bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatitis C Virus (HCV) Core Antigen Assay To Detect Ongoing HCV Infection in Thai Injection Drug Users
Authors: Netski Dale M. , Wang Xiao-Hong , Mehta Shruti H. , Nelson Kenrad , Celentano David , Thongsawat Satawat , Maneekarn Niwat , Suriyanon Vinai , Jittiwutikorn Jaroon , Thomas David L. , Ticehurst John R. 
Published: April 2004

ABSTRACTWe evaluated a quantitative enzyme immunoassay (trak-C) for hepatitis C virus core antigen (HCV core Ag) by testing serum specimens from 820 injection drug users in Thailand with anti-HCV antibodies. The HCV genotypes in this population include genotypes 3 and 6, which have not been extensively tested with this assay. Among these specimens, 629 (76.7%) yielded positive results, with HCV core Ag concentrations predominantly spanning (35.7%) or above (58.2%) the measurable range of 1.5 to 100 pg/ml. To assess reproducibility, we retested 30 specimens representing six core Ag ranges; the mean coefficient of variation for each range was ≤9.7% (highest for 1.5 to 25 pg/ml). We also tested 204 specimens of the 820-specimen set for HCV RNA: while 146 (71.6%) were core Ag positive, 168 (82.4%) had detectable HCV RNA, of which 96% were typeable as genotype 3 (39%), 1 (31%), or 6 (26%) by nested reverse transcription-PCR. Among RNA-positive specimens, 86.9% had core Ag; 94% of the RNA negatives were core Ag negative. While there was no apparent bias for detecting core Ag representing the tested genotypes, median quantified results were higher for types 1a and 6 than for genotype 3 (P= 0.01); similarly, the median core Ag concentration was higher in HCV-human immunodeficiency virus-coinfected subjects than in HCV-monoinfected subjects. Our results demonstrated a good correlation between core Ag and HCV RNA in this population with high frequencies of genotypes 3 and 6. Because most core Ag concentrations were greater than those in the measurable range, we recommend a 10-fold dilution of the specimen before quantification. Reproducibility, low technical requirements, and high throughput should make this assay useful for clinical or research monitoring of HCV levels during active infection.
Convenient Selective Differential Broth for Isolation of Vancomycin-Resistant
Enterococcus
from Fecal Material
Authors: Novicki Thomas J. , Schapiro Jeffrey M. , Ulness Bruce K. , Sebeste Ann , Busse-Johnston Laurel , Swanson Kristine M. , Swanzy Susan R. , Leisenring Wendy , Limaye Ajit P. 
Published: April 2004

ABSTRACT

Studies have shown that vancomycin broth enrichment is superior to direct plating for the detection of vancomycin-resistant enterococcus (VRE), but vancomycin selective broth is not generally commercially available. We developed an easy-to-prepare VRE selective differential broth and compared it to direct plating on bile esculin azide (BEA) agar for the isolation of VRE from fecal samples. A total of 528 consecutive rectal swabs and stools were inoculated onto BEA agar and into BEA broth with vancomycin at a concentration of 15 μg/ml (BEA VAN
15μg/ml
broth). After 1 to 2 days of incubation, broths were subcultured to BEA VAN
6μg/ml
agar. Bile esculin-positive colonies from the direct and broth subculture plates were evaluated for the presence of VRE by standard microbiological techniques. Addition of the broth enrichment step led to the detection of significantly more VRE isolates than did direct plating alone (28 versus 18 VRE isolates, respectively). In all, 30 VRE strains were isolated from 29 cultures, all of which were
Enterococcus faecium
. MICs of vancomycin ranged from 32 μg/ml (
n
= 2) to > 256 μg/ml (
n
= 28). Twenty-two VRE isolates were available for further testing: sixteen exhibited a VanA phenotype and six were of the VanB phenotype.
van
genotypes were in agreement with phenotypes for all VRE isolates except one, which could not be genotyped. The broth method also resulted in significantly fewer bile esculin-positive, non-VRE isolates requiring further workup. We have thus developed an easily prepared vancomycin selective differential broth that is significantly more sensitive and specific in the detection of VRE than is direct fecal plating to BEA agar.
Characterization of
ompA
Genotypes by Sequence Analysis of DNA from All Detected Cases of
Chlamydia trachomatis
Infections during 1 Year of Contact Tracing in a Swedish County
Authors: Lysén Maria , Österlund Anders , Rubin Carl-Johan , Persson Tina , Persson Ingrid , Herrmann Björn 
Published: April 2004

