bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction and Evaluation of Internal Control DNA for PCR Amplification of
Chlamydia trachomatis
DNA from Urine Samples
Authors: Betsou Fotini , Beaumont Katy , Sueur Jean Marie , Orfila Jeanne
Published: March 2003

An internal control DNA (ICD) with the same primer binding sequences as the target
Chlamydia trachomatis
DNA was constructed and evaluated in a PCR assay with immunoenzymatic detection. One hundred urine specimens were tested, and 23 were found to contain inhibitors of the PCR, if not subjected to DNA extraction prior to amplification. Coamplification and detection of the ICD appeared to be a useful method for estimating the effects of inhibitors on
C. trachomatis
DNA amplification.
Hepatitis B Virus Genotype C Takes a More Aggressive Disease Course Than Hepatitis B Virus Genotype B in Hepatitis B e Antigen-Positive Patients
Authors: Chan Henry Lik-Yuen , Wong May Ling , Hui Alex Yui , Hung Lawrence Cheung-Tsui , Chan Francis Ka-Leung , Sung Joseph Jao-Yiu
Published: March 2003

One hundred forty-six hepatitis B e antigen (HBeAg)-positive chronic hepatitis B patients were followed up for 32 ± 13 months. All six patients with hepatocellular carcinoma had hepatitis B virus (HBV) genotype C. Disease activity was greater in patients infected by HBV genotype C than in those infected by HBV genotype B in the HBeAg-positive phase but not after HBeAg seroconversion.
Molecular Characterization of Avian Paramyxovirus 1 Isolates Collected from Cormorants in Canada from 1995 to 2000
Authors: Weingartl H. M. , Riva J. , Kumthekar P.
Published: March 2003

Sequences encompassing cleavage sites of fusion protein genes were obtained for avian paramyxovirus 1 isolates from cormorants in Canada. All isolates have the virulent cleavage site SRGRRQKR*FVG. They form a distinct cluster within isolates obtained around the world and may represent a novel genotype closely related to genotype V.
Genotypic and Phenotypic Characteristics of
Corynebacterium diphtheriae
Strains Isolated from Patients in Belarus during an Epidemic Period
Authors: Titov Leonid , Kolodkina Valentina , Dronina Alina , Grimont Francine , Grimont Patrick A. D. , Lejay-Collin Monique , de Zoysa Aruni , Andronescu Constantin , Diaconescu Angela , Marin Byanca , Efstratiou Androulla
Published: March 2003

One hundred two
Corynebacterium diphtheriae
strains (93 of the gravis biotype and nine of the mitis biotype) isolated from clinical cases during the Belarus diphtheria epidemic were characterized by biotyping, toxigenicity testing by the Elek test and an indirect hemagglutination assay, phage typing, and ribotyping. The gravis biotype strains were characterized as high and medium toxin producers, and strains of biotype mitis were characterized as low and medium toxin producers. Most strains (82 of 102) were distributed among five phage types. Seventy-two strains (64 of the gravis biotype and 8 of the mitis biotype) belonged to phage type VI ls5,34add. Hybridization of genomic DNA digested with
Bst
EII and
Pvu
II revealed five ribotype patterns, namely, D1, D4, D6, D7, and D13. The majority of gravis biotype strains belonged to ribotypes D1 (49 of 93) and D4 (33 of 93) and included one clonal group of
C
.
diphtheriae
. This clone predominated in all regions in Belarus. There was a statistical association between ribotypes and phage types but not between ribotypes and levels of toxin production.
Paracoccus yeeii
sp. nov. (Formerly CDC Group EO-2), a Novel Bacterial Species Associated with Human Infection
Authors: Daneshvar Maryam I. , Hollis Dannie G. , Weyant Robbin S. , Steigerwalt Arnold G. , Whitney Anne M. , Douglas Michael P. , Macgregor John P. , Jordan Jean G. , Mayer Leonard W. , Rassouli Shadi M. , Barchet Winfred , Munro Cindy , Shuttleworth L. , Bernard Kathryn
Published: March 2003

CDC eugonic oxidizer group 2 (EO-2) is a group of unclassified gram-negative bacterial strains isolated from various human sources. As determined by biochemical tests and analyses of fatty acid compositions, these organisms form a homogeneous group that appears to be distinct from but related to other
Paracoccus
species. Molecular studies were performed on a set of 13 EO-2 strains from various clinical sources and geographic locations in the United States and Canada to determine their relationship to the
Paracoccus
genus. Control strains were
Paracoccus denitrificans
ATCC 17741
T
,
P. versutus
ATCC 25364
T
,
P. aminophilus
ATCC 49673
T
,
P. solventivorans
ATCC 700252
T
, and
Psychrobacter immobilis
ATCC 43116
T
, which are phenotypically similar to EO-2. Nearly complete (1,500-base) 16S rRNA gene sequencing of eight EO-2 strains showed a high level of sequence similarity (>99.3%) within the group, and a BLAST search of GenBank placed the EO-2 cluster in close proximity to
Paracoccus
species (95 to 97% similarity). DNA-DNA hybridization studies of 13 of the EO-2 strains showed all to be related at the species level, with >70% relatedness under stringent conditions and a divergence within the group of less than 2%. None of the
Paracoccus
control strains hybridized at >54% with any of the EO-2 strains. These results indicate that EO-2 represents a new
Paracoccus
species, the first isolated from human clinical specimens. A new species,
Paracoccus yeeii
, is proposed for the EO-2 strains. The type strain of
P. yeeii
is CDCG1212 (ATCC BAA-599 and CCUG 46822), isolated in Pennsylvania from dialysate of a 77-year-old male with peritonitis.
Identification of
Histoplasma
capsulatum
from Culture Extracts by Real-Time PCR
Authors: Martagon-Villamil Jose , Shrestha Nabin , Sholtis Mary , Isada Carlos M. , Hall Gerri S. , Bryne Terry , Lodge Barbara A. , Reller L. Barth , Procop Gary W.
Published: March 2003

