Netherlands eScience Center

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

LOFAR, the LOw-Frequency ARray, is a new-generation radio interferometer constructed in the north of the Netherlands and across europe. Utilizing a novel phased-array design, LOFAR covers the largely unexplored low-frequency range from 10–240 MHz and provides a number of unique observing capabilities. Spreading out from a core located near the village of Exloo in the northeast of the Netherlands, a total of 40 LOFAR stations are nearing completion. A further five stations have been deployed throughout Germany, and one station has been built in each of France, Sweden, and the UK. Digital beam-forming techniques make the LOFAR system agile and allow for rapid repointing of the telescope as well as the potential for multiple simultaneous observations. With its dense core array and long interferometric baselines, LOFAR achieves unparalleled sensitivity and angular resolution in the low-frequency radio regime. The LOFAR facilities are jointly operated by the International LOFAR Telescope (ILT) foundation, as an observatory open to the global astronomical community. LOFAR is one of the first radio observatories to feature automated processing pipelines to deliver fully calibrated science products to its user community. LOFAR’s new capabilities, techniques and modus operandi make it an important pathfinder for the Square Kilometre Array (SKA). We give an overview of the LOFAR instrument, its major hardware and software components, and the core science objectives that have driven its design. In addition, we present a selection of new results from the commissioning phase of this new radio observatory.

Abstract. Robust projections and predictions of climate variability and change, particularly at regional scales, rely on the driving processes being represented with fidelity in model simulations. The role of enhanced horizontal resolution in improved process representation in all components of the climate system is of growing interest, particularly as some recent simulations suggest both the possibility of significant changes in large-scale aspects of circulation as well as improvements in small-scale processes and extremes. However, such high-resolution global simulations at climate timescales, with resolutions of at least 50 km in the atmosphere and 0.25° in the ocean, have been performed at relatively few research centres and generally without overall coordination, primarily due to their computational cost. Assessing the robustness of the response of simulated climate to model resolution requires a large multi-model ensemble using a coordinated set of experiments. The Coupled Model Intercomparison Project 6 (CMIP6) is the ideal framework within which to conduct such a study, due to the strong link to models being developed for the CMIP DECK experiments and other model intercomparison projects (MIPs). Increases in high-performance computing (HPC) resources, as well as the revised experimental design for CMIP6, now enable a detailed investigation of the impact of increased resolution up to synoptic weather scales on the simulated mean climate and its variability. The High Resolution Model Intercomparison Project (HighResMIP) presented in this paper applies, for the first time, a multi-model approach to the systematic investigation of the impact of horizontal resolution. A coordinated set of experiments has been designed to assess both a standard and an enhanced horizontal-resolution simulation in the atmosphere and ocean. The set of HighResMIP experiments is divided into three tiers consisting of atmosphere-only and coupled runs and spanning the period 1950–2050, with the possibility of extending to 2100, together with some additional targeted experiments. This paper describes the experimental set-up of HighResMIP, the analysis plan, the connection with the other CMIP6 endorsed MIPs, as well as the DECK and CMIP6 historical simulations. HighResMIP thereby focuses on one of the CMIP6 broad questions, “what are the origins and consequences of systematic model biases?”, but we also discuss how it addresses the World Climate Research Program (WCRP) grand challenges.

Recent technological advances have transformed the research on physical activity initially based on questionnaire data to the most recent objective data from accelerometers. The shift to availability of raw accelerations has increased measurement accuracy, transparency, and the potential for data harmonization. However, it has also shifted the need for considerable processing expertise to the researcher. Many users do not have this expertise. The R package GGIR has been made available to all as a tool to convermulti-day high resolution raw accelerometer data from wearable movement sensors into meaningful evidence-based outcomes and insightful reports for the study of human daily physical activity and sleep. This paper aims to provide a one-stop overview of GGIR package, the papers underpinning the theory of GGIR, and how research contributes to the continued growth of the GGIR package. The package includes a range of literature-supported methods to clean the data and provide day-by-day, as well as full recording, weekly, weekend, and weekday estimates of physical activity and sleep parameters. In addition, the package also comes with a shell function that enables the user to process a set of input files and produce csv summary reports with a single function call, ideal for users less proficient in R. GGIR has been used in over 90 peer-reviewed scientific publications to date. The evolution of GGIR over time and widespread use across a range of research areas highlights the importance of open source software development for the research community and advancing methods in physical behavior research.

