bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Boundary Flexibility on the Vibration of a Continuum With a Moving Oscillator
Authors: Chen Yonghong , Tan C. A. , Bergman L. A.
Published: September 2002

In this paper, the problem of an oscillator traversing an elastically supported continuum is studied. The flexibility in the boundaries of the continuum is modeled by linear, transverse springs. The response of the continuum and the dynamic interaction force between the moving oscillator and the continuum are evaluated by an eigenfunction expansion series. To circumvent convergence difficulties associated with the jump in the shear force due to the moving interaction force, an improved series expansion employing the static Green’s function is derived. The coupled governing equations of motion are solved numerically and results are obtained to examine the effects of the boundary flexibility on the response, the dynamic interaction force, the shear force spatial and temporal distributions, as well as the convergence properties of the expansion series. It is found that high order modal terms contribute significantly to the shear force expansion series in the elastically supported model. The presence of large amplitude and high frequency components in the shear force is critical in understanding the cumulative fatigue failure of the structure. A useful and compact formula estimating the value of the support stiffness above which a boundary may be modeled as simply supported is also derived.
TeleDM: An Internet Web E-service Testbed for Fast Product Design Supported by Prototype Manufacturing
Authors: Jiang Pingyu , Fukuda Shuichi , Raper Stephen A.
Published: September 2002

This paper discusses developing an e-service testbed in order to verify an Internet web product design developed with the aid of a prototype manufacturing environment. A Java-enabled solution, together with web techniques, is employed for building such an infrastructure. By setting up a series of scenarios and running them under the guidance of the methodologies we developed, a global fast product design idea can be tested. Furthermore, the industrial practice perspective is also discussed in the paper.
Surface Feature Parametrization Analogous to Conductive Heat Flow
Authors: Marsan Anne L. , Chen Yifan , Stewart Paul J.
Published: September 2002

Direct Surface Manipulation (DSM) allows a designer to add a raised or indented feature to an existing surface. The user bounds the feature with a closed curve, and defines an influence center that indicates the point or curve of maximum displacement from the original surface. As we move radially outward from the influence center to the boundary curve, the magnitude of displacement is scaled gradually by a one-dimensional polynomial basis function whose values range from 0 to 1. In this paper we present a new technique for assigning parameter values in the radial direction, i.e., u, to points within a DSM feature. The new technique poses parameter distribution as a steady state heat conduction problem and uses a finite element method to solve for ux,y. The new method overcomes some stringent geometric conditions inherited from a fundamentally geometric-based reparameterization scheme and allows us to work with non-star-shaped and multiply connected DSM features. Thus it allows us to apply this surface feature technique to a wider variety of surface applications.
The STEP Modular Architecture
Authors: Feeney Allison Barnard
Published: September 2002

The first Technical Note in this series [1] introduced the international standard ISO 10303, informally known as STEP (STandard for the Exchange of Product model data). Subsequent Technical Notes discussed various issues faced by users of STEP and how the ISO TC184/SC4 committee is addressing these issues. This paper presents the current move to modularize the STEP application protocol architecture. This paper describes the initial STEP architecture, requirements for improvements to the architecture, features of the new modular architecture, status and issues.
Gene Expression During the Life Cycle of
Drosophila melanogaster
Authors: Arbeitman Michelle N. , Furlong Eileen E. M. , Imam Farhad , Johnson Eric , Null Brian H. , Baker Bruce S. , Krasnow Mark A. , Scott Matthew P. , Davis Ronald W. , White Kevin P.
Published: September 2002

Molecular genetic studies of
Drosophila melanogaster
have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all
Drosophila
genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes.
Quantum Dot Superlattice Thermoelectric Materials and Devices
Authors: Harman T. C. , Taylor P. J. , Walsh M. P. , LaForge B. E.
Published: September 2002

PbSeTe-based quantum dot superlattice structures grown by molecular beam epitaxy have been investigated for applications in thermoelectrics. We demonstrate improved cooling values relative to the conventional bulk (Bi,Sb)
2
(Se,Te)
3
thermoelectric materials using a n-type film in a one-leg thermoelectric device test setup, which cooled the cold junction 43.7 K below the room temperature hot junction temperature of 299.7 K. The typical device consists of a substrate-free, bulk-like (typically 0.1 millimeter in thickness, 10 millimeters in width, and 5 millimeters in length) slab of nanostructured PbSeTe/PbTe as the n-type leg and a metal wire as the p-type leg.
Conversion of Unc104/KIF1A Kinesin into a Processive Motor After Dimerization
Authors: Tomishige Michio , Klopfenstein Dieter R. , Vale Ronald D.
Published: September 2002

