bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Amphotericin B Resistance in Candida haemulonii and Closely Related Species by Use of the Etest, Vitek-2 Yeast Susceptibility System, and CLSI and EUCAST Broth Microdilution Methods
Authors: Shin Jong Hee , Kim Mi-Na , Jang Sook Jin , Ju Min Young , Kim Soo Hyun , Shin Myung Geun , Suh Soon Pal , Ryang Dong Wook 
Published: March 2012

ABSTRACT

The emerging fungal pathogens
Candida haemulonii
and
Candida pseudohaemulonii
often show high-level resistance to amphotericin B (AMB). We compared the utilities of five antifungal susceptibility testing methods, i.e., the Etest using Mueller-Hinton agar supplemented with glucose and methylene blue (Etest-MH), the Etest using RPMI agar supplemented with glucose (Etest-RPG), the Vitek-2 yeast susceptibility system, and the Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution methods, for the detection of AMB-resistant isolates of
C. haemulonii
and closely related species. Thirty-eight clinical isolates (8
C. haemulonii
, 10
C. pseudohaemulonii
, and 20
Candida auris
isolates) were analyzed. Of the 18
C. haemulonii
and
C. pseudohaemulonii
isolates, 18, 15, 18, 10, and 9 exhibited AMB MICs of >1 μg/ml by the Etest-MH, Etest-RPG, Vitek-2, CLSI, and EUCAST methods, respectively. All 20
C. auris
isolates showed AMB MICs of ≤1 μg/ml by all five methods. Of the methods, the Etest-MH generated the broadest distribution of AMB MICs for all 38 isolates and showed the best discrimination between the
C. haemulonii
and
C. pseudohaemulonii
isolates (4 to 32 μg/ml) and those of
C. auris
(0.125 to 0.5 μg/ml). Taking the Etest-MH as the reference method, the essential agreements (within two dilutions) for the Etest-RPG, Vitek-2, CLSI, and EUCAST methods were 84, 92, 55, and 55%, respectively; the categorical agreements were 92, 92, 79, and 76%, respectively. This study provides the first data on the efficacy of the Etest-MH and its excellent agreement with Vitek-2 for discriminating AMB-resistant from AMB-susceptible isolates of these
Candida
species.
A Multidrug-Resistant Staphylococcus epidermidis Clone (ST2) Is an Ongoing Cause of Hospital-Acquired Infection in a Western Australian Hospital
Authors: Widerström Micael , McCullough Cheryll A. , Coombs Geoffrey W. , Monsen Tor , Christiansen Keryn J. 
Published: March 2012

ABSTRACT

We report the molecular epidemiology of 27 clinical multidrug-resistant
Staphylococcus epidermidis
(MDRSE) isolates collected between 2003 and 2007 in an Australian teaching hospital. The dominant genotype (sequence type 2 [ST2]) accounted for 85% of the isolates tested and was indistinguishable from an MDRSE genotype identified in European hospitals, which may indicate that highly adaptable health care-associated genotypes of
S. epidermidis
have emerged and disseminated worldwide in the health care setting.
Detection of Dengue Virus Genome in Urine by Real-Time Reverse Transcriptase PCR: a Laboratory Diagnostic Method Useful after Disappearance of the Genome in Serum
Authors: Hirayama Takanori , Mizuno Yasutaka , Takeshita Nozomi , Kotaki Akira , Tajima Shigeru , Omatsu Tsutomu , Sano Kouichi , Kurane Ichiro , Takasaki Tomohiko 
Published: March 2012

ABSTRACT
The reemergence of dengue virus (DENV) infection has created a requirement for improved laboratory diagnostic procedures. In this study, DENV genome detection in urine was evaluated as a diagnostic method. The DENV genome was detected by real-time reverse transcriptase PCR (RT-PCR) in urine and serum of dengue patients. The detection rate of DENV genome in urine was 25% (2/8) on disease days 0 to 3 and 32% (7/22) on days 4 to 5. The rate was 50% or higher on days 6 to 16, 52% (11/21) on days 6 to 7, 78% (7/9) on days 8 to 9, 80% (4/5) on days 10 to 11, 50% (2/4) on days 12 to 13, and 60% (3/5) on days 14 to 16. The last positive urine sample was on day 16. The detection rates in serum were highest on days 0 to 3 and were greater than 50% on days 0 to 7. Detection rates decreased thereafter, and the last positive detection was on day 11. These results indicate that the time frames for positive detection differ between urine and serum samples, whereby detection rates of 50% or higher are evident between days 6 to 16 for urine samples and days 0 to 7 for serum samples. Nucleotide sequences of PCR products were identical between urine and serum samples. The detection of DENV genome in urine samples by real-time RT-PCR is useful to confirm DENV infection, particularly after viremia disappears.
Population Genetic Structures of Staphylococcus aureus Isolates from Cats and Dogs in Japan
Authors: Sasaki Takashi , Tsubakishita Sae , Tanaka Yoshikazu , Ohtsuka Masayuki , Hongo Isamu , Fukata Tsuneo , Kabeya Hidenori , Maruyama Soichi , Hiramatsu Keiichi 
Published: March 2012

