cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34973/qq9b-a864
title: Evaluating Cochlear Implant Outcomes in DFNA9 Subjects

description: This data collection contains the pre- peri- and post-implantation data of cochlear implant (CI) recipients with DFNA9.

DFNA9 is a progressive type of non-syndromic sensorineural hearing loss (SNHL) inherited in an autosomal dominant manner, typically emerging in mid-life due to mono-allelic pathogenic variants in COCH (1). It often includes vestibular deterioration, emerging between the third and seventh decade, depending on the genotype.
With this data set is was assessed whether the Fazekas score could account for the variability in cochlear implantation (CI) outcomes among individuals with DFNA9 and evaluated signal loss in the semicircular canals (SCCs) on magnetic resonance imaging (MRI) among individuals with DFNA9. It includes retrospective cross-sectional data of CI recipients with DFNA9, presenting the following variables: 
1. Demographic data: gender, self-reported age of onset of hearing loss, use of hearing aids before implantation, age at time of implantation 
2. Genetic data: identified pathogenic variant with the associated protein change(s). 
3. Cardiovascular risk factors: hypertension, diabetes mellitus (DM), elevated cholesterol levels, current or former smoking habits, the use of anticoagulant drugs, and a history of myocardial infarction and/or stroke.
4. The American Society of Anaesthesiologists (ASA) score 
5. Audiological measurements pre-implantation and outcome measurements post-implantation, including the pure tone average (PTA) aided and unaided, and phoneme scores measured at 65 dB SPL aided and unaided.
6. MRI findings: Fazekas score, additional brain or cochleovestibular abnormalities, and abnormalities at the level of the semicircular canals of the vestibular organ. 
7. Vestibular function.
DOI: 10.34973/32cm-2h58
title: Management and Outcome of Febrile Children in Europe

description: This study was part of the Management and Outcome of Fever in Children study (MOFICHE) within the Personalized Risk assessment in Febrile ilness to Optimise Real-life Management across the European Union project (PERFORM). PERFORM is a multifaceted study across different European study aiming to improve the diagnosis and management of febrile children across Europe. We retrospectively collected data of children presenting with fever in three levels of healthcare in Nijmegen area. Data were collected using an electronic case report form and entered in a secure Redcap database. After completion of the study and cleaning of the data, they were exported to the SPSS file which is attached to this repository.
DOI: 10.34973/4jn0-cp05
title: Longitudinal Mortality and Age Distributions of the Dutch Population with Long-term Care Indication related to Intellectual Disability

description: Aggregated results from CBS Microdata analyses towards identifying and describing primary characteristics of the Dutch population with Intellectual Disability related long-term care (WLZ) indications. This population as well as the remaining general population are described with age distributions at the start of each year over the period for which data was available (2015-2022 in this version). Similarly, there are approximate age distributions at times of death throughout each year.

Methodology is included with reflection on the promotion of replicability and information security surrounding population research. Attention was paid to techniques such as result tagging, system information logging, partial open source development, noise addition to privacy sensitive values.

Results are intentionally compact to facilitate various directions of downstream processing, e.g. derived value calculation and visualization, as separate units elsewhere.
DOI: 10.15468/dl.zdxfze
title: Occurrence Download

description: A dataset containing 712 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudomyrmex cubaensis (Forel, 1901)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 712 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004846-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34973/kknj-an72
title: Detailing organelle division and segregation in Plasmodium falciparum

description: This paper describes in detail division of the mitochondrion and apicoplast in the malaria parasite, Plasmodium falciparum. The raw images underlying the figures in this paper are available in this collection. A P. falciparum parasite line harbouring a fluorescent mitochondrial marker was generated and used for fluorescent confocal imaging of different developmental stages of the parasite. These images were used to reconstruct different mitochondrial division and development stages. This data collection contains the raw fluorescent images with different development stages of the parasite mitochondrion.
DOI: 10.34973/yffk-q479
title: Pharmacokinetic boosting of olaparib to improve exposure, tolerance and  cost-effectiveness part A

description: Background: Pharmacokinetic (PK) boosting is the intentional use of a drug-drug interaction to enhance systemic drug exposure. PK boosting of olaparib, a CYP3A-substrate, has the potential to reduce PK variability and financial burden. The aim of this study was to investigate equivalence of a boosted, reduced dose of olaparib compared to the non-boosted standard dose.