Wrist-worn accelerometers are increasingly being used for the assessment of physical activity in population studies, but little is known about their value for sleep assessment. We developed a novel method of assessing sleep duration using data from 4,094 Whitehall II Study (United Kingdom, 2012-2013) participants aged 60-83 who wore the accelerometer for 9 consecutive days, filled in a sleep log and reported sleep duration via questionnaire. Our sleep detection algorithm defined (nocturnal) sleep as a period of sustained inactivity, itself detected as the absence of change in arm angle greater than 5 degrees for 5 minutes or more, during a period recorded as sleep by the participant in their sleep log. The resulting estimate of sleep duration had a moderate (but similar to previous findings) agreement with questionnaire based measures for time in bed, defined as the difference between sleep onset and waking time (kappa = 0.32, 95%CI:0.29,0.34) and total sleep duration (kappa = 0.39, 0.36,0.42). This estimate was lower for time in bed for women, depressed participants, those reporting more insomnia symptoms, and on weekend days. No such group differences were found for total sleep duration. Our algorithm was validated against data from a polysomnography study on 28 persons which found a longer time window and lower angle threshold to have better sensitivity to wakefulness, while the reverse was true for sensitivity to sleep. The novelty of our method is the use of a generic algorithm that will allow comparison between studies rather than a "count" based, device specific method.

Being a morning person is a behavioural indicator of a person's underlying circadian rhythm. Using genome-wide data from 697,828 UK Biobank and 23andMe participants we increase the number of genetic loci associated with being a morning person from 24 to 351. Using data from 85,760 individuals with activity-monitor derived measures of sleep timing we find that the chronotype loci associate with sleep timing: the mean sleep timing of the 5% of individuals carrying the most morningness alleles is 25 min earlier than the 5% carrying the fewest. The loci are enriched for genes involved in circadian regulation, cAMP, glutamate and insulin signalling pathways, and those expressed in the retina, hindbrain, hypothalamus, and pituitary. Using Mendelian Randomisation, we show that being a morning person is causally associated with better mental health but does not affect BMI or risk of Type 2 diabetes. This study offers insights into circadian biology and its links to disease in humans.

Abstract. We present PCR-GLOBWB 2, a global hydrology and water resources model. Compared to previous versions of PCR-GLOBWB, this version fully integrates water use. Sector-specific water demand, groundwater and surface water withdrawal, water consumption, and return flows are dynamically calculated at every time step and interact directly with the simulated hydrology. PCR-GLOBWB 2 has been fully rewritten in Python and PCRaster Python and has a modular structure, allowing easier replacement, maintenance, and development of model components. PCR-GLOBWB 2 has been implemented at 5 arcmin resolution, but a version parameterized at 30 arcmin resolution is also available. Both versions are available as open-source codes on https://github.com/UU-Hydro/PCR-GLOBWB_model (Sutanudjaja et al., 2017a). PCR-GLOBWB 2 has its own routines for groundwater dynamics and surface water routing. These relatively simple routines can alternatively be replaced by dynamically coupling PCR-GLOBWB 2 to a global two-layer groundwater model and 1-D–2-D hydrodynamic models. Here, we describe the main components of the model, compare results of the 30 and 5 arcmin versions, and evaluate their model performance using Global Runoff Data Centre discharge data. Results show that model performance of the 5 arcmin version is notably better than that of the 30 arcmin version. Furthermore, we compare simulated time series of total water storage (TWS) of the 5 arcmin model with those observed with GRACE, showing similar negative trends in areas of prevalent groundwater depletion. Also, we find that simulated total water withdrawal matches reasonably well with reported water withdrawal from AQUASTAT, while water withdrawal by source and sector provide mixed results.

