bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus Sequence Typing of
Porphyromonas gingivalis
Strains from Different Geographic Origins
Authors: Enersen Morten , Olsen Ingar , van Winkelhoff Arie J. , Caugant Dominique A. 
Published: January 2006

ABSTRACT

Porphyromonas gingivalis
is an important periodontal pathogen that can be isolated from both active and inactive periodontal lesions. Apparently, differences in virulence between
P. gingivalis
strains exist, but the mechanisms underlying these differences are not yet fully understood. To obtain more information about pathogenicity and virulence of
P. gingivalis
, it is relevant to assess the genetic population structure of the species and to examine the occurrence of putative virulence factors against the genetic background. Presently, multilocus sequence typing (MLST) is the best method for analyzing bacterial population structures. Forty
P. gingivalis
strains from worldwide sources were analyzed by MLST. Internal 310- to 420-bp DNA fragments of the eight ubiquitous chromosomal genes,
ftsQ, hagB, gdpxJ, pepO, mcmA, recA, pga
, and
nah
, were amplified by PCR and then sequenced. The number of alleles at individual loci ranged from 2 to 19, and a total of 33 allelic profiles, or sequence types (STs), were identified. Nucleotide variation between alleles was located at one or a few sites. Identical or similar STs were found in isolates from different geographic regions. Our results showed signs of a clonal population structure with a level of recombination not as high as that previously suggested for the species. We also found that
P. gingivalis
isolates from individual patients were genetically heterogeneous.
Effects of Cow Age and Pregnancy on
Bartonella
Infection in a Herd of Dairy Cattle
Authors: Maillard R. , Grimard B. , Chastant-Maillard S. , Chomel B. , Delcroix T. , Gandoin C. , Bouillin C. , Halos L. , Vayssier-Taussat M. , Boulouis H.-J. 
Published: January 2006

ABSTRACT

Bartonella
spp. are small hemotropic bacteria infecting mammals. Four
Bartonella
species have been recently described in cattle and wild ruminants. To date, the biology and possible pathogenic role of
Bartonella
species isolated from ruminants are poorly understood. Therefore, a dairy herd of 448 cows and heifers was surveyed in order to establish the prevalence of
Bartonella bovis
and
B. chomelii
infections, the level of bacteremia, and the relationship between bacteremia and age or pregnancy status. The putative impact of
Bartonella
infection on production performance (individual milk cell count, milk yield) and reproductive status (success of artificial insemination [AI], placental retention, embryonic death, and abortion) was also assessed. The overall mean prevalence of
B. bovis
bacteremia was 59%, with the highest prevalence in heifers (92.5%). No
B. chomelii
was isolated, and 95% (114/120) of the
B. bovis
strains isolated and tested by PCR-restriction fragment length polymorphism belonged to type I. The level of bacteremia was higher in pregnant cows than in nonpregnant cows (
P
= 0.05), and the level of bacteremia rose during the last two-thirds of gestation (
P
< 0.001). There was no correlation between bacteremia and milk yield, individual milk cell count, success of first AI, interval between two calvings, or incidence of abortion and embryonic death. The interval from calving to first AI was shorter and the incidence of placental retention was lower in bacteremic animals than in nonbacteremic ones (
P
= 0.03 and
P
= 0.01, respectively).
Positive Correlation between Epstein-Barr Virus Viral Load and Anti-Viral Capsid Immunoglobulin G Titers Determined for Hodgkin's Lymphoma Patients and Their Relatives
Authors: Besson Caroline , Amiel Corinne , Le-Pendeven Catherine , Brice Pauline , Fermé Christophe , Carde Patrice , Hermine Olivier , Raphael Martine , Abel Laurent , Nicolas Jean-Claude 
Published: January 2006