We designed and tested a real-time LightCycler PCR assay for
Histoplasma
capsulatum
that correctly identified the 34
H
.
capsulatum
isolates in a battery of 107 fungal isolates tested and also detected
H
.
capsulatum
in clinical specimens from three patients that were culture positive for this organism.
Significant Improvement of the Recombinant
Borrelia
-Specific Immunoglobulin G Immunoblot Test by Addition of VlsE and a DbpA Homologue Derived from
Borrelia garinii
for Diagnosis of Early Neuroborreliosis
Authors: Schulte-Spechtel Ulrike , Lehnert Gisela , Liegl Gaby , Fingerle Volker , Heimerl Christiane , Johnson Barbara J. B. , Wilske Bettina
Published: March 2003

We investigated whether the recombinant
Borrelia
Western blot test previously described (B. Wilske, C. Habermann, V. Fingerle, B. Hillenbrand, S. Jauris-Heipke, G. Lehnert, I. Pradel, D. Rössler, and U. Schulte-Spechtel, Med. Microbiol. Immunol.
188:
139-144, 1999) can be improved by the addition of VlsE and additional DbpA and OspC homologues. By using a panel of sera from 36 neuroborreliosis patients and 67 control patients, the diagnostic sensitivity of the recombinant immunoblot test was significantly increased (86.1% versus 52.7%) without loss of specificity and was higher (86.1% versus 63.8%) than that of the conventional whole-cell lysate immunoblot test (U. Hauser, G. Lehnert, R. Lobentanzer, and B. Wilske, J. Clin. Microbiol.
35:
1433-1444, 1997). Improvement was mainly due to the presence of VlsE and DbpA.
Isolation of Sulfate-Reducing Bacteria from Human Thoracoabdominal Pus
Authors: Loubinoux Julien , Jaulhac Benoit , Piemont Yves , Monteil Henri , Le Faou Alain E.
Published: March 2003

To evaluate the prevalence of sulfate-reducing bacteria in septic processes, we searched for these bacteria by culture in 100 consecutive abdominal and pleural pus specimens. Twelve isolates were obtained from abdominal samples and were identified by a multiplex PCR as
Desulfovibrio piger
(formerly
Desulfomonas pigra
) (seven strains),
Desulfovibrio fairfieldensis
(four strains), and
Desulfovibrio desulfuricans
(one strain).
emmGene Distribution among Erythromycin-Resistant and -Susceptible Italian Isolates ofStreptococcus pyogenes
Authors: Zampaloni Claudia , Cappelletti Paola , Prenna Manuela , Vitali Luca Agostino , Ripa Sandro
Published: March 2003

The phenotypes and genetic determinants for macrolide resistance were determined for 167 erythromycin-resistantStreptococcus pyogenesstrains. A cMLS phenotype was shown in 18% of the erythromycin-resistant strains, while inducible resistance was apparent in 31% and the M phenotype was apparent in 50%. Theemmgene type of this set of resistant isolates and that of 48 erythromycin-sensitive isolates were determined.emm2 andemm48 were recorded only in the resistant strains of the M phenotype, while approximately all of the strains harboring theemm22 gene had the cMLS phenotype. More than 80% of theemm89-positive strains had the iMLS phenotype, and the same portion ofemm4 strains presented the M phenotype.emm3 is recorded only among sensitive strains. The distribution of frequencies of the genetic determinant for the virulence factor M protein was significantly different both among organisms of different types of resistance and between resistant and sensitive populations ofS.pyogenesunder study.
Identification of Mycobacterial Species by PCR Sequencing of Quinolone Resistance-Determining Regions of DNA Gyrase Genes
Authors: Dauendorffer Jean-Noël , Guillemin Isabelle , Aubry Alexandra , Truffot-Pernot Chantal , Sougakoff Wladimir , Jarlier Vincent , Cambau Emmanuelle
Published: March 2003

The determination of the amino acid sequence of quinolone resistance-determining regions (QRDRs) in the A and B subunits of DNA gyrase is the molecular test for the detection of fluoroquinolone resistance in mycobacteria. We looked to see if the assignment of mycobacterial species could be obtained simultaneously by analysis of the corresponding nucleotide sequences. PCR sequencing of
gyrA
and
gyrB
QRDRs was performed for 133 reference and clinical strains of 21 mycobacterial species commonly isolated in clinical laboratories. Nucleotide sequences of
gyrA
and
gyrB
QRDRs were species specific, regardless of fluoroquinolone susceptibility.
Stability of Allelic Frequencies and Distributions of
Candida albicans
Microsatellite Loci from U.S. Population-Based Surveillance Isolates
Authors: Lott Timothy J. , Fundyga Ruth E. , Brandt Mary E. , Harrison Lee H. , Sofair Andre N. , Hajjeh Rana A. , Warnock David W.
Published: March 2003

Allelic distributions and frequencies of five
Candida albicans
microsatellite loci have been determined for strains isolated from the bloodstream and obtained through active population-based surveillance in two U.S. metropolitan areas between 1998 and 2000. These data were compared to data for isolates obtained from two other U.S. regions in 1992 to 1993. In a majority of pairwise combinations between sites, no evidence was seen for shifts in microsatellite allelic frequencies. One to three alleles were highly predominant and correlated with major genotypes. These data both support the concepts of allelic stability and genetic equilibria and suggest that, in the United States, strains of
C
.
albicans
isolated from the bloodstream may form a defined, genetically homogeneous population across geographical distance and time.
Prospective Clinical Evaluation of the Serologic Tuberculous Glycolipid Test in Combination with the Nucleic Acid Amplification Test
Authors: Maekura Ryoji , Kohno Hiroaki , Hirotani Atsushi , Okuda Yoshinari , Ito Masami , Ogura Takeshi , Yano Ikuya
Published: March 2003

