8,202 research outputs found

    Technical Dimensions of Programming Systems

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    Programming requires much more than just writing code in a programming language. It is usually done in the context of a stateful environment, by interacting with a system through a graphical user interface. Yet, this wide space of possibilities lacks a common structure for navigation. Work on programming systems fails to form a coherent body of research, making it hard to improve on past work and advance the state of the art. In computer science, much has been said and done to allow comparison of programming languages, yet no similar theory exists for programming systems; we believe that programming systems deserve a theory too. We present a framework of technical dimensions which capture the underlying characteristics of programming systems and provide a means for conceptualizing and comparing them. We identify technical dimensions by examining past influential programming systems and reviewing their design principles, technical capabilities, and styles of user interaction. Technical dimensions capture characteristics that may be studied, compared and advanced independently. This makes it possible to talk about programming systems in a way that can be shared and constructively debated rather than relying solely on personal impressions. Our framework is derived using a qualitative analysis of past programming systems. We outline two concrete ways of using our framework. First, we show how it can analyze a recently developed novel programming system. Then, we use it to identify an interesting unexplored point in the design space of programming systems. Much research effort focuses on building programming systems that are easier to use, accessible to non-experts, moldable and/or powerful, but such efforts are disconnected. They are informal, guided by the personal vision of their authors and thus are only evaluable and comparable on the basis of individual experience using them. By providing foundations for more systematic research, we can help programming systems researchers to stand, at last, on the shoulders of giants

    Optimizing transcriptomics to study the evolutionary effect of FOXP2

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    The field of genomics was established with the sequencing of the human genome, a pivotal achievement that has allowed us to address various questions in biology from a unique perspective. One question in particular, that of the evolution of human speech, has gripped philosophers, evolutionary biologists, and now genomicists. However, little is known of the genetic basis that allowed humans to evolve the ability to speak. Of the few genes implicated in human speech, one of the most studied is FOXP2, which encodes for the transcription factor Forkhead box protein P2 (FOXP2). FOXP2 is essential for proper speech development and two mutations in the human lineage are believed to have contributed to the evolution of human speech. To address the effect of FOXP2 and investigate its evolutionary contribution to human speech, one can utilize the power of genomics, more specifically gene expression analysis via ribonucleic acid sequencing (RNA-seq). To this end, I first contributed in developing mcSCRB-seq, a highly sensitive, powerful, and efficient single cell RNA-seq (scRNA-seq) protocol. Previously having emerged as a central method for studying cellular heterogeneity and identifying cellular processes, scRNA-seq was a powerful genomic tool but lacked the sensitivity and cost-efficiency of more established protocols. By systematically evaluating each step of the process, I helped find that the addition of polyethylene glycol increased sensitivity by enhancing the cDNA synthesis reaction. This, along with other optimizations resulted in developing a sensitive and flexible protocol that is cost-efficient and ideal in many research settings. A primary motivation driving the extensive optimizations surrounding single cell transcriptomics has been the generation of cellular atlases, which aim to identify and characterize all of the cells in an organism. As such efforts are carried out in a variety of research groups using a number of different RNA-seq protocols, I contributed in an effort to benchmark and standardize scRNA-seq methods. This not only identified methods which may be ideal for the purpose of cell atlas creation, but also highlighted optimizations that could be integrated into existing protocols. Using mcSCRB-seq as a foundation as well as the findings from the scRNA-seq benchmarking, I helped develop prime-seq, a sensitive, robust, and most importantly, affordable bulk RNA-seq protocol. Bulk RNA-seq was frequently overlooked during the efforts to optimize and establish single-cell techniques, even though the method is still extensively used in analyzing gene expression. Introducing early barcoding and reducing library generation costs kept prime-seq cost-efficient, but basing it off of single-cell methods ensured that it would be a sensitive and powerful technique. I helped verify this by benchmarking it against TruSeq generated data and then helped test the robustness by generating prime-seq libraries from over seventeen species. These optimizations resulted in a final protocol that is well suited for investigating gene expression in comprehensive and high-throughput studies. Finally, I utilized prime-seq in order to develop a comprehensive gene expression atlas to study the function of FOXP2 and its role in speech evolution. I used previously generated mouse models: a knockout model containing one non-functional Foxp2 allele and a humanized model, which has a variant Foxp2 allele with two human-specific mutations. To study the effect globally across the mouse, I helped harvest eighteen tissues which were previously identified to express FOXP2. By then comparing the mouse models to wild-type mice, I helped highlight the importance of FOXP2 within lung development and the importance of the human variant allele in the brain. Both mcSCRB-seq and prime-seq have already been used and published in numerous studies to address a variety of biological and biomedical questions. Additionally, my work on FOXP2 not only provides a thorough expression atlas, but also provides a detailed and cost-efficient plan for undertaking a similar study on other genes of interest. Lastly, the studies on FOXP2 done within this work, lay the foundation for future studies investigating the role of FOXP2 in modulating learning behavior, and thereby affecting human speech

