1,720,992 research outputs found
Chromosomal assembly and comparative analysis of the red fox (Vulpes vulpes) genome
Full text linkIn the early days of genomics, the development of a reference genome was an expensive, collaborative undertaking reserved only for traditional and popular model organisms; however, in a theoretical shift highlighted most clearly by the goals of the Genome 10K Project, the advent of next-generation sequencing (NGS) technology has resulted in a shift of focus towards the development of reference genomes for a variety of species less commonly studied. One non-traditional model organism selected as a priority species for the Genome 10K Project is the red fox (Vulpes vulpes), and specifically a fox from an experimental breeding project in which silver foxes (a melanistic variant of the red fox) have been selected over the past several decades to exhibit extreme behavioral phenotypes. The population consists of a strain of hyper-aggressive foxes and a strain of hyper-docile foxes, offering a model system through which the genetic underpinnings of behavior, as well as the genetic correlates of domestication, can be investigated.
The draft red fox genome, which was developed at BGI, has a sequence depth of 94x and is assembled into 676,878 scaffolds with an N50 of 11.80 Mbp. However, in order for the reference genome to be integrated with previous work in the model system, it is necessary to understand the relationship between the scaffolds and the chromosomes they comprise. Therefore, the primary goal of the present study was to assemble the fox chromosomes from the scaffolds of the draft red fox genome assembly.
The draft genome was first analyzed to detect bioinformatic errors known to occur in NGS-assembled genomes that might influence the integrity of the chromosome assembly. Based on these findings, the 500 largest scaffolds were assembled into the 17 fox chromosomes (16 autosomes and the X) based both on nucleotide-level synteny among the fox, dog, and cat identified through pairwise alignment of the reference genomes and on interspecies synteny reported in previously developed comparative maps. The result of the current analysis is the development of a new version of the red fox reference genome that will serve as a valuable tool in ongoing research by increasing the resolution at which mapping studies can probe the genetic architecture of complex behavioral phenotypes in the domesticated fox system.Submission published under a 24 month embargo labeled 'U of I only', the embargo will last until 2017-08-01The student, Halie Rando, accepted the attached license on 2015-07-21 at 12:21.The student, Halie Rando, submitted this Thesis for approval on 2015-07-21 at 13:50.This Thesis was approved for publication on 2015-07-21 at 14:34.DSpace SAF Submission Ingestion Package generated from Vireo submission #8585 on 2015-09-29 at 15:00:54Made available in DSpace on 2015-09-29T20:50:22Z (GMT). No. of bitstreams: 3
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DSAD Module 4 - Python
No full textLectures for teaching data science tools in Python to graduate students from various disciplines on campus.Submitted by Diana Byrne ([email protected]) on 2016-08-03T21:41:06Z
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DSAD Module 4 - Python
No full textLectures for teaching data science tools in Python to graduate students from various disciplines on campus.UIUC Graduate College Focal PointU of I OnlyUIUC acces
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Correction for Rando et al., “Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure”
Full text linkVolume 6, no. 5, e00095-21, 2021, https://doi.org/10.1128/mSystems.00095-21. The author byline and affiliations should appear as shown in this correction. Page 3: The following should be added to the Fig. 1 legend. ‘This figure was adapted from “Human Coronavirus Structure,” by BioRender.com (2020), retrieved from https://app .biorender.com/biorender-templates.’ Page 21: In the 2nd paragraph of Acknowledgements, “S.M.B. is currently an employee at AstraZeneca, Gaithersburg, MD, USA, and may own stock or stock options; work was initially conducted at Georgetown University Medical Center, with writing, reviewing, and editing continued while working at AstraZeneca. Y.P. is now employed by Pfizer (subsequent to contributions to this project).” should read “S.M.B. is currently an employee at AstraZeneca, Gaithersburg, MD, USA, and may own stock or stock options. Y.P. is affiliated with Pfizer Worldwide Research; the author has no financial interests to declare and contributed as an author prior to joining Pfizer, and the work was not part of a Pfizer collaboration nor was it funded by Pfizer.” Copyright © 2022 Rando et al
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe 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
Full text linkWe 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
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