1,720,958 research outputs found
Characterisation of genetic diversity within chlamydia trachomatis in high-risk sexual networks
No full textChlamydia trachomatis is the most commonly diagnosed bacterial STI worldwide. Transmission of C. trachomatis within sexual networks is facilitated by high-risk sexual behaviours. C. trachomatis infections are frequently asymptomatic which allows for un-interrupted C. trachomatis transmission within sexual networks. C. trachomatis strains are characterised by their ompA genotype: strains with ompA genotypes A – C are associated with trachoma, D – K with sexually transmitted urogenital infections, and L1 – L3 with Lymphogranuloma venereum (LGV). The ompA gene is a mutational hotspot within the C. trachomatis genome, and extensive sequence variation within ompA has been reported amongst C. trachomatis strains. OmpA genotyping was applied to C. trachomatis DNA extracted from a conjunctival swab collected from a 10 year old female that had migrated to the UK from Afghanistan, to ascertain whether the child was infected with a trachoma-causing strain, or a strain associated with sexually transmitted urogenital tract infections (Chapter 3). Sequencing of the trpA gene was also conducted, as polymorphisms within this gene have been shown to distinguish ocular and genital C. trachomatis strains (Chapter 3). In recent years, multi-locus genotyping systems including multi-locus sequence typing (MLST), multi-sequence typing (MST), and multi-locus variable number tandem repeat (VNTR) analysis (MLVA), have been developed for C. trachomatis. Genotyping systems can elucidate diversity within C. trachomatis strains circulating in sexual networks. Multi-locus genotyping systems were evaluated to determine their suitability for application in a genotyping survey of LGV C. trachomatis strains in London (Chapter 4). The MLVA-ompA genotyping system was applied to genotype LGVpositive clinical specimens from London, to assess genotypic diversity within LGV C. trachomatis strains within this population (Chapter 5). The study detected several distinct LGV MLVA-ompA genotypes, in addition to a hybrid L2b/D ompA genotype that had previously been reported in Portugal. The data collected has added to the knowledge relating to the current LGV epidemic within MSM in the UK. Multi-locus typing systems cannot achieve the resolution provided by whole genome sequencing. Whole genome sequencing can provide insight into the genomic diversity within LGV C. trachomatis strains. Three LGV isolates collected from asymptomatic and symptomatic MSM in Brighton were whole genome sequenced in Chapter 6, to identify any genomic loci or key sequences that may account for the differences in symptomology between the three patients. The study identified several mutations within the genomes of the three isolates. Of these, SNPs were detected within genes associated with intracellular replication of C. trachomatis in the two isolates collected from symptomatic MSM, that were absent from the isolate obtained from an asymptomatic MSM
Reducing suspicion of sexual abuse in paediatric chlamydial conjunctivitis using ompA genotyping.
No full textChlamydia trachomatis is a Gram-negative bacterium that causes urogenital tract infections, and ocular infections including trachoma, neonatal conjunctivitis and adult chlamydial inclusion conjunctivitis. A positive C. trachomatis diagnosis in children often raises suspicions of sexual abuse. While outer membrane protein A (ompA) genotypes A–C are non-invasive and are associated with trachoma; ompA genotypes D–K are often associated with sexually transmitted urogenital infections or sexually acquired chlamydial conjunctivitis. A 10-year-old female presented with a 7-month history of unilateral conjunctivitis with itching, watering and hyperaemia. She had recently moved from an urban centre in Afghanistan to the UK. A conjunctival swab taken from the child tested positive for C. trachomatis. Application of ompA genotyping to conjunctival swab chlamydial DNA demonstrated that the C. trachomatis had an ompA genotype C. Chlamydial strains with this ompA genotype cause trachoma and have never previously been associated with urogenital infection. This result supported cessation of child protection investigations
Dataset in support of the Southampton doctoral thesis 'Characterisation of Genetic Diversity within Chlamydia trachomatis in High-Risk Sexual Networks'
No full textA zip file containing trimmed whole genome sequence reads, a spreadsheet indicating MLVA-ompA genotypes of DNA extracts obtained for the genotyping survey, and example nucleotide sequence traces.</span
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
High-resolution genotyping of Lymphogranuloma Venereum (LGV) strains of Chlamydia trachomatis in London using multi-locus VNTR analysis-ompA genotyping (MLVA-ompA).
No full textBackgroundLymphogranuloma venereum (LGV) is caused by Chlamydia trachomatis strains with ompA genotypes L1 to L3. An LGV epidemic associated with the L2b genotype has emerged in the past few decades amongst men who have sex with men (MSM). C. trachomatis genotypes can be discriminated by outer membrane protein A gene (ompA) sequencing, however this method has limited resolution. This study employed a high-resolution genotyping method, namely, multi-locus tandem repeat (VNTR) analysis with ompA sequencing (MLVA-ompA), to assess the distribution of LGV MLVA-ompA genotypes amongst individuals attending genitourinary medicine (GUM) clinics in London.MethodsClinical specimens were collected from individuals attending eight London-based GUM clinics. Specimens that tested positive for C. trachomatis by commercial nucleic acid amplification test (NAAT) were confirmed as LGV by pmpH real-time PCR. LGV-positive DNA extracts were subsequently genotyped using MLVA-ompA.ResultsTwo hundred and thirty DNA extracts were confirmed as LGV, and 162 (70%) yielded complete MLVA-ompA genotypes. Six LGV MLVA-ompA genotypes were identified: 1.9.2b-L2, 1.9.3b-L2b, 1.9.2b-L2b, 1.9.2b-L2b/D, 1.4a.2b-L2b, and 5.9.2b-L1. The following LGV ompA genotypes were identified (in descending order of abundance): L2, L2b, L2b/D, and L1. Eight ompA sequences with the hybrid L2b/D profile were detected. The hybrid sequence was identical to the ompA of a recombinant L2b/D strain detected in Portugal in 2017.ConclusionsThe L2 ompA genotype was found to predominate in the London study population. The study detected an unusual hybrid L2b/D ompA profile that was previously reported in Portugal. We recommend further monitoring and surveillance of LGV strains within the UK population
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
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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