Unc104/KIF1A belongs to a class of monomeric kinesin motors that have been thought to possess an unusual motility mechanism. Unlike the unidirectional motion driven by the coordinated actions of the two heads in conventional kinesins, single-headed KIF1A was reported to undergo biased diffusional motion along microtubules. Here, we show that Unc104/KIF1A can dimerize and move unidirectionally and processively with rapid velocities characteristic of transport in living cells. These results suggest that Unc104/KIF1A operates in vivo by a mechanism similar to conventional kinesin and that regulation of motor dimerization may be used to control transport by this class of kinesins.
Structural Basis for Gluten Intolerance in Celiac Sprue
Authors: Shan Lu , Molberg Øyvind , Parrot Isabelle , Hausch Felix , Filiz Ferda , Gray Gary M. , Sollid Ludvig M. , Khosla Chaitan
Published: September 2002

Celiac Sprue, a widely prevalent autoimmune disease of the small intestine, is induced in genetically susceptible individuals by exposure to dietary gluten. A 33-mer peptide was identified that has several characteristics suggesting it is the primary initiator of the inflammatory response to gluten in Celiac Sprue patients. In vitro and in vivo studies in rats and humans demonstrated that it is stable toward breakdown by all gastric, pancreatic, and intestinal brush-border membrane proteases. The peptide reacted with tissue transglutaminase, the major autoantigen in Celiac Sprue, with substantially greater selectivity than known natural substrates of this extracellular enzyme. It was a potent inducer of gut-derived human T cell lines from 14 of 14 Celiac Sprue patients. Homologs of this peptide were found in all food grains that are toxic to Celiac Sprue patients but are absent from all nontoxic food grains. The peptide could be detoxified in in vitro and in vivo assays by exposure to a bacterial prolyl endopeptidase, suggesting a strategy for oral peptidase supplement therapy for Celiac Sprue.
A Single P450 Allele Associated with Insecticide Resistance in
Drosophila
Authors: Daborn P. J. , Yen J. L. , Bogwitz M. R. , Le Goff G. , Feil E. , Jeffers S. , Tijet N. , Perry T. , Heckel D. , Batterham P. , Feyereisen R. , Wilson T. G. , ffrench-Constant R. H.
Published: September 2002

Insecticide resistance is one of the most widespread genetic changes caused by human activity, but we still understand little about the origins and spread of resistant alleles in global populations of insects. Here, via microarray analysis of all P450s in
Drosophila melanogaster
, we show that
DDT-R
, a gene conferring resistance to DDT, is associated with overtranscription of a single cytochrome P450 gene,
Cyp6g1
. Transgenic analysis of
Cyp6g1
shows that overtranscription of this gene alone is both necessary and sufficient for resistance. Resistance and up-regulation in
Drosophila
populations are associated with a single
Cyp6g1
allele that has spread globally. This allele is characterized by the insertion of an
Accord
transposable element into the 5′ end of the
Cyp6g1
gene.
RETRACTED: Severe Dopaminergic Neurotoxicity in Primates After a Common Recreational Dose Regimen of MDMA ("Ecstasy")
Authors: Ricaurte George A. , Yuan Jie , Hatzidimitriou George , Cord Branden J. , McCann Una D.
Published: September 2002

The prevailing view is that the popular recreational drug (±)3,4-methylenedioxymethamphetamine (MDMA, or “ecstasy”) is a selective serotonin neurotoxin in animals and possibly in humans. Nonhuman primates exposed to several sequential doses of MDMA, a regimen modeled after one used by humans, developed severe brain dopaminergic neurotoxicity, in addition to less pronounced serotonergic neurotoxicity. MDMA neurotoxicity was associated with increased vulnerability to motor dysfunction secondary to dopamine depletion. These results have implications for mechanisms of MDMA neurotoxicity and suggest that recreational MDMA users may unwittingly be putting themselves at risk, either as young adults or later in life, for developing neuropsychiatric disorders related to brain dopamine and/or serotonin deficiency.
Little Evidence for Developmental Plasticity of Adult Hematopoietic Stem Cells
Authors: Wagers Amy J. , Sherwood Richard I. , Christensen Julie L. , Weissman Irving L.
Published: September 2002

To rigorously test the in vivo cell fate specificity of bone marrow (BM) hematopoietic stem cells (HSCs), we generated chimeric animals by transplantation of a single green fluorescent protein (GFP)–marked HSC into lethally irradiated nontransgenic recipients. Single HSCs robustly reconstituted peripheral blood leukocytes in these animals, but did not contribute appreciably to nonhematopoietic tissues, including brain, kidney, gut, liver, and muscle. Similarly, in GFP
+
:GFP
−
parabiotic mice, we found substantial chimerism of hematopoietic but not nonhematopoietic cells. These data indicate that “transdifferentiation” of circulating HSCs and/or their progeny is an extremely rare event, if it occurs at all.
Efficient Photochemical Water Splitting by a Chemically Modified n-TiO
2
Authors: Khan Shahed U. M. , Al-Shahry Mofareh , Ingler William B.
Published: September 2002

