuitive formation of aggregate-like, non-spherical condensates near the critical point is attributed to stronger bending of the DNA by oppositely charged peptides as the system moves away from the critical point, deeper in the two-phase region. Overall, this work shows that enzymes can induce shape transformations of condensates, and that condensate material properties do not necessarily inform about their stability. In this collection, you can find the data underlying this study.
DOI: 10.34973/agxj-4j22
title: Phase-separated Droplets Can Direct Chemical Reaction Kinetics of Polymerization, Self-replication and Oscillating Networks

description: Supplementary Code for paper Phase-separated Droplets Can Direct Chemical Reaction Kinetics of Polymerization, Self-replication and Oscillating Networks (ChemSysChem). A numerical ODE based model is included to study how coacervate droplets can influence reaction rates, polymer length distributions, chemical self-replicators and the behavior of oscillatory networks, providing insights into their potential roles in both prebiotic chemistry and biological systems.
DOI: 10.34973/j5ax-am79
title: Identifying and controlling the order parameter for ultrafast photoinduced phase transitions in thermosalient materials

description: This data collection contains input files and trajectory movies associated with Ghasemlou et al. Identifying and controlling the order parameter for ultrafast photoinduced phase transitions in thermosalient materials
DOI: 10.34973/faps-jp08
title: Dataset for Quantum simulator to emulate lower-dimensional molecular structure

description: Raw data collection for the respective Science publication. 
Bottom-up quantum simulators have been developed to quantify the role of various interactions, dimensionality, and structure in creating electronic states of matter. In the associated paper, we demonstrated a solid-state quantum simulator emulating molecular orbitals, based solely on positioning individual cesium atoms on an indium antimonide surface. Using scanning tunneling microscopy and spectroscopy, combined with ab initio calculations, we showed that artificial atoms could be made from localized states created from patterned cesium rings. These artificial atoms served as building blocks to realize artificial molecular structures with different orbital symmetries. These corresponding molecular orbitals allowed us to simulate two-dimensional structures reminiscent of well-known organic molecules. This platform could further be used to monitor the interplay between atomic structures and the resulting molecular orbital landscape with submolecular precision.
In this collection you find the data to plot the figures of the paper and recreate the theoretical calculations.
DOI: 10.34973/qk29-f305
title: 2000HIV plasma proteome

description: In this collection, you can find the circulating plasma protein expression of 2932 proteins measured in 1930 samples from the 2000HIV cohort. In addition, you can find the metadata that accompany the  following study by Otten et al, “Impact of COVID-19, Lockdowns and Vaccination on Immune Responses in a HIV cohort in the Netherlands; Front. Immunol 15-2024; doi: 10.3389/fimmu.2024.1459593”.

The 2000HIV study is a prospective longitudinal cohort study of people living with HIV (PLHIV) on cART. It aims to discover new biological pathways and identify biomarkers that play a role in persistent inflammation, accelerated ageing, non-AIDS co-morbidities, extreme HIV-related clinical phenotypes (Elite controllers, immunological non-responders, and rapid progressors) and the HIV viral reservoir size and composition. To this end, 1895 PLHIV, divided into two independent cohorts (a discovery and validation cohort), recruited between 2019 and 2021, and followed-up for two  years. Extensive clinical data and measurements were registered, multi-omics data were generated,  and the latent viral reservoir size and composition were assessed in this cohort.