"Topic Modeling Assignment"

Curatorial note from Digital Pedagogy in the Humanities: As Elijah Meeks and Scott Weingart suggest in their introduction to a special issue of Journal of Digital Humanities, “[t]opic modeling could stand in as a synecdoche of digital humanities” because of its algorithmic complexity and potential obscurity. Joanna Swafford’s two-part topic modeling assignment for undergraduates makes it accessible by giving a clear explanation of the several steps required to prepare textual data, import it into the graphical user interface tool for MALLET, and explore the results. This assignment requires students to try the topic modeling process with different parameters and to assess the results of their experiments. This assignment helps students learn a specific method of text analysis as well as skills in visualizing and interpreting its results in relation to the historical and literary topics of the course

An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes.

OBJECTIVE: IKZF1 encoding Ikaros, an essential regulator of lymphopoiesis and immune homeostasis, has been implicated in the development of childhood acute lymphoblastic leukemia (C-ALL). Because recent genome-wide association (GWA) studies have linked a region of the 3'-UTR of IKZF1 with C-ALL susceptibility, we tested whether IKZF1 is associated with the autoimmune disease type 1 diabetes. RESEARCH DESIGN AND METHODS: rs10272724 (T>C) near IKZF1 at 7p12 was genotyped in 8,333 individuals with type 1 diabetes, 9,947 control subjects, and 3,997 families of European ancestry. Association was tested using logistic regression in the case-control data and by the transmission disequilibrium test in the families. Expression data for IKZF1 by rs10272724 genotype were obtained using quantitative PCR of mRNA/cDNA generated from peripheral blood mononuclear cells from 88 individuals, whereas expression data for five other neighboring genes were obtained from the online Genevar dataset. RESULTS: The minor allele of rs10272724 (C) was found to be protective from type 1 diabetes (odds ratio 0.87 [95% CI 0.83-0.91]; P = 1.1 × 10(-11)). rs10272724 was not correlated with levels of two transcripts of IKZF1 in peripheral blood mononuclear cells. CONCLUSIONS: The major susceptibility genotype for C-ALL confers protection from type 1 diabetes. Our finding strengthens the link between autoimmunity and lymphoid cancers. Further investigation is warranted for the genetic effect marked by rs10272724, its impact on IKZF1, and the role of Ikaros and other family members, Ailios (IKZF3) and Eos (IKZF4), in autoimmunity

"Topic Modeling Assignment"

Curatorial note from Digital Pedagogy in the Humanities: As Elijah Meeks and Scott Weingart suggest in their introduction to a special issue of Journal of Digital Humanities, “[t]opic modeling could stand in as a synecdoche of digital humanities” because of its algorithmic complexity and potential obscurity. Joanna Swafford’s two-part topic modeling assignment for undergraduates makes it accessible by giving a clear explanation of the several steps required to prepare textual data, import it into the graphical user interface tool for MALLET, and explore the results. This assignment requires students to try the topic modeling process with different parameters and to assess the results of their experiments. This assignment helps students learn a specific method of text analysis as well as skills in visualizing and interpreting its results in relation to the historical and literary topics of the course