bluuebunny/crossref_metadata_2025 huggingface dataset:
Lock-Exchange Flows in Non-Rectangular Cross-Section Channels
Authors: Thomas and Luis , Marino Beatriz
Published: May 2004

Lock-exchange flows driven by density differences in non-rectangular cross-section channels are investigated in situations that resemble estuaries, navigation canals and hydraulic engineering structures. A simple analytical model considering stratified flows suggests practical relationships corroborated by results of laboratory experiments carried out in a straight channel of triangular cross-section.
Dioxygen Binds End-On to Mononuclear Copper in a Precatalytic Enzyme Complex
Authors: Prigge Sean T. , Eipper Betty A. , Mains Richard E. , Amzel L. Mario
Published: May 2004

Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.
Early Proterozoic Ultrahigh Pressure Metamorphism: Evidence from Microdiamonds
Authors: Cartigny Pierre , Chinn Ingrid , Viljoen K. S. (Fanus) , Robinson Derek
Published: May 2004

Microdiamonds from the Akluilâk minette dykes (Nunavut, Canada) are similar to diamonds formed in subducted metamorphic rocks. High concentrations of unaggregated nitrogen and positive δ
15
N suggest that the microdiamonds formed within rocks subducted to ultrahigh pressures before being sampled by the minette magma 1.8 billion years ago. This ultrahigh pressure metamorphism in North America, probably related to the Trans-Hudson orogen (about 2 billion years ago), extends the occurrence of ultrahigh pressure metamorphism from 0.6 billion years to before 1.8 billion years ago and suggests that Phanerozoic-type subductions were active by the Early Proterozoic.
Side-On Copper-Nitrosyl Coordination by Nitrite Reductase
Authors: Tocheva Elitza I. , Rosell Federico I. , Mauk A. Grant , Murphy Michael E. P.
Published: May 2004

A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.
Degradation of Terrigenous Dissolved Organic Carbon in the Western Arctic Ocean
Authors: Hansell Dennis A. , Kadko David , Bates Nicholas R.
Published: May 2004

The largest flux of terrigenous organic carbon into the ocean occurs in dissolved form by way of rivers. The fate of this material is enigmatic; there are numerous reports of conservative behavior over continental shelves, but the only knowledge we have about removal is that it occurs on long unknown time scales in the deep ocean. To investigate the removal process, we evaluated terrigenous dissolved organic carbon concentration gradients in the Beaufort Gyre of the western Arctic Ocean, which allowed us to observe the carbon's slow degradation. Using isotopic tracers of water-mass age, we determined that terrigenous dissolved organic carbon is mineralized with a half-life of 7.1 ± 3.0 years, thus allowing only 21 to 32% of it to be exported to the North Atlantic Ocean.
Old World Fossil Record of Modern-Type Hummingbirds
Authors: Mayr Gerald
Published: May 2004

I report on tiny skeletons of stem-group hummingbirds from the early Oligocene of Germany that are of essentially modern appearance and exhibit morphological specializations toward nectarivory and hovering flight. These are the oldest fossils of modern-type hummingbirds, which had not previously been reported from the Old World. The findings demonstrate that early hummingbird evolution was not restricted to the New World. They further suggest that bird–flower coevolution dates back to the early Oligocene and open another view on the origin of ornithophily in Old World plants.
Direct Visual Observation of Thermal Capillary Waves
Authors: Aarts Dirk G. A. L. , Schmidt Matthias , Lekkerkerker Henk N. W.
Published: May 2004

We studied the free fluid-fluid interface in a phase-separated colloid-polymer dispersion with laser scanning confocal microscopy and directly observed thermally induced capillary waves at the interface in real space. Experimental results for static and dynamic correlation functions validate the capillary wave model down to almost the particle level. The ultralow interfacial tension, the capillary length, and the capillary time are found to be in agreement with independent measurements. Furthermore, we show that capillary waves induce the spontaneous breakup of thin liquid films and thus are of key importance in the process of droplet coalescence.
Distribution of Insertion Sequences Associated with Tn
1546
-Like Elements among
Enterococcus faecium
Isolates from Patients in Korea
Authors: Huh Ji Young , Lee Wee Gyo , Lee Kyungwon , Shin Wan Shik , Yoo Jin Hong
Published: May 2004

The
vanA
gene cluster is carried as a part of Tn
1546
-like elements. The genetic diversity in Tn
1546
-like elements has been documented previously. The differences described thus far have included the integration of insertion sequence (IS) elements IS
1216V
, IS
1251
, IS
1476
, and IS
1542
. Among these, IS
1216V
has been reported to be widespread in VanA enterococci of diverse geographic areas, whereas IS
1542
and IS
1476
have been reported only in the United Kingdom and Canada, respectively. We investigated the distribution of ISs among 20
vanA
-containing
Enterococcus faecium
isolates from human patients in nine different university hospitals in Korea. Pulsed-field gel electrophoresis (PFGE) was performed to identify the clonality of the isolates. Moreover, PCR amplification of the internal regions of Tn
1546
was performed for structural analysis of the
van
gene, and both DNA strands of the PCR amplicons were directly sequenced by the dideoxy termination method. The PFGE patterns revealed a high degree of clonal diversity. Structural analyses of the
van
gene detected IS
1542
and IS
1216V
in the genomes of all 20 isolates, whereas it did not detect IS
1476
or IS
1251
in the genomes of any of the isolates. In addition, IS
19
was detected in the
vanS
-
vanH
intergenic region of one isolate. These data indicate that identification of the IS within a
vanA
gene cluster could be a useful tool in epidemiological investigations. In addition, the distribution of ISs associated with Tn
1546
-like elements among the Korean isolates is therefore similar to that among European vancomycin-resistant enterococci.
Rapid Screening Method for Detection of Bacteria in Platelet Concentrates
Authors: Ribault S. , Harper K. , Grave L. , Lafontaine C. , Nannini P. , Raimondo A. , Besson Faure I.
Published: May 2004