ABSTRACT

In this study we aimed to characterize the
ompA
gene by sequencing DNA from all detected cases of
Chlamydia trachomatis
infection in a Swedish county during 2001, in order to improve the efficiency of contact tracing. Approximately 990 bp of the
ompA
gene was amplified, and sequence analysis was achieved in 678 (94%) of 725
C. trachomatis
-positive cases in this unselected population. The most prevalent genotype was serotype E (39%), followed by F (21%), G (11%), D (9%), K (9%), J (7%), H (2%), B (1%), and Ia (1%). Serotype E was found in five genotype variants, with the reference sequence comprising 96% of all E cases. Serotype D was the most variable, and of seven sequence variants, three were identified as recombinants with serotype E. Altogether 29 genetic variants were detected, and mutations and recombination events are discussed. Clinical manifestations were not associated with genotypes. Sequence variation was linked to sexual networks identified by contact tracing and improved epidemiological knowledge but was of limited benefit.
Identification of a Protein Biomarker Unique to the Pandemic O3:K6 Clone of
Vibrio parahaemolyticus
Authors: Williams Tracie L. , Musser Steven M. , Nordstrom Jessica L. , DePaola Angelo , Monday Steven R. 
Published: April 2004

ABSTRACT

The present method of characterizing
Vibrio parahaemolyticus
strains involves serotyping or detection methods based on assessment of the presence or absence of genes thought to be markers of an organism's pathogenicity. It is unclear whether these assays detect all pathogenic
V. parahaemolyticus
strains since a clear correlation between the presence of a particular gene and the organism's pathogenicity has not yet been observed. We have described a proteomics-based method to distinguish individual
V. parahaemolyticus
strains on the basis of their protein profiles and identified a specific protein that is characteristic of the pandemic O3:K6 strain and its clonal derivatives. In the pandemic clone of
V. parahaemolyticus
, a histone-like DNA-binding protein, HU-α, has a C-terminal amino acid sequence different from those of other strains of
V. parahaemolyticus
. Upon further study, it was discovered that the gene encoding this protein has a 16-kbp insert at the 3′ terminus of the open reading frame for this protein. By using the protein sequence of the unique biomarker for the pandemic clone of
V. parahaemolyticus
, it was possible to rationally design specific PCR-based probes and assays that permit the rapid and precise identification of pandemic strains of
V. parahaemolyticus
.
Significance of Amplified Fragment Length Polymorphism in Identification and Epidemiological Examination of
Candida
Species Colonization in Children Undergoing Allogeneic Stem Cell Transplantation
Authors: Ball L. M. , Bes M. A. , Theelen B. , Boekhout T. , Egeler R. M. , Kuijper E. J. 
Published: April 2004

ABSTRACT

Candida albicans
and non-
C. albicans Candida
species are increasingly being isolated from patients in high-risk categories, most notably, those who have undergone stem cell transplantation (SCT). Identification of the presence of non-
C. albicans Candida
species early in the course of the transplant procedure is important, as these species exhibit different sensitivities to the available antifungal treatments and cause mortality at rates that vary from those for
C. albicans
. Amplified fragment length polymorphism (AFLP) analysis has been shown to be a reliable method of reproducibly identifying medically important
Candida
species. We investigated the use of serial AFLP analysis of 54 routine surveillance cultures for the identification and epidemiological examination of
Candida
sp. colonization in five consecutive children undergoing allogeneic SCT. One child became colonized with a
C. albicans
strain and remained colonized with this strain during the whole admission period. Another child had persistent colonization with a
C. albicans
strain with striking variations in its AFLP patterns over time, which was considered indicative of microevolution.
Candida dubliniensis
,
Candida lusitaniae
, and
Saccharomyces cerevisiae
were identified in the three remaining patients, with two children being simultaneously and transiently colonized with different species. These findings show that colonization with yeasts during transplantation is a complex and dynamic interaction between the host and the organism(s). In our study three strains from eight separate time points were incorrectly identified as
C. albicans
by a rapid enzyme test. AFLP analysis of surveillance cultures allowed more accurate and informative epidemiological evaluations of pathogenic yeasts in children during transplantation.
Multilocus Short Sequence Repeat Sequencing Approach for Differentiating among
Mycobacterium avium
subsp.
paratuberculosis
Strains
Authors: Amonsin Alongkorn , Li Ling Ling , Zhang Qing , Bannantine John P. , Motiwala Alifiya S. , Sreevatsan Srinand , Kapur Vivek 
Published: April 2004