ABSTRACT

We determined the population genetic structures of feline and canine
Staphylococcus aureus
strains in Japan by multilocus sequence typing (MLST). Ecological analyses suggested that multiple feline-related
S. aureus
clones, including ST133, naturally occur as commensals and can cause endogenous infections in felines. In contrast,
S. aureus
populations do not likely include any clone that exhibits tropism in domestic dogs. Even if
S. aureus
infections occur in dogs, the pathologies are likely exogenous infections.
Automated Pangenomic Analysis in Target Selection for PCR Detection and Identification of Bacteria by Use of ssGeneFinder Webserver and Its Application to Salmonella enterica Serovar Typhi
Authors: Ho Chi-Chun , Wu Alan K. L. , Tse Cindy W. S. , Yuen Kwok-Yung , Lau Susanna K. P. , Woo Patrick C. Y. 
Published: March 2012

ABSTRACTWith the advent of high-throughput DNA sequencing, more than 4,000 bacterial genomes have been sequenced and are publicly available. We report a user-friendly web platform, ssGeneFinder Webserver (http://147.8.74.24/ssGeneFinder/), which is updated weekly for the automated pangenomic selection of specific targets for direct PCR detection and the identification of clinically important bacteria without the need of gene sequencing. To apply the ssGeneFinder Webserver for identifying specific targets forSalmonella entericaserovar Typhi, we analyzed 11S. Typhi genomes, generated two specific targets, and validated them using 40S. Typhi, 110 non-TyphiSalmonellaserovars (serovar Paratyphi A,n= 4; Paratyphi B,n= 1; Typhimurium,n= 5; Enteritidis,n= 12; non-Paratyphi group A,n= 6; non-Paratyphi group B,n= 29; non-Paratyphi group C,n= 12; non-Typhi group D,n= 35; group E and others,n= 6), 115Enterobacteriaceaeisolates (Escherichia,n= 78;Shigella,n= 2;Klebsiella,n= 13;Enterobacter,n= 9; others,n= 13), and 66 human stool samples that were culture negative forS. Typhi. Both targets successfully detected all typical and atypicalS. Typhi isolates, including an H1-j flagellin gene mutant, an aflagellated mutant which reacted with 2OSalmonellaantiserum, and the Vi-negative attenuated vaccine strain Ty21a. No false positive was detected from any of the bacterial isolates and stool samples. DNA sequencing confirmed the identity of all positive amplicons. The PCR assays have detection limits as low as 100 CFU per reaction and were tested using spiked stool samples. Using a pangenomic approach, ssGeneFinder Webserver generated targets specific toS. Typhi. These and other validated targets should be applicable to the identification and direct PCR detection of bacterial pathogens from uncultured, mixed, and environmental samples.
Evaluation of Pneumonia Virus of Mice as a Possible Human Pathogen
Authors: Brock Linda G. , Karron Ruth A. , Krempl Christine D. , Collins Peter L. , Buchholz Ursula J. 
Published: March 2012

