cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17026/dans-xyb-dxys
title: Wheat 2003 outdoor

description: This dataset containts the underlying data for the study:Evers JB, Vos J, Fournier C, Andrieu B, Chelle M, Struik PC. 2005. Towards a generic architectural model of tillering in Gramineae, as exemplified by spring wheat (Triticum aestivum). New Phytologist, 166: 801-812,http://dx.doi.org/10.1111/j.1469-8137.2005.01337.x•This paper presents an architectural model of wheat (Triticum aestivum), designed to explain effects of light conditions at the individual leaf level on tillering kinetics. Various model variables, including blade length and curvature, were parameterized for spring wheat, and compared with winter wheat and other Gramineae species.•The architectural model enables simulation of plant properties at the level of individual organs. Parameterization was based on data derived from an outdoor experiment with spring wheat cv. Minaret.•Final organ dimensions of tillers could be modelled using the concept of relative phytomer numbers. Various variables in spring wheat showed marked similarities to winter wheat and other species, suggesting possibilities for a general Gramineae architectural model.•Our descriptive model is suitable for our objective: investigating light effects on tiller behaviour. However, we plan to replace the descriptive modelling solutions by physiological, mechanistic solutions, starting with the localized production and partitioning of assimilates as affected by abiotic growth factors.
DOI: 10.17026/dans-zah-vs6x
title: Data from: Combined effects of land use and hunting on distributions of tropical mammals

description: In our paper “Combined effects of land use and hunting on distributions of tropical mammals.” (Conservation Biology, Available from: https://onlinelibrary.wiley.com/doi/abs/10.1111/cobi.13459) we provide the first pantropical-scale assessment on the combined effect of land use and hunting on the distributions of 1,884 tropical mammal species in the years 1992 and 2015.Here we provide the hunting database used in the article, including the (non-openaccess) raw data, R-scripts and final results of the manuscript.
DOI: 10.17026/dans-zwz-ukdn
title: Wheat 2006 outdoor

description: This dataset contains the underlying data for the study:Evers JB, Vos J, Yin X, Romero P, van der Putten PEL, Struik PC. 2010. Simulation of wheat growth and development based on organ-level photosynthesis and assimilate allocation. Journal of Experimental Botany, 61: 2203-2216http://dx.doi.org/10.1093/jxb/erq025Intimate relationships exist between form and function of plants, determining many processes governing their growth and development. However, in most crop simulation models that have been created to simulate plant growth and, for example, predict biomass production, plant structure has been neglected. In this study, a detailed simulation model of growth and development of spring wheat (Triticum aestivum) is presented, which integrates degree of tillering and canopy architecture with organ-level light interception, photosynthesis, and dry-matter partitioning. An existing spatially explicit 3D architectural model of wheat development was extended with routines for organ-level microclimate, photosynthesis, assimilate distribution within the plant structure according to organ demands, and organ growth and development. Outgrowth of tiller buds was made dependent on the ratio between assimilate supply and demand of the plants. Organ-level photosynthesis, biomass production, and bud outgrowth were simulated satisfactorily. However, to improve crop simulation results more efforts are needed mechanistically to model other major plant physiological processes such as nitrogen uptake and distribution, tiller death, and leaf senescence. Nevertheless, the work presented here is a significant step forwards towards a mechanistic functional–structural plant model, which integrates plant architecture with key plant processes.
DOI: 10.17026/dans-xg4-9mz7
title: Data from: Overcoming establishment thresholds for peat mosses in human-made bog pools

description: Data from: Overcoming establishment thresholds for peat mosses in human-made bog pools.Ecological Applications.In this study, we theoretically explore if a floating peat mat and an open human-made bog lake can be considered two alternative stable states using a simple model, and experimentally test in the field whether stable states are present, and whether a state shift can be accomplished using floating biodegradable structures that mimic buoyant peat. We transplanted two peat moss species into these structures (pioneer sp. Sphagnum cuspidatum and later-successional sp. S. palustre) with and without additional organic substrate.This dataset contains data of plant performance of the experimental plots and of surface water quality.
DOI: 10.17026/dans-z5m-kp67
title: FEM growth and yield data mixed species forest

