cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17026/dans-29y-ra9e
title: Melanoma ML

description: Files: *.csv1.csv-185.csv: indexed images (0-255) translated from dermoscopy RGB (2^24 bit) imageslabels.csv: class labels (1=melanoma, 0=dysplastic nevus)Forthcoming publication: The corresponding paper to this dataset will be available soon
DOI: 10.17026/dans-24y-xgpm
title: The Effect of Different Types of Prostate Biopsy Techniques on Post-Biopsy Infectious Complications

description: The aim of our study was to compare infectious complication rates between different prostate biopsy techniques with various number of biopsy cores. In this retrospective study, all patients from 2 hospitals who underwent prostate biopsy between 2012 and 2019 were identified. Cohorts with different types of prostate biopsies were compiled within these hospitals. Primary outcome measure was any registered infectious complication within 7 days post-biopsy. Secondary outcomes were infectious complications within 30 days, hospitalization and bacteremia. To compare the risk of infection following different prostate biopsy techniques, data was fitted into a logistic regression model adjusting for potential confounders. In total, 4,233 prostate biopsies in 3,707 patients were included: TRUSPB 12±1.4 biopsy cores; transperineal magnetic resonance imaging (MRI)-ultrasound fusion guided prostate biopsy 16±3.7 biopsy cores; transrectal targeted MRI-ultrasound fusion guided prostate biopsy 3.1±0.8 biopsy cores; transrectal targeted in-bore MRI guided prostate biopsy 2.8±0.8 biopsy cores.
DOI: 10.17026/dans-x38-abzq
title: Seagrass is protected from ragworm pressure by a newly discovered grazer-ragworm interaction; implications for restoration

description: 1. Coastal ecosystems are generally controlled by the combination of bottom-up (resourcedriven) and top-down (consumer-driven) trophic, and non-trophic interactions. Anthropogenic disruption of these interactions, e.g., through eutrophication or overfishing, leads to loss of the foundation species composing these ecosystems. Within degraded ecosystems, new interactions may become dominant, hampering restoration of foundation species.2. We demonstrate this concept in saltwater Lake Grevelingen, where seagrass restoration was seriously hampered by a newly discovered non-trophic interaction between the seagrass Zostera marina and the ragworm Platynereis dumerilii. Platynereis constructs dwelling tubes between seagrass leaves by gluing and entangling them, leading to loss of biomass and increased epiphyte cover. To test the roles of epiphyte grazing (top-down) and eutrophication (bottom-up) on this newfound interaction, we executed a field experiment introducing the snail Littorina littorea under natural nutrient concentrations and Platynereis densities, and performed a full factorial mesocosm experiment applying Littorina, Platynereis and nutrient treatments.3. Our field results show that survival of reintroduced Zostera in Lake Grevelingen is seriously hampered by Platynereis, which can be suppressed by grazer addition.4. In our mesocosm experiment we demonstrate that top-down control by Littorina protected seagrass through two pathways: (1) mitigating bottom-up regulated epiphyte growth by trophic top-down forcing and (2) hampering the non-trophic interaction between Zostera and Platynereis by grazing epiphytes and dwelling tubes.5. Synthesis and applications. With coastal ecosystems globally under pressure, our study emphasises the importance of understanding ecosystem-specific trophic and non-trophic key interactions when considering restoration. We show how negative interspecific interactions can become dominant in the absence of key facilitating interactions. Next, we show that negative interactions (leaf gluing), inhibiting foundation species restoration, can be overruled by the inclusion of positive interspecific interactions (epiphyte grazing by mesograzers). Finally, we provide a three-step co-introduction approach for restoration management.
DOI: 10.17026/dans-z4a-k5jy
title: Rewiring of peatland plant–microbe networks outpaces species turnover