ABSTRACT

Pneumonia virus of mice (PVM), a relative of human respiratory syncytial virus (RSV), causes respiratory disease in mice. There is serologic evidence suggesting widespread exposure of humans to PVM. To investigate replication in primates, African green monkeys (AGM) and rhesus macaques (
n
= 4) were inoculated with PVM by the respiratory route. Virus was shed intermittently at low levels by a subset of animals, suggesting poor permissiveness. PVM efficiently replicated in cultured human cells and inhibited the type I interferon (IFN) response in these cells. This suggests that poor replication in nonhuman primates was not due to a general nonpermissiveness of primate cells or poor control of the IFN response. Seroprevalence in humans was examined by screening sera from 30 adults and 17 young children for PVM-neutralizing activity. Sera from a single child (6%) and 40% of adults had low neutralizing activity against PVM, which could be consistent with increasing incidence of exposure following early childhood. There was no cross-reaction of human or AGM sera between RSV and PVM and no cross-protection in the mouse model. In native Western blots, human sera reacted with RSV but not PVM proteins under conditions in which AGM immune sera reacted strongly. Serum reactivity was further evaluated by flow cytometry using unfixed Vero cells infected with PVM or RSV expressing green fluorescent protein (GFP) as a measure of viral gene expression. The reactivity of human sera against RSV-infected cells correlated with GFP expression, whereas reactivity against PVM-infected cells was low and uncorrelated with GFP expression. Thus, PVM specificity was not evident. Our results indicate that the PVM-neutralizing activity of human sera is not due to RSV- or PVM-specific antibodies but may be due to low-affinity, polyreactive natural antibodies of the IgG subclass. The absence of PVM-specific antibodies and restriction in nonhuman primates makes PVM unlikely to be a human pathogen.
Molecular Genetic and Biochemical Characterization of the Vaccinia Virus I3 Protein, the Replicative Single-Stranded DNA Binding Protein
Authors: Greseth Matthew D. , Boyle Kathleen A. , Bluma Matthew S. , Unger Bethany , Wiebe Matthew S. , Soares-Martins Jamaria A. , Wickramasekera Nadi T. , Wahlberg James , Traktman Paula 
Published: March 2012

ABSTRACT
Vaccinia virus, the prototypic poxvirus, efficiently and faithfully replicates its ∼200-kb DNA genome within the cytoplasm of infected cells. This intracellular localization dictates that vaccinia virus encodes most, if not all, of its own DNA replication machinery. Included in the repertoire of viral replication proteins is the I3 protein, which binds to single-stranded DNA (ssDNA) with great specificity and stability and has been presumed to be the replicative ssDNA binding protein (SSB). We substantiate here that I3 colocalizes with bromodeoxyuridine (BrdU)-labeled nascent viral genomes and that these genomes accumulate in cytoplasmic factories that are delimited by membranes derived from the endoplasmic reticulum. Moreover, we report on a structure/function analysis of I3 involving the isolation and characterization of 10 clustered charge-to-alanine mutants. These mutants were analyzed for their biochemical properties (self-interaction and DNA binding) and biological competence. Three of the mutant proteins, encoded by the I3 alleles I3-4, -5, and -7, were deficient in self-interaction and unable to support virus viability, strongly suggesting that the multimerization of I3 is biologically significant. Mutant I3-5 was also deficient in DNA binding. Additionally, we demonstrate that small interfering RNA (siRNA)-mediated depletion of I3 causes a significant decrease in the accumulation of progeny genomes and that this reduction diminishes the yield of infectious virus.
Evidence for ACE2-Utilizing Coronaviruses (CoVs) Related to Severe Acute Respiratory Syndrome CoV in Bats
Authors: Demogines Ann , Farzan Michael , Sawyer Sara L. 
Published: March 2012

ABSTRACT

In 2002, severe acute respiratory syndrome (SARS)-coronavirus (CoV) appeared as a novel human virus with high similarity to bat coronaviruses. However, while SARS-CoV uses the human angiotensin-converting enzyme 2 (ACE2) receptor for cellular entry, no coronavirus isolated from bats appears to use ACE2. Here we show that signatures of recurrent positive selection in the bat
ACE2
gene map almost perfectly to known SARS-CoV interaction surfaces. Our data indicate that ACE2 utilization preceded the emergence of SARS-CoV-like viruses from bats.
Virus-Derived Gene Expression and RNA Interference Vector for Grapevine
Authors: Kurth Elizabeth G. , Peremyslov Valera V. , Prokhnevsky Alexey I. , Kasschau Kristin D. , Miller Marilyn , Carrington James C. , Dolja Valerian V. 
Published: March 2012

