1,721,168 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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Negative feedback confers mutational robustness in yeast transcription factor regulation
Full text linkOrganismal fitness depends on the ability of gene networks to function robustly in the face of environmental and genetic perturbations. Understanding the mechanisms of this stability is one of the key aims of modern systems biology. Dissecting the basis of robustness to mutation has proven a particular challenge, with most experimental models relying on artificial DNA sequence variants engineered in the laboratory. In this work, we hypothesized that negative regulatory feedback could stabilize gene expression against the disruptions that arise from natural genetic variation. We screened yeast transcription factors for feedback, and used the results to establish the hypoxia regulator Rox1 as a model system for the study of feedback in circuit behaviors and its impact across genetically heterogeneous populations. Mutagenesis experiments revealed the mechanism of Rox1 as a direct transcriptional repressor at its own gene, enabling a regulatory program of rapid induction during environmental change that reached a plateau of moderate steady-‐state expression. Additionally, in a given environmental condition, Rox1 levels varied widely across genetically distinct strains; the ROX1 feedback loop regulated this variation, as the range of expression levels across genetic backgrounds showed greater spread in ROX1 feedback mutants than among strains with the ROX1 feedback loop intact. Our findings indicate that the ROX1 feedback circuit is tuned to respond to perturbations arising from natural genetic variation, in addition to its role in induction behavior. We suggest that regulatory feedback may be an important element of the network architectures that confer mutational robustness across biology
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The genetic dissection of trait differences between species of Saccharomyces yeasts
Full text linkUnbiased genetic dissection of widely observable phenotypic traits in the wild haslong been the goal of evolutionary geneticists. Mice, bacteria, rice and stickleback fisheshave historically been among the prime model organisms in the field. Here, we leveragethe recent surge of Saccharomyces yeast as a model genus in ecology and evolution tobegin answering questions about the genetic basis of ancient trait differences that haveevolved between species, over long evolutionary time scales. Specifically, we want toknow what genetic mechanisms evolution has used to create new traits in the distantpast, and what biological functions have been the focus of adaptation in the past. Iintroduce the field and our questions of interest in the introductory Chapter 1. Next,Chapter 2 delves deeper into the methods that have been used in the past to dissectinterspecies genetics, reviewing the literature and drawing general conclusions fromwhat we have learned so far. In Chapter 3, we develop a new application of thereciprocal hemizygote test on a genome-wide scale to drill down to the single gene leveland dissect the ability of S. cerevisiae to grow at high temperatures relative to otherSaccharomyces species. We uncover a suite of housekeeping genes geneticallyresponsible for this derived phenotype and reveal a likely defect in cell division in S.paradoxus as the culprit for cell death at high temperatures. Finally, in Chapter 4, weinvestigate two more species-specific differences: 1) resistance to the drug benomyl, amicrotubule poison and 2) cold tolerance. Unexpectedly, while microtubules are themolecular target of benomyl, it is the genes encoding water channels in the cellmembrane tha seem to be at the genetic root of these phenotypes. Our data begin toconnect the dots between the growth advantage in S. paradoxus in benomyl and at lowtemperatures, relative to S. cerevisiae
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
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Regulation and function of antisense transcription in Saccharomyces yeast
Full text linkTranscription of RNA antisense to protein-coding genes is widespread in genomes from bacteria to human. For most antisense transcription, the methods by which it is regulated and its potential function remain unknown. We sought to address these questions, using budding yeast as a model system, with two complementary approaches. First, we mapped antisense expression in four Saccharomyces species. Antisense transcripts conserved across yeasts were predominantly detected at open reading frames in a tail-to-head orientation with respect to the next gene 3' to the reference gene. For such tandem gene pairs, the region between the genes exhibited distinctive signatures of binding by transcription factors, suggesting that these factors could regulate transcription of both the mRNA from the 3' gene and the upstream antisense transcript. Transcription factor deletion experiments supported this hypothesis, conferring decreased expression of both antisense and downstream sense transcripts at such gene pairs; often in these mutants, as an antisense transcript dropped in expression, its host gene mRNA level increased, a hallmark of antisense-mediated repression. To test this model, we focused on the stress-response gene YKL151C and its downstream neighbor GPM1, which was strongly expressed in rich media. Cis-regulatory mutation experiments showed that YKL151C antisense expression was co-regulated with GPM1 and repressed mRNA levels of its overlapping sense transcript. In a second body of work, we used natural variation rather than engineered mutations to access the impact of variants that modulate antisense expression levels. We mapped naturally occurring polymorphisms between yeast strains that showed linkage to sense and antisense expression. We identified cases where such regulatory polymorphisms mediated their effects through transcription factors that bound at the promoters of linked antisense transcripts; in all such cases, expression of the downstream gene also showed linkage to the polymorphism, and, in several cases, sense transcription overlapping the antisense was linked as well. Our studies thus converged on a model in which antisense transcription at one yeast gene frequently originates from and is co-regulated with the promoter of a neighboring gene, mediated by the action of transcription factors; at a fraction of such loci, antisense transcription acts to repress expression of its overlapping mRNA, enabling the joint control of adjacent genes specialized to opposing conditions
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Investigating genetic determinants of phenotypic variation in natural isolates of Saccharomyces cerevisiae
Full text linkThe causal link between genotype and phenotype is one of the fundamental principles of modern biology; yet there remain significant challenges to successfully identifying and validating the effect of a specific genetic variant on an organism. Much of the tremendous diversity observed in nature, even among individuals of the same species, remains unexplained. Here, we used the model eukaryote, Saccharomyces cerevisiae, to investigate naturally occurring variation and employ a candidate gene approach, through a combination of genome sequence analysis and mining functional gene annotations, to identify genetic determinants of the phenotypes observed. First, we took a look at morphological variation, a major source of biological diversity, in an environmental isolate of S. cerevisiae and found that its allele of CDC28 underlies multiple phenotypes: linearly arranged spores after meiosis, elongated cell shape during mitosis, and branching filaments during filamentous growth. Second, we studied a wild yeast population, using a comparative transcriptomics approach, which revealed divergence in iron metabolism that exhibited itself as slow growth in a high iron environment. We again identified two of the genetic determinants, YAP5 and CCC1, both essential for resistance to iron toxicity, that contribute to the phenotype and show evidence that genes involved in iron homeostasis have undergone non-neutral evolution. Our work illustrates the viability of using genomic data to successfully predict the genes responsible for phenotypes of interest as well as the power of yeast a model system for investigating natural variation
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