1,721,023 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
Structural and Functional Characterization of Aminoglycoside N-Acetyltransferases from Environmental Microbiomes
No full textAminoglycoside N-acetyltransferases (AACs) are widespread enzymes that catalyze the acetylation at amino groups of the aminoglycoside antibiotics. Significant number of AAC encoding genes have been identified in diverse microbial (meta)genomes. Such a prospect necessitates a study of AACs from environmental microbiomes in order to anticipate the rise of corresponding resistance elements in the clinic. Accordingly, I performed both functional and structural characterization of putative AACs identified in soil microbiomes, which we named ENV enzymes. Four ENV enzymes demonstrated robust AAC activity and conferred aminoglycoside resistance. Among them, ENV0020 was identified as a novel member of AAC family that catalyzed the acetylation reaction at the prime ring of the antibiotic substrate. The crystal structures of the ENV0020 enzyme obtained in my study provided the molecular framework of its substrate recognition mechanism, which could be useful in the design of novel drug variants less prone to modification by AACs.M.A.S
Structural and Functional Manipulation of the Eukaryotic Ubiquitination System by Pathogenic Bacteria
Full text linkThe pathogenic strategy of many Gram-negative bacteria involves the translocation of arsenals of proteins, termed effectors, directly into the eukaryotic host cell. These effectors control and manipulate the host cell to inhibit host defenses and promote bacterial infection. A primary target of many effectors is the eukaryotic ubiquitination system, a conserved eukaryotic signalling cascade culminating in the attachment of one or multiple copies of a small protein called ubiquitin to a target protein, leading to specific regulation of the target protein. Bacteria lack ubiquitination, yet pathogens have evolved many effectors to manipulate this process, which act to either impede ubiquitination machinery or mimic the ubiquitin protein ligases to hijack the ubiquitination system for the pathogens’ benefit. How many of these effectors function remains an open question. To better understand these mechanisms by which pathogens manipulate host ubiquitination, I aimed to characterise poorly understood effectors that interface with the ubiquitination system.
This dissertation details that effort, describing the characterisation of two previously poorly characterised effector families, the NleG family from the dangerous enterohaemorrhagic Escherichia coli O157:H7, and a pair of paralogous effectors from the pneumonia-causing Legionella pneumophila, MavC and MvcA. With 14 NleG effector homologs they represent the largest effector family in E. coli O157:H7. I was able to determine the N-terminal domain of NleG effectors represents a structurally unique effector fold. This N-terminal domain allows NleGs to bind human proteins and, in conjunction with their C-terminal U-box ubiquitin ligase domain, use ubiquitination to mark those human proteins for degradation during E. coli infection. By solving the crystal structures of the effectors MavC and MvcA from L. pneumophila, I was able to determine that MavC and MvcA are unique ubiquitin-deamidating effectors. In addition, MavC uses this catalytic activity and an additional unique binding domain to inhibit the E2 ubiquitin conjugating enzyme UBE2N and suppress NF-κB by limiting Lys63 ubiquitination. This dissertation expands our knowledge of bacterial pathogenesis by revealing new effector biology that allows these effectors to interface with host ubiquitination to disrupt signalling and further emphasizes ubiquitination as a key intracellular battleground during bacterial infection.Ph.D.2022-06-22 00:00:0
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
Structural and Functional Characterization of Aminoglycoside N-Acetyltransferases from Environmental Microbiomes
No full textAminoglycoside N-acetyltransferases (AACs) are widespread enzymes that catalyze the acetylation at amino groups of the aminoglycoside antibiotics. Significant number of AAC encoding genes have been identified in diverse microbial (meta)genomes. Such a prospect necessitates a study of AACs from environmental microbiomes in order to anticipate the rise of corresponding resistance elements in the clinic. Accordingly, I performed both functional and structural characterization of putative AACs identified in soil microbiomes, which we named ENV enzymes. Four ENV enzymes demonstrated robust AAC activity and conferred aminoglycoside resistance. Among them, ENV0020 was identified as a novel member of AAC family that catalyzed the acetylation reaction at the prime ring of the antibiotic substrate. The crystal structures of the ENV0020 enzyme obtained in my study provided the molecular framework of its substrate recognition mechanism, which could be useful in the design of novel drug variants less prone to modification by AACs.M.A.S
Developing a Non-aureus Staphylococci Transposon Mutant Library and Testing it in a Bovine Mammary Gland Infection Model
No full textBovine mastitis is a prevalent and costly disease impacting the mammary gland health of dairy cows, resulting in 300-400 million CAD in annual losses to the Canadian dairy industry. Although mastitis can be caused by numerous bacterial species, non-aureus staphylococci (NAS) collectively account for a significant number of chronic subclinical infections. Among these, Staphylococcus simulans and Staphylococcus chromogenes are among the most frequently isolated and host-adapted NAS species associated with bovine mastitis yet are greatly understudied. To better understand the mechanisms underlying S. simulans adaptation to the bovine mammary gland, we constructed a transposon mutant library containing approximately 100,000 unique mutants derived from a bovine S. simulans isolate. The library was produced by transforming a transposon-plasmid system then inducing transposon mutagenesis via high temperature and using negative selection to kill non-mutant cells. The mutant library was tested in all mammary glands of three lactating cows for 48 hours. Inoculation resulted in the development of clinical mastitis, characterized by inflammation and altered milk appearance. Mutant libraries were recovered from all six sets of supramammary lymph nodes and three mammary glands. Output libraries size averaged to 127,696 CFU per tissue. We attempted to develop and optimize a protocol to prepare isolated DNA from the mutant libraries for downstream next generation sequencing and analysis by targeting transposon insertions via probe hybridization and circularization. The protocol was tested successfully on a control plasmid template but requires further optimization for transposon libraries. We discuss what parts of the protocol require optimization and explore ways to further optimize the protocol, then describe which mutant knockouts we expect to see based on our previous analysis of putative virulence factors of S. simulans strains from our collection. We then conclude with alternative approaches and recommended changes to the project and future directions. This work represents the first use of a live bovine mammary gland model to screen a large transposon mutant library and offers a new tool for any researchers interested in identifying genes of interest for pathogens involved in mastitis such as other NAS species, Staphylococcus aureus, Streptococcus uberis, and E. coli
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