ABSTRACT

The improvement of the agricultural and wine-making qualities of the grapevine (
Vitis vinifera
) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction of desired traits into grapevine without heritable modifications to the genome. This vector expresses recombinant proteins in the phloem tissue that is involved in sugar transport throughout the plant, from leaves to roots to berries. Furthermore, the vector provides a powerful RNA interference (RNAi) capability of regulating the expression of endogenous genes via virus-induced gene-silencing (VIGS) technology. Additional advantages of this vector include superb genetic capacity and stability, as well as the swiftness of technology implementation. The most significant applications of the viral vector include functional genomics of the grapevine and disease control via RNAi-enabled vaccination against pathogens or invertebrate pests.
Establishment and Lineage Replacement of H6 Influenza Viruses in Domestic Ducks in Southern China
Authors: Huang Kai , Zhu Huachen , Fan Xiaohui , Wang Jia , Cheung Chung-Lam , Duan Lian , Hong Wenshan , Liu Yongmei , Li Lifeng , Smith David K. , Chen Honglin , Webster Robert G. , Webby Richard J. , Peiris Malik , Guan Yi 
Published: March 2012

ABSTRACT
Domestic ducks in southern China act as an important reservoir for influenza viruses and have also facilitated the establishment of multiple H6 influenza virus lineages. To understand the continuing evolution of these established lineages, 297 H6 viruses isolated from domestic ducks during 2006 and 2007 were genetically and antigenically analyzed. Phylogenetic analyses showed that group II duck H6 viruses had replaced the previously predominant group I lineage and extended their geographic distribution from coastal to inland regions. Group II H6 virus showed that the genesis and development of multiple types of deletions in the neuraminidase (NA) stalk region could occur in the influenza viruses from domestic ducks. A gradual replacement of the N2 NA subtype with N6 was observed. Significant antigenic changes occurred within group II H6 viruses so that they became antigenically distinguishable from group I and gene pool viruses. Gene exchange between group II H6 viruses and the established H5N1, H9N2, or H6N1 virus lineages in poultry in the region was very limited. These findings suggest that domestic ducks can facilitate significant genetic and antigenic changes in viruses established in this host and highlight gaps in our knowledge of influenza virus ecology and even the evolutionary behavior of this virus family in its aquatic avian reservoirs.
Murine Noroviruses Bind Glycolipid and Glycoprotein Attachment Receptors in a Strain-Dependent Manner
Authors: Taube Stefan , Perry Jeffrey W. , McGreevy Eoghan , Yetming Kristen , Perkins Cheryl , Henderson Kenneth , Wobus Christiane E. 
Published: March 2012

ABSTRACT

Human norovirus infections are the most common cause of acute nonbacterial gastroenteritis in humans worldwide, and glycan binding plays an important role in the susceptibility to these infections. However, due to the lack of an efficient cell culture system or small animal model for human noroviruses, little is known about the biological role of glycan binding during infection. Murine noroviruses (MNV) are also enteric viruses that bind to cell surface glycans, but in contrast to their human counterparts, they can be grown in tissue culture and a small animal host. In this study, we determined glycan-binding specificities of the MNV strains MNV-1 and CR3
in vitro
, identified molecular determinants of glycan binding, and analyzed infection
in vivo
. We showed that unlike MNV-1, CR3 binding to murine macrophages was resistant to neuraminidase treatment and glycosphingolipid depletion. Both strains depended on N-linked glycoproteins for binding, while only MNV-1 attachment to macrophages was sensitive to O-linked glycoprotein depletion.
In vivo
, CR3 showed differences in tissue tropism compared to MNV-1 by replicating in the large intestine. Mapping of a glycan-binding site in the MNV-1 capsid by reverse genetics identified a region topologically similar to the histo-blood group antigen (HBGA)-binding sites of the human norovirus strain VA387. The recombinant virus showed distinct changes in tissue tropism compared to wild-type virus. Taken together, our data demonstrate that MNV strains evolved multiple strategies to bind different glycan receptors on the surface of murine macrophages and that glycan binding contributes to tissue tropism
in vivo
.
Laterality, hand control and scholastic performance: a British birth cohort study
Authors: Björk Tabita , Brus Ole , Osika Walter , Montgomery Scott 
Published: March 2012

