Ontology engineering for simulation component reuse

Commercial-off-the-shelf (COTS) simulation packages (CSPs) are widely used in industry, although they have yet to operate across organizational boundaries. Reuse across organizations is restricted by the same semantic issues that restrict the inter-organizational use of web services. The current representations of web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging semantic web. Semantic models, in the form of ontology, utilized by web service discovery and deployment architectures provide one approach to support simulation model reuse. Semantic interoperation is achieved through the use of simulation component ontologies to identify required components at varying levels of granularity (including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The paper presents the development of an ontology, connector software and web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organizational simulation, adopting a less intrusive interface between participants. Although specific to CSPs the work has wider implications for the simulation community

Semantic web services for simulation component reuse and interoperability: An ontology approach

Commercial-off-the-shelf (COTS) Simulation Packages (CSPs) are widely used in industry primarily due to economic factors associated with developing proprietary software platforms. Regardless of their widespread use, CSPs have yet to operate across organizational boundaries. The limited reuse and interoperability of CSPs are affected by the same semantic issues that restrict the inter-organizational use of software components and web services. The current representations of Web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging Semantic Web. The authors present new research that partially alleviates the problem of limited semantic reuse and interoperability of simulation components in CSPs. Semantic models, in the form of ontologies, utilized by the authors’ Web service discovery and deployment architecture provide one approach to support simulation model reuse. Semantic interoperation is achieved through a simulation component ontology that is used to identify required components at varying levels of granularity (i.e. including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The research presented here is based on the development of an ontology, connector software, and a Web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organizational simulation, by adopting a less intrusive interface between participants Although specific to CSPs this work has wider implications for the simulation community. The reason being that the community as a whole stands to benefit through from an increased awareness of the state-of-the-art in Software Engineering (for example, ontology-supported component discovery and reuse, and service-oriented computing), and it is expected that this will eventually lead to the development of a unique Software Engineering-inspired methodology to build simulations in future

Joint inversion of receiver functions, surface wave dispersion, and magnetotelluric data

We present joint inversion of magnetotelluric, receiver function, and Raleigh wave dispersion data for a one‐dimensional Earth using a multiobjective genetic algorithm (GA). The chosen GA produces not only a family of models that fit the data sets but also the trade‐off between fitting the different data sets. The analysis of this trade‐off gives insight into the compatibility between the seismic data sets and the magnetotelluric data and also the appropriate noise level to assume for the seismic data. This additional information helps to assess the validity of the joint model, and we demonstrate the use of our approach with synthetic data under realistic conditions. We apply our method to one site from the Slave Craton and one site from the Kaapvaal Craton. For the Slave Craton we obtain similar results to our previously published models from joint inversion of receiver functions and magnetotelluric data but with improved resolution and control on absolute velocities. We find a conductive layer at the bottom of the crust, just above the Moho; a low‐velocity, low‐resistivity zone in the lithospheric mantle, previously termed the Central Slave Mantle Conductor; and indications of the lithosphere‐asthenosphere boundary in terms of a decrease in seismic velocity and resistivity. For the Kaapvaal Craton both the seismic and the MT data are of lesser quality, which prevents as detailed and robust an interpretation; nevertheless, we find an indication of a low‐velocity low‐resistivity zone in the mantle lithosphere. These two examples demonstrate the potential of joint inversion, particularly in combination with nonlinear optimization methods

The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design

Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice. There are still significant challenges to be overcome using an EM approach, not least the speed of structure determination, difficulties with low-occupancy ligands and the modest resolution that is available. However, with the anticipated developments in the field of EM, the potential of EM to become a key tool for structure-based drug design, often complementing X-ray and NMR studies, seems promising

