cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17026/dans-x4d-b642
title: Photographs of HMEC-1 spheroids. Part of article "Computational Screening of Tip and Stalk Cell Behavior Proposes a Role for Apelin Signaling in Sprout Progression”

description: This data set contains microscopic photographs of in vitro cultures of Human Microvascular Endothelial Cells (HMEC-1) spheroids used to test role of Apelin and its receptor in angiogenic sprouting. It is used to test a hypothesis developed using computational modeling of angiogenesis. Images in TIFF format, as used for the image analysis. The archive also includes the output files of the NeuronJ plugin to ImageJ (file extension .NDF) as well as XML-files containing microscopy settings.The dataset set is part of the publication Computational Screening of Tip and Stalk Cell Behavior Proposes a Role for Apelin Signaling in Sprout Progression”.
DOI: 10.17026/dans-z65-7j7h
title: Enhancing the role of the social network in activity (re)engagement post‑stroke: a focus group study with rehabilitation professionals

description: Two focus groups were executed. Content analysis was used to analyze the transcripts of the recordedconversations.
DOI: 10.17026/dans-zhe-rrv2
title: Pelvic Floor rehabilitation to improve functional Outcome and quality of life after surgery for Rectal CancEr: a randomized controlled trial. FORCE-trial

description: The datasets contain all raw data and corresponding sum scores used for analyses in the research described in the Trials-paper by van der Heijden and Colleagues.After sphincter-preserving rectal cancer surgery, many patients suffer from changes in their stool. This may have a negative influence on Quality of Life. The aim of this trial was to gain insight in the effectiveness of pelvic floor rehabilitation after sphincter-preserving rectal cancer surgery (in comparison with usual care without PFR). A total of 128 patients were included and investigated. No significant improvement in fecal incontinence scores was found after pelvic floor rehabilitation. We however found several groups of patients that did benefit from this treatment. They experienced improved continence and an improvement of quality of life. We suggest that this treatment should not be provided to all patients after surgery, but to a selection of patients.A full description of the program as well as all measures is giving in the Methodology section of the Trial article. Data are collected in a prospective manner via questionnaires.
DOI: 10.17026/dans-29s-gupc
title: Dairy farming and marketing in relation to market quality: household data

description: Household data for 170 smallholder dairy farms
DOI: 10.17026/dans-xvw-asku
title: Data from: Same strategies – different categories: An explorative card-sort study of plant-based proteins comparing omnivores, flexitarians, vegetarians and vegans – Study 2

description: To accelerate the protein transition it is important to understand how different consumer groups perceive and categorise plant-based proteins in comparison to animal-derived proteins.Using a quantitative (card-sort task) technique, we examined how omnivores, flexitarians, vegetarians and vegans categorise plant-based proteins.81 Dutch participants free-sorted 80 product cards. Demographics and other background variables are administered via a survey.
DOI: 10.17026/dans-xx2-s4c6
title: Data from: Mimicry of emergent traits amplifies coastal restoration success

description: Data from: Mimicry of emergent traits amplifies coastal restoration success.Nature CommunicationsIn this study, we experimentally tested how mimicking key emergent traits that locally suppress physical stress using biodegradable establishment structures can increase restoration success. Experiments across (sub)tropical and temperate seagrass and salt marsh systems demonstrate greatly enhanced yields when individuals are transplanted within structures mimicking emergent traits that suppress waves or sediment mobility. Specifically, belowground mimics of dense root mats most facilitated seagrasses via sediment stabilization, while mimics of aboveground plant structures most facilitated marsh grasses by reducing stem movement.This dataset contains data of plant performance of the experimental plots, sediment movement data of seagrass plots, and stem movement data of the flume experiment.
DOI: 10.17026/dans-xc8-3a2q
title: Kenya public weather processed by the Global Yield Gap Atlas project

