cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34973/0n4p-d459
title: Immune Response and Exhaled Breath Profile Changes after Initiation of CFTR-modulator Therapy in Children with Cystic Fibrosis

description: Study in pediatric population (n = 17) with Cystic Fibrosis initiating CFTR modulation therapy. We investigated the immune response changes after initiating therapy with whole blood stimulation assays and exhaled breath volatile organic component analysis. The 4 SPSS files in this repository show baseline characteristics of the study population (basisbestand CF immunity) and additional data on exacerbations (Exacerbaties CF immunity), growth (Groeigegevens CF immunity) and microbiological cultures ((Kweekuitslagen CF immunity). The 2 excell files show the results of Luminex and ELISA results of different cytokines in supernatant of the whole blood stimulation assays after stimulation with different stimuli. 
The data of the VOC analysis were performed in Maastricht University Medical Center and are stored on a secure drive there.
DOI: 10.34973/0c5r-yf32
title: Evaluating potential drug-drug interactions with pharmacokinetic boosting of olaparib

description: The aim of this study is to evaluate drug-drug interactions potential when 
applying pharmacokinetic boosting by reviewing a retrospective cohort of patients treated with olaparib.

Data from patients who received olaparib between April 2017 and February 2024 were collected from the hospital electronic patient files and the outpatient pharmacy records of the Radboud university medical center (Nijmegen, The Netherlands). We screened for potential drug-drug interactions between cobicistat and comedications at the start of olaparib treatment if boosting cobicistat would have been initiated in these patients.
DOI: 10.34973/4zgg-5j18
title: CT simulations for test data

description: Having sufficient data to test processing of reconstruction algorithms is often a challenge in medical CT imaging. Since, patient data is limited and cannot be shared easily. Additionally, quantitative evaluation on for instance accuracy is close to impossible for patient data considering the lack of ground truth. Therefore, we developed a CT simulator which is able to simulate the behavior of a clinical CT system. The simulator involves all steps of the CT image acquisition process. Starting with the number of x-ray photons send from the source towards the patient and detector. Followed by the interaction of the x-rays with the object, so patient, in the scanner and thus the subsequently the number of photons that reach the detector and are measured. The resolution characteristics of the detector, CT geometry, and rotation are considered, as well as the noise characteristics. By following all these steps realistic CT scans can be obtained of any voxelized phantom. Making this tool ideal for testing purposes.
DOI: 10.34973/2pvq-rk32
title: Very Early Health Technology Assessment for Potential Predictive Biomarkers in the Treatment of Advanced Non-Small Cell Lung Cancer

description: Various biomarkers are being studied for treatment response to immune-checkpoint inhibitors (ICIs) to save costly and potentially harmful treatment in non-responders. We evaluated the cost-effectiveness of implementing a hypothetical predictive biomarker for ICI-containing treatment response compared with standard of care (e.g., no implemented biomarker) for pembrolizumab-containing treatment in patients with advanced NSCLC in the Netherlands. Standard-of-care-based and predictive-biomarker-based strategies were compared using Markov models for three first-line pembrolizumab-containing treatments depending on a patient’s tumor programmed cell death ligand-1 (PD-L1) expression and histology. A Dutch healthcare system perspective was adopted. Assuming a receiver operating characteristic-area under the curve of 1.0 in identifying responders, alternative treatments were offered for non-responders in the predictive-biomarker-based strategy. Parameters and assumptions were based on real-world data from surveys, literature using a targeted search, expert opinion, and registries. Outcomes included differences in costs, survival (life years (LYs)), and survival corrected for health-related quality of life (QoL) quality-adjusted life-years (QALYs) between the predictive-biomarker- and standard-of-care-based strategy.