Methods: This cross-over, multicentre trial compared olaparib 300 mg twice daily (BID) with olaparib 100 mg BID boosted with the strong CYP3A-inhibitor cobicistat 150 mg BID. Patients were randomised to the standard therapy followed by the boosted therapy, or vice versa. After seven days of each therapy, dense PK sampling was performed for noncompartmental PK analysis. Equivalence was defined as a 90% Confidence Interval (CI) of the geometric mean ratio (GMR) of the boosted versus standard therapy area under the plasma concentration-time curve (AUC0-12 h) within no-effect boundaries. These boundaries were set at 0.57-1.25, based on previous pharmacokinetic studies with olaparib capsules and tablets.

Results: Of 15 included patients, 12 were eligible for PK analysis. The GMR of the AUC0-12 h was 1.45 (90% CI 1.27-1.65). No grade ≥3 adverse events were reported during the study.

Conclusions: Boosting a 100 mg BID olaparib dose with cobicistat increases olaparib exposure 1.45-fold, compared to the standard dose of 300 mg BID. Equivalence of the boosted olaparib was thus not established. Boosting remains a promising strategy to reduce the olaparib dose as cobicistat increases olaparib exposure Adequate tolerability of the boosted therapy with higher exposure should be established.

This collection contains the laboratory and pharmacokinetic data of the twelve participation subjects. This includes the olaparib and cobicistat plasma concentrations over one dosing interval with olaparib monotherapy and boosted therapy.
DOI: 10.34973/1ps3-by08
title: Data for "Transvitreal retinochoroidal biopsies of primary uveal melanoma reveal an association of low HLA class I and high NK cell abundance in low-risk disease"

description: This data was collected for research purposes. The findings and results have been published in a manuscript called "Transvitreal retinochoroidal biopsies of primary uveal melanoma reveal an association of low HLA class I and high NK cell abundance in low-risk disease"

In this study, transvitreal retinochoroidal biopsies were taken from a total of 41 patients with primary uveal melanoma as diagnosis. These biopsies were used for the analysis of immune cells by flow cytometry. Three flow cytometry panels were implemented to study tumor infiltrating lymphocytes (T cells, NK cells and B cells), including their activation/exhaustion markers, as well as HLA class I, HLA class II and PD-L1 and PD-L2 expression on tumor cells and T cells.
Additionally, on archived tissue samples from a total of 13 patients that underwent enucleation, we performed multiplex immunohistochemistry to study lymphocytes in the different components of the eye (tumor, choroid, iris and ciliary body). From multiplex immunohistochemistry, densities can also be calculated, rather than just percentages, thereby indicating absolute infiltration.
For all included patients, relevant clinical data was collected as well. This includes follow-up of tumor recurrence, tumor size measurements, and genetic risk factors.
DOI: 10.34973/q3d7-6w60
title: Reference intervals for serum 11-oxygenated androgens in children

description: This dataset corresponds to the article ‘Reference intervals for serum 11-oxygenated androgens in children’ (DOI: 10.1093/ejendo/lvae008.) published in the European Journal of Endocrinology (EJE).

This study aimed to establish pediatric reference values for eight androgens, including four 11-oxygenated androgens. For this purpose, a liquid-chromatography tandem mass spectrometry (LC-MS/MS) assay was developed and validated for clinical use. To establish pediatric reference values, we measured these androgens in 256 children. Blood was taken from these children before minor surgery or medical procedure. This group of children was previously described in ‘Standardized serum hepcidin values in Dutch children: Set point relative to body iron changes during childhood’ (DOI: 10.1002/pbc.28038). Data on demographics of the included patients can be requested by contacting the corresponding author of that article.

