Visualization for Biological Models, Simulation, and Ontologies

In this dissertation, I present three browsers that I have developed for the purpose of exploring, understanding, and analyzing models, simulations, and ontologies in biology and medicine. The first browser visualizes multidimensional simulation data as an animation. The second browser visualizes the equations of a complex model as a network and puts structure and organization on top of equations and variables. The third browser is an ontology viewer and editor, directly intended for the Foundational Model of Anatomy (FMA), but applicable to other ontologies as well. This browser has two contributions. First, it is a lightweight deliverable that lets someone easily dabble with the FMA. Second, it lets the user edit an ontology to create a view of it. For the ontology browser, I also conduct user studies to refine and evaluate the software

BOB CAT: a Large-Scale Review and Delphi Consensus for Management of Barrett’s Esophagus With No Dysplasia, Indefinite for, or Low-Grade Dysplasia

OBJECTIVES: Barrett’s esophagus (BE) is a common premalignant lesion for which surveillance is recommended. This strategy is limited by considerable variations in clinical practice. We conducted an international, multidisciplinary, systematic search and evidence-based review of BE and provided consensus recommendations for clinical use in patients with nondysplastic, indefinite, and low-grade dysplasia (LGD). METHODS: We defined the scope, proposed statements, and searched electronic databases, yielding 20,558 publications that were screened, selected online, and formed the evidence base. We used a Delphi consensus process, with an 80% agreement threshold, using GRADE (Grading of Recommendations Assessment, Development and Evaluation) to categorize the quality of evidence and strength of recommendations. RESULTS: In total, 80% of respondents agreed with 55 of 127 statements in the final voting rounds. Population endoscopic screening is not recommended and screening should target only very high-risk cases of males aged over 60 years with chronic uncontrolled reflux. A new international definition of BE was agreed upon. For any degree of dysplasia, at least two specialist gastrointestinal (GI) pathologists are required. Risk factors for cancer include male gender, length of BE, and central obesity. Endoscopic resection should be used for visible, nodular areas. Surveillance is not recommended for <5 years of life expectancy. Management strategies for indefinite dysplasia (IND) and LGD were identified, including a de-escalation strategy for lower-risk patients and escalation to intervention with follow-up for higher-risk patients. CONCLUSIONS: In this uniquely large consensus process in gastroenterology, we made key clinical recommendations for the escalation/de-escalation of BE in clinical practice. We made strong recommendations for the prioritization of future research

Waste, Industry and Romantic Leisure: Veblen's Theory of Recognition

types: ArticleVeblen’s work contains a neglected, since for the most part implicit, theory of recognition centred on his concepts of waste and workmanship. This article tries to develop this theory in order to shed new light on the theorem of conspicuous leisure and consumption. The legitimacy of violence at the ‘predatory stage’ of culture has been partly superseded by a legitimacy of industrial efficiency, so that the leisure classes need to disguise their conspicuous waste as socially useful productive endeavours. At the same time waste remains a powerful symbol of legitimate status, so that even the industrial classes turn to it in order to assert their social worth and demand social recognition. Waste - which is far more central in Veblen’s theory than is emulation - becomes an ambiguous symbol which can stand for both unproductive privilege and industrial efficiency. The utilitarian urge for efficiency and the meaninglessness of a struggle for recognition through conspicuous waste produce a desire for a romantic escape, also acknowledged by Veblen, but often overlooked in his sharp criticism of consumerism

Creating Smooth Implicit Surfaces from Polygonal Meshes

Implicit surfaces have long been used for a myriad of tasks in computer graphics, including modeling soft or organic objects, morphing, and constructive solid geometry. Although operating on implicit surfaces is usually straight-forward, creating them is not --- interactive techniques are impractical for complex models, and automatic techniques have been largely unexplored. We introduce a practical method for creating implicit surfaces from polygonal models that produces high-quality results for complex models. Whereas much previous work has been done with primitives such as ``blobbies,'' we use surfaces based on a variational interpolation technique (the 3D generalization of thin-plate interpolation). Given a polygonal mesh, we convert the data to a volumetric representation and use this as a guide to create the implicit surface iteratively. Carefully chosen metrics evaluate each intermediate surface and control further refinement. We have applied this method successfully to a variety of polygonal meshes