In this collection, you can find the raw OS and PFS rates over time extracted from literature to calculate transition probabilites, R-scripts for the calculation of transition probabilities and the resulting .RDS files containing parameters of the survival function for the transition probabilities and R-scripts for the Markov models used for each pembrolizumab-containing regimen.
DOI: 10.34973/ct2w-7n68
title: Proactive monitoring of drug–drug interactions between direct oral anticoagulants and small-molecule inhibitors in patients with non-small cell lung cancer

description: SMI-induced drug–drug interactions (DDIs) with frequently co-administered direct oral anticoagulants (DOACs), increase thromboembolic and bleeding risks. This study investigated and proactively managed the consequences of DOAC-SMI DDIs. This study enrolled patients with NSCLC concomitantly using a DOAC and SMI. Primary outcome was DOAC plasma trough and peak concentration. Data collection: descriptive characteristics, DOAC peak and trough concentrations, serious adverse events, bleeding and thromboembolic events.
DOI: 10.34973/mc42-3y98
title: Entrustable professional activities in the undergraduate medical curriculum

description: In this research we investigate the role of entrustable professional professional activities (EPAs) on the professional development of medical students in the undergraduate curriculum at the Radboud University Medical Center in Nijmegen, The Netherlands. The database of this research contains datasets with focus group interviews exploring the perspective of medical students on EPAs on their professional identity formation (PIF), and individual interviews and observations with/from medical student about the role of EPAs on PIF and especially on the transitions between different clerkships. Moreover, data from a questionnaire, with over 2000 anonymous responses from medical students measuring their PIF, is available in our dataset. This dataset only contains Dutch data.
DOI: 10.34973/9dsg-2618
title: Survival of cemented short Exeter femoral components in primary total hip arthroplasty: an analysis of 394 femoral components in total hip arthroplasties undertaken between 1993 and 2021

description: Aims: The aim of this study was to report the long-term follow-up of cemented short Exeter femoral components when used in primary total hip arthroplasty (THA).
Methods: We included all primary 394 THAs with a cemented short Exeter femoral component (≤ 125 mm) used in our tertiary referral centre between October 1993 and December 2021. A total of 83 patients (21%) were male. The median age of the patients at the time of surgery was 42 years (interquartile range (IQR) 30 to 55). The main indication for THA was a childhood hip disease (202; 51%). The median follow-up was 6.7 years (IQR 3.1 to 11.0). Kaplan-Meier survival analyses were performed to determine the rates of survival with femoral revision for any indication, for septic loosening, for fracture of the femoral component and for aseptic loosening as endpoints. The indications for revision were evaluated. Fractures of the femoral component were described in detail.
Results: The 20-year rate of survival was 85.4% (95% confidence interval (CI) 73.9 to 92.0) with revision for any indication, 96.2% (95% CI 90.5 to 98.5) with revision for septic loosening and 92.7% (95% CI 78.5 to 97.6) with revision for fracture of the femoral component. No femoral components were revised for aseptic loosening. There were 21 revisions of the femoral component; most (seven) as part of a two-stage management of infection. Fracture of the femoral component occurred in four THAs (1.0%) at 6.6, 11.6, 16.5, and 18.2 years of follow-up, respectively. Three of these were transverse fractures and occurred at the level of the lesser trochanter. In one THA, there was a fracture of the neck of the component.
Conclusion: THAs using cemented short Exeter femoral components showed acceptable rates of survival of the femoral component at long-term follow-up,
in this young cohort of patients. Although fracture is a rare complication of these components, surgeons should be aware of their incidence and possible risk factors.
DOI: 10.48597/gumf-4454
title: Measurement of Aerosol light scattering at Pallas (Sammaltunturi)

description: Measurement of Aerosol light scattering at Pallas (Sammaltunturi)
DOI: 10.34973/d34h-3f64
title: Supplementary material corresponding to the article 'free cortisol and free 21-deoxycortisol in the clinical evaluation of congenital adrenal hyperplasia'

description: Supplementary material corresponding to the article ‘Free cortisol and free 21-deoxycortisol in the clinical evaluation of congenital adrenal hyperplasia’ (DOI: 10.1210/clinem/dgae591) published in The Journal of Clinical Endocrinology & Metabolism (JCEM).

This study aimed to measure free cortisol and free 21-deoxycortisol concentrations in patients with congenital adrenal hyperplasia and compare this  to levels in patients with non-classic congenital adrenal hyperplasia, patients with other forms of adrenal insufficiency, and controls.