Abstract Sleep is an essential state of decreased activity and alertness but molecular factors regulating sleep duration remain unknown. Through genome-wide association analysis in 446,118 adults of European ancestry from the UK Biobank, we identify 78 loci for self-reported habitual sleep duration ( p < 5 × 10 −8 ; 43 loci at p < 6 × 10 −9 ). Replication is observed for PAX8 , VRK2 , and FBXL12/UBL5/PIN1 loci in the CHARGE study ( n = 47,180; p < 6.3 × 10 −4 ), and 55 signals show sign-concordant effects. The 78 loci further associate with accelerometer-derived sleep duration, daytime inactivity, sleep efficiency and number of sleep bouts in secondary analysis ( n = 85,499). Loci are enriched for pathways including striatum and subpallium development, mechanosensory response, dopamine binding, synaptic neurotransmission and plasticity, among others. Genetic correlation indicates shared links with anthropometric, cognitive, metabolic, and psychiatric traits and two-sample Mendelian randomization highlights a bidirectional causal link with schizophrenia. This work provides insights into the genetic basis for inter-individual variation in sleep duration implicating multiple biological pathways.

Wrist worn raw-data accelerometers are used increasingly in large-scale population research. We examined whether sleep parameters can be estimated from these data in the absence of sleep diaries. Our heuristic algorithm uses the variance in estimated z-axis angle and makes basic assumptions about sleep interruptions. Detected sleep period time window (SPT-window) was compared against sleep diary in 3752 participants (range = 60-82 years) and polysomnography in sleep clinic patients (N = 28) and in healthy good sleepers (N = 22). The SPT-window derived from the algorithm was 10.9 and 2.9 minutes longer compared with sleep diary in men and women, respectively. Mean C-statistic to detect the SPT-window compared to polysomnography was 0.86 and 0.83 in clinic-based and healthy sleepers, respectively. We demonstrated the accuracy of our algorithm to detect the SPT-window. The value of this algorithm lies in studies such as UK Biobank where a sleep diary was not used.

The FAIR Data Principles propose that all scholarly output should be Findable, Accessible, Interoperable, and Reusable. As a set of guiding principles, expressing only the kinds of behaviours that researchers should expect from contemporary data resources, how the FAIR principles should manifest in reality was largely open to interpretation. As support for the Principles has spread, so has the breadth of these interpretations. In observing this creeping spread of interpretation, several of the original authors felt it was now appropriate to revisit the Principles, to clarify both what FAIRness is, and is not.

Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value. The FAIR for Research Software (FAIR4RS) Working Group has adapted the FAIR Guiding Principles to create the FAIR Principles for Research Software (FAIR4RS Principles). The contents and context of the FAIR4RS Principles are summarised here to provide the basis for discussion of their adoption. Examples of implementation by organisations are provided to share information on how to maximise the value of research outputs, and to encourage others to amplify the importance and impact of this work.

