11,672 research outputs found

    Impact of language skills and system experience on medical information retrieval

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    Partitioning algorithms for induced subgraph problems

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    This dissertation introduces the MCSPLIT family of algorithms for two closely-related NP-hard problems that involve finding a large induced subgraph contained by each of two input graphs: the induced subgraph isomorphism problem and the maximum common induced subgraph problem. The MCSPLIT algorithms resemble forward-checking constrant programming algorithms, but use problem-specific data structures that allow multiple, identical domains to be stored without duplication. These data structures enable fast, simple constraint propagation algorithms and very fast calculation of upper bounds. Versions of these algorithms for both sparse and dense graphs are described and implemented. The resulting algorithms are over an order of magnitude faster than the best existing algorithm for maximum common induced subgraph on unlabelled graphs, and outperform the state of the art on several classes of induced subgraph isomorphism instances. A further advantage of the MCSPLIT data structures is that variables and values are treated identically; this allows us to choose to branch on variables representing vertices of either input graph with no overhead. An extensive set of experiments shows that such two-sided branching can be particularly beneficial if the two input graphs have very different orders or densities. Finally, we turn from subgraphs to supergraphs, tackling the problem of finding a small graph that contains every member of a given family of graphs as an induced subgraph. Exact and heuristic techniques are developed for this problem, in each case using a MCSPLIT algorithm as a subroutine. These algorithms allow us to add new terms to two entries of the On-Line Encyclopedia of Integer Sequences

    The Ephemeral City : Songs for the Ghost Quarters

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    The towers of the Stockholm skyline twine with radio transmissions, flying out over the city, drifting down through the streets and sinking into the underground telephone system below. Stockholm has buildings that have been there for centuries, but is also full of modern and contemporary architectures, all jostling for their place in parallel collective memory. In taking the city up as a subject, this artistic PhD project in music expands allegories to these architectural instruments into the world of the mechanical and the electrical. By taking up and transforming the materials of the cityscape, this project spins ephemeral cities more subtle than the colossal forces transforming the cityscape. The aim is to empower urban dwellers with another kind of ownership of their city.The materials in the project are drawn around themes of urban memory and transformation, psychogeography and the ghosts of the imagined city. There are three questions the artistic works of this project reflect on and address. The first is about the ability of city-dwellers to regain or create some sense of place, history or belonging through the power of their imaginations. The second reflects on the possibility for imagined alternatives to re-empower a sense of place for the people who encounter them. The third seeks out the points where stories, memories, or alternative futures are collective, at what point are they wholly individual, and how the interplay between them plays out in listening.There is an improvisatory practice in how we relate to urban environments: an ever-transforming inter-play between the animate and inanimate. Each individual draws phantoms of memory and imagination onto the cityscape, and this yields subtle ways people can be empowered in their surroundings. The artistic works of this project are made to illuminate those subtleties, centering around a group of compositions, improvisations, artistic collaborations and sound installations in music and sound, utilizing modular synthesizers, field recordings, pipe organs, multi-channel settings; PureData and SuperCollider programs, string ensembles with hurdy-gurdy and nyckelharpa or violin, and sound installations. This choice of instruments is as an allegory to the architecture of Stockholm. The final result is a collection of music and sound works, made to illuminate the imagined city. Taken as a whole, the works of the project create an imaginary city–The Ephemeral City–in order to argue that this evocation of ephemeral space is a way to empower urban dwellers through force of imagination, immune to the vast forces tearing through the fabric of Stockholm life by virtue of the ghostly, transitory and mercurial, as compelling to the inner eye as brick and mortar to the outer life

    High-throughput Tools and Techniques to Investigate Environmental Effects on Aging Behaviors in Caenorhabditis elegans

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    Aging is modulated by genetic and environmental cues; however, it is difficult to study how these perturbations modulate the aging process in a robust, high-throughput manner. Methods to gather large-scale behavioral data for aging studies are labor-intensive, lack individual-level resolution, or lack precise spatiotemporal environmental control. In addition, tools to analyze large-scale behavioral data sets are difficult to scale, unable to be broadly applied across complex environments, or fail to detect subtle behavioral changes. In this thesis I develop tools to enable robust, microfluidic culture and behavioral analysis of C. elegans to examine how environmental cues, such as dietary restriction, influence longevity and behavior with age. In Aim 1, I engineer a robust pipeline for the long-term longitudinal culture and behavioral monitoring of C. elegans in aging studies with precise spatiotemporal environmental control. In Aim 2, I develop a flexible deep learning based pipeline for detecting and extracting postural information from large-scale behavioral datasets across heterogeneous environments. In Aim 3, I characterize how the full behavioral repertoire of individuals change with age, along with examining how these age-related behavioral changes are modulated by different dietary restriction regimes. The completion of this thesis provides 1) a new toolset to robustly explore how genetic or environmental effects influence longevity and healthspan, 2) a flexible pipeline for analyzing large-scale behavioral data in C. elegans, and 3) insight into how environmental perturbations influence health through age-related changes in behavior.Ph.D