Public awareness has long focused on the risks of the transmission of viral agents through blood product transfusion. This risk, however, pales in comparison to the less publicized danger associated with the transfusion of blood products contaminated with bacteria, in particular, platelet concentrates. Up to 1,000 cases of clinical sepsis after the transfusion of platelet concentrates are reported annually in the United States. The condition is characterized by acute reaction symptoms and the rapid onset of septicemia and carries a 20 to 40% mortality rate. The urgent need for a method for the routine screening of platelet concentrates to improve patient safety has long been recognized. We describe the development of a rapid and highly sensitive method for screening for bacteria in platelet concentrates for transfusion. No culture period is required; and the entire procedure, from the time of sampling to the time that the final result is obtained, takes less than 90 min. The method involves three basic stages: the selective removal of platelets by filtration following activation with a monoclonal antibody, DNA-specific fluorescent labeling of bacteria, and concentration of the bacteria on a membrane surface for enumeration by solid-phase cytometry. The method offers a universal means of detection of live, nondividing, or dead gram-negative and gram-positive bacteria in complex cellular blood products. The sensitivity is higher than those of the culture-based methods available at present, with a detection limit of 10 to 102CFU/ml, depending upon the bacterial strain.
Comparison of a Duplex Quantitative Real-Time PCR Assay and the COBAS Amplicor CMV Monitor Test for Detection of Cytomegalovirus
Authors: Herrmann Björn , Cavaglia Larsson Viviana , Rubin Carl-Johan , Sund Fredrik , Eriksson Britt-Marie , Arvidson Johan , Yun Zhibing , Bondeson Kåre , Blomberg Jonas
Published: May 2004

A duplex quantitative real-time PCR (qPCR) assay was designed to detect both the polymerase gene (
pol
) and the glycoprotein gene (
gB
) of cytomegalovirus (CMV). The detection limit of the qPCR was determined to be 1 to 3 copies/reaction and the linear measure interval was 10
3
to 10
8
copies/ml. The qPCR system was compared to the COBAS Amplicor CMV Monitor test (COBAS) by an analysis of 138 plasma samples. Both systems detected CMV in 71 cases and had negative results for 33 samples. In addition, 34 samples were positive by qPCR and negative by the COBAS assay, but in no case was the COBAS result positive and the qPCR result negative. Thus, qPCR detected 48% more positive cases than the COBAS method. For samples with ≥10
5
copies/ml by qPCR, a saturation effect was seen in the COBAS assay and quantification required dilution. Copy numbers for
pol
and
gB
by qPCR generally agreed. However, the reproducibility of qPCR assays and the need for an international standard are discussed. Discrepant copy numbers for
pol
and
gB
by qPCR were found for samples from two patients, and sequence analysis revealed that the corresponding CMV strains were mismatched at four nucleotide positions compared with the
gB
fragment primer sequences. In conclusion, a duplex qPCR assay in a real-time format facilitates quantitative measurements and minimizes the risk of false-negative results.
Clinically Feasible Biofilm Susceptibility Assay for Isolates of
Pseudomonas aeruginosa
from Patients with Cystic Fibrosis
Authors: Moskowitz Samuel M. , Foster Jessica M. , Emerson Julia , Burns Jane L.
Published: May 2004

Pseudomonas aeruginosa
is the predominant cause of chronic airway infection in cystic fibrosis (CF). CF airway isolates are often tested for antibiotic susceptibility but are rarely eradicated by the antibiotics identified as potentially effective. The growth state of
P. aeruginosa
in CF airways is probably different from that exhibited under conventional susceptibility testing conditions and may represent a bacterial biofilm. Biofilm susceptibility testing methods were adapted to create an assay for implementation in a clinical microbiology laboratory. This assay gave reproducible results when examined in 300 paired determinations with 12 antimicrobial agents, with a serious error rate of 5.7%. The biofilm assay was used retrospectively to test these 12 agents against 94 isolates from 41 CF patients. The biofilm inhibitory concentrations (BICs) were much higher than the corresponding conventionally determined MICs for the β-lactam antibiotics (median values: aztreonam, >128 μg/ml versus 4 μg/ml; ceftazidime, 128 μg/ml versus 2 μg/ml; piperacillin-tazobactam, 256 μg/ml versus 4 μg/ml; and ticarcillin-clavulanate, 512 μg/ml versus 16 μg/ml, respectively) and doxycycline (>64 μg/ml versus 16 μg/ml); and similar for meropenem (4 μg/ml versus ≤ 1 μg/ml), ciprofloxacin (0.5 μg/ml versus 1 μg/ml), and the aminoglycosides amikacin (32 μg/ml versus 16 μg/ml), gentamicin (16 μg/ml versus 8 μg/ml), and tobramycin (4 μg/ml versus 2 μg/ml). The median BIC for azithromycin was 2 μg/ml, whereas isolates were uniformly resistant when tested by standard methods. This demonstrates the feasibility of adapting biofilm susceptibility methods to the clinical microbiology laboratory and opens the way to examining whether biofilm testing might be used to select more effective antibiotic combinations for CF airway infections than methods in current use.
Performance Assessment of DNA Fragment Sizing by High-Sensitivity Flow Cytometry and Pulsed-Field Gel Electrophoresis
Authors: Ferris Matthew M. , Yan Xiaomei , Habbersett Robbert C. , Shou Yulin , Lemanski Cheryl L. , Jett James H. , Yoshida Thomas M. , Marrone Babetta L.
Published: May 2004