ABSTRACT

We
describe a multilocus short sequence repeat (MLSSR) sequencing approach
for the genotyping of
Mycobacterium avium
subsp.
paratuberculosis
(
M. paratuberculosis
) strains.
Preliminary analysis identified 185 mono-, di-, and trinucleotide
repeat sequences dispersed throughout the
M. paratuberculosis
genome, of which 78 were perfect repeats. Comparative nucleotide
sequencing of the 78 loci of six
M. paratuberculosis
isolates
from different host species and geographic locations identified a
subset of 11 polymorphic short sequence repeats (SSRs), with an average
of 3.2 alleles per locus. Comparative sequencing of these 11 loci was
used to genotype a collection of 33
M. paratuberculosis
isolates representing different multiplex PCR for IS
900
loci
(MPIL) or amplified fragment length polymorphism (AFLP) types. The
analysis differentiated the 33
M. paratuberculosis
isolates
into 20 distinct MLSSR types, consistent with geographic and
epidemiologic correlates and with an index of discrimination of 0.96.
MLSSR analysis was also clearly able to distinguish between sheep and
cattle isolates of
M. paratuberculosis
and easily and
reproducibly differentiated strains representing the predominant MPIL
genotype (genotype A18) and AFLP genotypes (genotypes Z1 and Z2) of
M. paratuberculosis
described previously. Taken together, the
results of our studies suggest that MLSSR sequencing enables facile and
reproducible high-resolution subtyping of
M. paratuberculosis
isolates for molecular epidemiologic and population genetic
analyses.
Identification of
Bacteroides thetaiotaomicron
on the Basis of an Unexpected Specific Amplicon of Universal 16S Ribosomal DNA PCR
Authors: Teng Lee-Jene , Hsueh Po-Ren , Huang Yu-Hsuan , Tsai Jui-Chang 
Published: April 2004

ABSTRACT

We applied a set of commonly used universal primers (primers RW01 and DG74) to amplify partial fragments of 16S ribosomal DNA for bacterial identification and found an unexpected amplicon (547 bp), in addition to the expected 362-bp product, in samples containing
Bacteroides thetaiotaomicron
. It was demonstrated that the internal sequence (508 bp, excluding the primers) of the 547-bp amplicon was identical to the genomic sequence from nucleotide positions 165800 to 166307 of
B. thetaiotaomicron
type strain VPI-5482 by a BLAST search of the sequences in the GenBank database. The existence of this unexpected yet specific amplicon strongly indicated the presence of
B. thetaiotaomicron
in the sample, and it was found that it could be used to discriminate
B. thetaiotaomicron
from closely related species. Another set of PCR primers specific for
B. thetaiotaomicron
was developed on the basis of the sequence of this 547-bp genomic fragment. Both PCR-based assays showed the same sensitivity (88%) and specificity (100%).
Evaluation of the Velogene Genomic Assay for Detection of
vanA
and
vanB
Genes in Vancomycin-Resistant
Enterococcus
Species
Authors: Appleman Maria D. , Citron Diane M. , Kwok Richard 
Published: April 2004

ABSTRACT

The Velogene (VEL) genomic assay is a qualitative DNA probe for
vanA
and
vanB
in enterococci. 150 clinical isolates were tested with the VEL assay and characterized by pigment production, catalase levels, motility, growth in 6 μg of vancomycin/ml, vancomycin and teicoplanin susceptibility, API 20S assay, and genotyping by multiplex PCR. The VEL assay identified all enterococcal strains with
vanA
and
vanB
genes.
Reactivation of Porcine Cytomegalovirus through Allogeneic Stimulation
Authors: Guedes Maria Isabel M. C. , Risdahl Jack M. , Wiseman Barry , Molitor Thomas W. 
Published: April 2004

ABSTRACT

Reactivation of latent porcine cytomegalovirus after coculture of peripheral blood mononuclear cells (PBMCs) from pigs with different genetic backgrounds was investigated. Nine of 10 allogeneic coculture pairs were PCR (DNA) positive, whereas 7 coculture pairs had porcine cytomegalovirus (PCMV) RNA, an indication of virus replication. The cell subpopulations harboring PCMV were monocytes and CD8
+
T cells.
Nested PCR Assay for Detection of
Leishmania donovani
in Slit Aspirates from Post-Kala-Azar Dermal Leishmaniasis Lesions
Authors: Sreenivas Gannavaram , Ansari N. A. , Kataria Joginder , Salotra Poonam 
Published: April 2004