Although n-type titanium dioxide (TiO
2
) is a promising substrate for photogeneration of hydrogen from water, most attempts at doping this material so that it absorbs light in the visible region of the solar spectrum have met with limited success. We synthesized a chemically modified n-type TiO
2
by controlled combustion of Ti metal in a natural gas flame. This material, in which carbon substitutes for some of the lattice oxygen atoms, absorbs light at wavelengths below 535 nanometers and has a lower band-gap energy than rutile (2.32 versus 3.00 electron volts). At an applied potential of 0.3 volt, chemically modified n-type TiO
2
performs water splitting with a total conversion efficiency of 11% and a maximum photoconversion efficiency of 8.35% when illuminated at 40 milliwatts per square centimeter. The latter value compares favorably with a maximum photoconversion efficiency of 1% for n-type TiO
2
biased at 0.6 volt.
Climate Effects of Black Carbon Aerosols in China and India
Authors: Menon Surabi , Hansen James , Nazarenko Larissa , Luo Yunfeng
Published: September 2002

In recent decades, there has been a tendency toward increased summer floods in south China, increased drought in north China, and moderate cooling in China and India while most of the world has been warming. We used a global climate model to investigate possible aerosol contributions to these trends. We found precipitation and temperature changes in the model that were comparable to those observed if the aerosols included a large proportion of absorbing black carbon (“soot”), similar to observed amounts. Absorbing aerosols heat the air, alter regional atmospheric stability and vertical motions, and affect the large-scale circulation and hydrologic cycle with significant regional climate effects.
Chance Favors the Prepared Mind
Authors: Weiss Robin A.
Published: September 2002

Hepatitis B
The Hunt for a Killer Virus. Baruch S. Blumberg. Princeton University Press, Princeton, NJ, 2002. 256 pp. $27.95, £19.95. ISBN 0-691-00692-X.

Blumberg recounts the unanticipated twists and turns of the investigations that led to his 1976 Nobel Prize.
Hydrogen Clusters in Clathrate Hydrate
Authors: Mao Wendy L. , Mao Ho-kwang , Goncharov Alexander F. , Struzhkin Viktor V. , Guo Quanzhong , Hu Jingzhu , Shu Jinfu , Hemley Russell J. , Somayazulu Maddury , Zhao Yusheng
Published: September 2002

High-pressure Raman, infrared, x-ray, and neutron studies show that H
2
and H
2
O mixtures crystallize into the sII clathrate structure with an approximate H
2
/H
2
O molar ratio of 1:2. The clathrate cages are multiply occupied, with a cluster of two H
2
molecules in the small cage and four in the large cage. Substantial softening and splitting of hydrogen vibrons indicate increased intermolecular interactions. The quenched clathrate is stable up to 145 kelvin at ambient pressure. Retention of hydrogen at such high temperatures could help its condensation in planetary nebulae and may play a key role in the evolution of icy bodies.
Orbital Ordering Transition in La
4
Ru
2
O
10
Authors: Khalifah P. , Osborn R. , Huang Q. , Zandbergen H. W. , Jin R. , Liu Y. , Mandrus D. , Cava R. J.
Published: September 2002

We report experimental evidence for a full orbital ordering transition in the two-dimensional lanthanum ruthenate La
4
Ru
2
O
10
. The observable consequences of this orbital ordering include the loss of the Ru local moment, a structural distortion which partitions Ru-O bonds into axially oriented short and long sets, a sharp jump in electrical resistivity, and the opening of a spin gap that is visible in neutron scattering experiments. This is a rare example of a discrete orbital ordering transition in a 4
d
transition metal oxide and demonstrates that orbital effects can have an influence on the properties of layered ruthenates, a family of compounds that notably includes the
p
-wave superconductor Sr
2
RuO
4
and the field-tuned quantum critical metamagnet Sr
3
Ru
2
O
7
.
Role of Hec1 in Spindle Checkpoint Signaling and Kinetochore Recruitment of Mad1/Mad2
Authors: Martin-Lluesma Silvia , Stucke Volker M. , Nigg Erich A.
Published: September 2002

The spindle checkpoint delays sister chromatid separation until all chromosomes have undergone bipolar spindle attachment. Checkpoint failure may result in chromosome mis-segregation and may contribute to tumorigenesis. We showed that the human protein Hec1 was required for the recruitment of Mps1 kinase and Mad1/Mad2 complexes to kinetochores. Depletion of Hec1 impaired chromosome congression and caused persistent activation of the spindle checkpoint, indicating that high steady-state levels of Mad1/Mad2 complexes at kinetochores were not essential for checkpoint signaling. Simultaneous depletion of Hec1 and Mad2 caused catastrophic mitotic exit, making Hec1 an attractive target for the selective elimination of spindle checkpoint–deficient cells.
The Corpse of a Wearisome Debate
Authors: Bateson Patrick
Published: September 2002

The Blank Slate
The Modern Denial of Human Nature. Steven Pinker. Viking, New York, 2002. 527 pp. $27.95. ISBN 0-670-03151-8.