The sizing of restriction fragments is the chief analytical technique utilized in the production of DNA fingerprints. Few techniques have been able to compete with pulsed-field gel electrophoresis (PFGE), which is capable of discriminating among bacteria at species and strain levels by resolving restriction fragments. However, an ultrasensitive flow cytometer (FCM) developed in our lab has also demonstrated the ability to discriminate bacteria at species and strain levels. The abilities of FCM warrant a quantitative parallel comparison with PFGE to assess and evaluate the accuracy and precision of DNA fragment sizing by both techniques. Replicate samples of
Staphylococcus aureus
Mu50 were analyzed along with two clinical
S. aureus
isolates. The absolute fragment sizing accuracy was determined for PFGE (5% ± 2%) and FCM (4% ± 4%), with sequence-predicted Mu50 SmaI fragment sizes used as a reference. Precision was determined by simple arithmetic methods (relative standard deviation for PFGE [RSD
PFGE
] = 3% ± 2% and RSD
FCM
= 1.2% ± 0.8%) as well as by the use of dendrograms derived from Dice coefficient-unweighted pair group method with arithmetic averages (UPGMA) and Pearson-UPGMA analyses. All quantitative measures of PFGE and FCM precision were equivalent, within error. The precision of both methods was not limited by any single sample preparation or analysis step that was tracked in this study. Additionally, we determined that the curve-based clustering of fingerprint data provided a more informative and useful assessment than did traditional band-based methods.
High Seroprevalence of Human T-Cell Lymphotropic Virus Type 1 in Blood Donors in Guyana and Molecular and Phylogenetic Analysis of New Strains in the Guyana Shelf (Guyana, Suriname, and French Guiana)
Authors: Pouliquen Jean-François , Hardy Lynette , Lavergne Anne , Kafiludine Eric , Kazanji Mirdad
Published: May 2004

The prevalence of human T-cell lymphotropic virus type 1 (HTLV-1) and HTLV-2 in blood donors in Guyana has never been estimated. We evaluated the prevalence of these viruses in blood donors by enzyme-linked immunosorbent assay and Western blotting and showed a prevalence of HTLV-1 of 1.3%; no HTLV-2 was detected. Female donors had a much higher HTLV-1 seroprevalence (3.6%) than male donors (0.7%). HTLV-1-seropositive donors tended to be slightly older than the average age for the total pool of donors. We also investigated the phylogenetic and molecular characteristics of HTLV-1 strains in Guyana and compared them with those identified in Suriname and French Guiana. Analysis of portions of the
env
and long terminal repeat nucleotide sequences showed that all the strains in Guyana and Suriname, like those in French Guiana, belonged to the transcontinental group of cosmopolitan subtype A. The similarities were greater between strains from Suriname and Guyana than between strains from Suriname and Guyana and those from French Guiana. Nevertheless, our results confirm that the HTLV-1 strains in all three countries have a common African origin.
Detection of
Shigella
by a PCR Assay Targeting the
ipaH
Gene Suggests Increased Prevalence of Shigellosis in Nha Trang, Vietnam
Authors: Thiem Vu Dinh , Sethabutr Orntipa , von Seidlein Lorenz , Van Tung Tran , Canh Do Gia , Chien Bui Trong , Tho Le Huu , Lee Hyejon , Houng Huo-Shu , Hale Thomas L. , Clemens John D. , Mason Carl , Trach Dang Duc
Published: May 2004

Shigella
spp. are exquisitely fastidious gram-negative organisms which frequently escape detection by traditional culture methods. To get a more complete understanding of the disease burden caused by
Shigella
in Nha Trang, Vietnam, real-time PCR was used to detect
Shigella
DNA. Randomly selected rectal swab specimens from 60
Shigella
culture-positive patients and 500
Shigella
culture-negative patients detected by population-based surveillance of patients seeking care for diarrhea were processed by real-time PCR. The target of the primer pair is the invasion plasmid antigen H gene sequence (
ipaH
), carried by all four
Shigella
species and enteroinvasive
Escherichia coli. Shigella
spp. could be isolated from the rectal swabs of 547 of 19,206 (3%) patients with diarrhea.
IpaH
was detected in 55 of 60 (93%)
Shigella
culture-positive specimens, whereas it was detected in 87 of 245 (36%) culture-negative patients free of dysentery (
P
< 0.001). The number of PCR cycles required to detect a PCR product was highest for culture-negative, nonbloody diarrheal specimens (mean number of cycles to detection, 36.6) and was lowest for children with culture-positive, bloody diarrheal specimens (mean number of cycles, 25.3) (
P
< 0.001). The data from real-time PCR amplification indicate that the culture-proven prevalence of
Shigella
among patients with diarrhea may underestimate the prevalence of
Shigella
infections. The clinical presentation of shigellosis may be directly related to the bacterial load.
Clonal Diversity and Stability of Subgingival
Eikenella corrodens
Authors: Fujise O. , Chen W. , Rich S. , Chen C.
Published: May 2004

