Visualization of HIV-Associated Neurocognitive Disorders

It is widely known that human immunodeficiency virus type-1 (HIV-1) can cause acquired immune deficiency syndrome (AIDS), but treatments to prevent the virus from escalating to that severity have come a long way since the virus was first described in the 1980s. The medications, combined antiretroviral therapy (cART), keep the virus from replicating, thus stopping its progression to AIDS. However, this treatment does not seem to ultimately benefit the brain, in part because cART does not uniformly penetrate the blood-brain barrier (BBB), and in part because HIV-1 seems to permanently turn on the part of the immune system that causes neuroinflammation. This allows the virus to exist in white blood cells and brain-resident glia amongst the neurons, wreaking havoc on the body\u27s central nervous system (CNS). Harris Gelbard and his research laboratory aim to understand the molecules and pathways involved in neuroinflammation caused by HIV-1 and the resulting HIV-associated neurocognitive disorders (HAND). The lab\u27s research has revealed several of the key components of this disease\u27s progression and has even synthesized small molecules with drug-like properties that confer neuroprotection in models of HAND. Applications of these molecules in a pharmaceutical setting and its delivery method for humans have yet to be established. The artwork created for this Thesis will visualize some of the research through illustrations, an animation, and an interactive game. The artwork will be effective in communicating the complexity of the research with graphical representations due to the collaboration with and contributions from the members of the Gelbard laboratory

Three-dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication

All positive strand RNA viruses are known to replicate their genomes in close association with intracellular membranes. In case of the hepatitis C virus (HCV), a member of the family Flaviviridae, infected cells contain accumulations of vesicles forming a membranous web (MW) that is thought to be the site of viral RNA replication. However, little is known about the biogenesis and three-dimensional structure of the MW. In this study we used a combination of immunofluorescence- and electron microscopy (EM)-based methods to analyze the membranous structures induced by HCV in infected cells. We found that the MW is derived primarily from the endoplasmic reticulum (ER) and contains markers of rough ER as well as markers of early and late endosomes, COP vesicles, mitochondria and lipid droplets (LDs). The main constituents of the MW are single and double membrane vesicles (DMVs). The latter predominate and the kinetic of their appearance correlates with kinetics of viral RNA replication. DMVs are induced primarily by NS5A whereas NS4B induces single membrane vesicles arguing that MW formation requires the concerted action of several HCV replicase proteins. Three-dimensional reconstructions identify DMVs as protrusions from the ER membrane into the cytosol, frequently connected to the ER membrane via a neck-like structure. In addition, late in infection multi-membrane vesicles become evident, presumably as a result of a stress-induced reaction. Thus, the morphology of the membranous rearrangements induced in HCV-infected cells resemble those of the unrelated picorna-, corona- and arteriviruses, but are clearly distinct from those of the closely related flaviviruses. These results reveal unexpected similarities between HCV and distantly related positive-strand RNA viruses presumably reflecting similarities in cellular pathways exploited by these viruses to establish their membranous replication factories

Playing Smart - Artificial Intelligence in Computer Games

Abstract: With this document we will present an overview of artificial intelligence in general and artificial intelligence in the context of its use in modern computer games in particular. To this end we will firstly provide an introduction to the terminology of artificial intelligence, followed by a brief history of this field of computer science and finally we will discuss the impact which this science has had on the development of computer games. This will be further illustrated by a number of case studies, looking at how artificially intelligent behaviour has been achieved in selected games