We have conducted a prospective controlled multicenter study to evaluate differences in the levels of clinical utility of the tuberculous glycolipid (TBGL) serodiagnostic test and the nucleic acid amplification test in patients with smear-negative active pulmonary tuberculosis (TB). The TBGL test and the PCR test were individually not so useful for the rapid diagnosis of smear-negative active pulmonary TB. However, clinical utility was considerably improved by using the TBGL test and the PCR test in combination, especially in patients with smear-negative and culture-negative active pulmonary TB and in patients with minimally advanced lesions.
Age-Specific
Helicobacter pylori
Seropositivity Rates of Children in an Impoverished Urban Area of Northeast Brazil
Authors: Mitchell Anastasia , Silva Terezinha M. J. , Barrett Leah J. , Lima Aldo A. M. , Guerrant Richard L.
Published: March 2003

We determined age-specific
Helicobacter pylori
seropositivity rates of 166 children and 39 mothers in an urban shantytown in northeast Brazil. Seropositivity rates increased from 23.1% at 0 to 11 months of age to only 39.3% by 96 to 131 months of age and were 82.1% at maturity. We observed no correlation between the seropositivity of the mothers and the seropositivity of their children.
Horizontal In Utero Acquisition of Cytomegalovirus Infection in a Twin Pregnancy
Authors: Gabrielli Liliana , Lazzarotto Tiziana , Foschini Maria Pia , Lanari Marcello , Guerra Brunella , Eusebi Vincenzo , Landini Maria Paola
Published: March 2003

It is generally accepted that viral infections can be transmitted horizontally by direct or indirect contact with virus-excreting persons, and some viral infections can be transmitted vertically, either prenatally or perinatally, from mother to child. This report presents data strongly supporting a prenatal horizontal acquisition of human cytomegalovirus infection in a twin pregnancy.
Two Cases of Subcutaneous Infection Due to
Phaeoacremonium
spp
Authors: Guarro Josep , Alves Sydney Hartz , Gené Josepa , Grazziotin Neiva Aparecida , Mazzuco Rosemari , Dalmagro Cristiane , Capilla Javier , Zaror Luis , Mayayo Emilio
Published: March 2003

We describe two cases in Brazil of human subcutaneous infections due to
Phaeoacremonium
spp. The first case was caused by
Phaeoacremonium
aleophilum
. The patient presented with a unique fistulized nodule on the left ankle. The fungus was detected by direct microscopic examination and was isolated repeatedly from material collected from the lesion. This is the first reported case of human infection caused by this fungus. The second case was caused by
Phaeoacremonium
rubrigenum
. The patient presented with multiple nodules around the left ankle and foot. The fungus was detected by direct examination of pus and histological sections of the nodules. It was repeatedly isolated from the clinical specimens. This is the second reported case of human infection caused by this species.
Bacteremia Caused by
Acinetobacter ursingii
Authors: Loubinoux Julien , Mihaila-Amrouche Liliana , Le Fleche Anne , Pigne Etienne , Huchon Gerard , Grimont Patrick A. D. , Bouvet Anne
Published: March 2003

Acinetobacter ursingii
has not been reported in infectious processes apart from its recent description as a new species. A bacteremia caused by
A. ursingii
in a patient with a pulmonary adenocarcinoma confirms that this microorganism is an opportunistic human pathogen. The isolate was susceptible to imipenem, aminoglycosides, rifampin, and fluoroquinolones.
Septic Shock Caused by
Ochrobactrum anthropi
in an Otherwise Healthy Host
Authors: Kettaneh Adrien , Weill François-Xavier , Poilane Isabelle , Fain Olivier , Thomas Michel , Herrmann Jean-Louis , Hocqueloux Laurent
Published: March 2003

Reported is a case of life-threatening septic shock that occurred in an otherwise healthy host after administration of a peripheral venous infusion of a solution contaminated with
Ochrobactrum anthropi
, an unusual human pathogen. The rapid onset of shock may have been due to a large inoculum caused by nonsterile practices at the time of reconstitution.
Diagnosis of
Bartonella
Endocarditis by a Real-Time Nested PCR Assay Using Serum
Authors: Zeaiter Zaher , Fournier Pierre-Edouard , Greub Gilbert , Raoult Didier
Published: March 2003

Bartonella
endocarditis is a severe disease for which blood cultures frequently remain negative. We tested three PCR assays by using specimens of serum sampled early during the disease from 43 patients diagnosed in our laboratory as having
Bartonella
endocarditis on the basis of serological, culture, and/or valvular molecular detection. We tested a two-step nested PCR (TSN-PCR), a one-step nested PCR (OSN-PCR) with a regular thermal cycler, and a one-step nested PCR with the LightCycler (LCN-PCR). These assays were performed with primers derived from the riboflavin synthase-encoding gene
ribC
, never before amplified in our laboratory. Due to contamination of negative controls, the results of the TSN-PCR were not interpretable, and this technique was no longer considered. The LCN-PCR had a specificity of 100% and a sensitivity of 58.1%, higher than those of the OSN-PCR (18.6%;
P
< 0.01) and prolonged blood culturing (7.1%;
P
< 0.01). The LCN-PCR results correlated strictly with those of other direct diagnostic tests, when available, and identified the causative species for six patients previously diagnosed on the basis of serological analysis only. The efficacy of the LCN-PCR was not influenced by antibiotics (
P
= 0.96) but was altered by prolonged storage of serum specimens at −20°C (
P
= 0.04). Overall, the LCN-PCR is specific and more sensitive than traditional methods (i.e., culturing and/or PCR with EDTA-treated blood). It can easily be applied to the diagnosis of patients with suspected
Bartonella
endocarditis, especially when only serum is available.
stx
1c
Is the Most Common Shiga Toxin 1 Subtype among Shiga Toxin-Producing
Escherichia coli
Isolates from Sheep but Not among Isolates from Cattle
Authors: Brett Kim N. , Ramachandran Vidiya , Hornitzky Michael A. , Bettelheim Karl A. , Walker Mark J. , Djordjevic Steven P.
Published: March 2003