ABSTRACTMarkers of Epstein-Barr virus (EBV) infection include measures of specific serological titers and of viral load (VLo) in peripheral blood mononuclear cells. Few studies have investigated the correlation between these two phenotypes. Here, we found that there was no correlation between VLo and either anti-EBV nuclear antigen type 1 or anti-early antigen immunoglobulin G (IgG) titer but that anti-viral capsid antigen (VCA) IgG titer increased with VLo in peripheral blood mononuclear cells in patients with Hodgkin's lymphoma (P= 3.10−3). A similar pattern was observed in healthy first-degree relatives (parents and siblings) of patients (P= 6.10−4). Our results indicate that anti-VCA IgG titers and EBV VLo are specifically correlated EBV phenotypes.
Association between Preterm Birth and Vaginal Colonization by Mycoplasmas in Early Pregnancy
Authors: Kataoka Soromon , Yamada Takashi , Chou Kazutoshi , Nishida Ryutaro , Morikawa Mamoru , Minami Mashiho , Yamada Hideto , Sakuragi Noriaki , Minakami Hisanori 
Published: January 2006

ABSTRACT

To examine the association between colonization by two newly classified species of genital ureaplasmas (
Ureaplasma parvum
and
U. urealyticum
) in early pregnancy and subsequent late abortion or preterm birth at <34 weeks of gestation, four species of genital mycoplasmas—
Mycoplasma genitalium, M. hominis, U. parvum
, and
U. urealyticum—
as well as
Chlamydia trachomatis
and
Neisseria gonorrhoeae
were examined by PCR-based methods in a prospective cohort study of 877 women with singleton pregnancies at <11 weeks of gestation. Antibiotics were used only in cases in which
C. trachomatis
and/or
N. gonorrhoeae
was detected. Multivariate logistic-regression analysis was used to assess independent risk factors after taking maternal low body weight and past history of preterm birth into account.
M. genitalium, M. hominis, U. parvum, U. urealyticum, C. trachomatis
, and
N. gonorrhoeae
were detected in 0.8%, 11.2%, 52.0%, 8.7%, 3.2%, and 0.1% of these 877 women, respectively. Twenty-one (2.4%) women experienced late abortion or preterm birth at <34 weeks of gestation. Three factors—detection of
U. parvum
in the vagina (odds ratio [OR], 3.0; 95% confidence interval [CI], 1.1 to 8.5); use of antibiotics, such as penicillin and cefatrizine, for incidental inflammatory complications before 22 weeks of gestation (OR, 4.2; 95% CI, 1.6 to 10.0); and past history of preterm birth (OR, 10.4; 95% CI, 2.7 to 40.5)—were independently associated with late abortion and preterm birth. In conclusion, vaginal colonization with
U. parvum
, but not
U. urealyticum
, is associated with late abortion or early preterm birth.
Legionella anisa
, a Possible Indicator of Water Contamination by
Legionella pneumophila
Authors: van der Mee-Marquet Nathalie , Domelier Anne-Sophie , Arnault Laurence , Bloc Daniel , Laudat Patrice , Hartemann Philippe , Quentin Roland 
Published: January 2006

ABSTRACT

Legionella anisa
is one of the most frequent species of
Legionella
other than
Legionella pneumophila
in the environment and may be hospital acquired in rare cases. We found that
L. anisa
may mask water contamination by
L. pneumophila
, suggesting that there is a risk of
L. pneumophila
infection in immunocompromised patients if water is found to be contaminated with
Legionella
species other than
L. pneumophila
.
Direct Identification of Mycobacteria in Primary Liquid Detection Media by Partial Sequencing of the 65-Kilodalton Heat Shock Protein Gene
Authors: McNabb Alan , Adie Kathy , Rodrigues Mabel , Black William A. , Isaac-Renton Judith 
Published: January 2006