Layered Acting For Character Animation

We introduce an acting-based animation system for creating and editing character animation at interactive speeds. Our system requires minimal training, typically under an hour, and is well suited for rapidly prototyping and creating expressive motion. A real-time motion-capture framework records the user&apos;s motions for simultaneous analysis and playback on a large screen. The animator&apos;s realworld, expressive motions are mapped into the character&apos;s virtual world. Visual feedback maintains a tight coupling between the animator and character. Complex motion is created by layering multiple passes of acting. We also introduce a novel motion-editing technique, which derives implicit relationships between the animator and character. The animator mimics some aspect of the character motion, and the system infers the association between features of the animator&apos;s motion and those of the character. The animator modifies the mimic by acting again, and the system maps the changes onto the character. We demonstrate our system with several examples and present the results from informal user studies with expert and novice animators

Animating Explosions

In this paper, we introduce techniques for animating explosions and their effects. The primary effect of an explosion is a disturbance that causes a shock wave to propagate through the surrounding medium. This disturbance determines the behavior of nearly all other secondary effects seen in explosions. We simulate the propagation of an explosion through the surrounding air using a computational fluid dynamics model based on the equations for compressible, viscous flow. To model the numerically stable formation of shocks along blast wave fronts, we employ an integration method that can handle steep pressure gradients without introducing inappropriate damping. The system includes two-way coupling between solid objects and surrounding fluid. Using this technique, we can generate a variety of effects including shaped explosive charges, a projectile propelled from a chamber by an explosion, and objects damaged by a blast. With appropriate rendering techniques, our explosion model can be used to create such visual effects as fireballs, dust clouds, and the refraction of light caused by a blast wave

Implicit surfaces that interpolate

Implicit surfaces are often created by summing a collection of radial basis functions. Recently, researchers have begun to create implicit surfaces that exactly interpolate a given set of points by solving a simple linear system to assign weights to each basis function. Due to their ability to interpolate, these implicit surfaces are more easily controllable than traditional “blobby ” implicits. There are several additional forms of control over these surfaces that make them attractive for a variety of applications. Surface normals may be directly specified at any location over the surface, and this allows the modeller to pivot the normal while still having the surface pass through the constraints. The degree of smoothness of the surface can be controlled by changing the shape of the basis functions, allowing the surface to be pinched or smooth. On a point-by-point basis the modeller may decide whether a constraint point should be exactly interpolated or approximated. Applications of these implicits include shape transformation, creating surfaces from computer vision data, creation of an implicit surface from a polygonal model, and medical surface reconstruction. 1

Animating Explosions

In this paper, we introduce techniques for animating explosions and their effects. The primary effect of an explosion is a disturbance that causes a shock wave to propagate through the surrounding medium. This disturbance determines the behavior of nearly all other secondary effects seen in explosions. We simulate the propagation of an explosion through the surrounding air using a computational fluid dynamics model based on the equations for compressible, viscous flow. To model the numerically stable formation of shocks along blast wave fronts, we employ an integration method that can handle steep pressure gradients without introducing inappropriate damping. The system includes two-way coupling between solid objects and surrounding fluid. Using this technique, we can generate a variety of effects including shaped explosive charges, a projectile propelled from a chamber by an explosion, and objects damaged by a blast. With appropriate rendering techniques, our explosion model can be used to create such visual effects as fireballs, dust clouds, and the refraction of light caused by a blast wave

Clinical Practice Guidelines by the Infectious Diseases Society of America (IDSA): 2020 Guideline on Diagnosis and Management of Babesiosis

The purpose of this guideline is to provide evidence-based guidance for the most effective strategies for the diagnosis and management of babesiosis. The diagnosis and treatment of co-infection with babesiosis and Lyme disease will be addressed in a separate Infectious Diseases Society of America (IDSA), American Academy of Neurology (AAN), and American College of Rheumatology (ACR) guideline [1]. Recommendations for the diagnosis and treatment of human granulocytic anaplasmosis can be found in the recent rickettsial disease guideline developed by the Centers for Disease Control and Prevention [2]. The target audience for the babesiosis guideline includes primary care physicians and specialists caring for this condition, such as infectious diseases specialists, emergency physicians, intensivists, internists, pediatricians, hematologists, and transfusion medicine specialists