1,720,991 research outputs found
Identification of constrained sequence elements across 239 primate genomes
No full textAbstract Noncoding DNA is central to our understanding of human gene regulation and complex diseases 1,2 , and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome 3–9 . Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA 10 , the relatively short timescales separating primate species 11 , and the previously limited availability of whole-genome sequences 12 . Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis -regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals
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
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Identification and Interpretation of Causal Genetic Variants Underlying Human Phenotypes
No full textHuman genetics provides a powerful approach for the identification of genetic loci involved in the pathogenesis of human disease. Whole exome (WES), and increasingly whole genome, sequencing have allowed for the identification of rare, highly penetrant variants that result in severe disease. Scalable genotypic array approaches have similarly empowered the robust association of thousands of common genetic variants with modest effects on complex human traits. In both cases, it remains difficult to distinguish between pathogenic or benign and causal or passenger variants. In the following works, I develop and apply methodologies to better identify and understand the effects of a wide spectrum of variants in the human genome.
In Chapter 1, I analyze WES of 472 individuals with Diamond-Blackfan anemia (DBA), a classic Mendelian disease characterized by a pure red cell aplasia. By combining population genetic databases, RNA sequencing, and copy number variant analyses, I identify a pathogenic variant for 78% of DBA individuals, including a number of prominent phenocopies.
In Chapter 2, I identify associations for common variants in 115,000 individuals with heritable blood cell measurements. By applying fine-mapping, an approach to disentangle correlations between neighboring inherited variants, I pinpoint hundreds of likely causal variants contributing to differences in blood cell production.
In Chapter 3, I expand my fine-mapping studies to 360,000 individuals across 96 human phenotypes. After carefully benchmarking and evaluating these approaches, I apply them to identify 2,519 likely causal common genetic variants that influence physiological human traits. In
both this and the previous chapter, I use experimental and statistical approaches to dissect the molecular mechanisms of variants that regulate gene expression.
Finally, in several collaborative studies, I apply these methods to traits related to genome instability, show how different Bayesian priors can be used to improve causal variant resolution, extend these methods across genetic ancestry and genetic variant type, validate fine-mapped variants using high-throughput assays, develop a benchmark for commonly used target gene discovery methods, and finally demonstrate the usefulness of mitochondrial genome variants for lineage tracing applications. Together, these studies advance our understanding of how genetic variants alter human physiology.Medical SciencesMedical Science
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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