Pinker describes his latest book for a popular audience as an argument for a "truly honest science of human nature, one that would take into account both instinct and choice as well as the deep inherent structures of the mind."
Establishment and Maintenance of a Heterochromatin Domain
Authors: Hall Ira M. , Shankaranarayana Gurumurthy D. , Noma Ken-ichi , Ayoub Nabieh , Cohen Amikam , Grewal Shiv I. S.
Published: September 2002

The higher-order assembly of chromatin imposes structural organization on the genetic information of eukaryotes and is thought to be largely determined by posttranslational modification of histone tails. Here, we study a 20-kilobase silent domain at the mating-type region of fission yeast as a model for heterochromatin formation. We find that, although histone H3 methylated at lysine 9 (H3 Lys
9
) directly recruits heterochromatin protein Swi6/HP1, the critical determinant for H3 Lys
9
methylation to spread in cis and to be inherited through mitosis and meiosis is Swi6 itself. We demonstrate that a centromere-homologous repeat (
cenH
) present at the silent mating-type region is sufficient for heterochromatin formation at an ectopic site, and that its repressive capacity is mediated by components of the RNA interference (RNAi) machinery. Moreover,
cenH
and the RNAi machinery cooperate to nucleate heterochromatin assembly at the endogenous
mat
locus but are dispensable for its subsequent inheritance. This work defines sequential requirements for the initiation and propagation of regional heterochromatic domains.
The Origin of Aluminum Flocs in Polluted Streams
Authors: Furrer Gerhard , Phillips Brian L. , Ulrich Kai-Uwe , Pöthig Rosemarie , Casey William H.
Published: September 2002

About 240,000 square kilometers of Earth's surface is disrupted by mining, which creates watersheds that are polluted by acidity, aluminum, and heavy metals. Mixing of acidic effluent from old mines and acidic soils into waters with a higher pH causes precipitation of amorphous aluminum oxyhydroxide flocs that move in streams as suspended solids and transport adsorbed contaminants. On the basis of samples from nine streams, we show that these flocs probably form from aggregation of the
ɛ
-Keggin polyoxocation AlO
4
Al
12
(OH)
24
(H
2
O)
12
7+
(aq) (Al
13
), because all of the flocs contain distinct Al(O)
4
centers similar to that of the Al
13
nanocluster.
Collapse of a Degenerate Fermi Gas
Authors: Modugno Giovanni , Roati Giacomo , Riboli Francesco , Ferlaino Francesca , Brecha Robert J. , Inguscio Massimo
Published: September 2002

A degenerate gas of identical fermions is brought to collapse by the interaction with a Bose-Einstein condensate. We used an atomic mixture of fermionic potassium-40 and bosonic rubidium-87, in which the strong interspecies attraction leads to an instability above a critical number of particles. The observed phenomenon suggests a direction for manipulating fermion-fermion interactions on the route to superfluidity.
Evaluation of the Digene Hybrid Capture II Assay with the Rapid Capture System for Detection ofChlamydia trachomatisandNeisseria gonorrhoeae
Authors: Van Der Pol B. , Williams J. A. , Smith N. J. , Batteiger B. E. , Cullen A. P. , Erdman H. , Edens T. , Davis K. , Salim-Hammad H. , Chou V. W. , Scearce L. , Blutman J. , Payne W. J.
Published: September 2002

Screening for chlamydial and gonococcal infection has been strongly recommended for all sexually active women under the age of 26. Advances in the ability to detect infection by nucleic acid detection techniques have improved access to screening methods in routine clinical practices. To meet the increasing demand for testing, a high-throughput system is desirable. We evaluated the performance of the Hybrid Capture 2 CT/GC (HC2) assay with the Digene Rapid Capture System (HC2-RCS). The results of HC2-RCS for endocervical samples from 330 women were compared to those of culture and the COBAS Amplicor PCR. For detection of chlamydial infection, HC2-RCS had a sensitivity and a specificity similar to those of PCR (P> 0.5) and an improved sensitivity compared to that of culture (P= 0.007). For identification of gonococcal infections, all assays performed similarly (P> 0.5). The performance of HC2-RCS was also compared to that of the manual HC2 format (HC2-M) with these samples and with 911 endocervical samples collected previously. The performance of HC2-RCS was equivalent to that of HC2-M; the overall concordance rates for the detection of chlamydia and gonorrhea were 99.7% (κ = 0.97) and 99.8% (κ = 0.97), respectively. When the HC2 assay was performed with a semiautomated system application designed for high throughput, it demonstrated high sensitivity and a high specificity for detection of bothChlamydia trachomatisandNeisseria gonorrhoeae.
Molecular Epidemiological Analysis of the Changing Nature of a Meningococcal Outbreak following a Vaccination Campaign
Authors: Shlush Liran I. , Behar Doron M. , Zelazny Adrian , Keller Nathy , Lupski James R. , Beaudet Arthur L. , Bercovich Dani
Published: September 2002

