1,721,178 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
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
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Comparative Genomics and Chromosome Evolution
Full text linkViewed through the lens of comparative genomics, how have chromosomes and karyotypes evolved, particularly under extreme scenarios of rapid or torpid evolution? To examine this question, I produced and analyzed new high-quality, chromosome-scale genome assemblies, representing cases of extreme chromosome evolution. The interplay between convergent and divergent genomic architectures can further our understanding into the maintenance of chromosome structure and organization as well as the underlying biological mechanisms. Despite their recent divergence, muntjac deer show striking karyotype differences. In Chapter 2, I produced new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyzed their evolution and architecture. I identified six fusion events shared by both species relative to the cervid ancestor and, therefore, present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and 26 fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Although comparative Hi-C analysis uncovered differences in long-range genome contacts and A/B compartment structures, I discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. Analysis of the muntjac genomes revealed new insights into this unique case of rapid karyotype evolution and the resulting biological variation. In contrast to muntjacs, frogs are a more phylogenetically ancient order, with two prominent species, Xenopus laevis and Xenopus tropicalis, being utilized as vertebrate cell and developmental model systems. In Chapter 3, I reported new chromosome-scale genome assemblies for three distantly related frogs: the common coquí (Eleutherodactylus coqui), the túngara frog (Engystomops pustulosus), and the Zaire dwarf clawed frog (Hymenochirus boettgeri). Through comparative sequence analysis of these and other frog genomes, I identified long-range and even chromosome-scale synteny, denoting the stability and pervasiveness of this type of genomic conservation across the frog phylogeny. These chromosome-scale comparisons also revealed the 13 ancestral chromosomes, with limited Robertsonian translocations and end-to-end fusions explaining the observed chromosome variations. These assemblies, encompassing over a billion years of evolutionary divergence, unmasked insights into torpid karyotype evolution in frogs
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Molecular Mechanisms of Precise and Robust Gene Regulation in Drosophila
Full text linkThe ornate arrangement of diverse cells into specialized tissues, organs, and higher structures characteristic of multicellular organisms is all encoded from the same genome sequence. Despite their differences, morphologically distinct cells (e.g. muscle cells and neurons) must transcribe many of the same genes. Morphological indistinguishable cells must often transcribe distinct sets of genes (e.g. different odorant receptor cells). The ensemble of genes expressed in a given cell -- and the relative frequency they are expressed at, give each cell its characteristic identity more so than the presence of individual genes. Therefore understanding the genetic control of development and differentiation is a question not so much of the understanding the gene sequences themselves, but the regulatory structure of the genome which determines how they are deployed.In order for development to unravel in such a manner that each embryo makes it through the process with all the correct parts in the correct positions at the end, this process must be exceedingly precise. Though often taken for granted, this precision becomes particular impressive if one considers the frequency with which mistakes are made in intelligently designed human built assembly processes. The developing animal must position components correctly on scales of microns (e.g. tissue boundaries) and nanometers (e.g. neuron-junctions), has no external direction of assembly, and requires thermal noise to position many of its components (including essentially all transcription factors - proteins which regulate read access to the genome). It is not sufficient for the process to be precise. It must also be robust to changes in the conditions in which it operates, such as different thermal environments, nutrient conditions, and chemical environments. This robustness enables a certain degree of plasticity, such that some components of the system can change and evolve new functions, without causing catastrophic failure of the rest of the system. In my thesis research I have tried to explore some of the molecular mechanisms of gene regulation which support the precise and robust expression of multicellular genomes. Rapid advances in post-genomic technologies have exposed a broad range of fundamental differences in the organization and regulation of multicellular genomes such as Drosophila. I have worked primarily on two phenomena, the use of promoter proximal pausing as a regulatory strategy, and the use of multiple apparently redundant regulatory sequences to drive expression of the same gene. Discovery of both of these phenomena emerged from analysis of whole genome polymerase and transcription factor binding data. Using quantitative high resolution in situ and semi-automated computational image processing I have studied the detailed differences in the transcriptional activation and transcription frequency of genes regulated by these mechanisms. Through this analysis I have shown a strong correlation through more rapid and synchronous gene expression and regulation through release of promoter proximal paused polymerase. Theoretical modeling demonstrates that such an effect can be expected from regulating release of stable downstream state in a general assembly process (such as construction of the RNA Pol II pre-initiation complex). Analysis of gene expression driven by multiple enhancers with overlapping activity compared to constructs with only a single active enhancer revealed that the process by which an enhancer binds its target transcription factors and activates expression is often limiting enough that having a second independent copy can produce detectable changes in the frequency of transcription. This reduction of natural variation in gene activation is especially important under stress conditions, such as thermal stress or reduced levels of some of the activating factors. Robustness to this sort of variation may be important both for adaptation within a species and the flexibility to allow modification of interacting pathways in the course of evolutionary modification. These investigations also revealed a corrective propensity whereby the simultaneous activity of multiple enhancers, responding to repressors as well as activators, can give rise to correctly restricted gene expression even when the elements taken in isolation drive some degree of ectopic expression. So far both of these mechanisms have only been reliably documented in multicellular systems, suggesting that the precision and robustness they confer may be an innovation of metazoans in response to increased levels of coordination required to keep many cells functioning in the tight cooperation of a multicellular organism. Doubtless this is but scratching the surface of the mechanisms which ensure such precision and control. However the rapid improvements to both genomic tools and imaging technology make it like to be a promising field for further exploration for years to come
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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Four Statistical Explorations of Genetic Variation
Full text linkGenetic variation is the result of DNA sequence differences between individuals or populations. Our understanding of genetic variation has benefited greatly from advances in DNA sequencing, computational power, and statistical tools. I will present four statistical analyses of genetic variation related to genetic mapping, genome editing, evolutionary biology, and de novo genome assembly and annotation. First, I will present a novel methodology for genotype imputation and composite genetic marker construction. This technique, minimum spanning tree imputation, is designed to improve linkage maps in outbred F1 crosses, particularly from genetic markers derived from low confidence sequencing. I then use minimum spanning tree imputation to construct sex-specific genetic maps for Xenopus laevis, Branchiostoma floridae, and Miscanthus sinensis. Second, I will present a case of three mouse lines edited with the CRISPR/Cas9 system in order to delete an enhancer locus in the IL2RA gene. All three lines were confirmed to have the intended deletion. Curiously, one line displayed a severe immune deficient phenotype that persistently bred true. By resequencing mice from these lines, I was able to identify the occurrence of a tandem duplication as an off-target consequence of the editing in the immune compromised individuals that was absent in the other lines. The tandem duplication was then confirmed experimentally. I close by proposing a repair mechanism mediated by microhomology that might have caused the tandem duplication to form. Third, I will compare the chromosomal position of orthologous genes between lancelet amphioxus, Branchiostoma floridae (an early-branching living chordate) and five vertebrates. These comparisons will offer support for the “2R hypothesis,” that early vertebrate organisms underwent two rounds of whole genome duplication. This analysis takes advantage of a novel way of computing and visualizing mutual best hits between previously identified chordate linkage groups (CLGs) and segments of vertebrate chromosomes. Finally, I will present my contributions to the assembly and annotation of the genome of a regenerative model organism, Hofstenia miamia
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