1,721,094 research outputs found
Loss of the crumbs cell polarity complex disrupts epigenetic transcriptional control and cell cycle progression in the developing retina - code
No full text<p><strong>CRB Omics Manuscript Repo</strong><br>
Code for the _crb2a_ multi omics manuscript <a href="https://doi.org/10.1002/path.6056">https://doi.org/10.1002/path.6056</a></p>
<p>[](https://zenodo.org/badge/latestdoi/380179339)</p>
<p><br>
This is the analysis pipeline for the DNA methylation analysis and integration of RNA-seq and methylation (RRBS) data for the manuscript :</p>
<p><strong>Loss of the crumbs cell polarity complex disrupts epigenetic transcriptional control and cell cycle progression in the developing retina</strong></p>
<p>Owen, N., Toms, M., Tian, Y., Toualbi, L., Richardson, R., Young, R., Tracey-White, D., Dhami, P., Beck, S., Moosajee, M.</p>
<p>__Journal of Pathology 2023__ Apr;259(4):441-454. doi: [10.1002/path.6056](https://doi.org/10.1002/path.6056)</p>
<p> </p>
<p><strong>RRBS data analysis pipeline</strong></p>
<p> The code is organised for reviewers and reseachers to validate our analysis result. The RRBS data was generated from control (wt) and _crb2a_<sup>-/-</sup> zebrafish at 56 hpf. The raw NuGen generated bcl file are taken as input. The process of data analysis has been outlined in the following numbered section, indicating the sequence of analysis. Input for subsequent sections often requires results from the formal analysis.</p>
<p>In each folder, there is a R script called `main.R`, by running it in R session, in theory all results presented in this repo could be reproduced. Users need to install corresponding R packages, install corresponding R version (4.0.2+).</p>
<p>All analysis within are using Ensembl genome as genomic annotation ([version 98](ftp://ftp.ensembl.org/pub/release-98/)), except for CpG islands information used in ./05_GlobalIntegration, which is downloaded from USCS.</p>
<p><br>
<strong>Data</strong></p>
<p>The raw data for both RNA-seq and RRBS has been deposited within the NCBI Gene Expression Omnibus (GEO) at [GSE178709](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178709) and [GSE178842](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178842)</p>
<p><br>
</p>
<p> </p>
<p><strong>Full Changelog</strong>: <a href="https://github.com/nicholas-owen/crb_omics_manuscript/commits/v1.0.0">https://github.com/nicholas-owen/crb_omics_manuscript/commits/v1.0.0</a></p>
Tanner on Nicholas Owen: A Note
No full textAllan Fea, Secret Chambers and Hiding-Places (1901, 1904, 1908), pp. 20-21, quotes Mathias Tanner, Societas Iesu Militans … sive … Vita et Mors … (Prague, 1675), p. 75 (should be p. 73), as saying that Nicholas Owen ‘with incomparable skill knew how to conduct priests to a place of safety along subterranean passages, to hide them between walls and bury them in impenetrable recesses, and to entangle them in labyrinths and a thousand windings’. But, although there are reasons for supposing that Owen may have converted the medieval sewer at Baddesley Clinton into a hiding-place, Fea and others who have followed him are incautious in quoting the first part of this sentence at its face value. Tanner's Latin is reminiscent of Aeneid V, 588-591, and should perhaps be taken rather as an elegant tribute to a craftsman worthy to be compared with Daedalus:Ut quondam Creta fertur Labyrinthus in alta parietibus textum caecis iter ancipitemque mile viis habuisse dolum, qua signa sequendi frangeret indeprensus et inremeabilis error.The labyrinth of subterranean Crete: A legend for evasion and deceit; Where blind partitions wove a baffling maze, And sly devices turned a thousand ways.</jats:p
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
- …