Eikenella corrodens
is a commensal subgingival bacterium commonly found in both periodontally nondiseased and diseased subjects. The present study examined the clonal diversity and stability of subgingival
E. corrodens
over time. Ninety-five subjects were enrolled at the baseline examination, including 44 periodontally nondiseased subjects and 51 subjects with aggressive periodontitis. Twenty-two nondiseased subjects and 11 subjects with aggressive periodontitis were subsequently reexamined after an average interval of 14 months. Two subgingival plaque samples were obtained from each subject to determine the total cultivable bacteria. In addition, multiple
E. corrodens
isolates from each sample were recovered for clonal analysis by arbitrarily primed PCR. The mean numbers of distinct
E. corrodens
clones harbored by nondiseased subjects and subjects with aggressive periodontitis were 1.3 and 3.0, respectively. Thirty-nine percent of the nondiseased subjects and 63% of the subjects with aggressive periodontitis harbored multiple clones of
E. corrodens
. The numbers of distinct
E. corrodens
clones increased significantly (Mann-Whitney ranking test,
P
< 0.05) in sites from patients with aggressive periodontitis, in sites with pocket depths of 4 mm or greater, in sites with a clinical attachment loss of 2 mm or greater, and in sites coinfected with
Porphyromonas gingivalis
. Comparison of
E. corrodens
clones recovered at the baseline and those recovered at the follow-up examination showed that
E. corrodens
colonization was not stable. Thirty-eight of the 66 follow-up samples (58%) showed a complete change (including de novo colonization of the sites or complete elimination of the organism from the sites) of the subgingival
E. corrodens
clonal types between the baseline and the follow-up examinations. Our results suggest a complexity of subgingival microbiota not seen previously.
PCR-Based Assay for Differentiation of
Pseudomonas aeruginosa
from Other
Pseudomonas
Species Recovered from Cystic Fibrosis Patients
Authors: Spilker Theodore , Coenye Tom , Vandamme Peter , LiPuma John J.
Published: May 2004

Pseudomonas aeruginosa
is the major opportunistic bacterial pathogen in persons with cystic fibrosis (CF); pulmonary infection occurs in approximately 80% of adult CF patients. Much of CF patient management depends on accurate identification of
P. aeruginosa
from sputum culture. However, identification of this species may be problematic due to the marked phenotypic variability demonstrated by CF sputum isolates and the presence of other closely related species. To facilitate species identification, we used 16S ribosomal DNA (rDNA) sequence data to design PCR assays intended to provide genus- or species-level identification. Both assays yielded DNA fragments of the predicted size. We tested 42 culture collection strains (including 14
P. aeruginosa
strains and 28 strains representing 16 other closely related
Pseudomonas
species) and 43 strains that had been previously identified as belonging to 28 nonpseudomonal species also recovered from CF patient sputum. Based on these 85 strains, the specificity and sensitivity of both assays were 100%. To further assess the utility of the PCR assays, we tested 66 recent CF sputum isolates. The results indicated that preliminary phenotypic testing had misidentified several isolates. The 16S rDNA sequence was determined for 38 isolates, and in all cases it confirmed the results of the PCR assays. Thus, we have designed two PCR assays: one is specific for the genus
Pseudomonas
, while the other is specific for
P. aeruginosa
. Both assays show 100% sensitivity and specificity.
Development of a Bacteriophage Phage Replication Assay for Diagnosis of Pulmonary Tuberculosis
Authors: McNerney Ruth , Kambashi Bupe S. , Kinkese Juliana , Tembwe Ruth , Godfrey-Faussett Peter
Published: May 2004

Successful infection and replication of bacteriophages is indicative of the presence of viable bacteria. We describe here the development of a bacteriophage replication assay for the detection of
Mycobacterium tuberculosis
by using mycobacteriophage D29. Optimization of phage inoculate and incubation times allowed highly sensitive detection of
M. bovis
BCG. Fewer than 10 CFU (100 CFU/ml) were detected. No false-positive results were observed in negative samples. Application of the assay to 496 sputum specimens in the National Reference Laboratory of Zambia produced sensitivity, specificity, and positive and negative predictive values of 44.1, 92.6, 82.2, and 67.5%, respectively, compared to culture on Lowenstein-Jensen medium. The equivalent corresponding results for direct fluorescent smear microscopy were 42.3, 96.8, 91.2, and 67.6%. The small increase in sensitivity over that of direct microscopy does not justify the introduction of this technique for routine diagnosis of pulmonary tuberculosis at this time.
Incidence of Group C Human Rotavirus in Central Australia and Sequence Variation of the VP7 and VP4 Genes
Authors: Schnagl Roger D. , Boniface Karen , Cardwell Pauline , McCarthy Damien , Ondracek Caroline , Coulson Barbara , Erlich John , Morey Fran
Published: May 2004

Human group C rotavirus was identified in central Australia in each of eight years over a 16-year period between 1982 and 1997. Cases occurred either sporadically but over a relatively short period of time or as clustered outbreaks. These are the only reports of human group C rotavirus in Australia other than that of a single case reported approximately 1,800 km away in 1982. The electrophoretic genome profiles of isolates were identical for all those identified within the same year but different between those identified in different years. The VP7 genes of four isolates identified in four different years over a 7-year period between 1987 and 1993, and the VP4 genes of two of these isolates showed relatively little variation in genome and deduced amino acid sequence upon comparison of the equivalent genes between isolates. The sequences were also very similar to those from the corresponding genes from most of the human group C rotavirus isolates from other countries. This continues the observation of a high degree of gene sequence conservation among human group C rotaviruses worldwide.
DNA Microarray Format for Detection and Subtyping of Human Papillomavirus
Authors: Klaassen Corné H. W. , Prinsen Clemens F. M. , de Valk Hanneke A. , Horrevorts Alphons M. , Jeunink Marcel A. F. , Thunnissen Frederik B. J. M.
Published: May 2004

