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"Burdick, Anne"
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Digital humanities
A visionary report on the revitalization of the liberal arts tradition in the electronically inflected, design-driven, multimedia language of the twenty-first century. Digital_Humanities is a compact, game-changing report on the state of contemporary knowledge production. Answering the question “Whatis digital humanities?,” it provides an in-depth examination of an emerging field. This collaboratively authored and visually compelling volume explores methodologies and techniques unfamiliar to traditional modes of humanistic inquiry—including geospatial analysis, data mining, corpus linguistics, visualization, and simulation—to show their relevance for contemporary culture. Written by five leading practitioner-theorists whose varied backgrounds embody the intellectual and creative diversity of the field, Digital_Humanities is a vision statement for the future, an invitation to engage, and a critical tool for understanding the shape of new scholarship.
eBook
Langerhans cells utilize CD1a and langerin to efficiently present nonpeptide antigens to T cells
Langerhans cells (LCs) constitute a subset of DCs that initiate immune responses in skin. Using leprosy as a model, we investigated whether expression of CD1a and langerin, an LC-specific C-type lectin, imparts a specific functional role to LCs. LC-like DCs and freshly isolated epidermal LCs presented nonpeptide antigens of Mycobacterium leprae to T cell clones derived from a leprosy patient in a CD1a-restricted and langerin-dependent manner. LC-like DCs were more efficient at CD1a-restricted antigen presentation than monocyte-derived DCs. LCs in leprosy lesions coexpress CD1a and langerin, placing LCs in position to efficiently present a subset of antigens to T cells as part of the host response to human infectious disease.
Journal Article
Integrated Pathways for Neutrophil Recruitment and Inflammation in Leprosy
Neutrophil recruitment is pivotal to the host defense against microbial infection, but it also contributes to the immunopathology of disease.We investigated the mechanism of neutrophil recruitment in human infectious disease by means of bioinformatic pathways analysis of the gene expression profiles in the skin lesions of leprosy. In erythema nodosum leprosum (ENL), which occurs in patients with lepromatous leprosy and is characterized by neutrophil infiltration in lesions, the most overrepresented biological functional group was cell movement, including E-selectin, which was coordinately regulated with interleukin 1β (IL-1β). In vitro activation of Toll-like receptor 2 (TLR2), up-regulated in ENL lesions, triggered induction of IL-1β, which together with interferon γ induced E-selectin expression on and neutrophil adhesion to endothelial cells. Thalidomide, an effective treatment for ENL, inhibited this neutrophil recruitment pathway. The gene expression profile of ENL lesions comprised an integrated pathway of TLR2 and Fc receptor activation, neutrophil migration, and inflammation, providing insight into mechanisms of neutrophil recruitment in human infectious disease.
Journal Article
Use of Genetic Profiling in Leprosy to Discriminate Clinical Forms of the Disease
Leprosy presents as a clinical and immunological spectrum of disease. With the use of gene expression profiling, we observed that a distinction in gene expression correlates with and accurately classifies the clinical form of the disease. Genes belonging to the leukocyte immunoglobulin-like receptor (LIR) family were significantly up-regulated in lesions of lepromatous patients suffering from the disseminated form of the infection. In functional studies, LIR-7 suppressed innate host defense mechanisms by shifting monocyte production from interleukin-12 toward interleukin-10 and by blocking antimicrobial activity triggered by Toll-like receptors. Gene expression profiles may be useful in defining clinical forms of disease and providing insights into the regulation of immune responses to pathogens.
Journal Article
T-cell release of granulysin contributes to host defense in leprosy
A novel mechanism by which T cells contribute to host defense against microbial pathogens is release of the antimicrobial protein granulysin. We investigated the role of granulysin in human infectious disease using leprosy as a model. Granulysin-expressing T cells were detected in cutaneous leprosy lesions at a six-fold greater frequency in patients with the localized tuberculoid as compared with the disseminated lepromatous form of the disease. In contrast, perforin, a cytolytic molecule that colocalizes with granulysin in cytotoxic granules, was expressed at similar levels across the spectrum of disease. Within leprosy lesions, granulysin colocalized in CD4
+
T cells and was expressed in CD4
+
T-cell lines derived from skin lesions. These CD4
+
T-cell lines lysed targets by the granule exocytosis pathway and reduced the viability of mycobacteria in infected targets. Given the broad antimicrobial spectrum of granulysin, these data provide evidence that T-cell release of granulysin contributes to host defense in human infectious disease.
Journal Article
Meta!Meta!Meta!: A Speculative Design Brief for the Digital Humanities
Fictitious future scenarios are used in the technology industry to identify new opportunities, test high risk concepts, and rally teams toward a common goal. While such visions can play a crucial role in the technology development process, Digital Humanities futures are largely absent. This paper proposes a design approach that combines core concepts from critical theory with design's speculative inventiveness and introduces the subject-computer-interface as an alternative to industry's user-centered concept. Case studies investigate how this triad of meta processes -- the meta of critical interpretation, the meta of speculative reflexive design, and the meta of subject-computer-interface -- might work by using critical making to engage recent concepts from digital humanities theory to invent new digital affordances. The paper concludes with a speculative design brief that challenges designers, humanists, and computer scientists to use a meta-meta-meta approach that begins with core humanities concepts and designs outward to imagine digital humanities tools that don't yet exist.
Journal Article
Chronic Rhinitis: A Manifestation of Leprosy
Leprosy, or Hansen disease, is an infection that affects the mucous membranes of the respiratory tract and may manifest with nasal symptoms of chronic rhinitis, including nasal congestion, rhinorrhea, and intermittent epistaxis. We present a case of a woman diagnosed with leprosy as an incidental finding from a biopsy obtained during endoscopic sinus surgery for the management of chronic rhinitis. The diagnosis of leprosy should be considered in patients with nasal symptoms and presumptive chronic rhinitis who do not respond adequately to standard therapies.
Journal Article
Understanding Word Embedding Stability Across Languages and Applications
Despite the recent popularity of word embedding methods, there is only a small body of work exploring the limitations of these representations. In this thesis, we consider several aspects of embedding spaces, including their stability. First, we propose a definition of stability, and show that common English word embeddings are surprisingly unstable. We explore how properties of data, words, and algorithms relate to instability. We extend this work to approximately 100 world languages, considering how linguistic typology relates to stability. Additionally, we consider contextualized output embedding spaces. Using paraphrases, we explore properties and assumptions of BERT, a popular embedding algorithm. Second, we consider how stability and other word embedding properties affect tasks where embeddings are commonly used. We consider both word embeddings used as features in downstream applications and corpus-centered applications, where embeddings are used to study characteristics of language and individual writers. In addition to stability, we also consider other word embedding properties, specifically batching and curriculum learning, and how methodological choices made for these properties affect downstream tasks. Finally, we consider how knowledge of stability affects how we use word embeddings. Throughout this thesis, we discuss strategies to mitigate instability and provide analyses highlighting the strengths and weaknesses of word embeddings in different scenarios and languages. We show areas where more work is needed to improve embeddings, and we show where embeddings are already a strong tool.
Dissertation