ABSTRACT
A nested PCR assay to detect parasite DNA in slit aspirates from skin lesions of patients with post-kala-azar dermal lesihmaniasis (PKDL) is described. PCR results were positive in 27 of 29 (93%) samples by nested PCR assay, while only 20 of 29 (69%) were positive in a primary PCR assay. The nested PCR assay allowed reliable diagnosis of PKDL in a noninvasive manner.
Performance of a Commercial, Type-Specific Enzyme-Linked Immunosorbent Assay for Detection of Herpes Simplex Virus Type 2-Specific Antibodies in Ugandans
Authors: Laeyendecker Oliver , Henson Charla , Gray Ronald H. , Nguyen Ruby H.-N. , Horne Bobbi Jo , Wawer Maria J. , Serwadda David , Kiwanuka Noah , Morrow Rhoda Ashley , Hogrefe Wayne , Quinn Thomas C. 
Published: April 2004

ABSTRACT
Two hundred forty-eight human immunodeficiency virus (HIV)-positive and 496 HIV-negative subjects in Uganda were tested by HerpeSelect herpes simplex virus type 2 enzyme-linked immunosorbent assay (ELISA) and Western blotting to optimize the ELISA for use in this population. A higher index cutoff value was required for optimal sensitivity and specificity, and overall performance of the assay was not affected by HIV status.
Two Genotypes of Canine Coronavirus Simultaneously Detected in the Fecal Samples of Dogs with Diarrhea
Authors: Pratelli Annamaria , Decaro Nicola , Tinelli Antonella , Martella Vito , Elia Gabriella , Tempesta Maria , Cirone Francesco , Buonavoglia Canio 
Published: April 2004

ABSTRACT
Sixty-nine fecal samples from diarrheic puppies were examined by reverse transcription-PCR assays for the M and the S genes of canine coronaviruses (CCoVs). The isolates in 10 samples were recognized as CCoV type I, and the isolates in 6 samples were recognized as CCoV type II, while isolates of both genotypes were simultaneously detected in 53 samples.
Molecular Characterization of a Prophage of
Salmonella enterica
Serotype Typhimurium DT104
Authors: Tanaka Kiyoshi , Nishimori Kei , Makino Sou-Ichi , Nishimori Tomoko , Kanno Toru , Ishihara Ryoko , Sameshima Toshiya , Akiba Masato , Nakazawa Muneo , Yokomizo Yuichi , Uchida Ikuo 
Published: April 2004

ABSTRACT

Isolates of the
Salmonella enterica
serotype Typhimurium definitive phage type (DT104) were found to contain the same prophage (designated phage ST104). The complete sequence of the DNA genome of prophage ST104 was determined. The entire DNA sequence consisted of 41,391 bp, including 64 open reading frames, and exhibited high similarity to P22 and to phage type conversion phage ST64T.
Generalized Tuberculosis in Llamas (Lama glama) Due toMycobacterium microti
Authors: Oevermann A. , Pfyffer G. E. , Zanolari P. , Meylan M. , Robert N. 
Published: April 2004

ABSTRACTNecropsy of two llamas revealed numerous caseous nodules containing abundant acid-fast bacilli (AFB) in various organs. The AFB were identified by spoligotyping asMycobacterium microti, vole type. Infection caused byM. microtishould be considered in the differential diagnosis of debilitating diseases in New World camelids.
Effects of charge non-neutrality and finite beta on the electron temperature gradient modes in Tokamaks
Authors: Hirose A , Liu D Z , Livingstone S , Hirose A 
Published: April 2004

Local kinetic analysis of the electron temperature gradient (ETG) mode in Tokamaks indicates that the effects of charge non-neutrality are significant in the parameter regime of Tokamaks. The maximum growth rate occurs at (k/kDe)2 [Formula: see text] 0.5 when the electron temperature and density are varied over a wide range. The growth rate becomes dependent on the β factor even though the ETG mode is predominantly electrostatic. Finite β stabilization of the ETG mode requires a large ballooning parameter so as to cause an effective drift reversal. Mixing length estimate yields an electron thermal diffusivity χe [Formula: see text] qνTe (c/ωpe)2 [Formula: see text] / Ln where c/ωpe is the electron skin depth. PACS Nos.: 52.65.Tt, 52.55.Fa, 52.35.Py
THEOLOGY AND RELIGIOUS STUDIES IN THE POSTCOMMUNIST UKRAINE: History, Modern Status, Perspectives
Authors: Filipovych Lyudmyla , Kolodny Anatoly 
Published: April 2004

