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Borgdorff J.,Netherlands eScience Center | Krishna H.,Fields of View | Lees M.H.,University of Amsterdam
Procedia Computer Science | Year: 2015

Urban areas are characterised by high population densities and the resulting complex social dynamics. For urban planners to evaluate, analyse, and predict complex urban dynamics, a lot of scenarios and a large parameter space must be explored. In urban disasters, complex situations must be assessed in short notice. We propose the concept of an assisted decision support system to aid in these situations The system interactively runs a scenario exploration, which evaluates scenarios and optimize for desired properties. We introduce the SIM-CITY architecture to run such interactive scenario explorations and highlight a use case for the architecture, an urban fire emergency response simulation in Bangalore. © The Authors. Published by Elsevier B.V.

PubMed | Phortos Consultants, Stanford University, Cray, TU Eindhoven and 30 more.
Type: | Journal: Scientific data | Year: 2016

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.

Pelupessy F.I.,Leiden University | Van Elteren A.,Leiden University | De Vries N.,Leiden University | McMillan S.L.W.,Drexel University | And 2 more authors.
Astronomy and Astrophysics | Year: 2013

We present the open source Astrophysical Multi-purpose Software Environment (AMUSE), a component library for performing astrophysical simulations involving different physical domains and scales. It couples existing codes within a Python framework based on a communication layer using MPI. The interfaces are standardized for each domain and their implementation based on MPI guarantees that the whole framework is well-suited for distributed computation. It includes facilities for unit handling and data storage. Currently it includes codes for gravitational dynamics, stellar evolution, hydrodynamics and radiative transfer. Within each domain the interfaces to the codes are as similar as possible. We describe the design and implementation of AMUSE, as well as the main components and community codes currently supported and we discuss the code interactions facilitated by the framework. Additionally, we demonstrate how AMUSE can be used to resolve complex astrophysical problems by presenting example applications. © ESO, 2013.

Haren R.,Royal Netherlands Meteorological Institute | Haren R.,Netherlands eScience Center | Haarsma R.J.,Netherlands eScience Center | Oldenborgh G.J.,Netherlands eScience Center | And 3 more authors.
Journal of Climate | Year: 2015

In this study, the authors investigate the effect of GCM spatial resolution on modeled precipitation over Europe. The objectives of the analysis are to determine whether climate models have sufficient spatial resolution to have an accurate representation of the storm tracks that affect precipitation. They investigate if there is a significant statistical difference in modeled precipitation between a medium-resolution (~ 112-km horizontal resolution) and a high-resolution (~ 25-km horizontal resolution) version of a state-of-the-art AGCM (EC-EARTH), if either model resolution gives a better representation of precipitation in the current climate, and what processes are responsible for the differences inmodeled precipitation. The authors find that the highresolution model gives a more accurate representation of northern and central European winter precipitation. The medium-resolution model has a larger positive bias in precipitation inmost of the northern half of Europe. Storm tracks are better simulated in the high-resolution model, providing for a more accurate horizontal moisture transport and moisture convergence. Using a decomposition of the precipitation difference between the medium- and high-resolution model in a part related and a part unrelated to a difference in the distribution of vertical atmospheric velocity, the authors find that the smaller precipitation bias in central and northern Europe is largely unrelated to a difference in vertical velocity distribution. The smaller precipitation amount in these areas is in agreementwith lessmoisture transport over this area in the high-resolution model. In areas with orography the change in vertical velocity distribution is found to be more important. © 2015 American Meteorological Society.

Fleuren W.W.M.,Computational Discovery and oDesign Group CMBI | Fleuren W.W.M.,Netherlands eScience Center | Alkema W.,Computational Discovery and oDesign Group CMBI | Alkema W.,NIZO Food Research BV
Methods | Year: 2015

In recent years the amount of experimental data that is produced in biomedical research and the number of papers that are being published in this field have grown rapidly. In order to keep up to date with developments in their field of interest and to interpret the outcome of experiments in light of all available literature, researchers turn more and more to the use of automated literature mining. As a consequence, text mining tools have evolved considerably in number and quality and nowadays can be used to address a variety of research questions ranging from de novo drug target discovery to enhanced biological interpretation of the results from high throughput experiments. In this paper we introduce the most important techniques that are used for a text mining and give an overview of the text mining tools that are currently being used and the type of problems they are typically applied for. © 2015 Elsevier Inc.