Unlike Shiga toxin 2 (
stx
2
) genes, most nucleotide sequences of Shiga toxin 1 (
stx
1
) genes from Shiga toxin-producing
Escherichia coli
(STEC),
Shigella dysenteriae
, and several bacteriophages (H19B, 933J, and H30) are highly conserved. Consequently, there has been little incentive to investigate variants of
stx
1
among STEC isolates derived from human or animal sources. However
stx
1OX3
, originally identified in an OX3:H8 isolate from a healthy sheep in Germany, differs from other
stx
1
subtypes by 43 nucleotides, resulting in changes to 12 amino acid residues, and has been renamed
stx
1c
. In this study we describe the development of a PCR-restriction fragment length polymorphism (RFLP) assay that distinguishes
stx
1c
from other
stx
1
subtypes. The PCR-RFLP assay was used to study 378
stx
1
-containing STEC isolates. Of these, 207 were isolated from sheep, 104 from cattle, 45 from humans, 11 from meat, 5 from swine, 5 from unknown sources, and 1 from a cattle water trough. Three hundred fifty-five of the 378 isolates (93.9%) also possessed at least one other associated virulence gene (
ehxA
,
eaeA
, and/or
stx
2
); the combination
stx
1
,
stx
2
, and
ehxA
was the most common (175 of 355 [49.3%]), and 90 of 355 (25.4%) isolates possessed
eaeA
. One hundred thirty-six of 207 (65.7%) ovine isolates possessed
stx
1c
alone and belonged to 41 serotypes. Seventy-one of 136 (52.2%) comprised the common ovine serotypes O5:H
−
, O128:H2, and O123:H
−
. Fifty-two of 207 isolates (25.1%) possessed an
stx
1
subtype; 27 (51.9%) of these belonged to serotype O91:H
−
. Nineteen of 207 isolates (9.2%) contained both
stx
1c
and
stx
1
subtypes, and 14 belonged to serotype O75:H8. In marked contrast, 97 of 104 (93.3%) bovine isolates comprising 44 serotypes possessed an
stx
1
subtype, 6 isolates possessed
stx
1c
, and the remaining isolate possessed both
stx
1c
and
stx
1
subtypes. Ten of 11 (91%) isolates cultured from meat in New Zealand possessed
stx
1c
(serotypes O5:H
−
, O75:H8/H40, O81:H26, O88:H25, O104:H
−
/H7, O123:H
−
/H10, and O128:H2); most of these serotypes are commonly recovered from the feces of healthy sheep. Serotypes containing
stx
1
recovered from cattle rarely were the same as those isolated from sheep. Although an
stx
1c
subtype was never associated with the typical enterohemorrhagic
E. coli
serogroups O26, O103, O111, O113, and O157, 13 human isolates possessed
stx
1c
. Of these, six isolates with serotype O128:H2 (from patients with diarrhea), four O5:H
−
isolates (from patients with hemolytic-uremic syndrome), and three isolates with serotypes O123:H
−
(diarrhea), OX3:H8 (hemolytic-uremic syndrome), and O81:H6 (unknown health status) represent serotypes that are commonly isolated from sheep.
Epidemiologic Analysis of Invasive and Noninvasive Group A Streptococcal Isolates in Hong Kong
Authors: Ho P. L. , Johnson D. R. , Yue A. W. Y. , Tsang D. N. C. , Que T. L. , Beall B. , Kaplan E. L.
Published: March 2003

Since the mid-1980s, there has been a resurgence of severe forms of invasive group A streptococcal (GAS) disease in many Western countries. In Hong Kong, a similar increase has also been observed in recent years. One hundred seven GAS isolates collected from 1995 to 1998 from individuals with necrotizing fasciitis, toxic shock syndrome, meningitis, or other type of bacteremic sepsis (invasive group,
n
= 24) as well as from individuals with minor skin and throat infections (noninvasive group,
n
= 83) were characterized through serologic and/or
emm
sequence typing. Thirty-two M protein gene sequence types were identified. Types M1, M4, and M12 were the most prevalent in both the invasive group and the noninvasive group; together they accounted for 70.8 and 37.3% of the isolates, respectively. No clear pattern of skin and throat infection M types was observed. Type M1 was overrepresented in the invasive and pharyngeal isolates. The same pulsed-field gel electrophoresis pattern was shared by most invasive and all pharyngeal M1 isolates. Overall, resistance to erythromycin (32%) and tetracycline (53%) was high, but M1 isolates were significantly less likely to have resistance to either antimicrobial agent than non-M1 isolates. One novel
emm
sequence type,
stHK
, was identified in an isolate from a patient with necrotizing fasciitis. Minor
emm
gene sequence alterations were noted for 31 isolates, and for 13 of these isolates, deletion, insertion, or point mutations were seen in the hypervariable 50 N-terminal residues.
Competitive Enzyme-Linked Immunosorbent Assay Based on Monoclonal Antibody and Recombinant Hemagglutinin for Serosurveillance of Rinderpest Virus
Authors: Renukaradhya G. J. , Suresh K. B. , Rajasekhar M. , Shaila M. S.
Published: March 2003

A competitive enzyme-linked immunosorbent assay (C-ELISA) which detects antibodies unique to rinderpest virus (RPV) has been developed. This test can differentiate antibodies against RPV and those against peste des petits ruminants virus. The recombinant RPV hemagglutinin (H)-protein C-ELISA (recH C-ELISA) is based on the ability of a well-characterized monoclonal antibody (MAb) produced with the soluble, secreted form of the H protein (Sec H protein) of RPV made in a baculovirus expression system to compete with the binding of RPV antibodies in the serum of vaccinated or infected, recovered animals to the Sec H protein. The B-cell epitope recognized by the MAb corresponds to amino acids 575 to 583 on the H protein, which is not present on the antigenically closely related peste des petits ruminants virus hemagglutinin-neuraminidase protein. Initially, a positive-negative threshold cutoff value for percent inhibition of 34 was established with 500 known RPV-negative serum samples. The recH C-ELISA was developed with the enzyme immunoassay software of a commercial RPV C-ELISA kit. Comparative analysis of the test results for 700 serum samples obtained with the commercial kit gave a sensitivity of 112.4% and a specificity of 72.4%. Variations in percent inhibition values were observed for the two assay systems. These variations may have been due to the undefined amount of antigen present in the commercial kit as well as the use of a different MAb. The recH C-ELISA detected more positive serum samples compared to the number detected by the commercial kit, with the results confirmed by a virus neutralization test. Thus, recH C-ELISA is a sensitive tool for RPV serosurveillance in disease eradication programs.
Cost-Effectiveness Analysis of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test as Used Routinely on Smear-Positive Respiratory Specimens
Authors: Dowdy David W. , Maters Amelia , Parrish Nicole , Beyrer Christopher , Dorman Susan E.
Published: March 2003