description: A revised version of this dataset has been published: https://doi.org/10.17026/dans-zyu-xkhc. The files of this dataset are therefore no longer accessible.This dataset contains the underlying data for the study: Kenya public weather processed by the Global Yield Gap Atlas project. Open Journal for Agricultural Research : ODjAR.The Global Yield Gap Atlas project (GYGA - http://yieldgap.org ) has undertaken a yield gap assessment following the protocol recommended by van Ittersum et. al. (van Ittersum et. al., 2013). One part of the activities consists of collecting and processing weather data as an input for crop simulation models in sub-Saharan African countries including Kenya. This publication covers weather data for 10 locations in Kenya. The project looked for good quality weather data in areas where crops are pre-dominantly grown. As locations with good public weather data are sparse in Africa, the project developed a method to generate weather data from a combination of observed and other external weather data. One locations holds actually measured weather data, the other 9 locations show propagated weather data. The propagated weather data consist on TRMM rain data (or NASA POWER if TRMM is not available) and NASA POWER Tmax, Tmin, and Tdew data corrected based on calibrations with short-term (&lt;10 years) observed weather data. sources (Van Wart et.al. 2015).
DOI: 10.17026/dans-276-sda6
title: Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

description: This dataset contains supplemental tables and tracks for the study entitled: "Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation".FilesPMDs_CGIsThe included files contain:- Genome positions of detected PMDs with their mean methylation (weighted mean, see Methods)- Genome positions of CpG islands with their mean methylation (weighted mean)- The "Brinkman" directory contains files from breast cancer data produced in this study- The "normals" directory contains files from normal tissues (external data) analyzed in this study- The "tumors" directory contains files from tumors (external data) analyzed in this studyAll genome positions are based on GRCh37/hg19All files are TAB-delimited text files (.tsv)DNAme_bigwigsThe included files are BIGWIG files for viewing the DNA methylation profiles in a genome browser such as UCSC (http://genome.ucsc.edu). Each file represents a whole-Genome Bisulfite Sequencing (WGBS) DNA methylation profile from one tumor used in this study. The used genome build was GRCh37/hg19. For every CpG with a coverage of at least 4 reads, the DNA methylation value (range: 0-1) is included.MethodsDetection of PMDsDetection of partially methylated domains (PMDs) in all whole-genome bisulfite sequencing (WGBS) methylation profiles throughout this study was done using the MethylSeekR package for R (1). Before PMD calling, CpGs overlapping common SNPs (dbSNP build 137) were removed. The alpha distribution (1) was used to determine whether PMDs were present at all, along with visual inspection of WGBS profiles. After PMD calling, the resulting PMDs were further filtered by removing regions overlapping with centromers (undetermined sequence content).Mean methylation inside CpG islandsMean methylation values from WGBS inside CGIs were calculated using the ‘weighted methylation level’ (2).Mean methylation inside PMDsMean methylation values from WGBS inside PMDs were calculated using the ‘weighted methylation level’ (2). Calculation of mean methylation within PMDs involved removing all CpGs overlapping with CpG island(-shores) and promoters, as the high CpG densities within these elements yield unbalanced mean methylation values, not representative of PMD methylation.References(1) Burger, L., Gaidatzis, D., Schübeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Research 41, (2013).(2) Schultz, M. D., Schmitz, R. J. & Ecker, J. R. ’Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends in Genetics 28, 583–585 (2012).
DOI: 10.17026/dans-xaj-ysx8
title: Geomorphological development of aquatic mesohabitats in shore channels along longitudinal training dams

