3,772 research outputs found

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Guided rewriting and constraint satisfaction for parallel GPU code generation

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    Graphics Processing Units (GPUs) are notoriously hard to optimise for manually due to their scheduling and memory hierarchies. What is needed are good automatic code generators and optimisers for such parallel hardware. Functional approaches such as Accelerate, Futhark and LIFT leverage a high-level algorithmic Intermediate Representation (IR) to expose parallelism and abstract the implementation details away from the user. However, producing efficient code for a given accelerator remains challenging. Existing code generators depend on the user input to choose a subset of hard-coded optimizations or automated exploration of implementation search space. The former suffers from the lack of extensibility, while the latter is too costly due to the size of the search space. A hybrid approach is needed, where a space of valid implementations is built automatically and explored with the aid of human expertise. This thesis presents a solution combining user-guided rewriting and automatically generated constraints to produce high-performance code. The first contribution is an automatic tuning technique to find a balance between performance and memory consumption. Leveraging its functional patterns, the LIFT compiler is empowered to infer tuning constraints and limit the search to valid tuning combinations only. Next, the thesis reframes parallelisation as a constraint satisfaction problem. Parallelisation constraints are extracted automatically from the input expression, and a solver is used to identify valid rewriting. The constraints truncate the search space to valid parallel mappings only by capturing the scheduling restrictions of the GPU in the context of a given program. A synchronisation barrier insertion technique is proposed to prevent data races and improve the efficiency of the generated parallel mappings. The final contribution of this thesis is the guided rewriting method, where the user encodes a design space of structural transformations using high-level IR nodes called rewrite points. These strongly typed pragmas express macro rewrites and expose design choices as explorable parameters. The thesis proposes a small set of reusable rewrite points to achieve tiling, cache locality, data reuse and memory optimisation. A comparison with the vendor-provided handwritten kernel ARM Compute Library and the TVM code generator demonstrates the effectiveness of this thesis' contributions. With convolution as a use case, LIFT-generated direct and GEMM-based convolution implementations are shown to perform on par with the state-of-the-art solutions on a mobile GPU. Overall, this thesis demonstrates that a functional IR yields well to user-guided and automatic rewriting for high-performance code generation

    Introduction to Psychology

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    Introduction to Psychology is a modified version of Psychology 2e - OpenStax

    Subjective Excess: Aesthetics, Character, and Non-Normative Perspectives in Serial Television After 2000

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    This dissertation aims to fill gaps in contemporary television scholarship with regards to aesthetics and character subjectivity. By analyzing eight series that have all aired after 2000, there is a marked trend in series that use an excessive visual and aural style to not only differentiate themselves from other programming, but also to explore non-normative perspectives. Now more willing to explore previously taboo topics such as mental health, addiction, illness, and trauma, the shows featured in this dissertation show how a seemingly excessive televisual aesthetic works with television’s seriality to create narrative complexity and generate character development. Chapters are arranged by mode of production with the first chapter focusing on the series Grey’s Anatomy and Hannibal as a means of exploring the production and distribution practices surrounding network TV. The second chapter examines the basic cable series Crazy Ex-Girlfriend and Legion and posits how the narrowcasting of cable allows for more nuanced character representations through aesthetics. In the third chapter, the impact HBO has had on the television medium is explored through Carnivàle and Euphoria. The final chapter looks at contemporary series The Boys and Unbreakable Kimmy Schmidt as a way to better understand how the medium’s production and distribution has shifted during the convergence era. Ultimately, this dissertation will argue that in addition to further explorations of aesthetics, television studies is in need of a medium specific vernacular for creating meaningful textual analyses that avoid an overreliance on cinematic terminology

    Investigating the learning potential of the Second Quantum Revolution: development of an approach for secondary school students

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    In recent years we have witnessed important changes: the Second Quantum Revolution is in the spotlight of many countries, and it is creating a new generation of technologies. To unlock the potential of the Second Quantum Revolution, several countries have launched strategic plans and research programs that finance and set the pace of research and development of these new technologies (like the Quantum Flagship, the National Quantum Initiative Act and so on). The increasing pace of technological changes is also challenging science education and institutional systems, requiring them to help to prepare new generations of experts. This work is placed within physics education research and contributes to the challenge by developing an approach and a course about the Second Quantum Revolution. The aims are to promote quantum literacy and, in particular, to value from a cultural and educational perspective the Second Revolution. The dissertation is articulated in two parts. In the first, we unpack the Second Quantum Revolution from a cultural perspective and shed light on the main revolutionary aspects that are elevated to the rank of principles implemented in the design of a course for secondary school students, prospective and in-service teachers. The design process and the educational reconstruction of the activities are presented as well as the results of a pilot study conducted to investigate the impact of the approach on students' understanding and to gather feedback to refine and improve the instructional materials. The second part consists of the exploration of the Second Quantum Revolution as a context to introduce some basic concepts of quantum physics. We present the results of an implementation with secondary school students to investigate if and to what extent external representations could play any role to promote students’ understanding and acceptance of quantum physics as a personal reliable description of the world

    Talking about personal recovery in bipolar disorder: Integrating health research, natural language processing, and corpus linguistics to analyse peer online support forum posts

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    Background: Personal recovery, ‘living a satisfying, hopeful and contributing lifeeven with the limitations caused by the illness’ (Anthony, 1993) is of particular value in bipolar disorder where symptoms often persist despite treatment. So far, personal recovery has only been studied in researcher-constructed environments (interviews, focus groups). Support forum posts can serve as a complementary naturalistic data source. Objective: The overarching aim of this thesis was to study personal recovery experiences that people living with bipolar disorder have shared in online support forums through integrating health research, NLP, and corpus linguistics in a mixed methods approach within a pragmatic research paradigm, while considering ethical issues and involving people with lived experience. Methods: This mixed-methods study analysed: 1) previous qualitative evidence on personal recovery in bipolar disorder from interviews and focus groups 2) who self-reports a bipolar disorder diagnosis on the online discussion platform Reddit 3) the relationship of mood and posting in mental health-specific Reddit forums (subreddits) 4) discussions of personal recovery in bipolar disorder subreddits. Results: A systematic review of qualitative evidence resulted in the first framework for personal recovery in bipolar disorder, POETIC (Purpose & meaning, Optimism & hope, Empowerment, Tensions, Identity, Connectedness). Mainly young or middle-aged US-based adults self-report a bipolar disorder diagnosis on Reddit. Of these, those experiencing more intense emotions appear to be more likely to post in mental health support subreddits. Their personal recovery-related discussions in bipolar disorder subreddits primarily focussed on three domains: Purpose & meaning (particularly reproductive decisions, work), Connectedness (romantic relationships, social support), Empowerment (self-management, personal responsibility). Support forum data highlighted personal recovery issues that exclusively or more frequently came up online compared to previous evidence from interviews and focus groups. Conclusion: This project is the first to analyse non-reactive data on personal recovery in bipolar disorder. Indicating the key areas that people focus on in personal recovery when posting freely and the language they use provides a helpful starting point for formal and informal carers to understand the concerns of people diagnosed with bipolar disorder and to consider how best to offer support
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