A decision analysis was conducted to evaluate the cost-effectiveness of programs in which the Amplified Mycobacterium Tuberculosis Direct test (MTD) (Gen-Probe) is used to rapidly exclude
Mycobacterium tuberculosis
complex as a cause of disease in smear-positive respiratory specimens. MTD sensitivity, specificity, and probability of inhibition for smear-positive specimens were estimated from literature reports. Costs and laboratory performance characteristics were determined from review of records and practices at an urban hospital in the mid-Atlantic United States. In the base case, 31.4% of smear-positive specimens were assumed to be culture positive for
M. tuberculosis
. Under these conditions, the marginal cost of the MTD testing program was estimated as $338 per smear-positive patient, or $494 per early exclusion of tuberculosis based on negative MTD results. By comparison, the cost of respiratory isolation ($27.77/day) and drugs ($5.66/day) averted by MTD testing was estimated at $201 per early tuberculosis exclusion. MTD testing was therefore not cost-effective in this scenario. Sensitivity analysis revealed that cost-effectiveness estimates are sensitive to the number of smear-positive specimens processed annually, the relative prevalence of
M. tuberculosis
in smear-positive specimens, and the marginal daily cost of respiratory isolation. A decision tool is therefore presented for assessing the cost-effectiveness of MTD under various combinations of those three variables. While routine MTD testing of smear-positive specimens is not expected to be cost-saving for most individual hospitals, centralized reference laboratories may be able to implement MTD in a cost-effective manner across a wide range of situations.
Use of Fourier-Transform Infrared Spectroscopy for Typing of
Candida
albicans
Strains Isolated in Intensive Care Units
Authors: Sandt C. , Sockalingum G. D. , Aubert D. , Lepan H. , Lepouse C. , Jaussaud M. , Leon A. , Pinon J. M. , Manfait M. , Toubas D.
Published: March 2003

Comparative studies of
Candida
albicans
strains are essential for proving cross-infections in epidemiological investigations. Typing of
C
.
albicans
strains is mainly based on genotypic methods. Fourier-transform infrared (FTIR) spectroscopy is described in this study as a novel phenotypic approach to the typing of
C
.
albicans
. The first step in the approach was the standardization of sample preparation (culture conditions and sampling parameters) and acquisition and classification parameters (spectral acquisition, spectral window selection, classification algorithm, and heterogeneity threshold). The second step consisted of validating the established parameters with a set of 79 strains of
C
.
albicans
isolated over 4 months from nine patients hospitalized in two intensive care units. Strains were isolated from multiple anatomical sites with repeated sampling. FTIR spectroscopy results were compared to randomly amplified polymorphic DNA (RAPD) results; this analysis showed that the amplification patterns of strains isolated from a given patient were identical and that different patients had different profiles. FTIR spectroscopy data were analyzed by hierarchical clustering performed with the second-derivative spectra. This classification revealed nine groups, one per patient. Only one spectrum out of 79 was misclassified by the FTIR spectroscopy method. RAPD and FTIR spectroscopy results were in good agreement, showing that, when nosocomial candidiasis transmission is suspected and urgent information is needed, this technique may be useful as a quick identification tool to give solid clues before confirmation by a genotypic method.
Interaction between Porcine Reproductive-Respiratory Syndrome Virus and Bacterial Endotoxin in the Lungs of Pigs: Potentiation of Cytokine Production and Respiratory Disease
Authors: Van Gucht Steven , Van Reeth Kristien , Pensaert Maurice
Published: March 2003

Porcine reproductive-respiratory syndrome virus (PRRSV) is a key agent in multifactorial respiratory disease of swine. Intratracheal administration of bacterial lipopolysaccharides (LPSs) to PRRSV-infected pigs results in markedly enhanced respiratory disease, whereas the inoculation of each component alone results in largely subclinical disease. This study examines whether PRRSV-LPS-induced respiratory disease is associated with the excessive production of proinflammatory cytokines in the lungs. Gnotobiotic pigs were inoculated intratracheally with PRRSV and then with LPS at 3, 5, 7, 10, or 14 days of infection and euthanatized 6 h after LPS inoculation. Controls were inoculated with PRRSV or LPS only or with phosphate-buffered saline. Virus titers, (histo)pathological changes in the lungs, numbers of inflammatory cells, and bioactive tumor necrosis factor alpha (TNF-α), interleukin-1 (IL-1), and IL-6 levels in bronchoalveolar lavage fluids were examined. All pigs inoculated with PRRSV-LPS developed severe respiratory disease, whereas the controls that were inoculated with PRRSV or LPS alone did not. PRRSV infection significantly enhanced cytokine production in response to LPS. Peak TNF-α, IL-1, and IL-6 titers were 10 to 100 times higher in the PRRSV-LPS-inoculated pigs than in the pigs inoculated with PRRSV or LPS alone; and the titers correlated with the respiratory signs. The levels of neutrophil infiltration and the pathological changes detected in the lungs of PRRSV-LPS-inoculated pigs resembled those detected when the effects of PRRSV and LPS inoculated alone are combined, but with no synergistic effects between PRRSV and LPS. These data demonstrate a synergism between PRRSV and LPS in the induction of proinflammatory cytokines and an association between induction of these cytokines and disease.
Blastocystis
Isolates from a Pig and a Horse Are Closely Related to
Blastocystis hominis
Authors: Thathaisong Umaporn , Worapong Jeerapun , Mungthin Mathirut , Tan-Ariya Peerapan , Viputtigul Kwanjai , Sudatis Apichart , Noonai Adisak , Leelayoova Saovanee
Published: March 2003