description: Dataset for the article 'Geomorphological development of aquatic mesohabitats in shore channels along longitudinal training dams' published in Remote Sensing in Ecology and Conservation.AbstractLongitudinal training dams (LTDs) are novel hydraulic engineering structures in the river Waal intended to facilitate intensive navigation and safe discharges in the main channel while providing sheltered habitats for aquatic biota in shore channels. Monitoring data collected using light detection and ranging (LiDAR), multibeam echosounder (MBES) and aerial photography for the years during and after to construction of the LTDs were analyzed in order to determine patterns of erosion and deposition, the retreat rate of steep eroding banks and shoreline length change through time. The LTD shore channels and two traditional groyne fields (references) were divided into nine mesohabitats based on physical attributes. Net erosion was estimated for eight out of the nine mesohabitats for the 2015-2020 period. Generally, there is a pattern of riverbed aggradation towards the LTDs and degradation or bank erosion towards the littoral zones of the LTD shore channels. This kind of continuous behavior could be indicative of current or eminent channel and thus habitat stability. The bankline erosion in shore channels had mean retreat rates of 1.4-1.6 m/yr. The shorelines were longer in sand-dominated mesohabitats, which could be key for habitat heterogeneity. The LTD shore channels offered more complex relatively natural continuous littoral zones than the traditional groyne fields while maintaining the multifunctionality of the river. Thus, the development of sandy shorelines in the LTD shore channels should be encouraged through management in order to enhance biodiversity. Geomorphological monitoring of the shore channels should continue in the future in order to detect any long-term changes in the sedimentary processes and ecological functions.For detailed methods see the Readme.txt file.
DOI: 10.17026/dans-zss-9ams
title: Cannabinoid antagonist SLV326 induces convulsive seizures and changes in the interictal EEG in rats

description: Cannabinoid CB1 antagonists have been investigated for possible treatment of e.g. obesity-related disorders. However, clinical application was halted due to their symptoms of anxiety and depression. In addition to these adverse effects, we have shown earlier that chronic treatment with the CB1 antagonist rimonabant may induce EEG-confirmed convulsive seizures.In a regulatory repeat-dose toxicity study “muscle spasms” were observed in Wistar rats, daily dosed with the CB1 receptor antagonist SLV326 during 5 months. The aim of the present follow-up study was to investigate whether these spasms were of an epileptic origin.In selected SLV326-treated and control animals, EEG and behavior were monitored for 24 hours. 25% of SLV326 treated animals showed 1 to 21 EEG-confirmed generalized convulsive seizures, whereas controls were seizure-free. The behavioral seizures were typical for a limbic origin. Moreover, interictal spikes were found in 38% of treated animals. The frequency spectrum of the interictal EEG of the treated rats showed a lower theta peak frequency, as well as lower gamma power compared to the controls. These frequency changes were state-dependent: they were only found during high locomotor activity.It is concluded that long term blockade of the endogenous cannabinoid system can provoke limbic seizures in otherwise healthy rats. Additionally, SLV326 alters the frequency spectrum of the EEG when rats are highly active, suggesting effects on complex behavior and cognition.
DOI: 10.17026/dans-zy2-mkzc
title: Starting files for MD simulations in water and ions of haloalkane dehalogenase LinB and its mutants from Sphingomonas paucimobilis with substrates

description: The project aims to find key residues for haloalkane dehalogenase LinB from Sphingomonas paucimobilis (PDB id: 1mj5) that contribute to the binding of enzymes substrates on this enzymes surface. The dataset contains starting files for MD simulations in water and ions of haloalkane dehalogenase LinB and its mutants from Sphingomonas paucimobilis with substrates. It also contains scripts for running MD simulations (AMBER18).
DOI: 10.17026/dans-xhr-n8b9
title: A Phase I-II study of virus neutralizing antibodies against SARS-CoV-2. A focus on convalescent plasma and hyperimmune anti-SARS-CoV-2 immunoglobulines

description: In the ConvP/COVIg PK/PD study, we treated volunteers who were unable to produce antibodies against the coronavirus with convalescent plasma or hyperimmune globulins (COVig). Previously, no studies had been performed to investigate the amount of convalescent plasma or COVig needs to be administered to ensure that the transfused volunteer reaches a sufficient level of antibodies in his/her blood in the weeks or months after the administration of plasma or COVig.At several timepoints after the administration of the plasma or COVig, blood was taken and the level of antibodies against the coronavirus was measured. Based on these measurements, we built a model that can predict the concentration of antibodies in blood after administration of plasma or COVig in function of the antibody level in the transfused product.The study showed that plasma that had been collected during the first year of the pandemic from donors recently cured from COVID19 did not contain enough antibodies to provide long-term protection for people without antibodies. The model can however serve as a tool for the design of future studies into the preventive or therapeutic use of these agents.
DOI: 10.17026/dans-xxb-56zp
title: Data: Longitudinal study on the tonsillar microbiota of piglets

