1,721,086 research outputs found
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
Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania
Get PDFTrypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements - LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies) - that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are ∼70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3′-untranslated regions (3′UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3′UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function. © 2007 Bringaud et al
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
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
Differential expression analysis of TOR3 knockouts in arginine-starved Leishmania major
Get PDFThesis (Master's)--University of Washington, 2022The Arginine Deprivation Response (ADR) pathway is essential for Leishmania parasites to overcome host macrophage defense mechanisms and establish infection. The activation of this pathway appears to rely in part on regulation by target of rapamycin kinase 3 (TOR3), since TOR3 knockouts do not respond to arginine starvation consistent with ADR activation. Here, we investigate the role of TOR3 in response to arginine starvation via TOR3 knockout in Leishmania major. We analyzed mRNA abundance changes in L. major by differential gene expression analysis across four conditions: wild type (WT) in the presence of arginine, WT starved of arginine, knockout (KO) in arginine, and KO starved. As expected, we found a small number of changes between starved and unstarved WT samples, with relatively low magnitude (22 up-regulated, 1 down-regulated; fold change ≤ 2.5). Conversely, comparison of starved and unstarved knockout samples yielded man more differentially expressed genes (1263 up-regulated, 1158 down-regulated) with overall higher fold changes. Comparison of WT and KO samples under starved conditions showed similar results (1533 up-regulated, 1383 down-regulated) while comparison of WT and KO under unstarved showed fewer changes, even in the presence of arginine (463 up-regulated, 261 down-regulated). Together, our results support the hypothesis that TOR3 is involved in the ADR pathway and suggest that it also plays a wider regulatory role in cell homeostasis
Predicting Cancer Outcome with Multispectral Tumor Tissue Images
Get PDFThesis (Master's)--University of Washington, 2017-06Tumor tissue slides have been used by clinicians to assess cancer patient’s condition and indicate prognosis. Several recent studies have suggested that distribution of important immunological biomarkers on tumor tissue slides might help predict survival outcome. These studies rely upon non-parametric Kaplan-Meier survival analysis with Log-rank test to extract statistical insights, which, however, has several disadvantages such as prediction ambiguity and inability to directly model continuous variables. In this study, we engineered 676 features encoding cellular distribution information from multi- spectral tumor tissue images collected from 118 HPV-negative oral squamous cell cancer patients. We leveraged statistical methods and predictive models to explore the predictive power of these features. We identified 18 features as potential survival predictors through Kolmogorov- Smirnov test. Our best model, random forest model, has achieved 58.54% prediction accuracy rate on independent validation dataset. Although the model does not suggest strong predictive power of selected features, evaluation on large scale training data is still needed to further tune model parameters and generate more concrete results
Data Driven Methods for Scaffolding Genomes with Hi-C
No full textThesis (Ph.D.)--University of Washington, 2022High-quality reference genomes are once again in vogue with the publication of the telomere-to-telomere human genome and several challenging plant and animal genomes. Recent efforts in genome assembly have coalesced around two key technologies – ultra-long reads and genome chromatin conformation capture (Hi-C). Here, we used both to complete the protist genomes of Leishmania donovani, Leishmania tarentolae, Crithidia fasciculata, and Euglena gracilis, shedding light on their genomic organization and evolutionary history. To navigate the many Hi-C genome scaffolding methods, we benchmarked the most popular methods against a set of high-quality reference genomes. We found that while most can operate well under ideal circumstances, many struggle with using modern high-quality assemblies which contain near chromosome length contigs. Finally, we attempted to overcome these limitations using a machine learning approach by leveraging the recent bounty of genomes that have been published with Hi-C. Using an innovative convolutional neural network, we demonstrated a proof of concept for a data-driven approach to scaffolding genomes
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
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