bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Resequencing Oligonucleotide Microarrays for Identification of
Streptococcus pyogenes
and Associated Antibiotic Resistance Determinants
Authors: Davignon Louis , Walter Elizabeth A. , Mueller Kate M. , Barrozo Christopher P. , Stenger David A. , Lin Baochuan 
Published: November 2005

ABSTRACT

Group A streptococci (GAS) are responsible for a wide variety of human infections associated with considerable morbidity and mortality. Ever since the first systematic effort by Lancefield to group
Streptococcus
species by M protein variants, the detection and characterization of
Streptococcus
by different methods have been an evolving process. The ideal assay for GAS identification not only would provide quick and accurate diagnostic results but also would reveal antibiotic resistance patterns and genotype information, aiding not only in treatment but in epidemiologic assessment as well. The oligonucleotide microarray is a promising new technology which could potentially address this need. In this study, we evaluated the usefulness of oligonucleotide resequencing microarrays for identifying GAS and its associated antibiotic resistance markers. We demonstrated an assay platform that combines the use of resequencing DNA microarrays with either random nucleic acid amplification or multiplex PCR for GAS detection. When detecting
Streptococcus pyogenes
from coded clinical samples, this approach demonstrated an excellent concordance with a more established culture method. To this end, we showed the potential of resequencing microarrays for efficient and accurate detection of GAS and its associated antibiotic resistance markers with the benefit of sequencing information from microarray analysis.
Distribution of
tccP
in Clinical Enterohemorrhagic and Enteropathogenic
Escherichia coli
Isolates
Authors: Garmendia Junkal , Ren Zhihong , Tennant Sharon , Midolli Viera Monica Aparecida , Chong Yuwen , Whale Andrew , Azzopardi Kristy , Dahan Sivan , Sircili Marcelo Palma , Franzolin Marcia Regina , Trabulsi Luiz R. , Phillips Alan , Gomes Tânia A. T. , Xu Jianguo , Robins-Browne Roy , Frankel Gad 
Published: November 2005

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) and enteropathogenic
E. coli
(EPEC) are diarrheagenic pathogens that colonize the gut through the formation of attaching and effacing lesions, which depend on the translocation of effector proteins via a locus of enterocyte effacement-encoded type III secretion system. Recently, two effector proteins, EspJ and TccP, which are encoded by adjacent genes on prophage CP-933U in EHEC O157:H7, have been identified. TccP consists of a unique N-terminus region and several proline-rich domains. In this project we determined the distribution of
tccP
in O157:H7, in non-O157 EHEC, and in typical and atypical EPEC isolates. All the EHEC O157:H7 strains tested were
tccP
+
. Unexpectedly,
tccP
was also found in non-O157 EHEC, and in typical and atypical EPEC isolates, particularly in strains belonging to serogroups O26 (EHEC), O119 (typical EPEC), and O55 (atypical EPEC). We recorded some variation in the length of
tccP
, which reflects diversity in the number of the proline-rich repeats. These results show the existence of a class of “attaching and effacing” pathogens which express a combination of EPEC and EHEC virulence determinants.
Molecular Epidemiology of Clinical
Cryptococcus neoformans
Strains from India
Authors: Jain N. , Wickes B. L. , Keller S. M. , Fu J. , Casadevall A. , Jain P. , Ragan M. A. , Banerjee U. , Fries B. C. 
Published: November 2005

ABSTRACT

Little is known about the molecular epidemiology of the human pathogenic fungus
Cryptococcus neoformans
in India, a country now in the midst of an epidemic of AIDS-related cryptococcosis. We studied 57 clinical isolates from several regions in India, of which 51 were
C. neoformans
var.
grubii
, 1 was
C. neoformans
var.
neoformans
, and 5 were
C. neoformans
var.
gattii
. This strain set included 18 additional sequential isolates from 14 patients. Strains were characterized phenotypically by measuring the polysaccharide capsule and by determining the MICs of standard antifungals. Molecular typing was performed by a PCR-based method using the minisatellite-specific core sequence (M13), by electrophoretic karyotyping, by restriction fragment length polymorphisms with the
C. neoformans
transposon 1 (TCN-1), and by
URA5
DNA sequence analysis. Overall, Indian isolates were less heterogeneous than isolates from other regions and included a subset that clustered into one group based on
URA5
DNA sequence analysis. In summary, our results demonstrate (i) differences in genetic diversity of
C. neoformans
isolates from India compared to isolates from other regions in the world; (ii) that DNA typing with the TCN-1 probe can adequately distinguish
C. neoformans
var.
grubii
strains; (iii) that TCN-1 sequences are absent in many
C. neoformans
var.
gattii
strains, supporting previous studies indicating that these strains have a limited geographical dispersal; and (iv) that human cryptococcal infection can be associated with microevolution of the infecting strain and by simultaneous coinfection with two distinct
C. neoformans
strains.
PCR Analysis of Egyptian Respiratory Adenovirus Isolates, Including Identification of Species, Serotypes, and Coinfections
Authors: Metzgar David , Osuna Miguel , Yingst Samuel , Rakha Magda , Earhart Kenneth , Elyan Diaa , Esmat Hala , Saad Magdi D. , Kajon Adriana , Wu Jianguo , Gray Gregory C. , Ryan Margaret A. K. , Russell Kevin L. 
Published: November 2005