description: Interactions between plant and microbial communities in peatlands are complex, yet pivotal for the functioning of these carbon-dense ecosystems. Our understanding of how climate change affects important peatland processes such as carbon dynamics is often based on assumed fixed relationships between above-and belowground communities. Our work shows that the turnover in plant–microbial interactions along enviro–climatic gradients is faster than species turnover within both communities, resulting in a mismatch in alpha diversity between plant and microbial communities. Notably, warming and increased nutrient deposition weakens plant–microbe linkages, which may consequentially decrease the overall robustness of peatland ecosystem processes to future anthropogenic pressures.
DOI: 10.17026/dans-x8s-ns7y
title: Mite Diet Sequences Obtained by High Throughput Sequencing of Gut Contents of Freshly Collected Water Mites

description: Cytochrome oxidase subunit I (COI) barcode sequences in this file were obtained from gut DNA extracted from 54 freshly collected water mites, comprising 21 Lebertia quinquemaculosa, 30 Lebertia davidcooki , 1 Limnesia , and 2 Arrenurus specimens.
DOI: 10.17026/dans-27a-fj4k
title: STRAP

description: This research project aimed to safely reduce antibiotic prescriptions in children under five suspected of a lower respiratory tract infection (RTI) at the emergency department (ED), by implementing a clinical decision rule.DesignIn a stepped-wedge, cluster randomized trial we included children aged one month to five years presenting with fever and cough or dyspnoea to eight EDs in the Netherlands . In the pre-intervention phase children received usual care. During the intervention phase a validated clinical prediction model (Feverkidstool) including clinical characteristics and C-reactive protein was implemented as a decision rule guiding antibiotic prescription. We obtained data of 999 children (61% male, median age 17 months (IQR 9 to 30)) between January 1, 2016 and September 30, 2018; 402 during the intervention phase. Data include general and clinical characteristics, interventions (diagnostic tests, hospitalisation), and for a subset of patients microbiological data are available
DOI: 10.17026/dans-z3c-q2bs
title: Interview met prof. dr. E.J. Ruitenberg

description: Interview in het kader van promotieonderzoek (2012-2017) naar de omgang met door mensen en landbouwhuisdieren gedeelde infectieziekten ('zoönosen') in Nederland gedurende de twintigste eeuw, in het bijzonder met betrekking tot de casus BSE (1988-2001) in dat onderzoek. Het interview gaat niet alleen over Bovine Spongiforme Encefalopathie (BSE) / 'gekkekoeienziekte', maar ook over de professionele loopbaan van prof. dr. Ruitenberg in het algemeen en zijn werk bij het RIVM en het CLB.
DOI: 10.2909/886b22ee-b16c-4f7e-a82c-5c905a89f896
title: High Resolution Vegetation Phenology and Productivity: Fraction of Absorbed Photosynthetically Active Radiation (raster 10m) version 1 revision 1, Sep. 2021

description: This metadata refers to the Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) dataset, one of the near real-time (NRT) Vegetation Index products of the pan-European High Resolution Vegetation Phenology and Productivity (HR-VPP), component of the Copernicus Land Monitoring Service (CLMS). The Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) quantifies the fraction of the solar radiation absorbed by live leaves for the photosynthesis activity. Then, it refers only to the green and alive elements of the canopy. The FAPAR depends on the canopy structure, vegetation element optical properties, and illumination conditions. The FAPAR dataset is made available as raster files with 10 x 10m resolution, in UTM/WGS84 projection corresponding to the Sentinel-2 tiling grid, for those tiles that cover the EEA38 countries and the United Kingdom and for the period from October 2016 until today, with daily updates. Each file has an associated quality indicator (QFLAG2) to assist users with the screening of clouds, shadows from clouds and topography, snow and water surfaces.
DOI: 10.17026/dans-24b-zqa7
title: Differential diagnosis in children with infections

description: Differential diagnosis in children with infections
DOI: 10.17026/dans-zzt-9xs3
title: Trophic transfer of Cd, Cu, Pb, Zn, Se and P in Dutch storage water reservoirs

description: The datafile is part of a study to determine elemental -with a focus on heavy metal- contents in organisms of drinking water reservoirs (Brabantse Biesbosch, the Netherlands).Heavy metals are naturally omnipresent in aquatic systems. Excess amounts of heavy metals can accumulate in organisms of pollution impacted systems and biomagnify or biodilute across a food web. Analysing the food web structure and metal contents of the organisms can help unravel the pathways of biomagnification or biodilution and gain insight in trophic linkages. The measured heavy metals and other elements in organisms of the Biesbosch reservoirs were linked to stable isotopic signatures (as measured in a previous study by Verstijnen et al. (2019)).
DOI: 10.17026/dans-x7n-gspx
title: Online survey among Dutch urologists about prostate biopsy practices