Blastocystis
has a widespread distribution in a variety of animals, which is a potential source of infection for humans. However, the contribution of zoonotic transmission remains unclear due to the absence of molecular proof of these organisms being identical to those found in humans. We report herein the similar subgroup of
Blastocystis
isolates from humans, pigs, and a horse using a restriction fragment length polymorphism (RFLP) analysis of partial small-subunit ribosomal DNA (ssu rDNA). Additionally, sequence and phylogenic analysis of partial ssu rDNA of
Blastocystis
from a human, a pig, and a horse sharing a common subgroup shows that
Blastocystis
isolates from a pig and a horse were monophyletic and closely related to
B. hominis
, with 92 to 94% identity. These results suggest the possibility of zoonotic potential of
Blastocystis
.
Heterogeneity of
cag
Genotypes in
Helicobacter
pylori
Isolates from Human Biopsy Specimens
Authors: Tomasini Maria Luisa , Zanussi Stefania , Sozzi Michele , Tedeschi Rosamaria , Basaglia Giancarlo , De Paoli Paolo
Published: March 2003

The
Helicobacter
pylori
chromosomal cluster of genes known as the cytotoxin-associated gene (
cag
) island may have different compositions in infecting strains. In this study, we analyzed 150 single colonies obtained from gastric biopsy specimens from 10 patients infected with
cagA
-positive
H
.
pylori
strains and sweep isolates (isolates harvested with sweep in different points of the plate) from 6 patients infected with
cagA
-negative strains. Three loci in the
cag
island (
cagA
,
cagE
, and
virB11
) and the conserved gene
glmM
(
ureC
) were investigated by PCR. The levels of anti-
H
.
pylori
and anti-CagA antibodies in patient sera were also measured. For subjects infected with
cagA
-negative strains, all sweep isolates were also negative for
cagE
and
virB11
, suggesting the complete absence of the
cag
island. For subjects infected with
cagA
-positive strains, most of the isolates were positive for all three genes studied, whereas 24.7% of the isolates had a partial or total deletion of the
cag
island.
cagA
,
cagE
, and
virB11
were, respectively, present in 87.3, 77.3, and 90% of the colonies. The deletion of
virB11
was always associated with the deletion of
cagA
and/or
cagE
.
H
.
pylori
colonies with different
cag
genotypes were isolated within a single gastric biopsy specimen from 3 of the 10 patients and were further characterized by random amplified polymorphic DNA (RAPD) analysis and by sequencing of an arbitrarily selected gene segment. Although the colonies had different
cag
genotypes, their RAPD profiles were highly similar within each patient, and the nucleotide sequences of the selected gene segment were identical. All of the patients had detectable antibodies against
H
.
pylori
, and 9 of 10 had anti-CagA antibodies. In conclusion, we show that a single infecting
H
.
pylori
strain may include variable proportions of colony subtypes with different
cag
genotypes. The extension of our analysis to patients with well-characterized gastric diseases may provide significant information on the relationship between
cag
genotypes and clinical outcomes of
H
.
pylori
infections.
Molecular Epidemiological Analysis of
Cryptosporidium
Isolates from Humans and Animals by Using a Heteroduplex Mobility Assay and Nucleic Acid Sequencing Based on a Small Double-Stranded RNA Element
Authors: Leoni Francesca , Gallimore Chris I. , Green Jonathan , McLauchlin Jim
Published: March 2003

Two extrachromosomal double-stranded RNA (dsRNA) elements occur in
Cryptosporidium
parvum
. A heteroduplex mobility assay (HMA) was developed for the rapid characterization of sequence diversity in a 173-bp fragment of the small dsRNA element of
Cryptosporidium
with either a natural sequence from
Cryptosporidium
meleagridis
or a synthetic sequence as reference DNA. The 173-bp fragment was generated from 265 samples of whole feces (242 from humans and 18 from livestock with
C
.
parvum
genotype 1 or 2, 4 from humans with
Cryptosporidium
felis
, and 1 from a human with
C
.
meleagridis
). The HMA method identified 21 patterns in
C
.
parvum
(8 in genotype 1, 12 in genotype 2, and a type common to both genotypes), 4 patterns in
C
.
felis
, and 1 pattern in
C
.
meleagridis
. All patterns were confirmed as distinct by DNA sequencing. For genotype 1, a single HMA type was found in 89% of samples: 64 of 65 cases from three waterborne outbreaks, all 16 cases from eight intrafamilial outbreaks, and 17 of 28 sporadic cases. Among the remaining 11 sporadic cases due to genotype 1, seven other HMA types were detected. For genotype 2, a single HMA type was found in 72% of samples: 36 of 43 cases from three waterborne outbreaks, 11 of 15 cases from seven intrafamilial outbreaks, 44 of 75 sporadic cases, and all 18 samples from livestock. Within the intrafamilial outbreaks, two other HMA types were identified: the same HMA type was detected in samples from cases within the same outbreak. Among the sporadic cases due to genotype 2, 10 additional HMA types were detected.
Rapid Detection of
rpoB
Gene Mutations in Rifampin-Resistant
Mycobacterium tuberculosis
Isolates in Shanghai by Using the Amplification Refractory Mutation System
Authors: Fan Xiao-Yong , Hu Zhong-Yi , Xu Fan-Hong , Yan Zhi-Qiang , Guo Sheng-Qi , Li Zhong-Ming
Published: March 2003

Rapid detection of drug resistance in
Mycobacterium tuberculosis
is essential for efficient treatment and control of this pathogen. The amplification refractory mutation system (ARMS) was used to detect mutations in the rifampin resistance-determining region of the
rpoB
gene. A total of 39 rifampin-resistant
M. tuberculosis
isolates in Shanghai were analyzed by this assay, resulting in 92.3% sensitivity (36 of 39) and 87.2% concordance (34 of 39) relative to DNA sequencing, by which 41 mutations of 11 different types, including 9 point mutations and 2 deletions, were identified in the
rpoB
gene. The most frequent mutations were those associated with codon 531 (21 of 39 [53.8%]) and codon 526 (9 of 39 [23.1%]). The results suggest that the ARMS assay is rapid and simple to implement and could be performed for detection of rifampin resistance in
M. tuberculosis
to complement conventional culture-based methods.
Performance Characteristics of Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping Systems in Sequence-Based Analysis of Subtypes Other than HIV-1 Subtype B
Authors: Jagodzinski Linda L. , Cooley John D. , Weber Mark , Michael Nelson L.
Published: March 2003

