IMPACT: The Journal of the Center for Interdisciplinary Teaching and Learning. Volume 8, Issue 2, Summer 2019

Many of us look for ways to help students forge concrete connections between their academic studies and the real world. Universities encourage professors to develop community-based learning, allowing students to contribute to the community beyond their campus in a way that enhances their academic studies and enables them to create these connections. Scholars have theorized the many benefits of community-based learning, but professors have many questions about how to implement community-based learning in practice. What does a successful community-based learning assignment look like? What are the different ways to assess students’ learning experiences in community-based learning assignments? How can one build effective partnerships with community organizations? In these pages, you will find practical advice, theoretical framework, and firsthand accounts of community-engaged teaching across disciplines. Learn from professors who have designed assignments allowing students to complete community projects with refugees, prisoners, veterans, elementary school children, science museums, nursing homes, public libraries, and ESL populations. Students in an Anthropology course, for instance, conduct oral history interviews with refugees, and provide written transcriptions of the interviews that the refugees can then use as a learning tool in ESL classes. In a Science Methods class, students collaborate with an aquarium to produce meaningful exhibits that educate the public. First-year writing students work with veterans to create autobiographical films and write papers related to the project

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Educational outliers: exclusion as innovation in nineteenth-century British literature

Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.This dissertation traces a genealogy of literary resistance to dominant pedagogies in nineteenth-century Britain. Although politicians, religious leaders, and literary authors celebrated the expansion of schools for people outside of privileged classes, a persistent tradition of writers registers the loss of non-institutional forms of learning. Excluded from Oxford and Cambridge because of their class or gender, Jane Austen, Elizabeth Barrett Browning, Thomas Hardy, and Virginia Woolf use their position outside of educational institutions to critique rote learning at universities for the elite as well as utilitarian schools for the masses. Hardy describes the "mental limitations" of Angel's Cambridge-educated brothers in Tess of the d'Urbervilles (1891), for example, mocking them as "such unimpeachable models as are turned out yearly by the lathe of systematic tuition." The radicalism of educational outliers emerges when read alongside educational pamphlets, working-men's club reports, college newspapers, and parliamentary debates. Educational outliers investigate the role that literature plays in un-teaching readers. They model alternative pedagogies centered on active learning instead of rote memorization. With Mansfield Park (1814), Austen inaugurates this tradition; at a time when proclamations on women's education proliferated, she offers novels as anti-treatises that constantly disrupt the reading experience instead of offering simplistic truths, forcing us to rely on our own judgment to make sense of the disorder that characterizes her model of self-education. Several decades later in her "novel-poem" Aurora Leigh (1856), Barrett Browning instructs us in a "headlong," empathic reading of her text as part of her experiential learning approach for women of different classes that stresses reform from within. Writing after more working-class schools had opened, Hardy tests the novel's capacity to un-teach assumptions about categories like "autodidact" itself and rewrites the celebratory self-made man's narrative by placing the reader in the position from which to weigh the positives and negatives of self-education. In the early twentieth century, Woolf imagines an education that "unfixes" students from their rigid class mindset in her "essay-novel" The Pargiters. Educational outliers' innovations ultimately prompt us to think about what outsiders' perspectives might be helpful today

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

: Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w