A serogroup C meningococcal outbreak that occurred in an Israeli Arab village led to a massive vaccination campaign. During the subsequent 18 months, new cases of type B
Neisseria meningitidis
infection were revealed. To investigate the influence of vaccination on bacteriological epidemiology, bacteria were isolated from individuals at the outbreak location, patients with several additional other sporadic cases, and patients involoved in another outbreak. Haploid bacterial genomic DNA was mixed with a consensus PCR product to form a heteroduplex state that enabled multilocus sequence typing (MLST) to be combined with denaturing high-performance liquid chromatography (DHPLC) for a novel high-throughput molecular typing method called MLST-DHPLC. A 100% correlation was found to exist between the sequencing by MLST alone and the MLST-DHPLC method. Independent molecular typing by repetitive extragenic palindromic PCR discriminated the neisserial clones as well as the MLST-DHPLC method did. The occurrence of type B
N. meningitidis
in the postvaccination period might be attributed to the selection pressure applied to the bacteria by vaccination, suggesting a possible unwarranted outcome of vaccination with the quadrivalent vaccine for control of a serogroup C meningococcal outbreak. This is the first time that DHPLC has been applied to the genotyping of bacteria, and it proved to be more efficient than MLST alone.
Evaluation of PCR for Diagnosis of American Cutaneous Leishmaniasis in an Area of Endemicity in Northeastern Brazil
Authors: Rodrigues Eduardo Henrique Gomes , Felinto de Brito Maria Edileuza , Mendonça Mitzi Guedes , Werkhäuser Roberto P. , Coutinho Eridan M. , Souza Wayner V. , Militão de Albuquerque Maria de Fátima P. , Jardim Márcio L. , Abath Frederico G. C.
Published: September 2002

PCR-based approaches targeting kinetoplast DNA were evaluated for the diagnosis of American cutaneous leishmaniasis (ACL) in regions of endemicity in northeastern Brazil. A total of 119 cutaneous biopsy specimens from patients with ACL and nonleishmaniasis cutaneous lesions were studied. Two PCR-based systems were used; one was specific for the subgenus
Viannia
, and the other was specific for the genus
Leishmania
. The PCR specific for the subgenus
Viannia
had a sensitivity of 95.4%, whereas the genus-specific PCR detected the target DNA in 88.2% of the samples tested. The specificities of the assays, determined with samples from a group with nonleishmaniasis cutaneous lesions, was 100%. The results of the conventional tests indicate that the sensitivities of the PCR-based methods were significantly higher than those of smear examination, histological staining, and isolation by culture (
P
< 0.05). Antibodies specific for
Leishmania braziliensis
were detected by indirect immunofluorescence in 82.9% of the patients tested. Parasites were isolated from 40 of 86 patients (46.5%). Sixty-seven percent of dermal scrapings and 66.2% of stained tissue sections were positive by microscopy. Amplified products from the subgenus-specific PCR hybridized with the
Leishmania panamensis
minicircle, confirming infection consistent with
L. braziliensis
. The evidence available at present incriminates
L. braziliensis
as the only causative agent of ACL in the state of Pernambuco in Brazil.
Pilot Study of the Genetic Diversity of the Pneumococcal Nasopharyngeal Flora among Children Attending Day Care Centers
Authors: Sá-Leão Raquel , Tomasz Alexander , Santos Sanches Ilda , de Lencastre Hermínia
Published: September 2002

A pilot study was conducted to determine the genetic diversity of multiple colonies of pneumococci recovered from 37 nasopharyngeal (NP) samples of children. A total of 239 pneumococcal isolates (typically, six to eight colonies per sample) were typed by pulsed-field gel electrophoresis (PFGE). In most NP samples (89%) the multiple colonies shared common PFGE types and serotypes. However, four samples were heterogeneous (samples A through D): each contained two strains with different PFGE types, antibiotypes, and serotypes. Samples A and B each contained one strain of a vaccine capsular type and another expressing a non-vaccine type (according to the currently licensed seven-valent conjugate vaccine). In samples B and C the penicillin MIC for one strain was elevated and the other strain was susceptible. In each of the heterogeneous samples, one of the strains was a representative of an internationally disseminated clone. Samples A, C, and D contained strains which carried prophages that were inducible by mitomycin C and that could be visualized by electron microscopy. The
comC
gene allele (which encodes the competence-stimulating peptide) was the same in both strains found in each of samples A, B, and D. Carriage of multiple pneumococci with distinct properties should favor genetic exchange and provide a dynamic population structure for pneumococci in their ecological reservoir. Quantitative resolution of majority and minority components of the pneumococcal NP flora will be of importance for evaluation of the impact of intervention strategies such as vaccination or introduction of new antimicrobial agents.
Characterization of Multidrug-ResistantEscherichia coliIsolates Associated with Nosocomial Infections in Dogs
Authors: Sanchez Susan , McCrackin Stevenson M. A. , Hudson Charlene R. , Maier Marie , Buffington Tameka , Dam Quyen , Maurer John J.
Published: September 2002

