From Research Assistant to Researcher: Being Wakeful in a Mentorship Journey About Methodology, Poverty, and Deficit Thinking

This article explores how insights and new knowledge were incorporated about narrative inquiry methodology, poverty, and deficit ways of thinking through a journey of mentorship. The experiences of a graduate student, as she journeys through the roles of a research assistant and graduate researcher, all the while being part of a positive mentorship experience, are relayed. The article describes the journey of an evolving researcher who becomes wakeful through the narrative inquiry methodology while engaged as a research assistant as well as a graduate student alongside her supervisor

“GOOD, STEADY PROGRESS”: SUCCESS STORIES FROM ONTARIO ELEMENTARY SCHOOLS IN CHALLENGING CIRCUMSTANCE

This paper presents findings from a funded case study research project conducted in Ontario, Canada during the 2007-2008 school year. Together with the Elementary Teachers‘ Federation of Ontario (ETFO), the researchers undertook a qualitative investigation to identify and describe success stories from a diverse sample of 11 Ontario elementary schools working with students and communities affected by poverty. Through school visits, interviews, and document analysis, researchers identified three major findings: schools made connections with parents and the broader community; schools built a sense of collective endeavor and community within the school; and schools struggled with a persistent dilemma regarding students‘ social versus academic needs. The project contributes to the Canadian research literature on poverty and schooling and to the practical understanding of how schools can better work with students and communities affected by poverty

Problematizing Complexities and Pedagogy in Teacher Education Programs: Enacting Knowledge in a Narrative Inquiry Teacher Education Discourse Community

This article describes how a cross-Canada cohort of teacher educators identified the benefits of participating in a narrative inquiry teacher education discourse community. The community enables conscious dialogue regarding the legitimacy of teacher knowledge, identification of personal and professional issues within educational contexts, and connections between local issues and global trends. Three themes are explored: (1) development of a non-hierarchical community, (2) unravelling of complexities in light of external pressures, and (3) personal ethical responses to current challenges. Teacher educator knowledge is deepened by providing a relational venue to attend to educational reform and programmatic complexity by grounding practices in collaborative experience

Epidemiology of chronic pain in children and adolescents : a protocol for a systematic review update

Funding This work was supported by an operating grant from the Canadian Institutes of Health Research (FRN167902) awarded to CTC and funding from the Dalhousie Medical Research Foundation (DMRF). CTC is the senior author and is supported by a Tier 1 Canada Research Chair with infrastructure support from the Canada Foundation for Innovation. CLL is supported by an IWK Health Centre Summer Studentship (1025420). PRT is supported by a Research Nova Scotia Scholars Award, a Nova Scotia Graduate Scholarship and an IWK Graduate Studentship Award, and is a trainee member of Pain Child Health (PICH).Peer reviewedPublisher PD

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Integrated Molecular Characterization of Uterine Carcinosarcoma

SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified