1,721,095 research outputs found
Universal chromatin state annotation of the mouse genome
No full textGenome-wide chromatin states learned from integrating genome-wide maps of multiple epigenetic marks within the same cell type have been widely used to generate genome annotations of individual cell types. An alternative strategy based on ‘stacked modeling’ can provide a single ‘universal’ chromatin state annotation based jointly on data from many cell types. In human, such an approach was recently demonstrated and the resulting chromatin state annotation, denoted full-stack, was shown to have complementary advantages to per-cell-type annotations. However, an analogous annotation has not been previously available in mouse. Here, we produce a chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 different cell or tissue types. To characterize each chromatin state, we relate the states to other external annotations and compare them to analogously defined states in human. We expect the full-stack chromatin state annotation for mouse will be a useful resource for studying the genome of this key mammalian model organism
Universal chromatin state annotation of the mouse genome
No full textGenome-wide chromatin states learned from integrating genome-wide maps of multiple epigenetic marks within the same cell type have been widely used to generate genome annotations of individual cell types. An alternative strategy based on ‘stacked modeling’ can provide a single ‘universal’ chromatin state annotation based jointly on data from many cell types. In human, such an approach was recently demonstrated and the resulting chromatin state annotation, denoted full-stack, was shown to have complementary advantages to per-cell-type annotations. However, an analogous annotation has not been previously available in mouse. Here, we produce a chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 different cell or tissue types. To characterize each chromatin state, we relate the states to other external annotations and compare them to analogously defined states in human. We expect the full-stack chromatin state annotation for mouse will be a useful resource for studying the genome of this key mammalian model organism
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
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
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
No full textChromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.United States. Dept. of Energy (Contract DE-AC02-05CH11231)RC2 HG005639U01 HG004279R01 GM082798R37 GM45744R37 GM45744R01 GM071923U54 HG004592National Science Foundation (U.S.) (NSF 0905968
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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