Thesauri and other types of controlled vocabularies are increasingly re‐engineered into ontologies described using the Web Ontology Language (OWL), particularly in the life sciences. This has led to ...the perception by some that thesauri are ontologies once they are described by using the syntax of OWL while others have emphasized the need to re‐engineer a vocabulary to use it as ontology. This confusion is rooted in different perceptions of what ontologies are and how they differ from other types of vocabularies. In this article, we rigorously examine the structural differences and similarities between thesauri and meaning‐defining ontologies described in OWL. Specifically, we conduct (a) a conceptual comparison of thesauri and ontologies, and (b) a comparison of a specific thesaurus and a specific ontology in the same subject field. Our results show that thesauri and ontologies need to be treated as 2 orthogonal kinds of models with superficially similar structures. An ontology is not a good thesaurus, nor is a thesaurus a good ontology. A thesaurus requires significant structural and other content changes to become an ontology, and vice versa.
Electron tomography produces very high resolution 3D image volumes useful for investigating the structure and function of cellular components. Unfortunately, unavoidable discontinuities and physical ...constraints in the acquisition geometry lead to a range of artifacts that can affect the reconstructed image. In particular, highly electron dense regions, such as gold nanoparticles, can hide proximal biological structures and degrade the overall quality of the reconstructed tomograms. In this work we introduce a pre-reconstruction non-conservative non-linear isotropic diffusion (NID) filter that automatically identifies and reduces local irregularities in the tilt projections. We illustrate the improvement in quality obtained using this approach for reconstructed tomograms generated from samples of malaria parasite-infected red blood cells. A quantitative and qualitative evaluation for our approach on both simulated and real data is provided.
Electron tomography produces highly magnified 3D image volumes useful for investigating the structure and function of cellular components. Image quality is degraded by multiple scattering events and ...quantum noise, which depend on the angle at which individual tilt projections are collected. We have adapted a biomedical imaging approach to improve image quality by enhancing individual tilt projections prior to volumetric reconstruction. Specifically, we have developed a family of non-linear anisotropic diffusion (NAD) filters parameterized by the tilt angle. We give a quantitative and qualitative evaluation of our pre-processing approach and the NAD filter. We show an improvement in the reconstructed volumes for tomograms generated from both plastic-embedded and cryo-stabilized samples of malaria parasite-infected erythrocytes.
Technical skills are critical for dentists. Computer‐based simulation offers a range of potential benefits for surgical training, but to date the development of simulators has not been characterized ...by a structured investigation of specific mechanisms by which trainees attain competence. This two‐part study contributes to the understanding of the manner in which surgical psychomotor skills are acquired so that this knowledge can be incorporated into the design of training simulations. We studied participant groups of varying skill levels as they performed a drilling task in oral surgery. In this first part of our study, we investigated the elements of surgical technique and differences in the drilling performance of novice, competent, and expert dentists. Our results indicate that novice dentists employ a technique that differs considerably in drilling stroke length and duration from that employed by experts. Expert dentists perform faster, apply more force, lift the bur off the bone less, and produce superior results compared with novices.
The study of expertise in surgery aims to facilitate the development of improved training methods by understanding the characteristics of expert practitioners. In this article and its companion, we ...present our study of the characteristics of competence and expertise in the field of oral surgery. We observed participants of different skill levels as they performed an ex vivo drilling task designed to test the psychomotor skill of distinguishing the material boundaries between tooth and bone. Part 1 of this study examined the physical characteristics of drilling performance, while this article examines the cognitive aspects of performance. In this article we investigate the psychomotor cues used for decision making during drilling and explore other factors that affect a participant's ability to distinguish tooth from bone. Our results suggest that visual and tactile cues were the most important cues guiding drilling performance in all participant groups. Our results also suggest that when compared to experts, novices relied more on visual cues rather than tactile cues and lacked the psychomotor skills required to utilize the broader range of cues used by experts.
The use of virtual reality (VR) simulation for surgical training has gathered much interest in recent years. Despite increasing popularity and usage, limited work has been carried out in the use of ...automated objective measures to quantify the extent to which performance in a simulator resembles performance in the operating theatre, and the effects of simulator training on real world performance. To this end, we present a study exploring the effects of VR training on the performance of dentistry students learning a novel oral surgery task. We compare the performance of trainees in a VR simulator and in a physical setting involving ovine jaws, using a range of automated metrics derived by motion analysis. Our results suggest that simulator training improved the motion economy of trainees without adverse effects on task outcome. Comparison of surgical technique on the simulator with the ovine setting indicates that simulator technique is similar, but not identical to real world technique.
Safety analysis methods for safety-critical systems face new challenges as systems evolve more frequently and the interactions within systems rise in numbers and complexity. Two such challenges are: ...(1) the need to formally examine the impact of system interactions on safety and (2) the need to extract and readily integrate knowledge from past accidents into new systems. We propose an approach which exploits knowledge from past accidents to conduct quantitative safety analysis using interactions between system components. A case study is presented that shows how our approach provides a support mechanism to safety and design experts. Further, it shows how we identify critical interactions and their contributions to accidents. This is especially important when components have not failed but instead undesirable interactions have contributed to an accident.
Analyzing accidents is a vital exercise in the development of safety-critical software systems to prevent past accidents from reoccurring in the future. Current practices such as causal event ...analysis are insufficient in light of a growing trend of accidents involving complex interactions between components with and without the occurrence of failures. Furthermore, the reuse of accident knowledge in current practices relies heavily on human expert recall and interpretation. In this paper, we propose an ontological classification mechanism to acquire and reuse knowledge from past accidents that focuses on the interactions taking place in a system. A set of knowledge bases are constructed independently using a feature-based classification and a domain specific ontology to organize the term spaces of each feature. Similarity mechanisms are introduced to retrieve and integrate the acquired knowledge into the new system analyses. Our experiments show how our approach reuses accident knowledge to uncover potential safety concerns in future safety analysis that may otherwise have been incorrectly classified in traditional approaches.
It is desirable to automatically classify data samples for the assessment of quantitative performance of users of haptic devices as the haptic data volume may be much higher than is feasible to ...manually annotate. In this paper we compare the use of three k-metrics for automated classifaction of human motion: cosine, extrinsic curvature and symmetric centroid deviation. Such classification algorithms make predictions about data attributes, whose quality we assess via three mathematical methods of comparison: root mean square deviation, sensitivity error and entropy correlation coefficient. Our assessment suggests that k-cosine might be more promising at analysing haptic motion than our two other metrics.
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