This collection includes the supplementary materials: 

- Table S1: Genetic analyses of included CAH patients (n=34) with predicted phenotype based on residual enzyme activity and literature. 
- Table S2: liquid chromatography tandem mass spectrometry setting for measuring total cortisol and 21-deoxycortisol 
- Table S3: liquid chromatography tandem mass spectrometry setting for measuring total cortisol and 21-deoxycortisol 
- Figure S1: Flowchart of included patients for this research
- Figure S2: Percentage of free cortisol before (T0) and after (T60) administration of Synacthen® in patients with classic congenital adrenal hyperplasia (CAH), non-classic congenital adrenal hyperplasia (NCCAH), adrenal insufficiency but not CAH (AI), and controls. (S2A) Free cortisol percentage at T0; (S2B) Change in free cortisol percentages between T0 and T60; (S2C) Free cortisol percentage at T60. 
- Reference list of the references used in this document.
DOI: 10.34973/0fw3-4m22
title: Entrustable professional activities in the undergraduate medical curriculum

description: In this research we explore the role of entrustrable professional activities on the professional development of medical students in the undergraduate curriculum at the Radboud University Medical Center in Nijmegen, The Netherlands.
DOI: 10.34973/z1ev-st87
title: The conformation of tetraspanins CD53 and CD81 differentially affects their nanoscale organization and interaction with their partners

description: Tetraspanins, including CD53 and CD81, are four-transmembrane proteins that affect the membrane organization to regulate cellular processes including migration, proliferation and signaling. However, it is unclear how the organizing function of tetraspanins is regulated at the molecular level. Here we investigated whether recently proposed ‘open’ and ‘closed’ conformations of tetraspanins regulate the nanoscale organization of the plasma membrane of B cells. We generated conformational mutants of CD53 (F44E) and CD81 (4A, E219Q) that represent the ‘closed’ and ‘open’ conformation, respectively. Surface expression of these CD53 and CD81 mutants was comparable to that of wildtype (WT) protein. Localization of mutant tetraspanins into nanodomains was visualized by super-resolution dSTORM microscopy. Whereas the size of these nanodomains was unaffected by conformation, the clustered fraction of ‘closed’ CD53 was higher and of ‘open’ CD81 lower than respective WT protein. In addition, knock-out cells lacking CD53 showed an increased likelihood of clustering of its partner CD45. Interestingly, ‘closed’ CD53 interacted more with CD45 than WT CD53. Absence of CD81 lowered the cluster size of its partner CD19, and ‘closed’ CD81 interacted less with CD19 than WT CD81, but ’open’ CD81 did not affect CD19 interaction. However, none of the tetraspanin conformations made significant impact on the nanoscale organization of their partners CD19 or CD45. Taken together, conformational mutations of CD53 and CD81 differentially affect their nanoscale organization, but not the organization of their partner proteins. This study improves the molecular insight into cell surface nanoscale organization by tetraspanins.
DOI: 10.34973/chmw-nq46
title: FSHD-FOCUS 2 onderzoek

description: All data obtained during the five year follow-up natural history study on a large cohort (n=166) of patients in the entire clinical severity spectrum of FSHD. Data on clinical outcome measures, muscle ultrasound results and muscle MRI results
DOI: 10.34973/0hay-na22
title: Identification of a sorting motif for Tspan3 to MHCII compartments in human B cells

description: Tetraspanins are four-transmembrane proteins that play fundamental roles in the immune system by enabling processes like migration, proliferation, signaling and protein trafficking. While the importance of cell surface tetraspanins has been established, the function of intracellular tetraspanins is less well understood. Here, we investigated the role of tetraspanin 3 (Tspan3) in lymphocytes. Tspan3 expression was low in T cells and high in B cells which increased during B cell activation. Tspan3 localized to late endosomal structures where it colocalized with major histocompatibility complex II (MHCII) in the MHCII compartment. There, inhibiting the formation of intraluminal vesicles (ILVs) showed that Tspan3 localization was not affected in contrast to its homologue CD63. Using a peptide-pulldown approach, we identified that Tspan3 interacts with AP2 via its C-terminus that harbors a YXXΦ-based sorting motif. Interestingly, mutating this motif did not impair Tspan3 localization. Instead, leucine 246 was required for its intracellular localization, identifying an unrecognized leucine-based sorting motif responsible for Tspan3 localization to MHCII compartment in B cells. Taken together, we report a new sorting motif for Tspan3 to MHCII compartments in human B cells.
DOI: 10.34973/bshh-cv40
title: 42-Parameter (40-Color) Spectral Flow Cytometry Panel for Comprehensive Immunophenotyping of Human Peripheral Blood Leukocytes