description: The clinical landscape of prostate biopsy is evolving with changes in procedures and techniques. Moreover, antibiotic resistance is increasing and influences the efficacy of pre-biopsy prophylactic regimens. Therefore, increasing antibiotic resistance may impact on clinical care, which probably results in differences between hospitals. The objective of our study is to determine the (variability in) current practices of prostate biopsy in the Netherlands and to gain insight into Dutch urologists' perceptions of fluoroquinolone resistance and biopsy related infections. An online questionnaire was prepared using SurveyMonkey® platform and distributed to all 420 members of the Dutch Association of Urology, who work in 81 Dutch hospitals. Information about PB techniques and periprocedural antimicrobial prophylaxis was collected. Urologists' perceptions regarding pre-biopsy antibiotic prophylaxis in an era of antibiotic resistance was assessed. One hundred sixty-one responses were analyzed representing 65 (80.3%) of all Dutch hospitals performing prostate biopsy.
DOI: 10.17026/dans-24e-5sk7
title: Effects of allopurinol and febuxostat on uric acid transport and transporter expression in human umbilical vein endothelial cells (TURBO project)

description: Uric acid induces radical oxygen species formation, endothelial inflammation, and endothelial dysfunction which contributes to the progression of atherosclerosis. Febuxostat and allopurinol differentially alter uric acid transporter function in human embryonic kidney cells. We hypothesized that endothelial cells express uric acid transporters that regulate intracellular uric acid concentration and that modulation of these transporters by febuxostat and allopurinol contributes to their different impact on cardiovascular mortality. Gene expression of uric acid transporters was determined in isolated human umbilical vein endothelial cells (HUVEC) and in human aortic endothelial cells (HAEC). Cultured HUVEC were studied for the effect of allopurinol and febuxostat on intracellular uric acid concentrations, gene expression of uric acid transporters, and cell count after exposure to uric acid in medium. Data is reported as median (range). HUVEC and HAEC expressed glucose transporter 9 (GLUT9), multidrug resistance protein 4 (MRP4), breast cancer resistance protein (BRCP), and sodium-dependent dicarboxylate transporter (NaDC3) at mRNA level. Allopurinol did not affect intracellular uric acid concentrations. In contrast, febuxostat 10µM and 20µM increased intracellular uric acid concentration by 32% (0-42%) and 75 (21-111%) during exposure to 100µM uric acid; and by 62% (23-98%) and 88% (58-150%) during exposure to 350µM uric acid. Allopurinol did not alter mRNA expression of uric acid transporters. In contrast, febuxostat increased mRNA expression of GLUT9, reduced that of MRP4, and did not affect BCRP. These findings could explain the higher cardiovascular mortality for febuxostat as compared to allopurinol in patients with gout.
DOI: 10.17026/dans-zk4-ercv
title: Nature portrayed in images in Dutch Brazil - Appendix (S2): Sources of the plant woodcuts in the Historia Naturalis Brasiliae (1648) Database