AbstractPost-Soviet Ukrainian society has gone through drastic changes that have to be considered both at a secular and a theological level; the same can be said of Ukrainian society's attitude toward religion. The secular analysis of religion, including its individual and social dimensions, is now taking place within the framework of religious studies, the human sciences approach to religion being somewhat new in Ukraine. On the other hand, the theological interpretation of traditional and nontraditional religion is undergoing a reawakening. The causes for the undeveloped status of religious studies and theology have to do with the absence of Ukrainian statehood and Ukrainian churches, due to the domination of foreign and communist regimes. This domination led to the prohibition of religion as well as of its study; in present-day Ukraine, however, theology and religious studies appear as specific forms of knowledge about religion, and as subjects taught at schools and universities.
Individualized risks of first adverse events in patients with Fanconi anemia
Authors: Rosenberg Philip S. , Huang Yi , Alter Blanche P. 
Published: April 2004

Abstract
Fanconi anemia (FA) is an autosomal recessive condition associated with bone marrow failure (BMF) leading to death or hematopoietic stem cell transplantation, acute myeloid leukemia (AML), and solid tumors (STs). It is unclear which patients are most likely to develop each outcome. From a cohort of 144 North American patients with FA, we calculated individualized risks of each outcome, given the presence or absence of readily diagnosed congenital abnormalities that occur frequently in FA. Abnormal radii and a 5-item congenital abnormality score were significant risk factors for BMF. The cumulative incidence of BMF by age 10 years varied from 18% in the lowest BMF risk group to 83% in the highest. Because of competing risks, patients in the lowest BMF risk group were most likely to live long enough to develop AML or ST, and, conversely, patients in the highest BMF risk group were least likely to live long enough to develop AML or ST. By age 40, the cumulative incidence of ST ranged from 0.6% to 29% in the highest and lowest BMF risk groups, respectively. Abnormal radii are the strongest predictor of early BMF in FA; a congenital abnormality score separates patients with normal radii into distinct prognostic groups. (Blood. 2004;104:350-355)
Germ line tumor-associated immunoglobulin VH region peptides provoke a tumor-specific immune response without altering the response potential of normal B cells
Authors: Lou Qiang , Kelleher Raymond J. , Sette Alessandro , Loyall Jenni , Southwood Scott , Bankert Richard B. , Bernstein Steven H. 
Published: April 2004

AbstractPrevious studies have suggested that murine T cells are tolerant to epitopes derived from germ line variable regions of immunoglobulin (Ig) heavy (VH) or light chains. This has lead to the prediction that germ line VH-region epitopes found in neoplastic B cells cannot be used to provoke an antitumor immune response. To test these assumptions and address the question of how such a vaccine may alter the normal B-cell response, an antibody-forming B-cell hybridoma (1H6) expressing a conserved germ line VH gene with specificity for dextran was generated and used as a tumor model. Using algorithms for predicting major histocompatibility complex (MHC) binding, potential MHC class I and II binding peptides were identified within the 1H6 VH region, synthesized, and tested for MHC binding and immunogenicity. We show that germ line VH peptides, when presented by dendritic cells, are immunogenic in vitro and provoke a tumor-specific protective immune response in vivo. We conclude that (1) it is possible to induce a T-cell response to germ line VH peptides; (2) such peptides can be used to generate a B-cell tumor-specific vaccine; and (3) a vaccine targeting VH peptides expressed by the dominant dextran-specific B-cell clonotype had no effect upon the magnitude of the normal B-cell response to dextran.
Post-transcriptional regulation of proinflammatory proteins
Authors: Anderson Paul , Phillips Kristine , Stoecklin Georg , Kedersha Nancy 
Published: April 2004

AbstractPost-transcriptional mechanisms play a critical role in regulating the expression of numerous proteins that promote inflammatory arthritis. The mRNAs encoding a subset of these proteins possess adenine/uridine-rich elements (AREs) in their 3′-untranslated regions that profoundly influence the rate at which mRNA is degraded and translated into protein. Tristetraprolin (TTP) and T cell intracellular antigen-1 (TIA-1) are ARE-binding proteins that dampen the expression of this class of proteins by promoting mRNA degradation and protein translation, respectively. We have discovered that TIA-1 and TTP function as arthritis-suppressor genes: TIA-1−/− mice develop mild arthritis, TTP−/− mice develop severe arthritis, and TIA-1−/−TTP−/− mice develop very severe arthritis. Paradoxically, lipopolysaccharide (LPS)-activated macrophages derived from TIA-1−/−TTP−/− macrophages produce less tumor necrosis factor α (TNF-α) than TIA-1−/− or TTP−/− macrophages. The bone marrows of these mice exhibit increased cellularity, reflecting the presence of mature neutrophils that secrete TNF-α in response to LPS stimulation. We hypothesize that TIA-1−/−TTP−/− neutrophils are a source of arthritigenic TNF-α, which promotes severe erosive arthritis in these mice.