description: Profiling the human immune system is essential to understand its role in disease, but it requires advanced and novel technologies. Spectral flowcytometry (SFM) enables deep profiling at the single cell level. It is able to detect many fluorescent parameters within one measurement, therefore vastly useful when patient material is limited. However, designing and analyzing these high dimensional datasets remains complex. We optimized a 42-parameter panel (40 commercially available fluorochromes, one stacked fluorochrome and an autofluorescent (AF) parameter) that enables identification of innate and adaptive immune cell composition. It is the first 42-parameter panel that is optimized on peripheral whole blood and it outperforms other published  optimized multicolor immunofluorescence panels (OMIPs) of 40 colors in terms of complexity. With this panel we are able to identify neutrophils, basophils, eosinophils, monocytes, dendritic cells, CD4 T cells, CD8 T cells, regulatory T cells, mucosal-associated invariant T (MAIT) cells, γδ T cells, B cells, NK cells, dendritic cells, and innate lymphoid cells (ILCs). Furthermore, with the utilization of co-stimulatory, checkpoint, activation, homing and maturation markers this panel enables deeper phenotyping. Within one measurement, more than 80 distinct immune cell subsets were identified and annotated manually. In conclusion, with this high-dimensional SFM panel we aim to generate immune profiles to understand disease and monitor therapy response.
DOI: 10.34973/69jb-g827
title: Learning goals in an EPA-based curriculum

description: This dataset contains three files with data about medical students’ learning goals and assessments in/of their senior clerkship. The data is originates from two clerkship groups (‘cogroepen’), with in total 56 students. This data gives insight into explore the role of learning goals on the professional development of the students, and specifically examines if students create transition-related learning goals in their senior clerkship (the transition from medical student to junior doctor). The (numeric and written) assessments provide insight into how the students actually perform, and if ‘transitions’ are mentioned by the supervisors in the evaluations.
DOI: 10.34973/c32s-t468
title: Modular Breath Sampler in the Microbiological Diagnostics of Patients with Cystic Fibrosis

description: In this cross-sectional proof-of-concept study we investigated the yield of a newly developed two-way non-rebreathing device (Modular Breath Sampler, nowadays renamed Aerocep) to collect exhaled breath for PCR-based microbiological diagnostics in pediatric patients with Cystic Fibrosis. We investigated 93 samples of 44 pediatric CF patients and 32 samples of pediatric asthma patients serving as controls. All data, including results of microbiological investigations and PCR-based diagnostics, were prospectively collected in a secure online Castor database and exported to the SPSS file in this repository.
DOI: 10.5281/zenodo.15012366
title: Indomethacin-induced small intestinal inflammation and dysbiosis are associated with characteristic changes in the expression of toll-like receptors and antimicrobial peptides in rats

description: Abstract

Nonsteroidal anti-inflammatory drugs (NSAIDs) can cause small intestinal injury and dysbiosis. Although NSAID-induced dysbiosis is well-characterized and contributes to enteropathy, the changes in host-bacterial interactions during enteropathy remain largely unexplored. Here we assessed the expression pattern of six toll-like receptors (TLRs) and three antimicrobial peptides (AMPs) over the course of indomethacin (IND)-induced enteropathy in rats, and evaluated their correlations with inflammation and dysbiosis. In addition, we assessed for the first time the effect of IND on small intestinal mucosal biofilm structure. We found that TLR1, TLR2 and cathelicidin were upregulated, TLR5 was downregulated, whereas TLR6 and TLR9 were not significantly altered in enteropathy. TLR4 expression showed only subtle differences, but correlated with a-defensin 5 and β-defensin 2. We found several correlations between TLRs, AMPs, inflammation and gut bacteria in severe enteropathy, but in early disease stage TLR1, TLR2, TLR5 and cathelicidin expression were more strongly associated with inflammation, whereas TLR4 and defensins were more dependent on gut dysbiosis. IND treatment also caused mild damage to the mucosal microbiota biofilm. This is the first comprehensive characterization of the time-dependent changes in TLRs, AMPs and mucosal biofilm in NSAID-treated rats, which may help to identify new strategies for the treatment of enteropathy.
DOI: 10.5281/zenodo.15012367
title: Indomethacin-induced small intestinal inflammation and dysbiosis are associated with characteristic changes in the expression of toll-like receptors and antimicrobial peptides in rats