Given the diversity of human immunodeficiency virus type 1 (HIV-1) subtypes and the emergence of subtypes other than HIV-1 subtype B in the United States, genotypic assays must be capable of delivering sequence data on diverse HIV-1 subtypes. We evaluated the performance of Visible Genetics TRUGENE
HIV-1
genotyping kit and Applied Biosystems ViroSeq HIV-1 genotyping system on a panel of 34 well-characterized HIV-1 viral stocks (subtypes A through H). Both assays perform well on diverse HIV-1 subtypes despite being designed for HIV-1 subtype B. The TRUGENE assay produced sequence data for 31 isolates but not for one C and two G isolates. The TRUGENE assay using prototype 1.5 RT-PCR primers and the ViroSeq assay were both successful for all variants tested, although five isolates lacked double-strand sequence coverage in the ViroSeq assay. The availability of standardized HIV-1 genotyping kits that perform reliably with all HIV subtypes will facilitate broad implementation of HIV-1 resistance testing.
ACCELERATED LATTICE BOLTZMANN SCHEME FOR STEADY-STATE FLOWS
Authors: BERNASCHI MASSIMO , SUCCI SAURO
Published: March 2003

We discuss time-independent variants of the lattice Boltzmann method aimed at accelerating the computation of steady-state flows.
ON THE NUMERICAL SIMULATION OF FLOWS OF POLYMER SOLUTIONS USING HIGH-ORDER METHODS BASED ON THE FOKKER-PLANCK EQUATION
Authors: CHAUVIÈRE CÉDRIC , FANG JIANNONG , LOZINSKI ALEXEI , OWENS ROBERT G.
Published: March 2003

The present paper provides evidence of the affordability and competitiveness of Fokker-Planck-based methods when compared with stochastic simulation techniques. We apply an FP-based method to solve flow of a FENE fluid past a confined cylinder. We then solve uniaxial extensional flow for a reptation model due to Öttinger1 at a high extensional rate. In both cases the FP method is seen, for comparable levels of accuracy, to cost only a small fraction of the equivalent stochastic approach.
VISCOUS FINGERING IN MISCIBLE, IMMISCIBLE AND REACTIVE FLUIDS
Authors: GROSFILS PATRICK , BOON JEAN PIERRE
Published: March 2003

With the Lattice Boltzmann method (using the BGK approximation) we investigate the dynamics of Hele-Shaw flow under conditions corresponding to various experimental systems. We discuss the onset of the instability (dispersion relation), the static properties (characterization of the interface) and the dynamic properties (growth of the mixing zone) of simulated Hele-Shaw systems. We examine the role of reactive processes (between the two fluids) and we show that they have a sharpening effect on the interface similar to the effect of surface tension.
LATTICE BOLTZMANN SIMULATIONS OF DROP DEFORMATION AND BREAKUP IN SHEAR FLOWS
Authors: INAMURO T. , TOMITA R. , OGINO F.
Published: March 2003

A lattice Boltzmann method for multicomponent immiscible fluids is applied to simulations of drop deformation and breakup in shear flows for various capillary numbers and viscosity ratios at three different Revnolds numbers, Re = 0.2, 1, 10. The effect of the Reynolds number on drop deformation and breakup in shear flows is investigated. It is found that the drop is easier to deform and to be ruptured as the Reynolds number increases.
MOLECULAR DYNAMICS SIMULATIONS OF NON-NEWTONIAN EXTENSIONAL FLUID FLOWS
Authors: KOPLIK JOEL , BANAVAR JAYANTH R.
Published: March 2003

We discuss the use of molecular dynamics computer simulations in the extensional flow dynamics of polymeric, non-Newtonian liquids. The molecular model consists of Lennard-Jones monomers bound into linear chains by FENE potentials, a system known to exhibit characteristic non-Newtonian behavior such as shear thinning and normal stress differences. Here, we simulate liquid bridge flows in which cylinders of such liquids are placed between solid plates and extended to the point of rupture. Measurements of the local fluid stress tensor and interface shape provide information on extensional viscosity and rheology, coupled to microscopic information based on the evolution of molecular configurations. The simulations are in good agreement with laboratory data and with the results of macroscopic numerical calculations where available, but provide new and detailed information on the internal dynamics of liquids in extensional flow.
LARGE-EDDY SIMULATIONS WITH A MULTIPLE-RELAXATION-TIME LBE MODEL
Authors: KRAFCZYK MANFRED , TÖLKE JONAS , LUO LI-SHI
Published: March 2003

We include Smagorinsky's algebraic eddy viscosity approach into the multiple-relaxation-time (MRT) lattice Boltzmann equation (LBE) for large-eddy simulations (LES) of turbulent flows. The main advantage of the MRT-LBE model over the popular lattice BGK model is a significant improvement of numerical stability which leads to a substantial reduction of oscillations in the pressure field, especially for turbulent flow simulations near the numerical stability limit. The MRT-LBE model for LES is validated with a benchmark case of a surface mounted cube in a channel at Re = 40 000. Our preliminary results agree well with experimental data.
HYBRID FINITE-DIFFERENCE THERMAL LATTICE BOLTZMANN EQUATION
Authors: LALLEMAND PIERRE , LUO LI-SHI
Published: March 2003

We analyze the acoustic and thermal properties of athermal and thermal lattice Boltzmann equation (LBE) in 2D and show that the numerical instability in the thermal lattice Boltzmann equation (TLBE) is related to the algebraic coupling among different modes of the linearized evolution operator. We propose a hybrid finite-difference (FD) thermal lattice Boltzmann equation (TLBE). The hybrid FD-TLBE scheme is far superior over the existing thermal LBE schemes in terms of numerical stability. We point out that the lattice BGK equation is incompatible with the multiple relaxation time model.
FOLDING SIMULATIONS FOR A THREE-HELIX BUNDLE PROTEIN
Authors: HU LONGHUA , WANG JUN , WANG WEI
Published: March 2003