description: I designed this publication to accompany the research article Nature portrayed in images in Dutch Brazil: Tracing the sources of the plant woodcuts in the Historia Naturalis Brasiliae (1648) by Mireia Alcantara Rodriguez, Tinde van Andel, and Mariana Françozo. This visual database is directed to everyone attracted to the fascinating world of tropical plants and Renaissance and early modern botanical art, with the main focus on the flora of Dutch Brazil (the northeastern territories of Brazil colonized by the Dutch from 1630 to 1654). This PDF file was built with Filemaker Pro software in a database format, and both files are available open access in the repository of Leiden University via: https://doi.org/10.17026/dans-zk4-ercv.The main purpose of this file is to present in a visual form the potential sources used to create the plant woodcuts embedded in the Historia Naturalis Brasiliae (HNB). A brief text accompanies every plant entry in which I discuss the various levels of correlation among sources. The HNB is a western treatise that documents the flora, fauna, medicine, climate, and the inhabitants coexisting in Dutch Brazil as perceived by German naturalist George Marcgrave (1610-1643) and Dutch physician Willem Piso (1611-1678) – among others. This work was funded by count Johan Maurits of Nassau-Siegen (1604-1679), whose governorship in Dutch Brazil lasted from 1636 to 1644, and edited by cartographer Johannes de Laet (1581-1649), one of the directors of the Dutch West India Company. This file can be read independently but its main function is to complement and depict the data analyzed in the main paper, which is also displayed in an Excel spreadsheet (S1). The main paper aimed to answer what were the sources used to create the plant woodcuts in the HNB, first, by arranging together the woodcut images and their corresponding species in other visual sources from Dutch Brazil and analyzing their similarities; and second, by searching for the remaining sources in contemporary or older treatises that included engravings similar to the HNB woodcuts. By doing so, the various methods of visual-knowledge-making are discussed, including the methods of plant collection and flora representation. This publication presents a catalogue of the data on plant woodcuts in the HNB, accounting for 243 database entries with 1458 images that correspond to 237 taxa. Related to this research, I created a second dataset (S3) and its corresponding PDF file (Appendix S4) to analyze the sources of the plant woodcuts in the India Utriusque re Naturali et Medica (IURNM, Piso 1658). The images and text of this treatise were edited by Piso ten years after the publication of the HNB. It is recommended to check both visual files (S2 vs. S4) to observe the diversity of visual knowledge production in the HNB and the IURNM.
DOI: 10.17026/dans-zqg-e4vy
title: Images used for paper #sleepingbaby on Instagram: adherence to Dutch safe sleeping advice

description: Images scraped from Instagram using 22 hashtags and 10 accounts of Dutch companies/platforms focused on infants. Dataset can be found in another deposit.
DOI: 10.17026/dans-xzf-wh36
title: Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) – functional MRI data set

description: The Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) study is an open-label trial during which children with ADHD followed a 5-week few-foods diet (FFD). The ADHD rating scale (ARS) was used thrice to assess the childs behaviour: at the screening (T0), before the FFD (T1) and at the end of the FFD (T2). Functional MRI scanning was done at T1 and T2. Each scan session received a random measurement code (M-code). During data processing and initial data analyses researchers were aware of which T1 and T2 samples formed a pair, but they were blinded to changes in ADHD symptoms. All data were anonymized using a subject-code (CH-code).
DOI: 10.17026/dans-xay-scs6
title: Data for: Synergy between induction heating, antibiotics, and N-acetylcysteine eradicates Staphylococcus aureus from biofilm

description: Non-contact induction heating (NCIH) is a noninvasive treatment modality that can be used to cause thermal damage to bacterial biofilms on a metal implant surface in the context of a prosthetic joint infection. The purpose of this study was (1) to determine the effectiveness of NCIH on killing Staphylococcus aureus from biofilm and (2) to determine the possible synergistic effect of NCIH and cocktails of antibiotics and N-acetylcysteine (NAC).
DOI: 10.17026/dans-x2a-nmwr
title: Quantification of cell-mediated stiffening of synthetic extracellular matrices

description: Strain stiffening of extracellular matrices is increasingly recognized as a mechanical mechanism to tune cell behaviors and maintain tissue functions. Routinely, the mechanical properties of a matrix are determined using shear rheology in the absence of cells. However, this method lacks the cell-induced stiffening and consistently underestimate the (macroscopic) stiffness of biogels. We introduce a method using shear rheology in combination with cells and synthetic matrices, polyisocyanide hydrogels that possess nonlinear mechanics. Human adipose-derived stem cells (hASCs) were encapsulated in gels from polymers with different contour lengths but a constant peptide density and polymer concentration to study the cell-mediated nonlinear mechanical change of ECM quantitatively. Other parameters such as cell line, cell density, type of cell adhesion peptides were also changed systematically. Rheology results reveal that cells can adjust matrix stiffness to a similar value via contraction regardless of the cell-free elasticity of gels. Fluorescence imaging further shows the local physical matrix remodeling by cells. Our results suggest that biogels or their mimics with nonlinear mechanics possess dynamic mechanical properties that are highly responsive to cellular intervention. Our approach offers a new platform with synthetic semi-flexible polymer networks for research on the cell-matrix interface.
DOI: 10.17026/dans-z4g-fe9h
title: Data of "Do initial concentration and activated sludge seasonality affect pharmaceutical biodegradation rate constants?"