description: The current database is part of the FEM growth and yield database, a collection of growth and yield data from even-aged monocultures (douglas fir, common oak, poplar, Japanese Larch, Norway spruce, Scots pine, Corsican pine, Austrian pine, red oak and several other species with only a few plots like grand fir, even-aged mixed species forest plots, uneven-aged natural forest, uneven-aged selection forest and roadside plantations of poplar). The FEM growth and yield data base is currently supervised by Jan den Ouden and Frits Mohren.
DOI: 10.17026/dans-xp8-ncmh
title: Data from: Initiating and upscaling mussel reef establishment with life cycle informed restoration: successes and future challenges

description: Data from: Initiating and upscaling mussel reef establishment with life cycle informed restoration: successes and future challengesThe manuscript that has been based on these data is published in Ecological Engineering.These datafiles are part of a study in which we aimed to test whether the restoration approach life cycle informed restoration, which focusses on the amelioration of multiple bottlenecks throughout an organisms life cycle, can be scaled to ecosystem-relevant scales. To test this, we conducted a large-scale restoration experiment using blue mussel reefs as a model system. In our two-year experiment, we used biodegradable structures to temporarily facilitate mussel reef formation by providing early-life settlement substrates, and subsequently, reduce post-settlement predation on an intertidal flat in the Wadden Sea, the Netherlands.The structures were placed in 10x20m plots, mimicking bands found in natural mussel beds, spread out across 650m. As controls, unmanipulated bare plots were used. Our results show that the structures enhance mussel biomass and that mussels were absent in bare plots. However, biomass varied within plots; in intact structures it was 60 times higher than in those that became buried. Next to burial, 18-46% of the structures were lost due to technical failure, especially during winters at this exposed site.The datasets contain data obtained from this manipulative field experiment on mussel biomass and structure condition collected near Griend in the Netherlands.
DOI: 10.17026/dans-2c3-uv9a
title: Data from: Herbivore exclusion and active planting stimulate reed marsh development on a newly constructed archipelago

description: This datafile is part of a study that demonstrates, using a manipulative field experiment, that herbivory and the introduction of reed rhizomes strongly control early vegetation development and carbon dynamics on the bare soils on a newly constructed archipelago (Marker Wadden, the Netherlands). In this full-factorial field experiment, we excluded herbivores (with cage exclosures) and introduced reed. In six replicated blocks we applied each of four treatments: “no herbivory, planted reed”, “herbivory, planted reed”, “no herbivory, no planted reed” and “herbivory, no planted reed”. The study took place from 2017 till 2018 on a newly constructed archipelago (Marker Wadden) in the Netherlands. The dataset contains data on vegetation cover, reed shoot number and maximum reed height after one season of growth, as well as data on porewater nutrient concentrations and greenhouse gas fluxes (carbon dioxide and methane) in the experimental treatments.
DOI: 10.17026/dans-zyf-qvax
title: Variation in the outcome of septic patients after the institution of a patient-tailored therapy protocol in an Italian Intensive Care Unit: retrospective observational study.

description: Single-centre retrospective observational study including 100 consecutive patients (≥ 16 years) diagnosed with septic shock, according to the 2001 International Sepsis Definition Conference criteria, admitted to our ICU after the institution of a patient-tailored therapy protocol, compared with a historical control group of 100 patients. The patient-tailored therapy protocol included the use of IgM-enriched immunoglobulins for patients with low plasma IgM levels, blood purification strategies for patients with high plasma levels of cytokines or endotoxin, albumin correction and vasoactive agents modulation. Clinical and therapeutic parameters were noted at the time of septic shock diagnosis and for the first 24 hours. The primary outcome was ICU mortality. ICU-mortality was lower in the patient-tailored therapy cohort as compare to the standard therapy cohort (32% versus 57%, p&lt;0.001). An individualised therapeutic approach in septic patients may be associated with a survival benefit.
DOI: 10.17026/dans-zub-5dyv
title: Data from 'The impact of imidacloprid and thiacloprid on the mean species abundance in aquatic ecosystems'