A new human papillomavirus (HPV) assay using high-density DNA microarrays is described. An HPV DNA fragment from the 3′ end of the E1 gene was amplified and digoxigenin labeled by PCR, and the resulting amplicons were hybridized onto type-specific oligonucleotides immobilized on high-density DNA microarrays. For detection, a simple immunohistochemical staining procedure was used with a substrate that has both colorimetric and fluorescent properties. This detection chemistry enables the rapid identification of reactive spots by regular light microscopy and semiquantification by laser scanning. Both single and multiple HPV infections are recognized by this assay, and the corresponding HPV types are easily identified. With this assay, 53 mucosal HPV types were detected and identified. A total of 45 HPV types were identified by a single type-specific probe, whereas the remaining 8 mucosal HPV types could be identified by a specific combination of probes. The simple assay format allows usage of this assay without expensive equipment, making it accessible to all diagnostic laboratories with PCR facilities.
Use of the DNA Flow-Thru Chip, a Three-Dimensional Biochip, for Typing and Subtyping of Influenza Viruses
Authors: Kessler Nicole , Ferraris Olivier , Palmer Kevin , Marsh Wayne , Steel Adam
Published: May 2004

Influenza A viruses, which are further subtyped on the basis of antigenic differences in external hemagglutinin and neuraminidase glycoproteins, and influenza B viruses are prominent among the viral causes of respiratory diseases and can cause a wide spectrum of illness. Each year these viruses are responsible for recurrent epidemics, frequently in association with genetic variation. There is a requirement for sensitive and rapid diagnostic techniques in order to improve both the diagnosis of infections and the quality of surveillance systems. A new three-dimensional biochip platform (Flow-Thru Chip; MetriGenix) was used to develop a rapid and reliable molecular method for the typing and subtyping of influenza viruses. Oligonucleotide probes immobilized in microchannels of a silicon wafer were selected to recognize multiple fragments of the influenza A virus matrix protein gene; the influenza B virus NS gene; the H1, H3, and H5 hemagglutinin genes; and the N1 and N2 neuraminidase genes. Biotinylated amplicons resulting from either multiplex or random reverse transcription-PCR were hybridized to arrayed oligonucleotides on the influenza virus chip before they were stained with horseradish peroxidase-streptavidin and were imaged by use of a chemiluminescent substrate. The chip analysis procedure, from the time of pipetting of the sample into the chip cartridge to the time of analysis of the results, was performed in less than 5 h. The random PCR exhibited a higher level of performance than the multiplex PCR in terms of the specificity of product hybridization to the influenza virus chip. Analysis of influenza A viruses (H1N1, H3N2, H1N2, and H5N1) and influenza B viruses showed that this microarray-based method is capable of the rapid and unambiguous identification of all types and subtypes of viruses by use of random PCR products. The redundancy of the probes designed for each gene selected yielded an additional criterion of confidence for the subtyping of viruses which are known for antigenic variations in some of their components.
Comparison of VITEK 2 with ITS2-Fragment Length Polymorphism Analysis for Identification of Yeast Species
Authors: Massonet Caroline , Van Eldere Johan , Vaneechoutte Mario , De Baere Thierry , Verhaegen Jan , Lagrou Katrien
Published: May 2004

A total of 61 clinical yeast isolates of
Candida
,
Cryptococcus
,
Blastoschizomyces
, and
Saccharomyces
spp. were used to compare two identification techniques, VITEK 2 and ITS2-fragment length polymorphism analysis (ITS2-FLP), with ID32C as the reference method. ID32C identified 58 isolates correctly. ITS2-FLP with Instagene DNA extraction identified 59 isolates. ITS2-FLP combined with boiling-freezing DNA extraction identified 55 isolates. VITEK 2 identified 41 isolates correctly.
Development and Evaluation of a New Commercial Test Allowing the Simultaneous Detection of Noroviruses and Sapoviruses by Reverse Transcription-PCR and Microplate Hybridization
Authors: Bon F. , Giraudon H. , Sancey C. , Barranger C. , Joannes M. , Pothier P. , Kohli E.
Published: May 2004

This work describes the design and initial evaluation of a commercial test allowing the detection of noroviruses and sapoviruses by reverse transcription-PCR (RT-PCR) in a single tube followed by microplate hybridization, as well as the detection of PCR inhibitors. The test was shown to be broadly reactive (except for Melksham-like strains), sensitive, and specific and thus should be useful for calicivirus detection in clinical practice.
Detection of a Rickettsia Closely Related to
Rickettsia aeschlimannii
, “
Rickettsia heilongjiangensis
,”
Rickettsia
sp. Strain RpA4, and
Ehrlichia muris
in Ticks Collected in Russia and Kazakhstan
Authors: Shpynov Stanislav , Fournier Pierre-Edouard , Rudakov Nikolay , Tankibaev Marat , Tarasevich Irina , Raoult Didier
Published: May 2004