description: In our paper ‘Do initial concentration and activated sludge seasonality affect pharmaceutical biodegradation rate constants?’ we evaluated potential relationships between first-order biodegradation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from wastewater treatment plant (WWTP) Groesbeek, the Netherlands, of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC-MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing and kb values were calculated. Wastewater measurements during the experiment included: dissolved inorganic matter, total suspended solids, pH, ammonium, nitrate and nitrite concentrations. At the start of the experiment, WWTP conditions were collected on: ammonium and nitrate concentrations, total suspended solids, oxygen and temperature. The biodegradable pharmaceuticals, ranked from high to low biodegradation rates, were acetaminophen, metformin, metoprolol, terbutaline, and phenazone. Carbamazepine, diatrizoic acid, diclofenac and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetics theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP.The data can be found in the following files, containing primary data:i) Van_Bergen_etal_experimental_wastewater_conditions (.xlsx, .csv or .ods), with data of dissolved inorganic matter, total suspended solids, pH, ammonium, nitrate and nitrite concentrations during the experiment.ii) Van_Bergen_etal_WWTP_conditions (.xlsx, .csv or .ods), with data of ammonium and nitrate concentrations, total suspended solids, oxygen and temperature at the time of sampling at WWTP Groesbeek.iii) Van_Bergen_etal_pharmaceutical_concentration (.xlsx, .csv or .ods), with data of the concentrations over time of the following pharmaceuticals: acetaminophen, carbamazepine, diatrizoic acid, diclofenac, fluoxetine, metformin, metoprolol, phenazone and terbutaline.
DOI: 10.17026/dans-zjt-aehh
title: Cognitive-motor interference during goal-directed upper-limb movements

description: Data was collected within the NEURAS project (protocol registered as NL48497.058.14), aimed to separately assess the functioning of systems involved in motor control (i.e., motor, sensory, cognitive) and their functional integration in various contexts (i.e., using different tasks and systematic manipulations of the mechanical/visual environment) in order to understand how these factors contribute to activity limitations in two highly prevalent neurological disorders (Parkinson’s disease and stroke). Within this project, among others, the possibilities of ‘markerless’ movement tracking (MT) devices (based on KinectTM) were explored to relate unobtrusively assessed characteristics of motor performance to contributing motor, (sensory,) and cognitive factors.In this study, we evaluated cognitive-motor interference during an upper-limb motor task. We used the cognitive auditory Stroop task (Cohen and Martin, 1975). The motor task involved goal-directed upper-limb movements to control a virtual mouse, presented on a LED TV, to collect virtual pieces of cheese (targets) as fast as possible while avoiding a virtual cat (obstacle). Single-task performances as well as dual-task effects (DTEs) in both the cognitive and motor domain were evaluated. Patterns of CMI were explored to evaluate overall attentional capacity and attention allocation.
DOI: 10.17026/dans-z82-3v72
title: Better assessments of greenhouse gas emissions from global fish ponds needed to adequately evaluate aquaculture footprint

description: Overview of methods used to assess aquaculture greenhouse gas emissions: a literature review. The paper compilation was performed and published by Yuan et al (2019). This dataset was added as an appendix in pdf format to "Kosten, S., Almeida, R. M., Barbosa, I., Mendonça, R., Muzitano, I. S., Oliveira-Junior, E. S., et al. (2020). Better assessments of greenhouse gas emissions from global fish ponds needed to adequately evaluate aquaculture footprint. Science of The Total Environment, 141247. http://www.sciencedirect.com/science/article/pii/S0048969720347768 "