Process model comparison based on cophenetic distance

The automated comparison of process models has received increasing attention in the last decade, due to the growing existence of process models and repositories, and the consequent need to assess similarities between the underlying processes. Current techniques for process model comparison are either structural (based on graph edit distances), or behavioural (through activity profiles or the analysis of the execution semantics). Accordingly, there is a gap between the quality of the information provided by these two families, i.e., structural techniques may be fast but inaccurate, whilst behavioural are accurate but complex. In this paper we present a novel technique, that is based on a well-known technique to compare labeled trees through the notion of Cophenetic distance. The technique lays between the two families of methods for comparing a process model: it has an structural nature, but can provide accurate information on the differences/similarities of two process models. The experimental evaluation on various benchmarks sets are reported, that position the proposed technique as a valuable tool for process model comparison.Peer ReviewedPostprint (author's final draft

Nonlinear Finite Element Analysis of Nanoindentation of Viral Capsids

Recent Atomic Force Microscope (AFM) nanoindentation experiments measuring mechanical response of the protein shells of viruses have provided a quantitative description of their strength and elasticity. To better understand and interpret these measurements, and to elucidate the underlying mechanisms, this paper adopts a course-grained modeling approach within the framework of three-dimensional nonlinear continuum elasticity. Homogeneous, isotropic, elastic, thick shell models are proposed for two capsids: the spherical Cowpea Chlorotic Mottle Virus (CCMV), and the ellipsocylindrical bacteriophage $\phi 29$. As analyzed by the finite element method, these models enable parametric characterization of the effects of AFM tip geometry, capsid dimensions, and capsid constitutive descriptions. The generally nonlinear force response of capsids to indentation is shown to be insensitive to constitutive details, and greatly influenced by geometry. Nonlinear stiffening and softening of the force response is dependent on the AFM tip dimensions and shell thickness. Fits of the models capture the roughly linear behavior observed in experimental measurements and result in estimates of Young's moduli of $\approx$280--360 MPa for CCMV and $\approx$4.5 GPa for $\phi 29$.Comment: 24 pages, 10 figures, submitted to Biophysical Journa

Grey seals (Halichoerus grypus) in the Dutch North sea: population ecology and effects of wind farms

This study was setup to gain an understanding of the possible effects of large-scale development of wind farms in Dutch waters on grey seals (Halichoerus grypus). This should be considered a first step in doing so as up until now relatively little was known about the species in Dutch waters. The study was carried out in the framework of WE@SEA a foundation aimed at acquiring knowledge in the field of offshore wind energy

Water Resources Systems Planning and Management: An Introduction to Methods, Models and Applications

This 2005 version has been superseded by the 2017 edition, available in full here: http://hdl.handle.net/1813/48159Throughout history much of the world has witnessed ever-greater demands for reliable, high-quality and inexpensive water supplies for domestic consumption, agriculture and industry. In recent decades there have also been increasing demands for hydrological regimes that support healthy and diverse ecosystems, provide for water-based recreational activities, reduce if not prevent floods and droughts, and in some cases, provide for the production of hydropower and ensure water levels adequate for ship navigation. Water managers are challenged to meet these multiple and often conflicting demands. At the same time, public stakeholder interest groups have shown an increasing desire to take part in the water resources development and management decision making process. Added to all these management challenges are the uncertainties of natural water supplies and demands due to changes in our climate, changes in people's standards of living, changes in watershed land uses and changes in technology. How can managers develop, or redevelop and restore, and then manage water resources systems - systems ranging from small watersheds to those encompassing large river basins and coastal zones - in a way that meets society's changing objectives and goals? In other words, how can water resources systems become more integrated and sustainable

Biodiversity hotspots on the Dutch Continental Shelf: a marine strategy framework directive perspective

This report presenst hotspots of biodiversity for benthos, fish, birds, marine mammals and habitats on the Dutch Continental Shelf. These hotspots are based on a spatial application of biodiversity metrics developed in this study for the GES(Good Environmental Status)-descriptor 1 ‘Biological diversity is maintained’ of the Marine Strategy Framework Directive (MSFD) (EU 2008). The choice of the biodiversity metrics is based on the proposed indicators of biodiversity in the Commission Decision (EU 2010). The purpose of this study is to provide insight in possibilities for spatial protection measures in the framework of the MSFD. This report feeds information and ideas into further work for the MSFD in the Netherlands. IMARES has compiled this report for the Dutch Ministry of Economic Affairs, Agriculture and Innovation (Ministry of EL&I) and the Ministry of Infrastructure and the Environment (I&M)