ABSTRACT

We investigated extending the use of direct partial
hsp65
gene sequencing for the identification of mycobacteria to isolates in primary liquid detection media as an economical, feasible, and more rapid means of identification. During the course of the study, the
hsp65
sequence-based identifications for isolates from 670 primary liquid detection media determined to be positive for acid-fast bacilli were compared to the identifications derived from Accuprobes, biochemical test panels, or 16S rRNA gene sequencing. Preliminary analysis indicated a 97.6% concordance, with a final agreement of 99.1% between the identification algorithms.
hsp65
sequencing costs (US$32.84) were greater than the cost of identification with Accuprobe (US$19) but less than the cost of the biochemical test panel identification (average cost, US$98.90) and equivalent to the cost of 16S rRNA sequencing, although there was a referral cost (US$59.85) for the shipping of isolates to another reference laboratory. Analysis indicated that our laboratory would have recognized a cost savings of approximately $12,000 by using
hsp65
sequencing to identify isolates from specimens with a negative fluorescent- smear status and would have achieved further savings by using it as an alternative to biochemical panel testing for fluorescent-smear-positive specimens. The time to identification by
hsp65
gene sequencing was slightly longer than that required by the Accuprobe assay (1 versus 2 days), shorter than that required by the biochemical test panels (2 days versus 26 days on average), and more rapid than referral for 16S rRNA gene sequencing.
Armored RNA as Virus Surrogate in a Real-Time Reverse Transcriptase PCR Assay Proficiency Panel
Authors: Hietala S. K. , Crossley B. M. 
Published: January 2006

ABSTRACT
In recent years testing responsibilities for high-consequence pathogens have been expanded from national reference laboratories into networks of local and regional laboratories in order to support enhanced disease surveillance and to test for surge capacity. This movement of testing of select agents and high-consequence pathogens beyond reference laboratories introduces a critical need for standardized, noninfectious surrogates of disease agents for use as training and proficiency test samples. In this study, reverse transcription-PCR assay RNA targets were developed and packaged as armored RNA for use as a noninfectious, quantifiable synthetic substitute for four high-consequence animal pathogens: classical swine fever virus; foot-and-mouth disease virus; vesicular stomatitis virus, New Jersey serogroup; and vesicular stomatitis virus, Indiana serogroup. Armored RNA spiked into oral swab fluid specimens mimicked virus-positive clinical material through all stages of the reverse transcription-PCR testing process, including RNA recovery by four different commercial extraction procedures, reverse transcription, PCR amplification, and real-time detection at target concentrations consistent with the dynamic ranges of the existing real-time PCR assays. The armored RNA concentrations spiked into the oral swab fluid specimens were stable under storage conditions selected to approximate the extremes of time and temperature expected for shipping and handling of proficiency panel samples, including 24 h at 37°C and 2 weeks at temperatures ranging from ambient room temperature to −70°C. The analytic test performance, including the reproducibility over the dynamic range of the assays, indicates that armored RNA can provide a noninfectious, quantifiable, and stable virus surrogate for specific assay training and proficiency test purposes.
Validation of VITEK 2 Version 4.01 Software for Detection, Identification, and Classification of Glycopeptide-Resistant Enterococci
Authors: Abele-Horn Marianne , Hommers Leif , Trabold René , Frosch Matthias 
Published: January 2006

ABSTRACT

We evaluated the ability of the new VITEK 2 version 4.01 software to identify and detect glycopeptide-resistant enterococci compared to that of the reference broth microdilution method and to classify them into the
vanA, vanB, vanC1
, and
vanC2
genotypes. Moreover, the accuracy of antimicrobial susceptibility testing with agents with improved potencies against glycopeptide-resistant enterococci was determined. A total of 121 enterococci were investigated. The new VITEK 2 software was able to identify 114 (94.2%) enterococcal strains correctly to the species level and to classify 119 (98.3%) enterococci correctly to the glycopeptide resistance genotype level. One
Enterococcus casseliflavus
strain and six
Enterococcus faecium vanA
strains with low-level resistance to vancomycin were identified with low discrimination, requiring additional tests. One of the
vanA
strains was misclassified as the
vanB
type, and one glycopeptide-susceptible
E. facium
wild type was misclassified as the
vanA
type. The overall essential agreements for antimicrobial susceptibility testing results were 94.2% for vancomycin, 95.9% for teicoplanin, 100% for quinupristin-dalfopristin and moxifloxacin, and 97.5% for linezolid. The rates of minor errors were 9% for teicoplanin and 5% for the other antibiotic agents. The identification and susceptibility data were produced within 4 h to 6 h 30 min and 8 h 15 min to 12 h 15 min. In conclusion, use of VITEK 2 version 4.01 software appears to be a reliable method for the identification and detection of glycopeptide-resistant enterococci as well as an improvement over the use of the former VITEK 2 database. However, a significant reduction in the detection time would be desirable.
Internal Transcribed Spacer Sequencing versus Biochemical Profiling for Identification of Medically Important Yeasts
Authors: Ciardo D. E. , Schär G. , Böttger E. C. , Altwegg M. , Bosshard P. P. 
Published: January 2006