Sang E.T.K.,Netherlands eScience Center | Van Den Bosch A.,Radboud University Nijmegen
Computational Linguistics in the Netherlands Journal | Year: 2013

As data sets keep growing, computational linguists are experiencing more big data problems: challenging demands on storage and processing caused by very large data sets. An example of this is dealing with social media data: including metadata, the messages of the social media site Twitter in 2012 comprise more than 250 terabytes of structured text. Handling data volumes like this requires parallel computing architectures with appropriate software tools. In this paper we present our experiences in working with such a big data set, a collection of two billion Dutch tweets. We show how we collected and stored the data. Next we deal with searching in the data using the Hadoop framework and visualizing search results. In order to determine the usefulness of this tweet analysis resource, we have performed three case studies based on the data: relating word frequency to real-life events, finding words related to a topic, and gathering information about conversations. The three case studies are presented in this paper. Access to this current and expanding tweet data set is offered via the website © 2013 Erik Tjong Kim Sang and Antal van den Bosch.

Shamoun-Baranes J.,University of Amsterdam | Bouten W.,University of Amsterdam | Van Loon E.E.,University of Amsterdam | Meijer C.,Netherlands eScience Center | Camphuysen C.J.,University Utrecht
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

The aerial environment is heterogeneous in space and time and directly influences the costs of animal flight. Volant animals can reduce these costs by using different flight modes, each with their own benefits and constraints. However, the extent to which animals alter their flight modes in response to environmental conditions has rarely been studied in the wild. To provide insight into how a flight generalist can reduce the energetic cost of movement, we studied flight behaviour in relation to the aerial environmental and landscape using hundreds of hours of global positioning system and triaxial acceleration measurements of the lesser black-backed gull (Larus fuscus). Individuals differed largely in the time spent in flight, which increased linearly with the time spent in flight at sea. In general, flapping was used more frequently than more energetically efficient soaring flight. The probability of soaring increased with increasing boundary layer height and time closer to midday, reflecting improved convective conditions supportive of thermal soaring. Other forms of soaring flight were also used, including fine-scale use of orographic lift. We explore the energetic consequences of behavioural adaptations to the aerial environment and underlying landscape and implications for individual energy budgets, foraging ecology and reproductive success. © 2016 The Author(s) Published by the Royal Society. All rights reserved.

PubMed | University of Glasgow, Netherlands eScience Center and Laboratory of Biochemistry
Type: Journal Article | Journal: Mass spectrometry (Tokyo, Japan) | Year: 2016

The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed.

PubMed | Netherlands eScience Center and Norwegian School of Sport Sciences
Type: | Journal: Scandinavian journal of medicine & science in sports | Year: 2016

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 24h. 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 (Areaunder the curve=0.84-0.92). Greatest sensitivity (97-98%) and specificity (74-78%) were observed for thewrist 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 (+30min, P=0.3). Sensitivity and specificity for the developed thresholdsduring 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 comparedwith 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.

PubMed | Netherlands eScience Center, Freeman Hospital and Northumbria University
Type: Journal Article | Journal: BMC cardiovascular disorders | Year: 2016

Given the ongoing burden of cardiovascular disease and an ageing population, physical activity in patients with coronary artery disease needs to be emphasized. This study assessed whether sedentary behaviour and physical activity levels differed among older patients (75years) following percutaneous coronary intervention (PCI) for acute coronary syndrome (ACS) consisting of ST-segment elevation myocardial infarction (STEMI) and non STEMI (NSTEMI) versus an elective admission control group of stable angina patients.Sedentary behaviour and physical activity were assessed over a 7-day period using wrist-worn triaxial accelerometers (GENEActiv, Activinsights Ltd, UK) in 58 patients following PCI for, STEMI (n=20) NSTEMI (n=18) and stable angina (n=20) upon discharge from a tertiary centre. MeanStandard deviation age was 794years (31% female).STEMI and NSTEMI patients spent more time in the low acceleration category (0-40mg) reflecting sedentary time versus stable angina patients (129859 and 130566 vs. 124092min/day, p<0.05). STEMI and NSTEMI patients spent less time in the 40-80mg acceleration category reflecting low physical activity versus stable angina patients (9535 and 9441 vs. 13250min/day, p<0.05). Stable angina patients spent more time in the higher acceleration categories (80-120 and 120-160mg) and moderate-to-vigorous physical activity (defined as 1 and 5min/day bouts) versus NSTEMI patients (p<0.05). For acceleration categories 160mg, no differences were observed.Patients presenting with ACS and undergoing PCI spent more time in sedentary behaviour compared with stable angina patients.

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