    A Design Science Research Approach to Smart and Collaborative Urban Supply Networks

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    Urban supply networks are facing increasing demands and challenges and thus constitute a relevant field for research and practical development. Supply chain management holds enormous potential and relevance for society and everyday life as the flow of goods and information are important economic functions. Being a heterogeneous field, the literature base of supply chain management research is difficult to manage and navigate. Disruptive digital technologies and the implementation of cross-network information analysis and sharing drive the need for new organisational and technological approaches. Practical issues are manifold and include mega trends such as digital transformation, urbanisation, and environmental awareness. A promising approach to solving these problems is the realisation of smart and collaborative supply networks. The growth of artificial intelligence applications in recent years has led to a wide range of applications in a variety of domains. However, the potential of artificial intelligence utilisation in supply chain management has not yet been fully exploited. Similarly, value creation increasingly takes place in networked value creation cycles that have become continuously more collaborative, complex, and dynamic as interactions in business processes involving information technologies have become more intense. Following a design science research approach this cumulative thesis comprises the development and discussion of four artefacts for the analysis and advancement of smart and collaborative urban supply networks. This thesis aims to highlight the potential of artificial intelligence-based supply networks, to advance data-driven inter-organisational collaboration, and to improve last mile supply network sustainability. Based on thorough machine learning and systematic literature reviews, reference and system dynamics modelling, simulation, and qualitative empirical research, the artefacts provide a valuable contribution to research and practice

    Accurate and Interpretable Solution of the Inverse Rig for Realistic Blendshape Models with Quadratic Corrective Terms

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    We propose a new model-based algorithm solving the inverse rig problem in facial animation retargeting, exhibiting higher accuracy of the fit and sparser, more interpretable weight vector compared to SOTA. The proposed method targets a specific subdomain of human face animation - highly-realistic blendshape models used in the production of movies and video games. In this paper, we formulate an optimization problem that takes into account all the requirements of targeted models. Our objective goes beyond a linear blendshape model and employs the quadratic corrective terms necessary for correctly fitting fine details of the mesh. We show that the solution to the proposed problem yields highly accurate mesh reconstruction even when general-purpose solvers, like SQP, are used. The results obtained using SQP are highly accurate in the mesh space but do not exhibit favorable qualities in terms of weight sparsity and smoothness, and for this reason, we further propose a novel algorithm relying on a MM technique. The algorithm is specifically suited for solving the proposed objective, yielding a high-accuracy mesh fit while respecting the constraints and producing a sparse and smooth set of weights easy to manipulate and interpret by artists. Our algorithm is benchmarked with SOTA approaches, and shows an overall superiority of the results, yielding a smooth animation reconstruction with a relative improvement up to 45 percent in root mean squared mesh error while keeping the cardinality comparable with benchmark methods. This paper gives a comprehensive set of evaluation metrics that cover different aspects of the solution, including mesh accuracy, sparsity of the weights, and smoothness of the animation curves, as well as the appearance of the produced animation, which human experts evaluated

    A Decision Support System for Economic Viability and Environmental Impact Assessment of Vertical Farms