ABSTRACT

In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as
Candida rugosa
or
Candida utilis
. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region.
Absence of
Spiroplasma
or Other Bacterial 16S rRNA Genes in Brain Tissue of Hamsters with Scrapie
Authors: Alexeeva Irina , Elliott Ellen J. , Rollins Sandra , Gasparich Gail E. , Lazar Jozef , Rohwer Robert G. 
Published: January 2006

ABSTRACT

Spiroplasma
spp. have been proposed to be the etiological agents of the transmissible spongiform encephalopathies (TSEs). In a blind study, a panel of 20 DNA samples was prepared from the brains of uninfected hamsters or hamsters infected with the 263K strain of scrapie. The brains of the infected hamsters contained ≥10
10
infectious doses/g. The coded panel was searched for bacterial 16S rRNA gene sequences, using primers selective for spiroplasma sequences, primers selective for mollicutes in general, and universal bacterial primers. After 35 PCR cycles, no samples were positive for spiroplasma or any other bacterial DNA, while control
Spiroplasma mirum
genomic DNA, spiked at 1% of the concentration required to account for the scrapie infectivity present, was readily detected. After 70 PCR cycles, nearly all samples yielded amplified products which were homologous to various bacterial 16S rRNA gene sequences, including those of frequent environmental contaminants. These sequences were seen in uninfected as well as infected samples. Because the concentration of scrapie infectivity was at a known high level, it is very unlikely that a bacterial infection at the same concentration could have escaped detection. We conclude that the infectious agent responsible for TSE disease cannot be a spiroplasma or any other eubacterial species.
Establishing a Method of Inoculum Preparation for Susceptibility Testing of
Trichophyton rubrum
and
Trichophyton mentagrophytes
Authors: Santos D. A. , Barros M. E. S. , Hamdan J. S. 
Published: January 2006

ABSTRACT

A total of 92 clinical isolates of dermatophytes (52 of
Trichophyton rubrum
and 40 of
Trichophyton mentagrophytes
) were selected for testing with six antifungal drugs (terbinafine, griseofulvin, clotrimazole, miconazole, isoconazole, and fluconazole) and two pairs of drug combinations (ketoconazole-cyclopiroxolamine and itraconazole-cyclopiroxolamine). Two methods of inoculum preparation for susceptibility testing were evaluated that used (i) inocula consisting only of microconidia of dermatophytes filtered in Whatman filter model 40 and (ii) unfiltered inocula consisting of hyphae and microconidia. We followed the recommendations of approved document M38-A of CLSI (formerly NCCLS) with some adaptations, including an incubation period of 7 days and an incubation temperature of 28°C. Reference strains of
Candida parapsilosis, Candida krusei, Trichophyton rubrum
, and
Trichophyton mentagrophytes
were included as quality-control strains. MICs were consistently higher (usually 1 to 2 dilutions for drugs tested individually) when nonfiltered inocula were tested (
P
< 0.01) except for terbinafine. Larger MICs were seen when testing drugs with nonfiltered inocula. The curves of drug interaction were used to analyze the reproducibility of the test, and it was shown that high levels of reproducibility were achieved using the methodology that included the filtration step. The standardization of methodologies is the first step to yield reliability of susceptibility testing and to proceed with clinical laboratory studies to correlate MICs with clinical outcomes.
PERFORMANCE EVALUATION OF BLAS ON THE TRIDENT PROCESSOR
Authors: SOLIMAN MOSTAFA I. , SEDUKHIN STANISLAV G. 
Published: January 2006