description: Abstract

Nonsteroidal anti-inflammatory drugs (NSAIDs) can cause small intestinal injury and dysbiosis. Although NSAID-induced dysbiosis is well-characterized and contributes to enteropathy, the changes in host-bacterial interactions during enteropathy remain largely unexplored. Here we assessed the expression pattern of six toll-like receptors (TLRs) and three antimicrobial peptides (AMPs) over the course of indomethacin (IND)-induced enteropathy in rats, and evaluated their correlations with inflammation and dysbiosis. In addition, we assessed for the first time the effect of IND on small intestinal mucosal biofilm structure. We found that TLR1, TLR2 and cathelicidin were upregulated, TLR5 was downregulated, whereas TLR6 and TLR9 were not significantly altered in enteropathy. TLR4 expression showed only subtle differences, but correlated with a-defensin 5 and β-defensin 2. We found several correlations between TLRs, AMPs, inflammation and gut bacteria in severe enteropathy, but in early disease stage TLR1, TLR2, TLR5 and cathelicidin expression were more strongly associated with inflammation, whereas TLR4 and defensins were more dependent on gut dysbiosis. IND treatment also caused mild damage to the mucosal microbiota biofilm. This is the first comprehensive characterization of the time-dependent changes in TLRs, AMPs and mucosal biofilm in NSAID-treated rats, which may help to identify new strategies for the treatment of enteropathy.
DOI: 10.34973/cmg2-av85
title: Outcome prediction for CI users

description: This data collection contains the prediction data made by participants in the Outcome Prediction for CI users study. Research Aim This study aimed to investigate the accuracy and confidence of clinicians in predicting speech perception outcomes for adult CI users one-year post-implantation. Participants were presented with comprehensive information on pre-implantation, one-month post-implantation, and six-month post-implantation data for 10 case studies. The cases encompassed a range of one-year post-implantation phoneme scores, from low performers (27%) to high performers (92%). Participants were tasked with predicting the speech perception outcomes for these cases one year after implantation. These predictions were then compared to the true outcomes of the case studies to assess prediction accuracy and confidence in the predictions.
DOI: 10.34973/0qn1-jb59
title: Reactive Oxygen Species and Antioxidants in Cancer Treatment

description: These data pertain to 2 publications on the effect of tamoxifen and irradiation on ROS and antioxidants. Earlier, we reported that tamoxifen-resistant (TAM-R) breast cancer cells are cross-resistant to irradiation. In PMID: 36755288, we investigated the mechanisms associated with tamoxifen-induced radioresistance, aiming to prevent or reverse resistance and improve breast cancer treatment. Wild-type ERα-positive MCF7 and ERα-negative MDA-MB-231 breast cancer cells and their TAM-R counterparts were analyzed for cellular metabolism using the Seahorse metabolic analyzer. Real-time ROS production, toxicity, and antioxidant capacity in response to H2O2, tamoxifen, and irradiation were determined. 
Real-time measurement of ROS after tamoxifen and H2O2 exposure indicated lower ROS levels and toxicity in TAM-R cells. Consistently, higher antioxidant levels were found in TAM-R cells, providing protection from irradiation-induced ROS.
In PMID: 38292333, total antioxidant capacity (TAC) was analyzed in head and neck cancer (HNSCC) tumor cells in vitro and in serum of HNSCC patients before, during, and after radiotherapie
. We found that irradiation induced NRF2 expression and upregulated TAC, which may compromise the effect of RT-induced ROS.