description: Little is known about the development of the tonsillar microbiota and the factors determining the establishment and proliferation of disease-associated bacteria. In this study we sampled the tonsillar microbiota of 63 piglets from 21 different litters after birth and at week 1, 3, and 5 of life. The piglets were free from disease and antimicrobial treatment throughout the study period. 16S rRNA gene V3-V4 region Illumina NovaSeq sequencing produced a minimum of 42537 reads per sample after processing with DADA2. The dataset includes 252 piglet microbiota samples and 12 samples collected from unrelated sows at the same farm. Analysis revealed that a diverse tonsillar microbiota is established shortly after birth, and that gradual change takes place during the first 5 weeks of life without weaning having a large impact. We found a strong litter effect, with siblings sharing a more similar microbiota compared to non-sibling piglets. Co-housing in rooms, within which litters were housed in separate pens, also had a large impact on microbiota composition. Sow parity and pre-partum Streptococcus suis bacterin vaccination had weaker but significant associations with microbiota composition, with piglets of vaccinated sows having a lower S. suis abundance 1 week after birth.This dataset consists of 16S rRNA gene V3-V4 amplicon sequencing of tonsillar swabs of piglets. The piglets were sampled shortly after birth, at week 1, week 3, and (after being weaned at week 4), week 5. No antimicrobial treatment was applied, and all piglets were healthy; piglets that died during the experiment were not included for sequencing.
DOI: 10.17026/dans-xux-y5ja
title: Normalised read counts of all mapped genes across all samples of the thesis by Heim 2022

description: This file contains a table with the normalised read counts generated by RNAseq of multiple samples from brain areas HVC or CMM in female zebra finches that received a lentiviral knockdown of FoxP1 either as juveniles or as adults.
DOI: 10.17026/dans-zfj-mxkt
title: Should a patient with a suspected scaphoid fracture be treated with cast? An RCT’

description: The SUSPECT study is an open-labeled multicenter randomized controlled trial with non-inferiority design. A total of 180 adult patients with a clinically suspected scaphoid fracture and normal initial radiographs are randomized between two groups: 3 days supportive bandage or 14 days below-elbow cast. We aim to evaluate the functional outcome and cost-effectiveness of both treatments . The primary outcome is the difference in functional outcome after 3 months between both groups, assessed with the Quick Disability of the Arm, Shoulder and Hand score. Secondary outcomes include post-traumatic injuries, functional outcome, recovery of function, pain, patient satisfaction, quality of life and cost-effectiveness measured by medical consumption, absence from work or decreased productivity and quality of life.
DOI: 10.17026/dans-zyw-efav
title: Chinese Food Life Cycle Assessment Database

description: In the Chinese Food Life Cycle Assessment Database (CFLCAD), Greenhouse Gas Emissions (GHGE) for 80 food items, Water Use (WU) for 93 food items and Land Use (LU) for 50 food items are collected through a literature review. The CFLCAD applies conversion factors for the edible portion of food, food loss ratio and processing, storage, packaging, transportation, and food preparation stages to estimate the environmental footprints of food from production to consumption. Similar food groups and recipes are used to match those food items without LCA value in the Chinese food composition table, resulting in a total of 17 food groups in the database.
DOI: 10.17026/dans-x5w-4np3
title: Three-dimensional Printed Orthoses for Improving Daily Functioning in Chronic Hand Conditions

description: In chronic disabling hand conditions, symptoms like pain, muscle weakness, and joint and/or muscle contractures are common impairments that negatively affect activities of daily life (ADL). Wearing a hand orthosis can improve use of the hand in performing ADL. In the last decade, the application of three-dimensional (3D) printing has been increasingly used to manufacture hand orthoses, being a promising alternative to conventional custom-manufactured hand orthoses. However, evidence on the effectiveness, costs and production time of 3D-printed orthoses in chronic hand conditions is scarce. We assessed the preliminary effectiveness of 3D-printed orthoses compared to conventionally manufactured orthoses in persons with chronic hand conditions on ADL performance (assessed with the PROMIS-UE), orthosis satisfaction (assessed with the D-CSD), and quality of life (assessed with the EQ-5D-5L). Besides, production time and costs of both orthoses were recorded. As part of this study, to measure orthosis satisfaction, we translated the English Client Satisfaction with Device (CSD) module of the Orthotics and Prosthetics Users’ Survey into Dutch (D-CSD), and assessed its content validity, structural validity and reliability in persons with chronic hand conditions. Furthermore, we assessed the reliability of the PROMIS-UE the measure ADL performance in chronic users of hand orthoses.
DOI: 10.17026/dans-2ct-j737
title: Nature portrayed in images in Dutch Brazil - Dataset (S5): Correlations between the plant woodcuts in the HNB and the botanical annotations in De Laet’s manuscript.