Health surveillance for occupational asthma in the UK

Background Periodic health surveillance (HS) of workers can identify early cases of occupational asthma. Information about its uptake and its content in the UK is lacking. Aims To identify the overall levels of uptake and quality of HS for occupational asthma within three high risk industry sectors in the UK. Methods A telephone survey of employers, and their occupational health (OH) professionals, carried out in three sectors with exposures potentially capable of causing occupational asthma (bakeries, wood working and motor vehicle repair). Results A total of 457 organizations participated (31% response rate). About 77% employed <10 people, 17% between 10 and 50 and 6% >50. Risk assessments were common (67%) and 14% carried out some form of HS for occupational asthma, rising to 19% if only organizations reporting asthma hazards and risks were considered. HS was carried out both by in-house (31%) and external providers (69%). Organizational policies were often used to define HS approaches (80%), but infrequently shared with the OH provider. OH providers described considerable variation in practice. Record keeping was universal, but worker-held records were not reported. HS tools were generally developed in-house. Lung function was commonly measured, but only limited interpretation evident. Referral of workers to local specialist respiratory services was variable. Conclusions This study provided new insights into the real world of HS for occupational asthma. We consider that future work could and should define simpler, more practical and evidence-based approaches to HS to ensure maximal consistency and use of high-quality approaches

Structure and evolution of the intracratonic Congo Basin

Surface wave tomography, heat flow, and crustal thickness measurements have demonstrated that the thickness of the continental lithosphere varies by at least a factor of 2. Since the thermal time constant of the lithosphere depends upon the square of its thickness, subsidence records of extensional sedimentary basins offer a potential way of extending these observations into the past. Here we examine the Congo basin, a large and iconic intracratonic sedimentary basin in Central Africa. This roughly circular basin covers an area in excess of 1.4 × 106 km2 with more than 5 km thickness of sedimentary rocks, the oldest parts of which are late Precambrian in age. First, we assess the thickness of the lithosphere. We have estimated its thickness across Africa using maps of shear wave velocity obtained by inversion of fundamental and higher-mode surface waveforms. The Congo Basin sits on 220 ± 30 km thick lithosphere and appears to be part of a southern core to the continent encompassing both Archean cratons and Proterozoic mobile belts. This thickness is consistent with published estimates from kimberlites. Reappraisal of legacy seismic reflection images demonstrates that the sedimentary section is underlain by a Late Precambrian rift zone and that the basin is still subsiding today. Subsidence modeling of two deep wells is consistent with uniform extension and cooling of the lithosphere by a factor of 1.2 during latest Precambrian and Cambrian time; we argue that the exceptional 0.55 Ga history of the basin is a direct consequence of the lithospheric thermal time constant being a factor of 4 longer than normal. Today, the basin coincides with a long-wavelength −30 to −40 mGal gravity anomaly. We interpret this gravity anomaly as the surficial manifestation of 400–600 m of recent mantle convective drawdown in response to the onset of upwelling plumes around the flanks of the southern African continent. The alternative explanation, that it is the static manifestation of locally thick lithosphere, is inconsistent with global trends of mantle density depletion. Our interpretation is consistent with fast seismic velocities observed throughout the sublithospheric upper mantle underneath the basin and recent geodynamic modeling

Tris-N-alkylpyridinium-functionalised cyclotriguaiacylene hosts as axles in branched [4]pseudorotaxane formation

A series of [4]pseudorotaxanes composed of three-way axle threads based on the cyclotriguaiacylene family of crown-shaped cavitands and three threaded macrocyclic components has been achieved. These exploit the strong affinity for electron-poor alkyl-pyridinium units to reside within the electron-rich cavity of macrocycles, in this case dimethoxypillar[5]arene (DMP). The branched [4]pseudorotaxane= assemblies {(DMP)3∙L}3+,where L = N-alkylated derivatives of the host molecule (±)-tris-(isonicotinoyl)cyclotriguaiacylene, were characterised by NMR spectroscopy and mass spectrometry, and an energy-minimised structure of {(DMP)3∙(tris-(N-propyl-isonicotinoyl)cyclotriguaiacylene)}3+ was calculated. Crystal structures of N-ethyl-isonicotinoyl)cyclotriguaiacylene hexafluorophosphate and N-propyl-isonicotinoyl)cyclotriguaiacylene hexafluorophosphate each show ‘hand-shake’ self-inclusion motifs occurring between the individual cavitands