This dataset only comprises the patient number, the age (in years), and the concentrations (in nmol/L) of eight androgens: dehydroepiandrosterone (DHEA), androstenedione (A4), testosterone (TES), dihydrotestosterone (DHT), 11-hydroxyandrostenedione (11OHA4), 11-ketoandrostenedione (11KA4), 11-hydroxytestosterone (11OHT), and 11-ketotestosterone (11KT). Concentration below the lower limit of quantification (LLOQ) with a signal-to-noise (S/N) ratio ≤5 are given as half the LLOQ-value. Concentrations <LLOQ with a S/N-ratio >5 are given as absolute measured value.
DOI: 10.15468/dl.wdtwb4
title: Occurrence Download

description: A dataset containing 770 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.41947 42.40212,-71.26868 42.40212,-71.26868 42.50896,-71.41947 42.50896,-71.41947 42.40212))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Apidae",
 "Year 1950-2025"
 ]
}

 The dataset includes 770 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004844-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34973/23c2-h979
title: Diurnal salivary androstenedione and 17‐hydroxyprogesterone levels in healthy volunteers

description: This dataset corresponds to the article ‘Diurnal salivary androstenedione and 17-hydroxyprogesterone levels in healthy volunteers for monitoring treatment efficacy of patients with congenital adrenal hyperplasia’ (DOI: 10.1111/cen.14690) published in Clinical Endocrinology (Clin Endo). 

This study aimed to establish age-adjusted reference values for salivary androstenedione and 17-hydroxyrprogesterone. We wanted to get insight into the diurnal variation of these adrenal steroids in the heatlhy population and therefore measured these hormones in saliva that was collected in the morning, afternoon, and evening. For this dataset, we used saliva of healthy volunteers from schools in Nijmegen, the Netherlands and also asked (grand)parents / caregivers of these children to collected saliva at these times to enable inclusion of volunteers with a broad age range. With this data set, age-adjusted reference values for these three time points could be established. 

The attached file contains the raw data used for conducting this study. For each participant the sex, menstruation status, and age (in years) are given. Thereafter, the time of saliva collection is given in a 24-hour data notation for the morning, afternoon, and evening. Then, the androstenedione and 17-hydroxyprogesterone levels (in pmol/L) are given for the morning, afternoon, and evening samples. If the concentration of the measured steroid was below the lower limit of quantification (LLOQ) and the signal-to-noise ratio was <10, the value was assigned half of the LLOQ. The LLOQ for androstenedione is 7 pmol/L, and for 17-hydroxyprogesterone 20 pmol/L.
DOI: 10.34973/axb6-bx55
title: A mapping review on preoperative prognostic factors and outcome measures of revision total knee arthroplasty

description: Chapter 2 from PhD thesis Towards better outcomes of revision total knee arthroplasty. Contains protocol, data and script.

To map literature on prognostic factors related to outcomes of revision total knee arthroplasty (rTKA), to identify extensively studied factors and to guide future research into what domains need further exploration. We performed a systematic literature search in MEDLINE, Embase, and Web of Science. The search string included multiple synonyms of the following keywords: "revision TKA", "outcome" and "prognostic factor". We searched for studies assessing the association between at least one prognostic factor and at least one outcome measure after rTKA surgery. Data on sample size, study design, prognostic factors, outcomes, and the direction of the association was extracted and included in an evidence map. After screening of 5,660 articles, we included 166 studies reporting prognostic factors for outcomes after rTKA, with a median sample size of 319 patients (30 to 303,867). Overall, 50% of the studies reported prospectively collected data, and 61% of the studies were performed in a single centre. In some studies, multiple associations were reported; 180 different prognostic factors were reported in these studies. The three most frequently studied prognostic factors were reason for revision (213 times), sex (125 times), and BMI (117 times). Studies focusing on functional scores and patient-reported outcome measures as prognostic factor for the outcome after surgery were limited (n = 42). The studies reported 154 different outcomes. The most commonly reported outcomes after rTKA were: re-revision (155 times), readmission (88 times), and reinfection (85 times). Only five studies included costs as outcome. Outcomes and prognostic factors that are routinely registered as part of clinical practice (e.g. BMI, sex, complications) or in (inter)national registries are studied frequently. Studies on prognostic factors, such as functional and sociodemographic status, and outcomes as healthcare costs, cognitive and mental function, and psychosocial impact are scarce, while they have been shown to be important for patients with osteoarthritis.
DOI: 10.34973/tfwt-0x10
title: development of SDM intervention