Report of the Horse Mackerel Exchange and Workshop 2006

Following a recommendation from PGCCDBS, a workshop on age calibration of horse mackerel was carried out. The workshop was preceded by an exchange. The objectives were: to improve the quality of horse mackerel readings by international calibration. In particular, attempt to resolve the observed differences between countries. Estimate the accuracy and precision of the age readings before and after the intercalibration. Take into account differences between areas and methods. Training of new horse mackerel readers

Zeezoogdieren in de Eems Evaluatie van de Vliegtuigtellingen van zeezoogdieren tussen oktober 2007 en september 2008

Groningen Seaports heeft de ambitie om de Eemshaven te ontwikkelen tot een belangrijk energiecentrum onder de naam "Energy Park Eemshaven". Bovendien worden de Eemshaven en de vaargeul naar de Noordzee verruimd en verdiept. Er komen drie soorten zeezoogdieren in het gebied voor. De meest algemene soort is de gewone zeehond, Phoca vitulina; ook worden er grijze zeehonden Halichoerus grypus en bruinvissen Phocoena phocoena in het gebied gezien. In Brasseur (2007) worden leemtes in de beschikbare kennis van de grijze zeehond en de bruinvis geconstateerd, en tevens over de winterverspreiding van de gewone zeehond. Aangezien de ontbrekende kennis noodzakelijk is om te komen tot een gedegen afweging van de mogelijke effecten van de geplande activiteiten wordt verder onderzoek aanbevolen naar: A. De ruimtelijke en temporele spreiding van de drie soorten in het gebied; B. Migratiegedrag van de drie soorten; C. Voor de zeezoogdieren frequentiespecifieke geluidscontouren van de bouwactiviteiten – met en zonder mitigatie

Indexing and efficient instance-based retrieval of process models using untanglings

Process-Aware Information Systems (PAISs) support executions of operational processes that involve people, resources, and software applications on the basis of process models. Process models describe vast, often infinite, amounts of process instances, i.e., workflows supported by the systems. With the increasing adoption of PAISs, large process model repositories emerged in companies and public organizations. These repositories constitute significant information resources. Accurate and efficient retrieval of process models and/or process instances from such repositories is interesting for multiple reasons, e.g., searching for similar models/instances, filtering, reuse, standardization, process compliance checking, verification of formal properties, etc. This paper proposes a technique for indexing process models that relies on their alternative representations, called untanglings. We show the use of untanglings for retrieval of process models based on process instances that they specify via a solution to the total executability problem. Experiments with industrial process models testify that the proposed retrieval approach is up to three orders of magnitude faster than the state of the art

Effects of caffeine intake prior to stress cardiac magnetic resonance perfusion imaging on regadenoson- versus adenosine-induced hyperemia as measured by T1 mapping

The antagonistic effects of caffeine on adenosine receptors are a possible cause of false-negative stress perfusion imaging. The purpose of this study was to determine the effects of coffee intake <4 h prior to stress perfusion cardiac magnetic resonance imaging (CMR) in regadenoson- versus adenosine-induced hyperemia as measured with T1-mapping. 98 consecutive patients with suspected coronary artery disease referred for either adenosine or regadenoson perfusion CMR were included in this analysis. Twenty-four patients reported coffee consumption <4 h before CMR (15 patients with adenosine, and 9 patients with regadenoson); 74 patients reported no coffee intake (50 patients with adenosine, and 24 patients with regadenoson). T1 mapping was performed using a modified look-locker inversion recovery sequence. T1 reactivity was determined by subtracting T1(rest) from T1(stress). T1(rest), T1(stress), and T1 reactivity in patients referred for regadenoson perfusion CMR were not significantly different when comparing patients with <4 h coffee intake and patients who reported no coffee intake (976 +/- 4 ms, 1019 +/- 48 ms, and 4.4 +/- 3.2% vs 971 +/- 33 ms, 1023 +/- 43 ms, and 5.4 +/- 2.4%) (p = 0.70, 0.79, and 0.40), and similar to values in patients without coffee intake undergoing adenosine CMR. In patients with <4 h coffee intake, T1(stress), and T1 reactivity were significantly lower for adenosine (898 +/- 51 ms, and -7.8 +/- 5.0%) compared to regadenoson perfusion CMR (p <0.001). Coffee intake <4 h prior to regadenoson perfusion CMR has no effect on stress-induced hyperemia as measured with T1 mapping