description: In our paper 'The impact of imidacloprid and thiacloprid on the mean species abundance in aquatic ecosystems' (10.1016/j.scitotenv.2022.153626), we used species sensitivity distributions and mean species abundance relationships to estimate the impact of two pesticides (imidacloprid and thiacloprid) on aquatic species. Despite data scarcity, uncertainty and variability, especially on emerging neonicotinoids, our study has shown that the Mean Species Abundance Relationship (MSAR) is a better indicator of effects in ecological studies than the Potentially Affected Fraction (PAF), a common metric in risk assessment. As such we are gradually moving from ad hoc comparisons of correlations between lab and field effects to theoretical underpinning of lab-field extrapolation. In this repository we provide data from literature underlying the analyses in the paper.
DOI: 10.17026/dans-xcg-ncur
title: Supplementary Figures and tables Eenjes et al AJP-LCM revision 4-6-21

description: Supplementary Figures and tables with revision Eenjes et al AJP-LCMB June 4, 2021
DOI: 10.17026/dans-x9d-ytww
title: Increased temperature reduces the positive effect of sulfide-detoxification mutualism on Zostera noltii nutrient uptake and growth

description: Seagrass meadows form essential ecological components in coastal zones but are rapidly declining worldwide due to anthropogenic impacts, including eutrophication and climate change-related heat waves. An important consequence of increased eutrophication is organic matter input in the sediment, which, together with raised temperatures, stimulates the production of toxic sulfide. Although multiple recent studies have highlighted that seagrass can engage in a mutualistic relationship with lucinid bivalves alleviating sulfide toxicity in the rhizosphere, it remains unclear how this mutualism is affected by temperature and eutrophication. To unravel this relation, we investigated the response of the seagrass Zostera noltii to contrasting sediment organic matter conditions, temperatures and presence/absence of the lucinid clam Loripes orbiculatus in a full-factorial mesocosm experiment. Results demonstrate that temperature increased porewater sulfide and nutrient levels, particularly in treatments with high sediment organic matter content. Interestingly, L. orbiculatus reduced not only sulfide levels, but also porewater nutrients. The removal of sulfide in turn stimulated Z. noltii growth, despite lower nutrient availability. Finally, increased temperature suppressed the mutualistic benefit for Z. noltii as sulfide detoxification became hampered. We conclude that, as eutrophication remains an issue in the coastal zone and temperature extremes will likely become more common in the future, seagrass meadows where lucinids occur may need to increasingly rely on its this mutualism. At the same time, however, this interaction will become increasingly more strained, with an inherent increasing risk of mutualism breakdown.The datafile is part mesocosm experiment showing the effect of eutrofication and heat stress on the mutualistic interaction between Lucinid bivalves and seagrass. The lab experiment conducted at the lab facilities of Radboud university, faculty of Science. The result of the experiment shows that increased temperature reduces the positive effect of sulfide-detoxification mutualism on Zostera noltii nutrient uptake and growth. Lab data analysed at the Faculty of Science at the General Instrumentation. Statistical analyses in open source R software. The dataset is a CSV file with the data results from the experiment which includes the treatments in the experiment (yes/no: organic matter injection, yes/no: lucinid addition, yes/no: heat stress), seagrass dry biomass, sulfide concentrations, porewater nutrients (PO4, NH4) and total nutrient content in the seagrass leafs (phosphor and nitrogen).
DOI: 10.17026/dans-xky-zh99
title: FEM growth and yield data - Poplar roadside plantations (revised version)

description: The current database is part of the FEM growth and yield database, a collection of growth and yield data from even-aged monocultures (douglas fir, common oak, poplar, Japanese Larch, Norway spruce, Scots pine, Corsican pine, Austrian pine, red oak and several other species with only a few plots, even-aged mixed species forest plots, uneven-aged natural forest, uneven-aged selection forest and roadside plantations of poplar. The FEM growth and yield data base is currently supervised by Jan den Ouden and Frits Mohren.The growth and yield research on poplar roadside and other line plantation was initiated by prof. dr. J.H. Becking in 1951. During almost five decades the project was supervised by A. van Laar, P.G. de Vries, J.H. Hildebrand and H.H. Bartelink. The project stopped after measuring the last remaining stand in 1997. Within the overall database it is called study 13.
DOI: 10.17026/dans-274-a78v
title: Trained neural network used in "OrganoidTracker: efficient cell tracking using machine learning and manual error correction"