description: This repository  contains workflowdata and the intervention itself. The data describe the process of developing the decision aid and includes the flowchart of the development process of the decision aid for advanced therapies in Parkinson's disease. The complete decision aid is included. Data gained from other studies to develop the decision aid are stored in the associated repositories (DAC). This repository does not contain data on humans/personal data as it only describes the processs of developing the decision aid and the decision aid itself. The data are (mostly) decribed in Dutch.
DOI: 10.34973/c7cr-0z09
title: Rehabilitation and Capability care in NeuroMuscular Diseases

description: In this Data Acquisition Collection data collected for the Rehabilitation and Capability Care in NeuroMuscular Diseseas (ReCap-NMD) study are stored. In this DAC, the quantitative raw data and SPSS syntaxes for analyses of the primary and secondary outcome measures of this study can be found. With these analyses, the effectiveness of capability care (care based on the capability approach) for persons with neuromuscular diseases is evaluated, compared to usual care for persons with NMD.
DOI: 10.34973/pa1d-2e92
title: Aberrant APOBEC3B Expression in Breast Cancer Is Linked to Proliferation and Cell Cycle Phase

description: APOBEC3B (A3B) is aberrantly overexpressed in a subset of breast cancers, where it associates with advanced disease, poor prognosis, and treatment resistance, yet the causes of A3B dysregulation in breast cancer remain unclear. In the associated publication, A3B mRNA and protein expression levels were quantified in different cell lines and breast tumors and related to cell cycle markers using RT-qPCR and multiplex immunofluorescence imaging. The inducibility of A3B expression during the cell cycle was additionally addressed after cell cycle synchronization with multiple methods. First, we found that A3B protein levels within cell lines and tumors are heterogeneous and associate strongly with the proliferation marker Cyclin B1 characteristic of the G2/M phase of the cell cycle. Second, in multiple breast cancer cell lines with high A3B, expression levels were observed to oscillate throughout the cell cycle and again associate with Cyclin B1. Third, induction of A3B expression is potently repressed throughout G0/early G1, likely by RB/E2F pathway effector proteins. Fourth, in cells with low A3B, induction of A3B through the PKC/ncNF-κB pathway occurs predominantly in actively proliferating cells and is largely absent in cells arrested in G0. Altogether, these results support a model in which dysregulated A3B overexpression in breast cancer is the cumulative result of proliferation-associated relief from repression with concomitant pathway activation during the G2/M phase of the cell cycle. This repository contains all quantitative data pertaining to this paper PMID37190094.
DOI: 10.34973/tpsf-nv76
title: A cardiac-rehab behaviour intervention to reduce sedentary time in coronary artery disease patients: the SIT LESS study

description: This data sharing collection contains materials used and data collected as part of the ‘SIT LESS (Sedentary behaviour IntervenTion as a personaLisEd Secondary prevention Strategy) study’. 

Background: As high sedentary times (ST) are highly prevalent in patients with coronary artery disease (CAD), we developed and evaluated the 12-week, hybrid behavioural change intervention SIT LESS. We examined the immediate and medium-term effect of the SIT LESS intervention on changes in ST among CAD patients enrolled in cardiac rehabilitation (CR).

Methods: CAD patients participating in CR at 2 regional hospitals were included in this randomized controlled trial (1:1, stratified for gender and hospital). The control group received CR, whereas SIT LESS participants additionally received a 12-week hybrid behaviour change intervention. The primary outcome was the change in accelerometer-derived ST from pre-CR to post-CR and 3 months post-CR. Secondary outcomes included changes in ST and physical activity characteristics, subjective outcomes, and cardiovascular risk factors. A baseline constrained linear mixed-model was used.

