1,720,963 research outputs found
Whole genome sequencing and comparative genomics in lactic acid bacteria
Full text linkIn the present thesis, the genomes of different microbial species, belonging to the lactic acid bacteria and including Lactobacillus crispatus, Streptococcus pneumoniae and Enterococcus faecalis, were obtained and analyzed using comparative genomics tools. In the first part of the thesis was described the genome of the probiotic L. crispatus strain M247, which contains a novel integrative and mobilizable element named Tn7088. Tn7088 carries a biosynthetic gene cluster coding for a class I bacteriocin which is homologous to the listeriolysin S gene cluster of Listeria monocytogenes and may confer selective advantages towards related bacterial species. Chromosomal rearrangements mediated by insertion sequences and involving two regions of 69.9- kb and 15.4-kb, were detected in the M247 strain. A L. crispatus M247 laboratory strain carried in our laboratory strain collection since 1990 and named M247_Siena, showed an unusual duplication of the 69.9-kb DNA region resulting in the generation of two long inverted repeats (LIRs) and the deletion of the 15.4-kb region. Analysis of ultra-long DNA Nanopore reads showed that the presence of LIRs in strain M247_Siena increased the intrinsic genome instability of strain M247. In the second part, a collection of 41 E. faecalis strains isolated from genital tract samples of infertile couples, was subjected to antimicrobial susceptibility testing and whole genome sequencing. Multi locus sequence typing and antimicrobial susceptibility testing results suggested clonality of infertility-associated E. faecalis isolates resistant to high-level aminoglycosides. Analysis of the genomic location of aminoglycoside modifying enzyme (AME) genes led to the identification of a family of novel composite transposons, whose reference element was denominated Tn7086. Tn7086 and Tn7086-like elements in infertility-associated E. faecalis shared the following traits: i) are flanked by two direct repeats of the IS1216E element, ii) employ the same chromosomal panE gene integration site, iii) excise from the bacterial chromosome leaving an IS1216E copy in the chromosome and form circular intermediates in which the ends are joined by the other IS1216E copy. Finally, the whole genome sequences of the L. crispatus type strain ATCC 33820 and of S. pneumoniae laboratory strains Rx1 and R36A, were obtained and analyzed
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
A family cluster of Streptococcus pyogenes associated with a fatal early-onset neonatal sepsis
No full textA 69.9-kb long inverted repeat increases genome instability in a strain of Lactobacillus crispatus
Full text linkLong inverted repeats (LIRs) of DNA sequences longer than 30 kb are rare in prokaryotes. Here, we identified two 69.9-kb LIRs in the genome of Lactobacillus crispatus M247_Siena, a derivative of strain M247. Complete genome sequence of M247_Siena was determined using Nanopore and Illumina technologies, while genome structure was analyzed using ultra-long Nanopore read mapping and polymerase chain reaction (PCR). In the parental M247 genome, there was only one copy of the 69.9-kb segment, while a 15.4-kb DNA segment was present instead of the second 69.9-kb segment copy. Both segments were delimited by the same insertion sequences (IS1201 and ISLcr2), and PCR analysis of the M247 population revealed low rates (∼1.28 per 104 chromosomes) of chromosomal rearrangements involving these regions. In contrast, the 69.9-kb LIRs in M247_Siena increased genomic instability, as evidenced by two alternative chromosomal structures detected at frequencies of 23.3% and 76.7% (∼1 out of 5 chromosomes). Comparative analysis of L. crispatus genomes revealed no LIRs similar to those of M247_Siena. However, long repeats of other DNA segments and chromosomal rearrangements, mostly associated with insertion sequences, were detected in 8 and 9 out of 25 L. crispatus genomes, respectively, highlighting genomic instability as a trait of the species
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
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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