description: Convolutional neural network and minimal set of Python scripts to detect nuclei in confocal microscopy images.
DOI: 10.17026/dans-zgd-v62z
title: Who cares: combining informal care and work

description: Information on demographics, working conditions, informal care giving, work-related outcomes and health. Information of employees, of which most had 1 cross-sectional measurement. Employees of one organization additionally invited participants at one year follow-up.
DOI: 10.17026/dans-x3x-aft8
title: Good Psychometric Properties of the Addiction Version of the Revised Illness Perception Questionnaire for Health Care Professionals

description: The current study involved 1072 participants from Indonesia and the Netherlands. Participants were healthcare professionals and master students with different educational backgrounds (medical doctors, psychologists, nurses, and social workers; medicine, psychology, educational science respectively). They were recruited from various addiction-training programs in the Netherlands and Indonesia. We adapted the Illness Perception Questionnaire (the IPQ) to the addiction version (the IPQ-A) and evaluate the psychometric properties of the IPQ-A: factor structure, internal consistency, and discriminant validity, when applied to evaluate healthcare professionals’ perceptions of addiction. The data set includes the statistic data (the SPSS files), the codebook that describes the study and the questionnaires: the IPQ-A, IPQ and IPQ-R.
DOI: 10.17026/dans-zkr-pyrc
title: Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase

description: Molecular dynamics (MD) trajectories for lytic polysaccharide monooxygenases (LPMO) based on neutron structure. These simulations were performed using AMBER package (ff14SB force-field) with explicit solvent and counter-ions. The durations of each trajectory is 1 microsecond. 1,000 snapshots each separated by 1 nanosecond are provided here in PDB format. The water molecules and counter-ions have been removed from these PDB frames. These files can be viewed using a biomolecular visualization software, such as PyMOL.
DOI: 10.17026/dans-zwb-87ha
title: The impact of the implementation of physician assistants in inpatient care: a multicenter matched-controlled study

description: Medical care for admitted patients is increasingly reallocated to physician assistants (PAs), because of an increased appreciation of continuity of care, pressure to deliver healthcare efficiently, and local shortages of medical doctors (MDs). A PA is a non-physician healthcare professional licensed to practice medicine in defined domains, with variable degrees of professional autonomy. PAs who are employed for medical care for admitted patients usually work in a team compromising both PAs and MDs (i.e. residents, staff physicians or hospitalists). Although there is a worldwide trend of an increase of PAs in the management of hospitalized patients, evidence about the consequences of reallocating inpatient care from MDs to PAs for healthcare outcomes is limited.This study aimed to determine the effects of substitution of inpatient care from MDs to PAs on patients’ lenght of stay, quality and safety of care, patient experiences and costs. Also the impact on guideline adherence on medication prescribing has been investigated.In a multicenter matched-controlled study, the traditional model in which only MDs are employed for inpatient care was compared with a mixed model in which besides MDs also PAs are employed. Thirty-four wards were recruited across the Netherlands. Patients were followed from admission till one month after discharge. In total, 2,307 patients were included
DOI: 10.17026/dans-z4b-6krm
title: Mitigation of inland navigation effects on biodiversity by longitudinal training dams