ABSTRACT
Eighty-eight adenovirus (Ad) isolates and associated clinical data were collected from walk-in patients with influenza-like illness in Egypt during routine influenza surveillance from 1999 through 2002. Respiratory Ad distributions are geographically variable, and serotype prevalence has not been previously characterized in this region. Serotype identity is clinically relevant because it predicts vaccine efficacy and correlates strongly with both clinical presentation and epidemiological pattern. Species and serotype identities were determined using several well-validated multiplex PCR protocols culled from the literature and supplemented with a few novel primer sets designed to identify rare types. The isolates included common species B1 serotypes (Ad3 and Ad7), common species C serotypes (Ad1, Ad2, and Ad5), the less common species B2 serotype Ad11, and three isolates of the rare species B1 serotype Ad16. Two isolates that appear to be variant Ad16 were also identified. Fifteen coinfections of multiple adenoviral types, primarily AdB/AdC and Ad3/Ad7 dual infections, were detected. The majority of these were verified using redundant PCR tests targeted at multiple genes. PCR is able to resolve coinfections, in contrast to traditional serum neutralization tests. PCR is also comparatively rapid and requires very little equipment. Application of the method allowed an inclusive determination of the serotypes found in the Egyptian respiratory sample set and demonstrated that coinfections are common and may play a previously unrecognized role in adenovirus pathogenesis, evolution, and epidemiology. In particular, coinfections may influence adenoviral evolution, as interserotypic recombination has been identified as a source of emerging strains.
Microbial Risk Indicators of Early Childhood Caries
Authors: Corby P. M. , Lyons-Weiler J. , Bretz W. A. , Hart T. C. , Aas J. A. , Boumenna T. , Goss J. , Corby A. L. , Junior H. M. , Weyant R. J. , Paster B. J. 
Published: November 2005

ABSTRACT

The aim of this study was to use molecular identification methods, such as 16S RNA gene sequence and reverse-capture checkerboard hybridization, for identification of the bacteria associated with dental caries and with dental health in a subset of 204 twins aged 1.5 to 7 years old. A total of 448 plaque samples (118 collected from caries-free subjects and 330 from caries-active subjects) were used for analysis. We compared the bacteria found in biofilms of children exhibiting severe dental caries, with different degrees of lesion severity, with those found in biofilms of caries-free children. A panel of 82 bacterial species was selected, and a PCR-based reverse-capture checkerboard method was used for detection. A simple univariate test was used to determine the overabundance and underabundance of bacterial species in the diseased and in the healthy groups. Features identified with this univariate test were used to construct a probabilistic disease prediction model. Furthermore, a method for the analysis of global patterns of gene expression was performed to permit simultaneous analysis of the abundance of significant species by allowing cross-bacterial comparisons of abundance profiles between caries-active and caries-free subjects. Our results suggested that global patterns of microbial abundance in this population are very distinctive. The top bacterial species found to be overabundant in the caries-active group were
Actinomyces
sp. strain B19SC,
Streptococcus mutans
, and
Lactobacillus
spp., which exhibited an inverse relationship to beneficial bacterial species, such as
Streptococcus parasanguinis
,
Abiotrophia defectiva
,
Streptococcus mitis
,
Streptococcus oralis
, and
Streptococcus sanguinis
.
Supplementation of CHROMagar Candida Medium with Pal's Medium for Rapid Identification of
Candida dubliniensis
Authors: Sahand Ismail H. , Moragues María D. , Eraso Elena , Villar-Vidal María , Quindós Guillermo , Pontón José 
Published: November 2005