Using PCR, we screened 411 ticks from four genera collected in Russia and Kazakhstan for the presence of rickettsiae and ehrlichiae. In Russia, we detected “
Rickettsia heilongjiangensis
,”
Rickettsia
sp. strain RpA4, and
Ehrlichia muris
. In Kazakhstan, we detected
Rickettsia
sp. strain RpA4 and a rickettsia closely related to
Rickettsia aeschlimannii
. These agents should be considered in a differential diagnosis of tick-borne infections in these areas.
Helcococcus ovis
Isolated from a Pulmonary Abscess in a Horse
Authors: Rothschild Chantal M. , Oaks J. Lindsay , Schaupp Jennifer K. , Rurangirwa Fred R. , Sellon Debra C. , Hines Melissa T.
Published: May 2004

Helcococcus ovis
, a recently described organism cultured from sheep, was isolated in pure culture from a pulmonary abscess in a horse. This is the first report of this organism in horses and the first report in veterinary medicine to clearly demonstrate a pathogenic role for this organism.
Molecular Fingerprinting ofMycobacterium bovissubsp.capraeIsolates from Central Europe
Authors: Erler Wilfried , Martin Gerald , Sachse Konrad , Naumann Ludmila , Kahlau Dagmar , Beer Jörg , Bartos Milan , Nagy György , Cvetnic Zeljko , Zolnir-Dovc Manca , Pavlik Ivo
Published: May 2004

To study the dissemination ofMycobacterium bovissubsp.caprae, 79 European isolates from cattle, humans, and other hosts were examined by spoligotyping and IS6110restriction fragment length polymorphism (RFLP) analysis. Among a total of 11 different spoligotypes identified, type C1 proved to be predominant (n= 62). Five of the spoligotypes are described for the first time. A total of 43 different RFLP types were identified, thus allowing further differentiation for epidemiological tracking. Isolates from a series of outbreaks in one village proved to be of the same spoligotype and of identical or closely related RFLP types.
Comparison of Flow Cytometric and Alamar Blue Tests with the Proportional Method for Testing Susceptibility of
Mycobacterium tuberculosis
to Rifampin and Isoniazid
Authors: Reis Roberto S. , Neves Ivan , Lourenço Sergio L. S. , Fonseca Leila S. , Lourenço Maria Cristina S.
Published: May 2004

The performance of flow cytometry and the microplate Alamar Blue assay in determining susceptibility of
Mycobacterium tuberculosis
was assessed by testing 150 Brazilian isolates. The overall agreement was 97.3 and 98% for isoniazid and 94.7 and 100% for rifampin by flow cytometry and MABA, respectively. This study was entirely done in a developing country.
Quantitative Microbiological Study of Subgingival Plaque by Real-Time PCR Shows Correlation between Levels of
Tannerella forsythensis
and
Fusobacterium
spp
Authors: Suzuki Nao , Yoshida Akihiro , Saito Toshiyuki , Kawada Miki , Nakano Yoshio
Published: May 2004

A TaqMan-based real-time PCR assay was established to quantify the periodontopathic bacteria
Tannerella forsythensis
and
Fusobacterium
spp. With this assay, the prevalence and proportion of these bacteria in clinical specimens were evaluated. Our preliminary results suggest a positive colocalization of
T. forsythensis
and
Fusobacterium
spp. in periodontal pockets.
Accuracy and Appropriateness of Antimicrobial Susceptibility Test Reporting for Bacteria Isolated from Blood Cultures
Authors: Diekema Daniel J. , Lee Kathleen , Raney Patti , Herwaldt Loreen A. , Doern Gary V. , Tenover Fred C.
Published: May 2004

Accurate antimicrobial susceptibility testing (AST) and appropriate reporting of AST results for pathogens isolated from blood cultures are critical functions of the microbiology laboratory. We studied AST performance and reporting from positive blood cultures at hospital microbiology laboratories in Iowa. One hundred sixteen episodes of bacteremia from 14 participating hospitals were examined. We detected AST or identification errors for 18 episodes (16%) and judged reporting of AST results to be inappropriate for 38 episodes (33%). Further study is necessary to determine the impact of testing errors and suboptimal reporting of results on the management of bloodstream infection.
Presence of Bacterial Phage-Like DNA Sequences in Commercial
Taq
DNA Polymerase Reagents
Authors: Newsome Tamara , Li Bing-Jie , Zou Nianxiang , Lo Shyh-Ching
Published: May 2004

Many studies have reported the presence of bacterial DNA contamination in commercial
Taq
DNA polymerase reagents. This is the first report of the presence of phage-like DNA sequences in certain commercial
Taq
DNA polymerase reagents. Precautions are needed when using amplification reagents with exogenous DNAs.
Survey of Rodents and Ticks in Human Babesiosis Emergence Area in Japan: First Detection of
Babesia microti
-Like Parasites in
Ixodes ovatus
Authors: Saito-Ito Atsuko , Yano Yasuhiro , Dantrakool Anchalee , Hashimoto Tetsuo , Takada Nobuhiro
Published: May 2004

Babesia microti
-like parasites were detected for the first time in
Ixodes ovatus
in Hyogo Prefecture, Japan, where two reported types of
B. microti-
like parasites were recognized in many rodents. Of 80 adult
I. ovatus
ticks collected, 5 possessed the reported type and 1 possessed a new type of
B. microti
-like parasite.
Asymptomatic and Symptomatic Excretion of Noroviruses during a Hospital Outbreak of Gastroenteritis
Authors: Gallimore Chris I. , Cubitt David , du Plessis Nelita , Gray Jim J.
Published: May 2004