description: This table shows the correlation between the plants that presumably originated from a sketch or drawing that came from Brazil in a numbered booklet (marked with the word ‘Icon’ in the recto folios of the manuscript), the plant woodcuts in the HNB, and their corresponding images in other sources from Dutch Brazil (like the Theatrum and Marcgrave's herbarium). The verso folios of the manuscript correspond to plant drawings or proof woodcuts glued to these folios
DOI: 10.17026/dans-zpr-rjm6
title: Development of an Automatic Pollen Classification System

description: This research applied image processing and machine learning techniques to develop an automatic process for the identification of 5 pollen species using images from a digital microscope.
DOI: 10.17026/dans-xqs-kdnn
title: Rapid stem cell spreading induced by high affinity α5β1 integrin-selective bicyclic RGD peptide in biomimetic hydrogels

description: Cell-matrix interactions form a crucial parameter for the design of synthetic ECM as these dictate cell fate and cell functions. Most commonly, synthetic biomaterials are conjugated with a linear or cyclic Arg-Gly-Asp (RGD) peptide. These peptides, however, lack selectivity towards integrin subtypes presented on the cell membrane and present low binding affinities. We conjugated bicyclic peptides with a strong affinity towards specific integrin subtypes to a synthetic fibrous hydrogel (polyisocyanide, PIC) and studied cell behavior in 3D cultures. In gels functionalized with an optimized bicyclic α5β1¬-integrin binder, human adipose-derived stem cells (hASCs) spread within 24 hours, which is much faster than in other PIC gels, including the default RGD-decorated gel, but also much faster than in the positive Matrigel control. YAP/TAZ staining showed that the rapid morphological change in the 3D microenvironments is YAP-independent. Our data highlights that the design of synthetic matrices with appropriate, optimized guiding signals is key to guide cells towards a predetermined outcome.
DOI: 10.17026/dans-zcm-q8fq
title: Decoding sensorimotor rhythms during robotic-assisted treadmill walking for brain computer interface (BCI) applications

description: Locomotor malfunction represents a major problem in some neurological disorders like stroke and spinal cord injury. Robot-assisted walking devices have been used during rehabilitation of patients with these ailments for regaining and improving walking ability.Previous studies showed the advantage of brain-computer interface (BCI) based robot-assisted training combined with physical therapy in the rehabilitation of the upper limb after stroke. Therefore, stroke patients with walking disorders might also benefit from using BCI robot-assisted training protocols. In order to develop such BCI, it is necessary to evaluate the feasibility to decode walking intention from cortical patterns during robot-assisted gait training.Spectral patterns in the electroencephalogram (EEG) related to robot-assisted active and passive walking were investigated in 10 healthy volunteers (mean age 32.3?10.8, six female) and in three acute stroke patients (all male, mean age 46.7?16.9, Berg Balance Scale 20?12.8). A logistic regression classifier was used to distinguish walking from baseline in these spectral EEG patterns. Mean classification accuracies of 94.0?5.4% and 93.1?7.9%, respectively, were reached when active and passive walking were compared against baseline. The classification performance between passive and active walking was 83.4?7.4%. A classification accuracy of 89.9?5.7% was achieved in the stroke patients when comparing walking and baseline. Furthermore, in the healthy volunteers modulation of low gamma activity in central midline areas was found to be associated with the gait cycle phases, but not in the stroke patients.Our results demonstrate the feasibility of BCI-based robotic-assisted training devices for gait rehabilitation.