    AIUCD 2022 - Proceedings

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    L’undicesima edizione del Convegno Nazionale dell’AIUCD-Associazione di Informatica Umanistica ha per titolo Culture digitali. Intersezioni: filosofia, arti, media. Nel titolo è presente, in maniera esplicita, la richiesta di una riflessione, metodologica e teorica, sull’interrelazione tra tecnologie digitali, scienze dell’informazione, discipline filosofiche, mondo delle arti e cultural studies

    Platform protocol place: a practice-based study of critical media art practice (2007-2020)

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    This practice-based research project focuses on critical media art practices in contemporary digital culture. The theoretical framework employed in this inquiry draws from the work of the Frankfurt School, in particular Theodor Adorno and Max Horkheimer’s The Culture Industry: Enlightenment as Mass Deception. Using Adorno & Horkheimer’s thesis as a theoretical guide, this research project formulates the concept of the digital culture industry - a concept that refers to the contemporary era of networked capitalism, an era defined by the unprecedented extraction, accumulation and manipulation of data and the material and digital infrastructures that facilitate it. This concept is used as a framing mechanism that articulates certain techno-political concerns within networked capitalism and responds to them through practice. The second concept formulated within this research project is Platform Protocol Place. The function of this second concept is to frame and outline the body of practice-based work developed in this study. It is also used to make complex technological issues accessible and to communicate these issues through public exhibition and within this written thesis. The final concept developed in this research project is tactical media archaeology. This concept describes the techniques and approaches employed in the development of the body of practice-based work that are the central focus of this research project. This approach is a synthesis of two subfields of media art practice and theory, tactical media and media archaeology. Through practice, tactical media archaeology critiques the geopolitical machinations and systems beneath the networked devices and interfaces of the digital culture industry

    Gamification of Education and Learning: Heuristic Elements, Player Types, and Learning Outcomes for Art History Games

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    The technology of virtual reality (VR) and the gamification of education and learning has had proven educational benefits, especially in secondary education. However, there remains little to no research on the heuristic elements and mechanics that contribute to learning at the postsecondary level of education. Most research conducted has been refined to science programs, but even in these instances, a study of the effects and interests of different demographics has yet to be considered. Given the visual nature of how the discipline of art history has traditionally been taught, there are a number of virtual reality (VR) applications to assist instructors in the field better engage students in immersive environments to provide a more accurate understanding of subjects covered. In order to capitalize on the strengths of the new digital medium, including immersion, engagement, and presence, the end user needs to be considered. This heuristic study investigates the different experiences, preferences, learning styles, and expectations relating to educational gaming of art history students at a private, Midwestern college. Results demonstrate that effective game design and development need consider the target audience to optimize user experience and learning outcomes

    Principles of Massively Parallel Sequencing for Engineering and Characterizing Gene Delivery

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    The advent of massively parallel sequencing and synthesis technologies have ushered in a new paradigm of biology, where high throughput screening of billions of nucleid acid molecules and production of libraries of millions of genetic mutants are now routine in labs and clinics. During my Ph.D., I worked to develop data analysis and experimental methods that take advantage of the scale of this data, while making the minimal assumptions necessary for deriving value from their application. My Ph.D. work began with the development of software and principles for analyzing deep mutational scanning data of libraries of engineered AAV capsids. By looking at not only the top variant in a round of directed evolution, but instead a broad distribution of the variants and their phenotypes, we were able to identify AAV variants with enhanced ability to transduce specific cells in the brain after intravenous injection. I then shifted to better understand the phenotypic profile of these engineered variants. To that end, I turned to single-cell RNA sequencing to seek to identify, with high resolution, the delivery profile of these variants in all cell types present in the cortex of a mouse brain. I began by developing infrastructure and tools for dealing with the data analysis demands of these experiments. Then, by delivering an engineered variant to the animal, I was able to use the single-cell RNA sequencing profile, coupled with a sequencing readout of the delivered genetic cargo present in each cell type, to define the variant’s tropism across the full spectrum of cell types in a single step. To increase the throughput of this experimental paradigm, I then worked to develop a multiplexing strategy for delivering up to 7 engineered variants in a single animal, and obtain the same high resolution readout for each variant in a single experiment. Finally, to take a step towards translation to human diagnostics, I leveraged the tools I built for scaling single-cell RNA sequencing studies and worked to develop a protocol for obtaining single-cell immune profiles of low volumes of self-collected blood. This study enabled repeat sampling in a short period of time, and revealed an incredible richness in individual variability and time-of-day dependence of human immune gene expression. Together, my Ph.D. work provides strategies for employing massively parallel sequencing and synthesis for new biological applications, and builds towards a future paradigm where personalized, high-resolution sequencing might be coupled with modular, customized gene therapy delivery.</p

    MIXING IT UP: THE IMPACT OF EPISODIC INTROGRESSION ON THE EVOLUTION OF HIGH-LATITUDE MESOCARNIVORES

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    At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude species. To understand the role of episodic isolation and gene flow on the evolution and diversification of high-latitude species, my dissertation integrates genetic, genomic, and morphometric characters across multiple high-latitude mesocarnivore mammals within the hyper-diverse Mustelidae family. Overall, I identified substantial cryptic diversity in the Arctic and highlight the complementary roles of glacial and interglacial cycles in the evolution and structuring of high latitude biota
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