During an investigation of a hospital outbreak of norovirus gastroenteritis identified as being caused by a recombinant genogroup II (rGII-3a) strain, fecal specimens collected from asymptomatic staff and patients were tested by nested PCR. A GII-4 norovirus strain, the predominant strain associated with outbreaks in hospitals over the last few years, was detected in 26 and 33% of asymptomatic staff and patients, respectively. No rGII-3a (Harrow/Mexico) norovirus strains were detected in the samples of asymptomatic staff or patients.
Detection ofCandida albicansmRNA in Archival Histopathology Samples by Reverse Transcription-PCR
Authors: Beggs Kyle T. , Holmes Ann R. , Cannon Richard D. , Rich Alison M.
Published: May 2004

The feasibility of detectingCandida albicansmRNA in formalin-fixed paraffin-embedded archival human histopathology specimens by reverse transcription-PCR (RT-PCR) was investigated. RT with gene-specific primers was used to detect five single-copyC. albicansgene transcripts, including those of two housekeeping genes, in oral candidiasis samples up to 8 years of age.
Correlation betweenHelicobacter pyloriOipA Protein Expression andoipAGene Switch Status
Authors: Kudo Takahiko , Nurgalieva Zhannat Z. , Conner Margaret E. , Crawford Sue , Odenbreit Stefan , Haas Rainer , Graham David Y. , Yamaoka Yoshio
Published: May 2004

Polyclonal antisera to either a synthetic OipA peptide or a recombinant OipA protein detected OipA expression inHelicobacter pyloriand correlated with functionaloipAstatus determined by PCR sequence (sensitivity and specificity of >94%). Immunoblotting is a simple and accurate method for detecting expression of the important virulence factor OipA.
Frequent Detection of Viral Nucleic Acids in Heart Valve Tissue
Authors: Donoso Mantke Oliver , Meyer Rudolf , Prösch Susanna , Niedrig Matthias
Published: May 2004

Due to a paucity of published data concerning the prevalence of viral nucleic acid in homografts, we analyzed tissue from 30 donor hearts for the presence of viral genome sequences of enteroviruses, adenoviruses, human cytomegalovirus, and influenza virus using different PCR techniques. Viral DNA was amplified in 64 and 52% of the subvalvular myocardial tissue and non-coronary valve samples, respectively. These findings, compared with clinical history and histologic and serologic analysis, demonstrate the importance of viral safety measures in heart valve banking.
Molecular Epidemiology of the
fsr
Locus and of Gelatinase Production among Different Subsets of
Enterococcus faecalis
Isolates
Authors: Roberts Jill C. , Singh Kavindra V. , Okhuysen Pablo C. , Murray Barbara E.
Published: May 2004

We examined 215
Enterococcus faecalis
isolates and found that neither the two-component regulatory locus
fsr
(
E. faecalis
regulator) nor gelatinase production was more common in disease-associated isolates than in isolates colonizing healthy individuals (ca. 60 to 65%). The majority of gelatinase-negative isolates, including 14 endocarditis isolates (of 80 isolates tested), contained the previously described 23.9-kb deletion and lacked
fsrA
and
fsrB
. While these findings indicate that neither
fsr
nor gelatinase is required for
E. faecalis
to cause infection, this study did not address whether
fsr
or gelatinase affects the severity of disease, as it does in animal models.
Glycerophosphodiester Phosphodiesterase Gene (
glpQ
) of
Borrelia lonestari
Identified as a Target for Differentiating
Borrelia
Species Associated with Hard Ticks (Acari:Ixodidae)
Authors: Bacon Rendi Murphree , Pilgard Mark A. , Johnson Barbara J. B. , Raffel Sandra J. , Schwan Tom G.
Published: May 2004

A
glpQ
ortholog was identified in DNA from
Borrelia lonestari-
positive
Amblyomma americanum
, providing further evidence that
B. lonestari
is more closely related to the relapsing fever group spirochetes than to borreliae that cause Lyme disease. This finding provides a basis for developing diagnostic assays to differentiate species of borrelia transmitted by hard ticks.
Phylogenetic Relationships among Virulent Newcastle Disease Virus Isolates from the 2002-2003 Outbreak in California and Other Recent Outbreaks in North America
Authors: Pedersen Janice C. , Senne Dennis A. , Woolcock Peter R. , Kinde Hailu , King Daniel J. , Wise Mark G. , Panigrahy Brundaban , Seal Bruce S.
Published: May 2004

Isolates from the 2002-2003 virulent Newcastle disease virus (v-NDV) outbreak in southern California, Nevada, Arizona, and Texas in the United States were compared to each other along with recent v-NDV isolates from Mexico and Central America and reference avian paramyxovirus type 1 strains. Nucleotide sequencing and phylogenetic analyses were conducted on a 1,195-base genomic segment composing the 3′ region of the matrix (M) protein gene and a 5′ portion of the fusion (F) protein gene including the M-F intergenic region. This encompasses coding sequences for the nuclear localization signal of the M protein and the F protein cleavage activation site. A dibasic amino acid motif was present at the predicted F protein cleavage activation site in all v-NDVs, including the California 2002-2003, Arizona, Nevada, Texas, Mexico, and Central America isolates. Phylogenetic analyses demonstrated that the California 2002-2003, Arizona, Nevada, and Texas viruses were most closely related to isolates from Mexico and Central America. An isolate from Texas obtained during 2003 appeared to represent a separate introduction of v-NDV into the United States, as this virus was even more closely related to the Mexico 2000 isolates than the California, Arizona, and Nevada viruses. The close phylogenetic relationship between the recent 2002-2003 U.S. v-NDV isolates and those viruses from countries geographically close to the United States warrants continued surveillance of commercial and noncommercial poultry for early detection of highly virulent NDV.
Chronic Cholangitis Caused by
Bordetella hinzii
in a Liver Transplant Recipient
Authors: Arvand Mardjan , Feldhues Rita , Mieth Markus , Kraus Thomas , Vandamme Peter
Published: May 2004