Multidrug-resistant opportunistic pathogens have become endemic to the veterinary hospital environment.Escherichia coliisolates resistant to 12 antibiotics were isolated from two dogs that were housed in the intensive care unit at The University of Georgia Veterinary Teaching Hospital within 48 h of each other. Review of 21 retrospective and prospective hospital-acquiredE. coliinfections revealed that the isolates had similar antibiotic resistance profiles, characterized by resistance to most cephalosporins, β-lactams, and the β-lactamase inhibitor clavulanic acid as well as resistance to tetracycline, spectinomycin, sulfonamides, chloramphenicol, and gentamicin.E. coliisolates with similar resistance profiles were also isolated from the environment in the intensive care unit and surgery wards. MultipleE. coligenetic types were endemic to the hospital environment, with the pulsed-field gel electrophoresis fingerprint identified amongE. coliisolates from diseased animals and the hospital environment matching. The extended-spectrum cephalosporin resistance in these nosocomialE. coliisolates was attributed to the cephamycinase-encoding gene,blaCMY2. Chloramphenicol resistance was due in part to the dissemination of the florfenicol resistance gene,flo, among these isolates. Resistance encoded by both genes was self-transmissible. AlthoughblaCMY2andflowere common to the polyclonal, nosocomialE. coliisolates, there was considerable diversity in the genetic compositions of class 1 integrons, especially among isolates belonging to the same genetic type. Two or more integrons were generally present in these isolates. The gene cassettes present within each integron ranged in size from 0.6 to 2.4 kb, although a 1.7-kb gene cassette was the most prevalent. The 1.7-kb gene cassette contained spectinomycin resistance geneaadA5and trimethoprim resistance genedfrA17.
Duration of Persistence of Gonococcal DNA Detected by Ligase Chain Reaction in Men and Women following Recommended Therapy for Uncomplicated Gonorrhea
Authors: Bachmann Laura H. , Desmond Renee A. , Stephens Joan , Hughes Annalee , Hook Edward W.
Published: September 2002

Neisseria gonorrhoeae
infection remains relatively common in the United States, representing a public health challenge. Ligase chain reaction (LCR) is both highly sensitive and specific for the detection of
N. gonorrhoeae
in urine and patient-obtained vaginal swab specimens. Because of the LCR test's exquisite sensitivity, it may potentially detect DNA from nonviable organisms following effective therapy, leading to false-positive test results and unnecessary additional treatment. The purpose of the present study was to determine the duration that gonococcal DNA is detectable by LCR following therapy for uncomplicated gonococcal infection. One hundred thirty men and women between the ages of 16 and 50 years presenting to a sexually transmitted disease clinic with urogenital gonorrhea were enrolled. After the standard history was taken and a genital examination was done, the patients were asked to submit either a urine specimen (men) or a urine specimen plus a self-obtained vaginal swab specimen (women) for
N. gonorrhoeae
testing by LCR at the initial visit and each day during the study period. At enrollment, patients were treated with single doses of ofloxacin, cefixime, or ceftriaxone. The median time to a negative urine LCR test result was 1 day for the men (mean, 1.6 ± 0.14 days) and 2 days for the women (mean, 1.7 ± 0.19 days). Among the women the clearance time was significantly longer for vaginal specimens (mean, 2.8 ± 0.30 days) than for urine specimens (mean, 1.7 ± 0.11 days). Irrespective of patient gender and specimen type, gonococcal DNA can be expected to be absent from urogenital specimens within 2 weeks following successful therapy.
Identification of
Candida glabrata
by a 30-Second Trehalase Test
Authors: Freydière A.-M. , Parant F. , Noel-Baron F. , Crepy M. , Treny A. , Raberin H. , Davidson A. , Odds F. C.
Published: September 2002

Rapid (30-s) trehalase tests done with material from colonies of 482 yeasts suspended in a drop of trehalose solution on a commercially supplied glucose test strip were positive for 225 (99.1%) of 227
Candida glabrata
isolates grown on either of two differential media, Candida ID medium or CandiSelect medium. The test was positive for only 3 (1.2%) and 12 (4.7%) of 255 isolates of other medically important yeast species grown on the same two media, respectively. A rapid maltase test done with a subset of 255 yeast isolates was negative for all but 1 of 64 trehalase-positive
C. glabrata
isolates, raising the specificity of the rapid testing for
C. glabrata
to 98.4 to 100%, depending on the isolation medium used. Rapid trehalase and maltase tests done independently in two laboratories with 217 yeast isolates showed sensitivities of 96.0 to 98.0% and specificities of 98.2 to 99.4% for identification of
C. glabrata
from colonies grown on Candida ID medium. The specificity was much lower because of frequent false-positive trehalose test results when the source of colonies was Sabouraud agar formulated with 4% glucose. We conclude that direct recognition of
C. albicans
as blue colonies on Candida ID isolation medium coupled with the performance of the 30-s trehalase and maltase tests for
C. glabrata
among the white colonies on this medium will allow the rapid presumptive identification of the two yeast species most commonly encountered in clinical samples.
Identification of
Bartonella bacilliformis
Genotypes and Their Relevance to Epidemiological Investigations of Human Bartonellosis
Authors: Birtles Richard J. , Fry Norman K. , Ventosilla Palmira , Cáceres Abraham G. , Sánchez Eduardo , Vizcarra Hugo , Raoult Didier
Published: September 2002