The aim was to develop sedentary (sitting/lying) thresholds from hip and wrist worn raw tri-axial acceleration data from the ActiGraph and GENEActiv, and to examine the agreement between free-living time spent below these thresholds with sedentary time estimated by the activPAL. Sixty children and adults wore an ActiGraph and GENEActiv on the hip and wrist while performing six structured activities, before wearing the monitors, in addition to an activPAL, for 24 h. Receiver operating characteristic (ROC) curves were used to determine sedentary thresholds based on activities in the laboratory. Agreement between developed sedentary thresholds during free-living and activPAL were assessed by Bland-Altman plots and by calculating sensitivity and specificity. Using laboratory data and ROC-curves showed similar classification accuracy for wrist and hip thresholds (Area under the curve = 0.84-0.92). Greatest sensitivity (97-98%) and specificity (74-78%) were observed for the wrist thresholds, with no large differences between brands. During free-living, Bland-Altman plots showed large mean individual biases and 95% limits of agreement compared with activPAL, with smallest difference for the ActiGraph wrist threshold in children (+30 min, P = 0.3). Sensitivity and specificity for the developed thresholds during free-living were low for both age groups and for wrist (Sensitivity, 68-88%, Specificity, 46-59%) and hip placements (Sensitivity, 89-97%, Specificity, 26-34%). Laboratory derived sedentary thresholds generally overestimate free-living sedentary time compared with activPAL. Wrist thresholds appear to perform better than hip thresholds for estimating free-living sedentary time in children and adults relative to activPAL, however, specificity for all the developed thresholds are low.

In the debate about filter bubbles caused by algorithmic news recommendation, the conceptualization of the two core concepts in this debate, diversity and algorithms, has received little attention in social scientific research. This paper examines the effect of multiple recommender systems on different diversity dimensions. To this end, it maps different values that diversity can serve, and a respective set of criteria that characterizes a diverse information offer in this particular conception of diversity. We make use of a data set of simulated article recommendations based on actual content of one of the major Dutch broadsheet newspapers and its users (N=21,973 articles, N=500 users). We find that all of the recommendation logics under study proved to lead to a rather diverse set of recommendations that are on par with human editors and that basing recommendations on user histories can substantially increase topic diversity within a recommendation set.

The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility, interoperability and reusability of digital research objects for both humans and machines. Until now the FAIR principles have been mostly applied to research data. The ideas behind these principles are, however, also directly relevant to research software. Hence there is a distinct need to explore how the FAIR principles can be applied to software. In this work, we aim to summarize the current status of the debate around FAIR and software, as basis for the development of community-agreed principles for FAIR research software in the future. We discuss what makes software different from data with regard to the application of the FAIR principles, and which desired characteristics of research software go beyond FAIR. Then we present an analysis of where the existing principles can directly be applied to software, where they need to be adapted or reinterpreted, and where the definition of additional principles is required. Here interoperability has proven to be the most challenging principle, calling for particular attention in future discussions. Finally, we outline next steps on the way towards definite FAIR principles for research software.

Abstract Sleep is an essential human function but its regulation is poorly understood. Using accelerometer data from 85,670 UK Biobank participants, we perform a genome-wide association study of 8 derived sleep traits representing sleep quality, quantity and timing, and validate our findings in 5,819 individuals. We identify 47 genetic associations at P < 5 × 10 −8 , of which 20 reach a stricter threshold of P < 8 × 10 −10 . These include 26 novel associations with measures of sleep quality and 10 with nocturnal sleep duration. The majority of identified variants associate with a single sleep trait, except for variants previously associated with restless legs syndrome. For sleep duration we identify a missense variant (p.Tyr727Cys) in PDE11A as the likely causal variant. As a group, sleep quality loci are enriched for serotonin processing genes. Although accelerometer-derived measures of sleep are imperfect and may be affected by restless legs syndrome, these findings provide new biological insights into sleep compared to previous efforts based on self-report sleep measures.

Addendum to: Scientific Data https://doi.org/10.1038/sdata.2016.18, published online 15 March 2016
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\nSince publication, the URL at which the FAIR principles ‘living document’ is hosted and maintained has changed from http://datafairport.org/fair-principles-living-document-menu to https://www.go-fair.org/fair-principles/.