ABSTRACT

CHROMagar Candida medium is used for the isolation and identification of
Candida
species, but it does not differentiate
Candida albicans
from
Candida dubliniensis
. This differentiation can be achieved by using Pal's agar, which cannot be used in primary isolation. We have combined both media to obtain a new medium that can be used for the isolation and identification of
C. dubliniensis
in primary cultures.
Comparison of the RSV Respi-Strip with Direct Fluorescent-Antigen Detection for Diagnosis of Respiratory Syncytial Virus Infection in Pediatric Patients
Authors: Gregson D. , Lloyd T. , Buchan S. , Church D. 
Published: November 2005

ABSTRACT
The RSV Respi-Strip was compared to the SimulFluor respiratory screen for detecting respiratory syncytial virus in nasopharyngeal aspirates from pediatric patients. Of samples tested, 115/239 (49%) were positive by direct fluorescent-antigen detection. The sensitivity and specificity of the RSV Respi-Strip were 92% (95% confidence interval [CI], 86% to 96%) and 98% (95% CI, 94% to 100%), respectively, with a diagnostic efficiency of 95%.
Use of Four Dengue Virus Antigens for Determination of Dengue Immune Status by Enzyme-Linked Immunosorbent Assay of Immunoglobulin G Avidity
Authors: Matheus Séverine , Deparis Xavier , Labeau Bhety , Lelarge Josiane , Morvan Jacques , Dussart Philippe 
Published: November 2005

ABSTRACT
We used an enzyme-linked immunosorbent assay (ELISA) of immunoglobulin G avidity to determine the dengue immune status of 105 pairs of serum samples from patients infected with dengue virus. This study shows that a simple avidity test, for which only one acute-phase serum sample is required, is potentially more useful than the hemagglutination inhibition test for the discrimination of primary from secondary dengue virus infection, whatever the type of dengue antigen used.
Epidemiology and Molecular Analysis of Intestinal Colonization by Vancomycin-Resistant Enterococci in Greek Hospitals
Authors: Gikas Achilleas , Christidou Athanasia , Scoulica Efstathia , Nikolaidis Paulos , Skoutelis Athanasios , Levidiotou Stamatina , Kartali Sofia , Maltezos Efstratios , Metalidis Simeon , Kioumis John , Haliotis George , Dima Sofia , Roumbelaki Maria , Papageorgiou Nikoleta , Kritsotakis Evangelos I. , Tselentis Yannis 
Published: November 2005

ABSTRACT
From 1,246 specimens collected from 13 Greek hospitals, 266 vancomycin-resistant enterococci strains were isolated from 255 patients (20.5%). The VanA phenotype was present in 82 (30.8%) strains, the VanB phenotype in 17 (6.4%) strains, the VanC1 phenotype in 152 (57.1%) strains, and the VanC2/C3 phenotypes in 15 (5.6%) strains. When only VanA and VanB phenotypes were considered, the overall prevalence was 7.5%. Eighty-six isolates exhibiting the VanA or VanB phenotype were analyzed by pulsed-field gel electrophoresis (PFGE), and 46 PFGE groups were found.
Broth Microdilution Susceptibility Testing of
Brucella
Species: Quality Control Limits for Ten Antimicrobial Agents against Three Standard Quality Control Strains
Authors: Brown Steven D. , Traczewski Maria M. 
Published: November 2005

ABSTRACT

Brucella broth without supplementation is the recommended medium for broth microdilution susceptibility tests of
Brucella abortus
,
B. melitensis
, and
B. suis
. Based on an eight-laboratory collaborative study using a pH-adjusted modification of this medium, we propose MIC quality control ranges for three control strains against 10 antimicrobials that are potentially efficacious for treating infections caused by these agents of bioterrorism.
Laryngeal Scleroma Associated with
Klebsiella pneumoniae
subsp.
ozaenae
Authors: De Champs C. , Vellin J. F. , Diancourt L. , Brisse S. , Kemeny J. L. , Gilain L. , Mom T. 
Published: November 2005

ABSTRACT

Klebsiella pneumoniae
subsp.
ozaenae
was isolated from the pharynx of a woman with laryngeal scleroma.
K. pneumoniae
subsp.
ozaenae
is rarely isolated from clinical infections and has never been reported in laryngeal scleroma, which is usually caused by
K. pneumoniae
subsp.
rhinoscleromatis
.
Three Nonfatal Cases of Neonatal Adenovirus Infection
Authors: Elnifro Elfateh M. , Cooper Robert J. , Dady Ian , Hany Sa'id , Mughal Zolf M. , Klapper Paul E. 
Published: November 2005

