1,720,963 research outputs found
Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III
Full text linkTwo new species, Candida orthopsilosis and C. metapsilosis, are proposed to replace the existing designations
of C. parapsilosis groups II and III, respectively. The species C. parapsilosis is retained for group I isolates.
Attempts to construct a multilocus sequence typing scheme to differentiate individual strains of C. parapsilosis
instead revealed fixed DNA sequence differences between pairs of subgroups in four genes: COX3, L1A1, SADH,
and SYA1. PCR amplicons for sequencing were obtained for these four plus a further seven genes from 21 group
I isolates. For nine group II isolates, PCR products were obtained from only 5 of the 11 genes, and for two group
III isolates PCR products were obtained from a different set of 5 genes. Three of the PCR products from group
II and III isolates differed in size from the group I products. Cluster analysis of sequence polymorphisms from
COX3, SADH, and SYA1, which were common to the three groups, consistently separated the isolates into three
distinct sets. All of these differences, together with DNA sequence similarities <90% in the ITS1 sequence,
suggest the subgroups should be afforded species status. The near absence of DNA sequence variability among
isolates of C. parapsilosis and relatively high levels of sequence variability among isolates of C. orthopsilosis
suggest that the former species may have evolved very recently from the latter
Multilocus sequence typing of the pathogenic fungus Aspergillus fumigatus
Full text linkA multilocus sequence typing (MLST) scheme was devised for Aspergillus fumigatus. The system involved
sequencing seven gene fragments and was applied to a panel of 100 isolates of A. fumigatus from diverse
sources. Thirty different sequence types were found among the 100 isolates, and 93% of the isolates differed
from the other isolates by only one allele sequence, forming a single clonal cluster as indicated by the eBURST
algorithm. The discriminatory power of the MLST method was only 0.93. These results strongly indicate that
A. fumigatus is a species of a relatively recent origin, with low levels of sequence dissimilarity. Typing methods
based on variable numbers of tandem repeats offer higher levels of strain discrimination. Mating type data for
the 100 isolates showed that 71 isolates were type MAT1-2 and 29 isolates were MAT1-1
Population structure and properties of Candida albicans, as determined by multilocus sequence typing
Full text linkWe submitted a panel of 416 isolates of Candida albicans from separate sources to multilocus sequence typing
(MLST). The data generated determined a population structure in which four major clades of closely related
isolates were delineated, together with eight minor clades comprising five or more isolates. By Fisher’s exact
test, a statistically significant association was found between particular clades and the anatomical source,
geographical source, ABC genotype, decade of isolation, and homozygosity versus heterozygosity at the mating
type-like locus (MTL) of the isolates in the clade. However, these associations may have been influenced by
confounding variables, since in a univariate analysis of variance, only the clade associations with ABC type and
anatomical source emerged as statistically significant, providing the first indication of possible differences
between C. albicans strain type clades and their propensity to infect or colonize different anatomical locations.
There were no significant differences between clades with respect to distributions of isolates resistant to
fluconazole, itraconazole, or flucytosine. However, the majority of flucytosine-resistant isolates belonged to
clade 1, and these isolates, but not flucytosine-resistant isolates in other clades, bore a unique mutation in the
FUR1 gene that probably accounts for their resistance. A significantly higher proportion of isolates resistant
to fluconazole, itraconazole, and flucytosine were homozygous at the MTL, suggesting that antifungal pressure
may trigger a common mechanism that leads both to resistance and to MTL homozygosity. The utility of MLST
for determining clade assignments of clinical isolates will form the basis for strain selection for future research
into C. albicans virulence
Multilocus sequence typing for differentiation of strains of Candida tropicalis
Full text linkA system is described for typing isolates of the pathogenic fungus Candida tropicalis, based on sequence
polymorphisms in fragments of six genes: ICL1, MDR1, SAPT2, SAPT4, XYR1, and ZWF1a. The system
differentiated 87 diploid sequence types (DSTs) among a total of 106 isolates tested or 80 DSTs among 88
isolates from unique sources. Replicate isolates from the same source clustered together with high statistical
similarity, with the exception of one isolate. However, a clade of very closely related isolates included replicate
isolates from three different patients, as well as single isolates from eight other patients. This clade, provisionally
designated clade 1, was one of three clusters of isolates with high statistical similarity. Five of six
isolates in one cluster that may acquire clade status were resistant to flucytosine. This study adds C. tropicalis
to Candida albicans and Candida glabrata as Candida species for which a multilocus sequence typing (MLST)
system has been set up. The C. tropicalis MLST database can be accessed at http://pubmlst.org/ctropicalis/
Collaborative consensus for optimized multilocus sequence typing of Candida albicans
Full text linkA panel of 86 different Candida albicans isolates was subjected to multilocus sequence typing (MLST) in two
laboratories to obtain sequence data for 10 published housekeeping gene fragments. Analysis of data for all
possible combinations of five, six, seven, eight, and nine of the fragments showed that a set comprising the
fragments AAT1a, ACC1, ADP1, MPIb, SYA1, VPS13, and ZWF1b was the smallest that yielded 86 unique diploid
sequence types for the 86 isolates. This set is recommended for future MLST with C. albicans
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
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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