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    Vertical farming (VF) is the practice of growing crops or animals using the vertical dimension via multi-tier racks or vertically inclined surfaces. In this thesis, I focus on the emerging industry of plant-specific VF. Vertical plant farming (VPF) is a promising and relatively novel practice that can be conducted in buildings with environmental control and artificial lighting. However, the nascent sector has experienced challenges in economic viability, standardisation, and environmental sustainability. Practitioners and academics call for a comprehensive financial analysis of VPF, but efforts are stifled by a lack of valid and available data. A review of economic estimation and horticultural software identifies a need for a decision support system (DSS) that facilitates risk-empowered business planning for vertical farmers. This thesis proposes an open-source DSS framework to evaluate business sustainability through financial risk and environmental impact assessments. Data from the literature, alongside lessons learned from industry practitioners, would be centralised in the proposed DSS using imprecise data techniques. These techniques have been applied in engineering but are seldom used in financial forecasting. This could benefit complex sectors which only have scarce data to predict business viability. To begin the execution of the DSS framework, VPF practitioners were interviewed using a mixed-methods approach. Learnings from over 19 shuttered and operational VPF projects provide insights into the barriers inhibiting scalability and identifying risks to form a risk taxonomy. Labour was the most commonly reported top challenge. Therefore, research was conducted to explore lean principles to improve productivity. A probabilistic model representing a spectrum of variables and their associated uncertainty was built according to the DSS framework to evaluate the financial risk for VF projects. This enabled flexible computation without precise production or financial data to improve economic estimation accuracy. The model assessed two VPF cases (one in the UK and another in Japan), demonstrating the first risk and uncertainty quantification of VPF business models in the literature. The results highlighted measures to improve economic viability and the viability of the UK and Japan case. The environmental impact assessment model was developed, allowing VPF operators to evaluate their carbon footprint compared to traditional agriculture using life-cycle assessment. I explore strategies for net-zero carbon production through sensitivity analysis. Renewable energies, especially solar, geothermal, and tidal power, show promise for reducing the carbon emissions of indoor VPF. Results show that renewably-powered VPF can reduce carbon emissions compared to field-based agriculture when considering the land-use change. The drivers for DSS adoption have been researched, showing a pathway of compliance and design thinking to overcome the ‘problem of implementation’ and enable commercialisation. Further work is suggested to standardise VF equipment, collect benchmarking data, and characterise risks. This work will reduce risk and uncertainty and accelerate the sector’s emergence

    Multiscale structural optimisation with concurrent coupling between scales

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    A robust three-dimensional multiscale topology optimisation framework with concurrent coupling between scales is presented. Concurrent coupling ensures that only the microscale data required to evaluate the macroscale model during each iteration of optimisation is collected and results in considerable computational savings. This represents the principal novelty of the framework and permits a previously intractable number of design variables to be used in the parametrisation of the microscale geometry, which in turn enables accessibility to a greater range of mechanical point properties during optimisation. Additionally, the microscale data collected during optimisation is stored in a re-usable database, further reducing the computational expense of subsequent iterations or entirely new optimisation problems. Application of this methodology enables structures with precise functionally-graded mechanical properties over two-scales to be derived, which satisfy one or multiple functional objectives. For all applications of the framework presented within this thesis, only a small fraction of the microstructure database is required to derive the optimised multiscale solutions, which demonstrates a significant reduction in the computational expense of optimisation in comparison to contemporary sequential frameworks. The derivation and integration of novel additive manufacturing constraints for open-walled microstructures within the concurrently coupled multiscale topology optimisation framework is also presented. Problematic fabrication features are discouraged through the application of an augmented projection filter and two relaxed binary integral constraints, which prohibit the formation of unsupported members, isolated assemblies of overhanging members and slender members during optimisation. Through the application of these constraints, it is possible to derive self-supporting, hierarchical structures with varying topology, suitable for fabrication through additive manufacturing processes.Open Acces

    Targeting Fusion Proteins of HIV-1 and SARS-CoV-2

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    Viruses are disease-causing pathogenic agents that require host cells to replicate. Fusion of host and viral membranes is critical for the lifecycle of enveloped viruses. Studying viral fusion proteins can allow us to better understand how they shape immune responses and inform the design of therapeutics such as drugs, monoclonal antibodies, and vaccines. This thesis discusses two approaches to targeting two fusion proteins: Env from HIV-1 and S from SARS-CoV-2. The first chapter of this thesis is an introduction to viruses with a specific focus on HIV-1 CD4 mimetic drugs and antibodies against SARS-CoV-2. It discusses the architecture of these viruses and fusion proteins and how small molecules, peptides, and antibodies can target these proteins successfully to treat and prevent disease. In addition, a brief overview is included of the techniques involved in structural biology and how it has informed the study of viruses. For the interested reader, chapter 2 contains a review article that serves as a more in-depth introduction for both viruses as well as how the use of structural biology has informed the study of viral surface proteins and neutralizing antibody responses to them. The subsequent chapters provide a body of work divided into two parts. The first part in chapter 3 involves a study on conformational changes induced in the HIV-1 Env protein by CD4-mimemtic drugs using single particle cryo-EM. The second part encompassing chapters 4 and 5 includes two studies on antibodies isolated from convalescent COVID-19 donors. The former involves classification of antibody responses to the SARS-CoV-2 S receptor-binding domain (RBD). The latter discusses an anti-RBD antibody class that binds to a conserved epitope on the RBD and shows cross-binding and cross-neutralization to other coronaviruses in the sarbecovirus subgenus.</p

    Differential Models, Numerical Simulations and Applications

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    This Special Issue includes 12 high-quality articles containing original research findings in the fields of differential and integro-differential models, numerical methods and efficient algorithms for parameter estimation in inverse problems, with applications to biology, biomedicine, land degradation, traffic flows problems, and manufacturing systems
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