ABSTRACT
Neonatal adenovirus infection is considered a rare and fatal disease. Three nonfatal neonatal adenovirus infections manifesting as conjunctivitis or conjunctivitis with other nonspecific symptoms are described. Adenovirus DNA was detected by PCR in eye swabs from two patients and in both cerebrospinal fluid and eye swabs in the third patient.
Group A Streptococcal Meningitis in a Pediatric Patient following Cochlear Implantation: Report of the First Case and Review of the Literature
Authors: Pettersen Géraldine , Ovetchkine Philippe , Tapiero Bruce 
Published: November 2005

ABSTRACTThe Food and Drug Administration published a public health warning on the association of bacterial meningitis and cochlear implants in June 2002. This article reports the first case of group A streptococcal (GAS) meningitis in a cochlear-implanted patient, followed by a review on cochlear implantation and GAS meningitis.
Molecular Identification of
Rhizomucor pusillus
as a Cause of Sinus-Orbital Zygomycosis in a Patient with Acute Myelogenous Leukemia
Authors: Iwen Peter C. , Freifeld Alison G. , Sigler Lynne , Tarantolo Stefano R. 
Published: November 2005

ABSTRACT

Sinus-orbital zygomycosis caused by
Rhizomucor pusillus
in a patient with acute myelogenous leukemia is described. Identification was achieved by sequencing of the internal transcribed spacer (ITS) regions of the rRNA gene and by expression of zygospores in mating. This report highlights the value of ITS sequencing as a diagnostic tool for the identification of
R. pusillus
and expands the understanding of infection types caused by this zygomycete.
Non-Culture-Based Analysis of Bacterial Populations from Patients with Chronic Rhinosinusitis
Authors: Power Daniel A. , Burton Jeremy P. , Chilcott Chris N. , Tagg John R. , Dawes Patrick J. 
Published: November 2005

ABSTRACT
Middle meatus aspirates from patients with chronic rhinosinusitis were analyzed by bacterial culture, denaturing gradient gel electrophoresis (DGGE), and antibiotic sensitivity techniques. DGGE detected a greater bacterial diversity than culture methods. Although resistance to antibiotics was low, there was evidence of changes in the composition of the bacterial microbiota over time, and the presence of noncultured bacteria was demonstrated.
Intraabdominal Zygomycosis Caused bySyncephalastrum racemosumInfection Successfully Treated with Partial Surgical Debridement and High-Dose Amphotericin B Lipid Complex
Authors: Schlebusch Sanmarié , Looke David F. M. 
Published: November 2005

ABSTRACTInvasive zygomycosis rarely complicates trauma. We describe the first recorded case of invasive infection of the anterior abdominal wall and omentum with the zygomyceteSyncephalastrum racemosum, which was successfully treated with partial surgical debridement and amphotericin B lipid complex.
RGFGA: An Efficient Representation and Crossover for Grouping Genetic Algorithms
Authors: Tucker Allan , Crampton Jason , Swift Stephen 
Published: November 2005

There is substantial research into genetic algorithms that are used to group large numbers of objects into mutually exclusive subsets based upon some fitness function. However, nearly all methods involve degeneracy to some degree. We introduce a new representation for grouping genetic algorithms, the restricted growth function genetic algorithm, that effectively removes all degeneracy, resulting in a more efficient search. A new crossover operator is also described that exploits a measure of similarity between chromosomes in a population. Using several synthetic datasets, we compare the performance of our representation and crossover with another well known state-of-the-art GA method, a strawman optimisation method and a well-established statistical clustering algorithm, with encouraging results.
Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni
Authors: Laha Thewarach , Kewgrai Nonglack , Loukas Alex , Brindley Paul J 
Published: November 2005

Abstract

Background
It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of the schistosome genome. Of more than 12 recognized clades of non-LTR retrotransposons, only members of the CR1, RTE, and R2 clades have been reported from the schistosome genome.

Results
Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 from chromosome 1 of the genome of Schistosoma mansoni (GenBank AC093105) revealed the likely presence of several RTE-like retrotransposons. Among these, a new non-LTR retrotransposon designated SR3 was identified and is characterized here. Analysis of gene structure and phylogenetic analysis of both the reverse transcriptase and endonuclease domains of the mobile element indicated that SR3 represented a new family of RTE-like non-LTR retrotransposons. Remarkably, two full-length copies of SR3-like elements were present in BAC 49-J-14, and one of 3,211 bp in length appeared to be intact, indicating SR3 to be an active non-LTR retrotransposon. Both were flanked by target site duplications of 10–12 bp. Southern hybridization and bioinformatics analyses indicated the presence of numerous copies (probably >1,000) of SR3 interspersed throughout the genome of S. mansoni. Bioinformatics analyses also revealed SR3 to be transcribed in both larval and adult developmental stages of S. mansoni and to be also present in the genomes of the other major schistosome parasites of humans, Schistosoma haematobium and S. japonicum.

