1,720,973 research outputs found
Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
No full textATAC-Seq reports local chromatin accessibility and provides a snapshot of active regulatory regions and genomic regions occupied by DNA-binding proteins in a given tissue. We used ATAC-Seq to identify open chromatin sites in FGFR3-positive spermatogonial cells isolated from dissociated human testicular samples. FGFR3 is most highly expressed in self-renewing spermatogonial stem cells, with low expression also being detected in early differentiating spermatogonia; its expression thus overlaps with the onset of PRDM9 expression in pre-meiotic spermatogonia. Open chromatin in FGFR3-positive cells was identified using standard peak detection analysis with MACS2 software.Talmane, Lana; Kaiser, Vera; Kumar, Yatendra; Semple, Fiona; MacLennan, Marie; Semple, Colin; Fitzpatrick, David; Taylor, Martin. (2021). Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome, [dataset]. University of Edinburgh. MRC IGC. MRC Human Genetics Unit. https://doi.org/10.7488/ds/3053
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
The role of the nuclear basket in regulating the senescence-associated secretory phenotype
Full text linkOncogene-induced senescence is a state of irreversible cell cycle arrest, accompanied by the secretion of signalling molecules, including pro-inflammatory cytokines and chemokines. These are collectively known as the senescence-associated secretory phenotype (SASP). The SASP enhances immune cell recruitment, aiding the clearance of senescent cells, but can also contribute to tumorigenesis. TPR, a protein in the nuclear basket of the nuclear pore complex, is known to be necessary for SASP induction in fibroblasts undergoing Ras-induced senescence.
In this thesis I investigate the mechanism by which TPR impacts the SASP. Using ATAC-seq, I show that potential enhancer elements, often close to key SASP genes, become active in senescent cells, but that this activity is lost when TPR is knocked down. I identify that these putative enhancers contain binding sites for NF-κB, a transcription factor known to regulate the SASP and I show that NF-κB activation is reduced in senescent cells without TPR.
Decreased NF-κB activation is already evident after three days of Ras activation and TPR knockdown, preceding induction of the SASP. RNA-seq carried out at the same timepoint shows transcriptional downregulation of STING upon TPR depletion. This is accompanied by reduced levels of cytoplasmic chromatin fragments (CCFs), which are known to activate NF-κB and the SASP through cGAS-STING signalling. This suggests that the nuclear pore complex may play a role in the blebbing off of the nuclear membrane to form CCFs in senescent cells.
I also investigate a potential role in senescence for the recently discovered nuclear basket protein ZC3HC1. I confirm that ZC3HC1 is present at the nuclear periphery and its localisation is dependent on TPR. However, contrary to previous reports, TPR localisation to nuclear pores does not depend on ZC3HC1. Unlike TPR, ZC3HC1 knockdown does not affect the SASP, and knockdown of ZC3HC1 causes different transcriptional changes from those that occur on TPR knockdown, suggesting distinct roles for the two nuclear basket proteins
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
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
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