Genotypic diversity among 26 isolates of
Bartonella bacilliformis
obtained from different areas of Peru, and at different times, was assessed by comparison of DNA sequences derived from 16S-23S ribosomal DNA intergenic spacer regions (ISR) and a citrate synthase gene (
gltA
) fragment and by amplified fragment length polymorphism (AFLP) analysis.
gltA
comparison divided the isolates into two groups, whereas ISR comparison revealed six sequences. AFLP analysis using a selective primer delineated five profiles that correlated well with those obtained by sequence comparison. Combination of all three data sets divided the isolates into six genotypes. One of these genotypes was common to isolates collected from a large area in western Peru that corresponded to the region of endemicity for bartonellosis; however, isolates belonging to two other genotypes were also found within this region. Two of these genotypes were found in isolates isolated more than 35 years apart. The remaining three genotypes were each specifically associated with three outbreaks of bartonellosis that have recently occurred in areas where the disease had not previously been recognized. Demonstration of the unique nature of these isolates indicates that the outbreaks with which they were associated did not result from the introduction of disease by individuals who acquired their infection in the recognized region of endemicity. The sources of these outbreaks remain unknown. A consensus approach to bacterial typing using comparative sequence analysis of multiple genetic loci and the pan-genomic sampling of AFLP appears to offer a well-supported assessment of
B. bacilliformis
diversity, and the genotypic differences identified appear to have epidemiological significance.
Detection in
Escherichia coli
of the Genes Encoding the Major Virulence Factors, the Genes Defining the O157:H7 Serotype, and Components of the Type 2 Shiga Toxin Family by Multiplex PCR
Authors: Wang Gehua , Clark Clifford G. , Rodgers Frank G.
Published: September 2002

Strains of Shiga toxin-producing
Escherichia coli
(STEC) have been associated with outbreaks of diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome in humans. Most clinical signs of disease arise as a consequence of the production of Shiga toxin 1 (Stx1), Stx2 or combinations of these toxins. Other major virulence factors include enterohemorrhagic
E. coli
hemolysin (EHEC
hlyA
), and intimin, the product of the
eaeA
gene that is involved in the attaching and effacing adherence phenotype. In this study, a series of multiplex-PCR assays were developed to detect the eight most-important
E. coli
genes associated with virulence, two that define the serotype and therefore the identity of the organism, and a built-in gene detection control. Those genes detected were
stx
1
,
stx
2
,
stx
2c
,
stx
2d
,
stx
2e
,
stx
2f
, EHEC
hlyA
, and
eaeA
, as well as
rfbE
, which encodes the
E. coli
O157 serotype;
fliC
, which encodes the
E. coli
flagellum H7 serotype; and the
E. coli
16S rRNA, which was included as an internal control. A total of 129
E. coli
strains, including 81 that were O157:H7, 10 that were O157:non-H7, and 38 that were non-O157 isolates, were investigated. Among the 129 samples, 101 (78.3%) were
stx
positive, while 28 (21.7%) were lacked
stx
. Of these 129 isolates, 92 (71.3%) were EHEC
hlyA
positive and 96 (74.4%) were
eaeA
positive. All STEC strains were identified by this procedure. In addition, all Stx2 subtypes, which had been initially identified by PCR-restriction fragment length polymorphism, were identified by this method. A particular strength of the assay was the identification of these 11 genes without the need to use restriction enzyme digestion. The proposed method is a simple, reliable, and rapid procedure that can detect the major virulence factors of
E. coli
while differentiating O157:H7 from non-O157 isolates.
Improved Culture from Lymph Nodes of Patients with Cat Scratch Disease and Genotypic Characterization of
Bartonella henselae
Isolates in Australia
Authors: Fournier Pierre-Edouard , Robson Jenny , Zeaiter Zaher , McDougall Rodney , Byrne Shane , Raoult Didier
Published: September 2002

