Library Beautification: Decorating a Denuded Library That Has Only Three Months Left to Live (in Its Current Location)

In the last semester of its tenure in Lehman Hall, after its book stacks were removed Barnard librarians found ways to make the library cozy and fun. With limited resources College Archivist Shannon O'Neill led a task force's efforts to bring in inexpensive furniture and the Communications Committee, chaired by communications director and zine librarian Jenna Freedman devised an activity to ignite students' feeling of ownership of the space

Sound design and music as part of the adapted and performed text in narrative theatre

This study is based on the narrative theatre production of The Time Traveler's Wife, a collaborative production with adaptor/director J. Lauren Shouse and musical director/sound designer/composer Shannon M. Murphy O'Neill, performed in October 2005 in Studio Six of Swain Hall on the campus of the University of North Carolina at Chapel Hill. This study examines the importance of music and sound design as a part of the adapted and performed text in a narrative theatre production that is not a musical. Specifically this study examines a.) relevant literature pertaining to music and sound design, b.) the collaboration between the adaptor/director and musical director/sound designer/composer to create the text, and c.) the development of an artistic aesthetic through the study.Master of Art

Associative Transcriptomics Study Dissects the Genetic Architecture of Seed Glucosinolate Content in Brassica napus

Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines

A reexamination of information theory-based methods for DNA-binding site identification

<p>Abstract</p> <p>Background</p> <p>Searching for transcription factor binding sites in genome sequences is still an open problem in bioinformatics. Despite substantial progress, search methods based on information theory remain a standard in the field, even though the full validity of their underlying assumptions has only been tested in artificial settings. Here we use newly available data on transcription factors from different bacterial genomes to make a more thorough assessment of information theory-based search methods.</p> <p>Results</p> <p>Our results reveal that conventional benchmarking against artificial sequence data leads frequently to overestimation of search efficiency. In addition, we find that sequence information by itself is often inadequate and therefore must be complemented by other cues, such as curvature, in real genomes. Furthermore, results on skewed genomes show that methods integrating skew information, such as <it>Relative Entropy</it>, are not effective because their assumptions may not hold in real genomes. The evidence suggests that binding sites tend to evolve towards genomic skew, rather than against it, and to maintain their information content through increased conservation. Based on these results, we identify several misconceptions on information theory as applied to binding sites, such as negative entropy, and we propose a revised paradigm to explain the observed results.</p> <p>Conclusion</p> <p>We conclude that, among information theory-based methods, the most unassuming search methods perform, on average, better than any other alternatives, since heuristic corrections to these methods are prone to fail when working on real data. A reexamination of information content in binding sites reveals that information content is a compound measure of search and binding affinity requirements, a fact that has important repercussions for our understanding of binding site evolution.</p

The Detection of an Extremely Bright Fast Radio Burst in a Phased Array Feed Survey

We report the detection of an ultra-bright fast radio burst FRB)from a modest, 3.4-day pilot survey with the Australian Square Kilometre Array Pathfinder. The survey was conducted in a wide- field fly’s-eye configuration using the phased-array-feed technology deployed on the array to instantaneously observe an effective area of 160 deg2, and achieve an exposure totalling 13200 deg2 hr. We constrain the position of FRB 170107 to a region 8 ́ x 8 ́ in size(90% containment)and its fluence to be 58 ± 6 Jy ms. The spectrum of the burst shows a sharp cutoff above 1400 MHz, which could be due to either scintillation or an intrinsic feature of the burst. This confirms the existence of an ultra-bright (> 20 Jy ms) population of FRBs

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

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

Generating route-level mutually exclusive service areas: comparative study of alternative methods

Willing-to-walk distance was investigated as a means of measuring spatial accessibility of bus stops and of examining the effectiveness of alternative methods of generating mutually exclusive transit service areas at the route level. First, the walking distance to and from a transit stop was investigated with onboard survey data. Two methods in geographical information systems - the combination of Thiessen polygon and buffer and the network distance-based service area - were compared as strategies for generating mutually exclusive service areas. For the examination of the effectiveness of these two methods, all mutually exclusive service areas were validated with a spider diagram generated from an onboard survey. Measures of urban form were also statistically tested for comparison of the two methods. A case study of a single route, serving the Minneapolis-Saint Paul, Minnesota, metropolitan area, was performed with data from various sources, such as Google's General Transit Feed Specification, an onboard survey, parcel-level land uses, and the U. S. Census street network. Validation with onboard survey data demonstrates the strengths of each method. Results also show that the network-based service area, a popular geographical information system method for service area analysis, does not yield a more meaningful strategy for generating mutually exclusive transit catchment areas, especially when spacing between stops is very small