1,720,970 research outputs found
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
CaTCHing the functional and structural properties of chromosome folding
Full text linkProper development requires that genes are expressed at the right time, in the right tissue, and at the right transcriptional level. In metazoans, this involves long-range cis-regulatory elements such as enhancers, which can be located up to hundreds of kilobases away from their target promoters. How enhancers find their target genes and avoid aberrant interactions with non-target genes is currently under intense investigations. The predominant model for enhancer function involves its direct physical looping between the enhancer and target promoter. The three-dimensional organization of chromatin, which accommodates promoter- enhancer interactions, therefore might play an important role in the specificity of these interactions. In the last decade, the development of a class of techniques called chromosome conformation capture (3C) and its derivatives have revolutionized the field of chromatin folding. In particular, the genome-wide version of 3C, Hi-C, revealed that mammalian chromosomes possess a rich hierarchy of folding layers, from multi-megabase compartments corresponding to mutually exclusive associations of active and inactive chromatin to topologically associating domains (TADs), which reflect regions with preferential internal interactions. Although the mechanisms that give rise to this hierarchy are still poorly understood, there is increasing evidence to suggest that TADs represent fundamental functional units for establishing the correct pattern of enhancer-promoter interactions. This is thought to occur through two complementary mechanisms: on the one hand, TADs are thought to increase the chances that regulatory elements meet each other by confining them within the same domain; on the other hand, by segregation of physical interactions across the boundary to avoid unwanted events to occur frequently.
It is however unclear whether the properties that have been attributed to TADs are specific to TADs, or rather common features among the whole hierarchy. To address this question, I have implemented an algorithm named Caller of Topological Chromosomal Hierarchies (CaTCH). CaTCH is able to detect nested hierarchies of domains, allowing a comprehensive analysis of structural and functional properties across the folding hierarchy. By applying CaTCH to published Hi-C data in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs), I showed that TADs emerge as a functionally privileged scale. In particular, TADs appear to be the scale where accumulation of CTCF at domain boundaries and transcriptional co-regulation during differentiation is maximal. Moreover, TADs appear to be the folding scale where the partitioning of interactions within transcriptionally active domains (and notably between active enhancers and promoters) is optimized.
3C-based methods have enabled fundamental discoveries such as the existence of TADs and CTCF-mediated chromatin loops. 3C methods detect chromatin interactions as ligation products after crosslinking the DNA. Crosslinking and ligation have been often criticized as potential sources of experimental biases, raising the question of whether TADs and CTCF- mediated chromatin loops actually exist in living cells. To address this, in collaboration with Josef Redolfi, we developed a new method termed ‘DamC’ which combines DNA methylation with physical modeling to detect chromosomal interactions in living cells, at the molecular scale, without relying on crosslinking and ligation. By applying DamC to mouse ESCs, we provide the first in vivo and crosslinking- and ligation-free validation of chromosomal structures detected by 3C-methods, namely TADs and CTCF-mediated chromatin loops.
DamC, together with 3C-based methods, thus have shown that mammalian chromosomes possess a rich hierarchy of folding layers. An important challenge in the field is to understand the mechanisms that drive the establishment these folding layers. In this sense, polymer physics represent a powerful tool to gain mechanistic insights into the hierarchical folding of mammalian chromosomes. In polymer models, the scaling of contact probability, i.e. the contact probability as a function of genomic distance, has been often used to benchmark polymer simulations and test alternative models. However, the scaling of contact probability is only one of the many properties that characterize polymer models raising the question of whether it would be enough to discriminate alternative polymer models. To address this, I have built finite-size heteropolymer models characterized by random interactions. I showed that finite-size effects, together with the heterogeneity of the interactions, are sufficient to reproduce the observed range of scaling of contact probability. This suggests that one should be careful in discriminating polymer models of chromatin folding based solely on the scaling.
In conclusion, my findings have contributed to achieve a better understanding of chromatin folding, which is essential to really understand how enhancers act on promoters. The comprehensive analyses using CaTCH have provided conceptually new insights into how the architectural functionality of TADs may be established. My work on heteropolymer models has highlighted the fact that one should be careful in using solely scaling to discriminate physical models for chromatin folding. Finally, the ability to detect TADs and chromatin loops using DamC represents a fundamental result since it provides the first orthogonal in vivo validation of chromosomal structures that had essentially relied on a single technology
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
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
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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