Immersive analytics for oncology patient cohorts

This thesis proposes a novel interactive immersive analytics tool and methods to interrogate the cancer patient cohort in an immersive virtual environment, namely Virtual Reality to Observe Oncology data Models (VROOM). The overall objective is to develop an immersive analytics platform, which includes a data analytics pipeline from raw gene expression data to immersive visualisation on virtual and augmented reality platforms utilising a game engine. Unity3D has been used to implement the visualisation. Work in this thesis could provide oncologists and clinicians with an interactive visualisation and visual analytics platform that helps them to drive their analysis in treatment efficacy and achieve the goal of evidence-based personalised medicine. The thesis integrates the latest discovery and development in cancer patients’ prognoses, immersive technologies, machine learning, decision support system and interactive visualisation to form an immersive analytics platform of complex genomic data. For this thesis, the experimental paradigm that will be followed is in understanding transcriptomics in cancer samples. This thesis specifically investigates gene expression data to determine the biological similarity revealed by the patient's tumour samples' transcriptomic profiles revealing the active genes in different patients. In summary, the thesis contributes to i) a novel immersive analytics platform for patient cohort data interrogation in similarity space where the similarity space is based on the patient's biological and genomic similarity; ii) an effective immersive environment optimisation design based on the usability study of exocentric and egocentric visualisation, audio and sound design optimisation; iii) an integration of trusted and familiar 2D biomedical visual analytics methods into the immersive environment; iv) novel use of the game theory as the decision-making system engine to help the analytics process, and application of the optimal transport theory in missing data imputation to ensure the preservation of data distribution; and v) case studies to showcase the real-world application of the visualisation and its effectiveness

Visualisation of Large-Scale Call-Centre Data

The contact centre industry employs 4% of the entire United King-dom and United States’ working population and generates gigabytes of operational data that require analysis, to provide insight and to improve efficiency. This thesis is the result of a collaboration with QPC Limited who provide data collection and analysis products for call centres. They provided a large data-set featuring almost 5 million calls to be analysed. This thesis utilises novel visualisation techniques to create tools for the exploration of the large, complex call centre data-set and to facilitate unique observations into the data.A survey of information visualisation books is presented, provid-ing a thorough background of the field. Following this, a feature-rich application that visualises large call centre data sets using scatterplots that support millions of points is presented. The application utilises both the CPU and GPU acceleration for processing and filtering and is exhibited with millions of call events.This is expanded upon with the use of glyphs to depict agent behaviour in a call centre. A technique is developed to cluster over-lapping glyphs into a single parent glyph dependant on zoom level and a customizable distance metric. This hierarchical glyph repre-sents the mean value of all child agent glyphs, removing overlap and reducing visual clutter. A novel technique for visualising individually tailored glyphs using a Graphics Processing Unit is also presented, and demonstrated rendering over 100,000 glyphs at interactive frame rates. An open-source code example is provided for reproducibility.Finally, a novel interaction and layout method is introduced for improving the scalability of chord diagrams to visualise call transfers. An exploration of sketch-based methods for showing multiple links and direction is made, and a sketch-based brushing technique for filtering is proposed. Feedback from domain experts in the call centre industry is reported for all applications developed

Department of Computer Science Activity 1998-2004

This report summarizes much of the research and teaching activity of the Department of Computer Science at Dartmouth College between late 1998 and late 2004. The material for this report was collected as part of the final report for NSF Institutional Infrastructure award EIA-9802068, which funded equipment and technical staff during that six-year period. This equipment and staff supported essentially all of the department\u27s research activity during that period

Exploring Environmental and Geographical Factors Influencing the Spread of Infectious Diseases with Interactive Maps

Publisher Copyright: © 2022 by the authors.Environmental problems due to human activities such as deforestation, urbanisation, and large scale intensive farming are some of the major factors behind the rapid spread of many infectious diseases. This in turn poses significant challenges not only in as regards providing adequate healthcare, but also in supporting healthcare workers, medical researchers, policy makers, and others involved in managing infectious diseases. These challenges include surveillance, tracking of infections, communication of public health knowledge and promotion of behavioural change. Behind these challenges lies a complex set of factors which include not only biomedical and population health determinants but also environmental, climatic, geographic, and socioeconomic variables. While there is broad agreement that these factors are best understood when considered in conjunction, aggregating and presenting diverse information sources requires effective information systems, software tools, and data visualisation. In this article, weargue that interactive maps, which couple geographical information systems and advanced information visualisation techniques, provide a suitable unifying framework for coordinating these tasks. Therefore, we examine how interactive maps can support spatial epidemiological visualisation and modelling involving distributed and dynamic data sources and incorporating temporal aspects of disease spread. Combining spatial and temporal aspects can be crucial in such applications. We discuss these issues in the context of support for disease surveillance in remote regions, utilising tools that facilitate distributed data collection and enable multidisciplinary collaboration, while also providing support for simulation and data analysis. We show that interactive maps deployed on a combination of mobile devices and large screens can provide effective means for collection, sharing, and analysis of health data.Peer reviewe