Results: Participants (23% female; SIT LESS: n = 108, control: n = 104) were 63 ± 10 years. Greater ST reductions were found for SIT LESS compared to control post-CR (-1.7 (95% confidence interval (CI): -2.0; -1.4) versus - 1.1 (95% CI: -1.4; -0.8) h/day, pinteraction=0.009), but not at 3 months post-CR (pinteraction=0.61). Besides, larger light-intensity physical activity (LIPA) increases were found for SIT LESS compared to control post-CR (+ 1.4 (95% CI: +1.2; +1.6) versus + 1.0 (95% CI: +0.8; +1.3) h/day, pinteraction=0.020). Changes in other secondary outcomes did not differ among groups.

Conclusion: SIT LESS transiently reduced ST and increased LIPA, but group differences were no longer significant 3 months post-CR. These findings highlight the challenge to induce sustainable behaviour changes in CAD patients without any continued support.
DOI: 10.34973/v43r-vr06
title: Prognostic Value of Nivolumab Clearance in Non-Small Cell Lung Cancer Patients for Survival Early in Treatment

description: Immune checkpoint inhibitors have improved survival in advanced-stage non-small cell lung cancer, but a reliable biomarker to identify non-responders is still needed. This study investigated the prognostic potential of nivolumab clearance for overall survival early in treatment and evaluated its performance as a biomarker. Nivolumab clearance at early time points was associated with survival outcomes, showing high sensitivity but low specificity. Data collected: baseline characteristics, nivolumab plasma concentrations, survival data.
DOI: 10.34973/dwqt-gd74
title: RadboudUMC TAVI program datasets concerning transaxillary TAVI

description: This data repository contains the databases used in our publications concerning transaxillary TAVI in the RadboudUMC. These publications concern transaxillary access as preferred access, i.e., irrespective of transfemoral accessibility. 

1. Aortic regurgitation index ratio: this database was used to publish the article 

Aortic Regurgitation Index ratio is a strong predictor of one-year mortality after transcatheter aortic valve implantation using self-expanding devices, published in Seminars in Thoracic Surgery 2020; 33: 923-930

2. Delirium after TAVI under general anesthesia: this database was used to publish the article

Delirium after Transcatheter Aortic Valve Implantation under general anesthesia
Incidence, predictors and relation to long-term survival published in Journal of the American Geriatrics Society, 2019; 67: 2325-2330

3. Feasibility and outcomes of TAVI using the left axillary artery as primary access site: this database was used to publish the article 

Feasibility and outcomes of TAVI using the left axillary artery as primary access site, published in  The Annals of Thoracic Surgery 2019;107:546-552

4. Geriatric assessment in the prediction of delirium and long-term survival after Transcatheter Aortic Valve Implantation was used to publish the article

Geriatric assessment in the prediction of delirium and long-term survival after Transcatheter Aortic Valve Implantation, published inThe Journal of Thoracic and Cardiovascular Surgery 2021;161:2095-102

5. Procedural success and clinical outcome of the Portico Transcatheter Aortic Valve using the left subclavian artery as primary access: this database was used to publish the article

Research correspondence : Procedural success and clinical outcome of the Portico Transcatheter Aortic Valve using the left subclavian artery as primary access published in JACC Cardiovascular Interventions  2018: 11(13); 1311-12

4.
DOI: 10.34973/dphh-2c44
title: A remote booster program to attenuate sedentary behaviour in patients with coronary artery disease: (SIT LESS) Booster

description: This data sharing collection contains materials used and data collected as part of the (SIT LESS) Booster study. 

Aims: Sedentary time (ST) can be reduced in patients with coronary artery disease (CAD) during cardiac rehabilitation (CR), but most patients relapse to sedentarism within months. We examined the effectiveness of a 3-week remote booster intervention on ST changes in CAD patients.

Methods: CAD patients who previously (2.0 [1.9 – 2.2] years) completed CR were included in this randomized controlled trial (1:1, stratified for gender). All participants received usual care, whereas booster participants additionally received a 3-week remote behavioral change intervention. The primary outcome was the change in accelerometer-derived ST from baseline to post-intervention and secondary outcomes included changes in sedentary behaviour and physical activity (PA) characteristics. A baseline constrained linear mixed-model on an intention-to-treat basis was used.