Excessive daytime sleepiness (EDS) affects 10-20% of the population and is associated with substantial functional deficits. Here, we identify 42 loci for self-reported daytime sleepiness in GWAS of 452,071 individuals from the UK Biobank, with enrichment for genes expressed in brain tissues and in neuronal transmission pathways. We confirm the aggregate effect of a genetic risk score of 42 SNPs on daytime sleepiness in independent Scandinavian cohorts and on other sleep disorders (restless legs syndrome, insomnia) and sleep traits (duration, chronotype, accelerometer-derived sleep efficiency and daytime naps or inactivity). However, individual daytime sleepiness signals vary in their associations with objective short vs long sleep, and with markers of sleep continuity. The 42 sleepiness variants primarily cluster into two predominant composite biological subtypes - sleep propensity and sleep fragmentation. Shared genetic links are also seen with obesity, coronary heart disease, psychiatric diseases, cognitive traits and reproductive ageing.

Mind wandering is an ubiquitous phenomenon in everyday life. In the cognitive neurosciences, mind wandering has been associated with several distinct neural processes, most notably increased activity in the default mode network (DMN), suppressed activity within the anti-correlated (task-positive) network (ACN), and changes in neuromodulation. By using an integrative multimodal approach combining machine-learning techniques with modeling of latent cognitive processes, we show that mind wandering in humans is characterized by inefficiencies in executive control (task-monitoring) processes. This failure is predicted by a single-trial signature of (co)activations in the DMN, ACN, and neuromodulation, and accompanied by a decreased rate of evidence accumulation and response thresholds in the cognitive model.

ABSTRACT In Galaxy And Mass Assembly Data Release 4 (GAMA DR4), we make available our full spectroscopic redshift sample. This includes 248 682 galaxy spectra, and, in combination with earlier surveys, results in 330 542 redshifts across five sky regions covering ∼250 deg2. The redshift density, is the highest available over such a sustained area, has exceptionally high completeness (95 per cent to rKiDS = 19.65 mag), and is well-suited for the study of galaxy mergers, galaxy groups, and the low redshift (z < 0.25) galaxy population. DR4 includes 32 value-added tables or Data Management Units (DMUs) that provide a number of measured and derived data products including GALEX, ESO KiDS, ESO VIKING, WISE, and HerschelSpace Observatory imaging. Within this release, we provide visual morphologies for 15 330 galaxies to z < 0.08, photometric redshift estimates for all 18 million objects to rKiDS ∼ 25 mag, and stellar velocity dispersions for 111 830 galaxies. We conclude by deriving the total galaxy stellar mass function (GSMF) and its sub-division by morphological class (elliptical, compact-bulge and disc, diffuse-bulge and disc, and disc only). This extends our previous measurement of the total GSMF down to 106.75 M$_{\odot } \, h_{70}^{-2}$ and we find a total stellar mass density of ρ* = (2.97 ± 0.04) × 108 M$_{\odot } \, h_{70}$ Mpc−3 or $\Omega _*=(2.17 \pm 0.03) \times 10^{-3} \, h_{70}^{-1}$. We conclude that at z < 0.1, the Universe has converted 4.9 ± 0.1 per cent of the baryonic mass implied by big bang Nucleosynthesis into stars that are gravitationally bound within the galaxy population.

Functional magnetic resonance imaging (MRI) data are usually registered into standard anatomical space. However, standard atlases, such as LPBA40, the Harvard-Oxford atlas, FreeSurfer, and the Jülich cytoarchitectonic maps all lack important detailed information about small subcortical structures like the substantia nigra and subthalamic nucleus. Here we introduce a new subcortical probabilistic atlas based on ultra-high resolution in-vivo anatomical imaging from 7 T MRI. The atlas includes six important but elusive subcortical nuclei: the striatum, the globus pallidus internal and external segment (GPi/e), the subthalamic nucleus, the substantia nigra, and the red nucleus. With a sample of 30 young subjects and carefully cross-validated delineation protocols, our atlas is able to capture the anatomical variability within healthy populations for each of the included structures at an unprecedented level of detail. All the generated probabilistic atlases are registered to MNI standard space and are publicly available.