description: This dataset is for the report titled "Mitigation of inland navigation effects on biodiversity by longitudinal training dams". The report focuses on assessing the effects that inland navigation has on the ecology of the river Waal and the mitigation of these effects by the three novel longitudinal training dams (LTDs) constructed in 2015 as a pilot project by Rijkswaterstaat (RWS). Moreover, fish and abiotic conditions monitoring performed in the period 2016 – 2020 was continued during 2021. Several techniques were used to measure the effects of ships on biodiversity, including the monitoring mussel behavior through Hall sensors, seine net fishing to assess fish densities, the use of hydrophones to measure underwater sound levels and remote sensing techniques to evaluate the ambient conditions at the LTD shore channels during 2020 and 2021.This report aims at answering the following research questions: 1) How do ship effects differ between the LTD shore channels and groyne fields? 2) Does the behaviour of mussels differ between habitats exposed and protected to ship effects? 3) What EPT species are using the LTD shore channels as habitats? 4) Do dreissenids occur more often in wave exposed or protected areas of the LTDs themselves? 5) Do the young of the year fish in the LTD shore channels react to the introduction of sound from inland navigation? 6) How did fish densities differ between the LTD shore channels and groyne fields during high river discharges in 2021? 7) What were the patterns of erosion in the shore channels and how did the shoreline length change in the period 2019-2020?METHODS SUMMARY:1. Fish density shore channels:After the construction of the LTDs, several monitoring techniques have been used to assess the fish biodiversity and densities in the LTD shore channels. In this study we focus on data collected throughout 2021 using seine nets in the Dreumel and Ophemert shore channels and reference groynes. The fork lengths of each fish caught were recorded as well as species and sampled surface area.2. Underwater sound and freshwater fish:Monitoring of fish with a seine net was done in the littoral zone at night during two campaigns in 2021 including high and low river discharges. The monitoring entailed the introduction of an underwater speaker to play pre-recorded sounds of inland navigation that passed in a nearby groyne field to quantify the response of fish densities. This sampling was done in the Ophemert shore channels with controls taking place in both the shore channel and reference groyne fields nearby.3. Mussel behaviour:To assess whether there is a significant difference in habitat quality for freshwater mussels between the Dreumel shore channel and a nearby groyne field their behaviour was measured with a Hall sensor to quantify their level of activity (i.e. closures).4. Ship effects:Sensors were deployed to assess parameters such as water level, light intensity underwater, temperature, sound and acceleration.
DOI: 10.17026/dans-zft-hgda
title: A comparison of 7T imaging with 8- and 2-channel transmit systems.

description: The quality of MRI scans on the multi-channel transmit was compared to that of the classic 2-channel system. An MP2RAGE sequence was used to acquire high-resolution anatomical data. Two echo planar imaging acquisitions were used to compare functional MRI data quality. The first was a standard 2mm acquisition, the second a high-resolution 3D-EPI acquisition.
DOI: 10.17026/dans-zqm-d9zh
title: Data from problematic and non-problematic Facebook users who performed a Go/Nogo task with Facebook-related, pleasant, unpleasant, and neutral pictures and a self assessment manikin (SAM)

description: We investigated the modulation of Facebook-related stimuli on response inhibition in Problematic Facebook Use (PFU) by recording the event-related potentials during an emotional Go/Nogo Task. Twenty-two Problematic Facebook users and 23 Non-problematic users were recruited based on their score on the Problematic Facebook Use Scale. The Go/Nogo task included Facebook-related, unpleasant, pleasant, and neutral pictures. The amplitudes of the Nogo-N2 and the Nogo-P3 were computed as measures of the detection of response conflict and response inhibition, respectively. Reaction times and accuracy were also measured.
DOI: 10.17026/dans-xzh-ydsu
title: Thorax-Pelvis Coordination During Gait

description: Gait kinematics and kinetics of fifteen healthy subjects and fifteen subjects with chronic low back pain.Supplementary data of the journal article (Open Access):"Axial Thorax-Pelvis Coordination During Gait is not Predictive of Apparent Trunk Stiffness"In Nature Scientific ReportsDOI:10.1038/s41598-018-37549-9By Maarten R. Prins, Sjoerd M. Bruijn, Onno G. Meijer, Peter van der Wurff and Jaap H. van DieënThe methods of data collection are described in the journal article.The .mat file ("ExperimentalData") and .csv file contain identical information.Dataset consists of [Units] (Variable Names):- Subject characteristicsWeight [kg] (Weight)Height [m] (Height)Thorax inertia around longitudinal axis [kgm2] (InertiaThorax)- Kinematics in 100 [samples/s]3D Thorax angular velocity in [rad/sec] (KinematicsThoraxOmega)3D Pelvis angular velocity [rad/sec] (KinematicsPelvisOmega)3D Trunk angle [rad] (KinematicsTrunkPhi)3D Left and right arm center of mass trajectory [m](KinematicsRArmCOMX)- Kinetics in 100 [samples/s]1D Arm swing moment around longitudinal axis trunk through L5S1 [Nm](KineticsRArmIAlphaL5S1X)3D Net trunk torque [Nm] (KineticsTrunkTorqueX)