ObjectivesTo use simple measures of laterality and hand control that can identify a greater risk of poorer scholastic ability, potentially signalling suboptimal hemispheric lateralisation.DesignAnalysis of material from a birth cohort study.SettingMembers of the National Child Development Study, a British birth cohort study following people born in 1958.Participants10 612 children who undertook tests at age 11 years.Primary outcome measuresTeacher-administered tests of non-verbal general ability, verbal general ability, reading comprehension and mathematics.ResultsLinear regression produced associations (and 95% CIs) with tests of verbal general ability, non-verbal general ability, reading comprehension and mathematics scores for the lowest third (compared with highest) of a left-hand control test involving picking up matches of −1.21 (−1.73 to −0.68; p<0.001), −0.72 (−1.14 to −0.29; p=0.001), −0.70 (−1.06 to −0.35; p<0.001) and −1.32 (−1.90 to −0.73; p<0.001). Among those in the lowest third of the right-hand control test score, mixed-handedness compared with right-handedness was associated with poorer scholastic performance, with regression coefficients (and 95% CIs; p values) of 1.90 (−3.01 to −0.80; p=0.001), −1.25 (−2.15 to −0.35; p=0.007), −1.28 (2.04 to −0.53; p=0.001) and −1.33 (−2.53 to −0.13; p=0.030). The estimates are for a point change in the scholastic test scores, after adjustment for sex, left-hand motor function and social class. Statistically significant associations with mixed-handedness were only observed for the lowest third of right-hand motor function.ConclusionsMeasures involving poorer left-hand motor function may represent useful markers of reduced cognitive function possibly reflecting suboptimal hemispheric lateralisation. Crude measures of laterality such as reported non-right-handedness may be more useful for research when combined with measures of motor function.
Track and trigger in an emergency department: an observational evaluation study
Authors: Wilson Sarah J , Wong David , Clifton David , Fleming Susannah , Way Rob , Pullinger Richard , Tarassenko Lionel 
Published: March 2012

ObjectiveTo evaluate the utilisation of paper-based track and trigger (T&T) charts in a UK emergency department (ED).MethodsA single-centre prospective observational cohort study was conducted in the ED of a medium-sized teaching hospital. Charted vital-sign data were collected from adults attending the resuscitation room, majors or observation ward. These data were examined in parallel with clinical notes to identify ‘escalation’ events. For each set of vital signs, the authors calculated the T&T score retrospectively.ResultsData from 472 patient episodes (2965 sets of vital signs) were examined. 85.8% of patients had at least one full set of observations (CEM standard) and 60.6% had at least one T&T score documented. However, only 34.5% of observation sets had a corresponding T&T score. 20.6% of T&T score totals (1024) were incorrect, potentially preventing a ‘trigger’ from being recognised. 204 patient episodes had at least one recorded escalation. Physiological escalations were associated with vital-sign scores that met the triggering thresholds (98/104), while patients who had non-physiological escalations or no escalations were more likely to have scores below the triggering thresholds (88/100). Only 26.9% of physiological escalations were associated with a documented T&T score above the triggering threshold. Retrospective completion of the charts increased that figure to 94.2%.ConclusionT&T in the ED is challenged by poor completion rates and numerical errors made during score calculation. However the potential for recognition of a deteriorating patient should not be ignored. The future work of the authors intends to evaluate an electronic system for automatically calculating T&T scores within the ED environment.
Morphodiversity, complexity and macroevolution: revealed by the megascopic life of the Palaeo-Neoproterozoic Vindhyan Supergroup, India
Authors: Srivastava Purnima 
Published: March 2012

Abstract
Evidence of past life found in the Vindhyan Supergroup exhibits extensive diversity and taxonomically unresolved morphological complexities indicating varied biological affinities, advanced life and macroevolutionary dynamics of evolving clades. The megascopic life of the supergroup documents possibly two macroevolutionary modes, demarcated as: (i) the Palaeo-Mesoproterozoic transitional period, which is represented by the fossil assemblages of the Semri and Rewa groups, and exhibits the domination of a diversified prokaryotic cyanobacterial community and moderately diversified megascopic life; (ii) the Neoproterozoic (Bhander groups, Uppermost Vindhyans), represented by the diversified and morphologically complex megascopic eukaryotes, and the emergence of multicellularity among plant and animal clades, viz. structures resembling bryophytes, sporophyte and Ediacara fauna. The overall Vindhyan fossils exhibit episodes of adaptive innovations and the emergence of complex morphologies in separate lineages of evolutionary history, resulting in extensive morphodiversity.

The present assemblage can be represented by that of prokaryotes, eukaryotes, possibly a symbiotic association, a
Jacutianema
-like Neoproterozoic form, specimens possibly of vaucheriacean affinity, mesoscopic intermediate forms inferred as transitional forms of microscopic–megascopic evolution, discs with process-like structures, the emergence of animal life (Ediacaran fauna) and a number of other complex morphologies that have no parallels in time and space. Traditionally and conventionally, the age of the Vindhyan Supergroup is considered to be that of Palaeoproterozoic–Neoproterozoic.