1,720,953 research outputs found
Identification of structural variations from whole genome sequencing of cancer patients
Get PDFCancer is largely driven by accumulation of somatic mutations that can be subdivided into small mutations (single nucleotide variations (SNVs), small insertions and deletions) and large structural variations (SVs). While SNVs affect single nucleotide, SVs can affect large stretches of DNA. Reliable identification of all mutations is key to understanding genetic diseases like cancer.
SVs can be identified by whole genome sequencing with conventional Illumina short-read sequencing (cWGS) being the most widely used approach. However, reliable prediction of SVs with short-reads (50-150bp) from fragmented DNA (~0.5kb) is challenging due to ambiguous mapping reads at repetitive regions and typically only few short reads span rearranged SV breakpoints with limited sequence overlap (due to read length). The 10X Genomics linked- reads sequencing (10XWGS) technology aims to mitigate limitations by linking short-reads to the original larger fragment of DNA (~10kb). In this study, we performed an unbiased evaluation of these two technologies with different types and sizes of SVs and compared their performance. The SVs commonly identified by both the technologies were highly specific, while the validation rate dropped for uncommon SVs. Despite the technological advantage, a particularly high false discovery rate (FDR) was observed for SVs found only by 10XWGS without any significant improvement in sensitivity. We proposed a sensitive and specific statistical approach to improve SV predictions from both technologies and characterized SVs from MCF7 breast cancer cell line and a primary breast tumor with high precision.
Due to the limited benefit of 10XWGS for sensitivity, we trained a random forest classifier in FuseSV for accurate predictions only from cWGS sequencing data. FuseSV integrates SV predictions from multiple bioinformatics tools and mitigates high FDR of cWGS with a novel set of features derived from alignment of reads to the reference genome, biological mechanisms of SVs and breakpoints of SVs clustered together to consider complex genomic rearrangements (CGRs). The performance of FuseSV classifiers was superior to all individual bioinformatics tools as well as combined use with 10XWGS.
SVs whether simple or complex can form chimeric fusion transcripts (CMTs). CMTs can be predicted from RNA-sequencing (RNA-seq) data but include also transcripts that occur without underlying mutation and are also present in healthy tissues. Here we propose a novel pipeline, FUdGE, that predict three types of CMT directly from somatic SVs: These include direct fusion transcripts or classical fusion genes, transcripts with intron (IR) and intergenic region retained (INR). FUdGE allows independent confirmation of expressed CMTs from matched RNA-seq data. We validated the approach in the same MCF7 cell line and a primary breast tumor sample and investigate CMTs in a cohort of liposarcoma samples. Here we observed that the majority of confirmed SV driven CMTs were classical fusion genes with a much smaller number of IR and INR events.
Conclusively, FuseSV enables accurate prediction of somatic SVs in cancer using only cWGS. While FUdGE provides an RNA-seq independent strategy for direct prediction of CMTs formed due to somatic SV event. The respective expressed CMT candidates can be confirmed independently with RNA-seq data. This alternative approach only predicts tumor-specific somatic SV driven CMTs, which is advantageous for personalized immunotherapy interventions considering CMTs as neo-antigen candidates.XII, 91 Seiten ; Illustrationen, Diagramm
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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