Bordetella hinzii
was isolated in four biliary specimens collected over 6 months from a liver transplant recipient with cholangitis. The isolates were resistant to most β-lactam antibiotics and fluoroquinolones. Molecular typing was performed by pulsed-field gel electrophoresis. These data add cholangitis to the spectrum of disease manifestations caused by
B. hinzii
.
Invasive Pneumococcal Infection in a Healthy Infant Caused by Two Different Serotypes
Authors: de Andrade Ana Lucia S. Sgambatti , Pimenta Fabiana Cristina , Laval Cristina Aparecida Borges , de Andrade João Guimarães , Guerra Maria Luiza , Brandileone Maria Cristina C.
Published: May 2004

We present a case of invasive pneumococcal infection in a healthy 10-month-old infant from whom
Streptococcus pneumoniae
serotype 23F was isolated from the blood and serotype 23B was isolated from the cerebrospinal fluid. Both serotypes were penicillin nonsusceptible. Pulsed-field gel electrophoresis analysis demonstrated that the two serotypes had distinct DNA patterns, indicating that infection did not occur as a result of capsular transformation but as a result of a mixed infection with two distinct pneumococcal serotypes.
Posttransplantation Disseminated Coccidioidomycosis Acquired from Donor Lungs
Authors: Miller Melissa B. , Hendren Ryan , Gilligan Peter H.
Published: May 2004

A North Carolinian developed fatal coccidioidomycosis immediately after bilateral lung transplantation. The donor had previously traveled to Mexico, and the recipient had no travel history to an area where
Coccidioides immitis
is endemic. Immunosuppresive therapy of the transplant recipient likely reactivated latent
Coccidioides
infection in the donor lungs, leading to posttransplant coccidioidomycosis.
GEOMETRY OF RELATIVISTIC PARTICLES WITH TORSION
Authors: BARROS MANUEL , FERRÁNDEZ ANGEL , JAVALOYES MIGUEL ANGEL , LUCAS PASCUAL
Published: May 2004

We consider the motion of relativistic particles described by an action that is linear in the torsion (second curvature) of the particle path. The Euler–Lagrange equations and the dynamical constants of the motion associated with the Poincaré group, the mass and the spin of the particle, are expressed in a simple way in terms of the curvatures of the embedded worldline. The moduli spaces of solutions are completely exhibited in four-dimensional background spaces and in the five-dimensional case we explicitly obtain the curvatures of the worldline.
NEW STRING AMPLITUDES FROM OLD FERMAT (HYPER)SURFACES
Authors: KHOLODENKO A. L.
Published: May 2004

The bosonic string theory evolved as an attempt to find a multidimensional analogue of Euler's beta function to describe the multiparticle Veneziano amplitudes. Such an analogue had in fact been known in mathematics at least in 1922. Its mathematical meaning was studied subsequently from different angles by mathematicians such as Selberg, Weil and Deligne among others. The mathematical interpretation of multidimensional beta function that was developed subsequently is markedly different from that described in physics literature. This paper aims to bridge the gap between the mathematical and physical treatments of such beta functions thus providing new topological, algebro-geometric, number-theoretic and combinatorial treatments of the multiparticle Veneziano and Veneziano-like amplitudes. As a result, the entirely new physical meaning of these amplitudes is emerging: they are periods connected with differential forms living on Fermat (hyper)surfaces. Such surfaces are considered as complex projective varieties of Hodge type. Obtained results allow to interpret the particle mass spectrum in terms of the Hodge spectrum of underlying Fermat (hyper)surface. The computational formalism although resembles that used in mirror symmetry calculations employs many additional results from topology, number theory, theory of singularities, etc. It allows to obtain the correlation functions in particle physics and conformal field theories using the same type of the Picard–Fuchs equations.
A UNIFIED APPROACH TO NNLO SOFT AND VIRTUAL CORRECTIONS IN ELECTROWEAK, HIGGS, QCD, AND SUSY PROCESSES
Authors: KIDONAKIS NIKOLAOS
Published: May 2004

I present a unified approach to calculating the next-to-next-to-leading order (NNLO) soft and virtual QCD corrections to cross-sections for electroweak, Higgs, QCD, and SUSY processes. I derive master formulas that can be used for any of these processes in hadron–hadron and lepton–hadron collisions. The formulas are based on a unified threshold resummation formalism and can be applied to both total and differential cross-sections for processes with either simple or complex color flows and for various factorization schemes and kinematics. As a test of the formalism, I rederive known NNLO results for Drell–Yan and Higgs production, deep inelastic scattering, and W+γ production, and I obtain expressions for several two-loop anomalous dimensions and other quantities needed in next-to-next-to-leading-logarithm (NNLL) resummations. I also present new results for the production of supersymmetric charged Higgs bosons; massive electroweak vector bosons; photons; heavy quarks in lepton–hadron and hadron–hadron collisions and in flavor-changing neutral current processes; jets; and squarks and gluinos. The NNLO soft and virtual corrections are often dominant, especially near threshold, and they reduce the scale dependence of the cross-section. Thus, a unified approach to these corrections is important in the search for new physics at present and future colliders.