Conclusion
Numerous copies of SR3, a novel non-LTR retrotransposon of the RTE clade are present in the genome of S. mansoni. Non-LTR retrotransposons of the RTE clade including SR3 appear to have been remarkably successful in colonizing, and proliferation within the schistosome genome.
The effect of motor control exercise versus placebo in patients with chronic low back pain [ACTRN012605000262606]
Authors: Maher Chris G , Latimer Jane , Hodges Paul W , Refshauge Kathryn M , Moseley G Lorimer , Herbert Robert D , Costa Leonardo OP , McAuley James 
Published: November 2005

Abstract

Background
While one in ten Australians suffer from chronic low back pain this condition remains extremely difficult to treat. Many contemporary treatments are of unknown value. One potentially useful therapy is the use of motor control exercise. This therapy has a biologically plausible effect, is readily available in primary care and it is of modest cost. However, to date, the efficacy of motor control exercise has not been established.

Methods
This paper describes the protocol for a clinical trial comparing the effects of motor control exercise versus placebo in the treatment of chronic non-specific low back pain. One hundred and fifty-four participants will be randomly allocated to receive an 8-week program of motor control exercise or placebo (detuned short wave and detuned ultrasound). Measures of outcomes will be obtained at follow-up appointments at 2, 6 and 12 months after randomisation. The primary outcomes are: pain, global perceived effect and patient-generated measure of disability at 2 months and recurrence at 12 months.

Discussion
This trial will be the first placebo-controlled trial of motor control exercise. The results will inform best practice for treating chronic low back pain and prevent its occurrence.
Cost and efficiency of public sector sexually transmitted infection clinics in Andhra Pradesh, India
Authors: Dandona Lalit , Sisodia Pratap , Prasad TLN , Marseille Elliot , Chalapathi Rao M , Kumar A Anod , Kumar SG Prem , Ramesh YK , Over Mead , Someshwar M , Kahn James G 
Published: November 2005

Abstract

Background
Control of sexually transmitted infections (STIs) is an important part of the effort to reduce the risk of HIV/AIDS. STI clinics in the government hospitals in India provide services predominantly to the poor. Data on the cost and efficiency of providing STI services in India are not available to help guide efficient use of public resources for these services.

Methods
Standardised methods were used to obtain detailed cost and output data for the 2003–2004 fiscal year from written records and interviews in 14 government STI clinics in the Indian state of Andhra Pradesh. The economic cost per patient receiving STI treatment was calculated, and the variations of total and unit costs across the STI clinics analysed. Multivariate regression technique was used to estimate incremental unit costs. The optimal number of STIs that could be handled by the clinics was estimated.

Results
18807 STIs were diagnosed and treated at the 14 STI clinics in fiscal year 2003–2004 (range 323–2784, median 1199). The economic cost of treating each STI varied 5-fold from Indian Rupees (INR) 225.5 (US$ 4.91) to INR 1201.5 (US$ 26.15) between 13 clinics, with one other clinic having a very high cost of INR 2478.5 (US$ 53.94). The average cost per STI treated for all 14 clinics combined was INR 729.5 (US$ 15.88). Personnel salaries made up 76.2% of the total cost. The number of STIs treated per doctor full-time equivalent and cost-efficiency for each STI treated had a significant direct non-linear relation (p < 0.001, R2 = 0.81; power function). With a multiple regression model, apart from the fixed costs, the incremental cost for each STI detected and cost of treatment was INR 55.57 (US$ 1.21) and for each follow-up visit was INR 3.75 (US$ 0.08). Based on estimates of optimal STI cases that could be handled without compromising quality by each doctor full-time equivalent available, it was projected that at 8 of the 14 clinics substantially more STI cases could be handled, which could increase the total STI cases treated at the 14 clinics combined by 38% at an additional cost of only 3.5% for service provision.

Conclusion
There is un-utilised capacity in the public sector STI clinics in this Indian state. Efforts to facilitate utilisation of this capacity would be useful, as this would enable more poor patients with STIs to be served at minimal additional cost, and would also reduce the cost per STI treated leading to more efficient use of public resources.