Different subtasks of an application usually have different computational, memory, and I/O requirements that result in different needs for computer capabilities. Thus, the more appropriate approach for both high performance and simple programming model is designing a processor having multi-level instruction set architecture (ISA). This leads to high performance and minimum executable code size. Since the fundamental data structures for a wide variety of existing applications are scalar, vector, and matrix, our research Trident processor has three-level ISA executed on zero-, one-, and two-dimensional arrays of data. These levels are used to express a great amount of fine-grain data parallelism to a processor instead of the dynamical extraction by a complicated logic or statically with compilers. This reduces the design complexity and provides high-level programming interface to hardware. In this paper, the performance of Trident processor is evaluated on BLAS, which represent the kernel operations of many data parallel applications. We show that Trident processor proportionally reduces the number of clock cycles per floating-point operation by increasing the number of execution datapaths.
GENERALIZING MONOTONICITY: ON RECOGNIZING SPECIAL CLASSES OF POLYGONS AND POLYHEDRA
Authors: BOSE PROSENJIT , VAN KREVELD MARC 
Published: January 2006

A simple polyhedron is weakly-monotonic in direction [Formula: see text] provided that the intersection of the polyhedron and any plane with normal [Formula: see text] is simply-connected (i.e. empty, a point, a line-segment or a simple polygon). Furthermore, if the intersection is a convex set, then the polyhedron is said to be weakly-monotonic in the convex sense. Toussaint10 introduced these types of polyhedra as generalizations of the 2-dimensional notion of monotonicity. We study the following recognition problems: Given a simple n-vertex polyhedron in 3-dimensions, we present an O(n log n) time algorithm to determine if there exists a direction [Formula: see text] such that when sweeping over the polyhedron with a plane in direction [Formula: see text], the cross-section (or intersection) is a convex set. If we allow multiple convex polygons in the cross-section as opposed to a single convex polygon, then we provide a linear-time recognition algorithm. For simply-connected cross-sections (i.e. the cross-section is empty, a point, a line-segment or a simple polygon), we derive an O(n2) time recognition algorithm to determine if a direction [Formula: see text] exists. We then study variations of monotonicity in 2-dimensions, i.e. for simple polygons. Given a simple n-vertex polygon P, we can determine whether or not a line ℓ can be swept over P in a continuous manner but with varying direction, such that any position of ℓ intersects P in at most two edges. We study two variants of the problem: one where the line is allowed to sweep over a portion of the polygon multiple times and one where it can sweep any portion of the polygon only once. Although the latter problem is slightly more complicated than the former since the line movements are restricted, our solutions to both problems run in O(n2) time.
Southern High-Latitude Ensemble Data Assimilation in the Antarctic Mesoscale Prediction System
Authors: Barker D. M. 
Published: January 2006

Abstract
Ensemble data assimilation systems incorporate observations into numerical models via solution of the Kalman filter update equations, and estimates of forecast error covariances derived from ensembles of model integrations. In this paper, a particular algorithm, the ensemble square root filter (EnSRF), is tested in a limited-area, polar numerical weather prediction (NWP) model: the Antarctic Mesoscale Prediction System (AMPS).
For application in the real-time AMPS, the number of model integrations that can be run to provide forecast error covariances is limited, resulting in an ensemble sampling error that degrades the analysis fit to observations. In this work, multivariate, climatologically plausible forecast error covariances are specified via averaged forecast difference statistics. Ensemble representations of the “true” forecast errors, created using randomized control variables of the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) three-dimensional variational (3DVAR) data assimilation system, are then used to assess the dependence of sampling error on ensemble size, data density, and localization of covariances using simulated observation networks. Results highlight the detrimental impact of ensemble sampling error on the analysis increment structure of correlated, but unobserved fields—an issue not addressed by the spatial covariance localization techniques used to date.
A 12-hourly cycling EnSRF/AMPS assimilation/forecast system is tested for a two-week period in December 2002 using real, conventional (surface, rawinsonde, satellite retrieval) observations. The dependence of forecast scores on methods used to maintain ensemble spread and the inclusion of perturbations to lateral boundary conditions are studied.