The folding thermodynamics and kinetics of a three-helix bundle protein with off-lattice model are studied using Monter Carlo simulations over a wide range of temperatures. By varying the strength of the dihedral angle potential, the effect of dihedral angle in folding is examined and it is demonstrated that the dihedral angle potential has much influence on protein folding thermodynamics and kinetics.
COMPUTER SIMULATIONS ON MELTING PHENOMENA OF QUANTIZED FLUX LINES IN TYPE-II SUPERCONDUCTORS
Authors: HU XIAO , CHEN QING-HU
Published: March 2003

Large scale Monte Carlo simulations are performed in order to clarify thermodynamic properties of vortex states of extremely type-II, layered superconductors. The first-order normal to superconductivity transition is observed accompanied by the melting of the flux-line lattice. If the magnetic field is applied parallel to the layer, there exists a critical field above which the melting becomes continuous. Dynamics of current-driven vortices in a random potential has also been investigated and it is found that for certain currents the moving Bragg glass melts first into moving smectic and then to liquid.
DESIGN AND CONTROL OF SELF-ASSEMBLED STRUCTURES IN A PHASE-SEPARATING SYSTEM UNDER OSCILLATORY PARTICLES
Authors: MA YU-QIANG , ZHU YUE-JIN
Published: March 2003

We study the self organization of a binary mixture in the presence of periodic oscillatory particles with special addictive to one of the two immiscible phases. By changing the oscillatory frequency ω and amplitude γ, we observe the striped domain structures either parallel or perpendicular to the oscillatory direction, and obtain a γ - ω phase diagram describing the orientational transition of structures. The results indicate the possibility of producing radically different oriented structures from the same particles, by only changing the amplitude of periodic forcing.
THE ELASTIC THEORY OF SINGLE-MOLECULE DNA
Authors: OU-YANG ZHONG-CAN
Published: March 2003

Our recent work on the elastic responses of double- (ds) and single-stranded (ss) DNA at external force fields is reviewed. By constructing as elastic model of dsDNA in which the base-pair stacking interaction is included, we demonstrate that dsDNA entropic elasticity, cooperative extensibility, and supercoiling property can all be understood from a unified viewpoint. The base-pair stacking interaction is also found to determine the cooperativity of the stretch-induced hairpin-coil transition is ssDNA.
STRAIN FIELD INDUCED ANISOTROPIC PHASE SEPARATION OF POLYMER BLENDS
Authors: YANG YULIANG , ZHANG HONGDONG , QIU FENG
Published: March 2003

Using a small angle light scattering (SALS) technique, we investigated the anisotropic SALS patterns formed in a phase separating polystyrene (PS) and poly (vinyl methyl ether) (PVME) blend under strain fields. We have found that, in addition to the interfacial relaxations, the stretching of the polymer chains plays an important role in the phase separation of the PS/PVME blend under a strain field. Two novel scattering patterns and the strain induced slowing down of the phase separation dynamics are observed. The experimental results are compared to a theoretical calculation based on a time-dependent Ginzburg-Landau equation incorporated with the chain stretching effect.
SIMULATION OF DIFFUSING-WAVE SPECTROSCOPY FOR STUDYING THE INTERACTIONS OF ELECTRORHEOLOGICAL PARTICLES
Authors: ZHANG L. F. , JIANG H. , XU J. , ZHOU L. W.
Published: March 2003

The temporal intensity autocorrelation function of diffusing wave spectroscopy (DWS) in electrorheological (ER) fluids is obtained with the molecular dynamics (MD) simulation method. The photons are introduced to the pattern of temporal microstructure and the light scattering procedure is regarded as Mie scattering. The fluctuations of the light intensity of different photon paths are calculated from the phase changes generated by the motion of the particles. Analyses of the decay of the time-dependent autocorrelation function provide information about the microscopic dynamics including the interactions between particles under high electric field. The results of this MD simulation method are consistent with that from CCD based DWS experiment and thus enable us to interpret our former experimental results.
SIMULATION OF A SYSTOLIC CYCLE IN A REALISTIC ARTERY WITH THE LATTICE BOLTZMANN BGK METHOD
Authors: ARTOLI A. M. , HOEKSTRA A. G. , SLOOT P. M. A.
Published: March 2003

We present an analysis of the accuracy of the lattice Boltzmann BGK (LBGK) method in simulating pulsatile blood flow in a model of the Human Abdominal Aorta. The flow is driven by a systolic pressure cycle. As a benchmark, we consider fully developed pulsatile flow in a straight tube. We compare velocity profiles and shear stress to the analytical Womersley solutions. The accuracy of the bounce-back on the links and a curved boundary condition is compared at different Mach numbers. Preliminary results of systolic flow in the human abdominal aorta are presented.
LATTICE BOLTZMANN SIMULATION OF THE FLOW OF NON-NEWTONIAN FLUIDS IN POROUS MEDIA
Authors: BOEK EDO S. , CHIN JONATHAN , COVENEY PETER V.
Published: March 2003

We present a LB study of the flow of single-phase non-Newtonian fluids, using a power law relationship between the effective viscosity and the local shear rate. Channel flow experiments were carried out to measure the velocity profiles. The simulation results are found to be in good agreement with theory. We also report simulations of the flow of non-Newtonian fluids in a 2-D porous medium.
A MASS CONSERVING BOUNDARY CONDITION FOR LATTICE BOLTZMANN MODELS
Authors: CHOPARD BASTIEN , DUPUIS ALEXANDRE
Published: March 2003

This paper proposes a new boundary condition which conserves mass exactly and exhibits a faster convergence than the halfway bounce-back in a Poiseuille flow. This boundary condition has some free parameters that can be used to improve significantly the accuracy of the simulation.