Over a 4-year period we detected
Bartonella henselae
isolates in 104 of 297 specimens (35.1%) from Australian patients clinically suspected of having cat scratch disease by amplification of a fragment of the
htrA
gene. We isolated 17
B. henselae
strains (20.5%) from the 83 PCR-positive human specimens available for culture. Our culture method was based on prolonged incubation in a moist atmosphere of blood agar to which hemin was added. We obtained more
B. henselae
isolates than the number of all other isolates from lymph nodes reported in the literature. In order to identify and study the genetic variation of Australian
B. henselae
isolates, we determined the sequence of a fragment of the
pap31
gene from our 17 human isolates and also from 8 Australian cat isolates. Thirteen of the human
B. henselae
isolates belonged to the Houston genotype, variant Houston-1 (76.5%), and four belonged to the Marseille genotype, variant CAL-1 (23.5%). In contrast, seven cat isolates were classified as
B. henselae
Marseille, variant CAL-1 (87.5%), and one was classified as
B. henselae
Houston, variant Houston-1 (12.5%). Our study describes an efficient culture method for the diagnosis of cat scratch disease and contributes to the description of the genotypic distribution of
B. henselae
in Australia.
Comparative Sequence Analysis of the Core Protein and Its Frameshift Product, the F Protein, of Hepatitis C Virus Subtype 1b Strains Obtained from Patients with and without Hepatocellular Carcinoma
Authors: Ogata Satoshi , Nagano-Fujii Motoko , Ku Yonson , Yoon Seitetsu , Hotta Hak
Published: September 2002

The core protein of hepatitis C virus (HCV) has been implicated in hepatocarcinogenesis. In order to determine whether there is a correlation between mutations of the core protein and the development of hepatocellular carcinoma (HCC), the core protein-coding sequence of the viral genome of HCV subtype 1b (HCV-1b) obtained from patients with and without HCC was analyzed. We found that 12 (40.0%) of 30 HCV-1b isolates from patients with HCC but none of 29 isolates from patients without HCC had a point mutation(s) in an N-terminal region of 20 residues. Similarly, 10 (33.3%) of 30 isolates from patients with HCC had mutations in a limited region between residues 141 and 160, whereas only 2 (6.9%) of 29 isolates from patients without HCC did. The differences between the two groups were statistically significant. The mutations were found in isolates from both cancerous and adjacent noncancerous tissues of patients with HCC, suggesting that the mutations were present before the development of HCC. The other regions of the core protein of some isolates also had mutations, but no significant difference was observed between isolates from patients with HCC and those from patients without HCC. The F protein, a frameshift product that is still hypothetical for HCV-1b strains, showed more sequence diversity than the core protein among the isolates analyzed, but there were no significant differences in the mutation rates or positions between isolates from patients with HCC and isolates from patients without HCC, except for a short N-terminal sequence of ∼11 residues that is shared with the core protein.
Quantification of
Chlamydia trachomatis
Elementary Bodies in Urine by Ligase Chain Reaction
Authors: Blocker Michael E. , Krysiak Robert G. , Behets Frieda , Cohen Myron S. , Hobbs Marcia M.
Published: September 2002

Modification of the standard
Chlamydia trachomatis
ligase chain reaction (LCR) detection assay resulted in a quantitative test. Sample rates from
C. trachomatis
standards ranging from 32 to 1,048,576 elementary bodies (EB)/ml of urine exhibited a linear correlation with concentration. Quantitative LCR (qLCR) was used to measure the number of EB per milliliter in 158 urine samples from women in Madagascar that tested positive for
C. trachomatis
by the standard LCR detection assay.
C. trachomatis
concentrations displayed an apparent bimodal distribution, with approximately one-third of samples (37%) in a peak ranging from 32 to 1,015 EB/ml (median = 297 EB/ml) and the remainder (63%) in a grouping with relatively higher concentrations, ranging from 1,086 to 218,670 EB/ml (median = 7,389 EB/ml). qLCR will be useful for studies of chlamydial infection aimed at understanding the associations of organism burden with clinical manifestations and transmission.
Detection of Herpes Simplex Virus Type 2-Specific Immunoglobulin G Antibodies in African Sera by Using Recombinant gG2, Western Blotting, and gG2 Inhibition
Authors: Hogrefe Wayne , Su Xin , Song James , Ashley Rhoda , Kong Lilly
Published: September 2002

Sera (
n
= 781) from four African countries were used to determine the prevalence of herpes simplex virus type 2 (HSV-2) antibodies by using the HerpeSelect HSV-2 enzyme-linked immunosorbent assay (ELISA; Focus Technologies) and Western blotting (WB). Also, an HSV inhibition assay was developed to evaluate the discordant sample results between HerpesSelect and WB. The seroprevalence of HSV-2 ranged from 17% in the South African panel to nearly 70% in panels from Kenya, Uganda, and Zimbabwe. Overall, HerpeSelect was 100% sensitive and 88% specific compared to WB and 100% sensitive and 96% specific compared to the inhibition assay. There was 100% concordance among all three assays for samples from South Africa and Zimbabwe. The discordant results occurred in samples from Kenya and Uganda.
Genetic Classification and Differentiation of
Bartonella
Species Based on Comparison of Partial
ftsZ
Gene Sequences
Authors: Zeaiter Zaher , Liang Zhongxing , Raoult Didier
Published: September 2002

Currently, 19 species are recognized in the genus
Bartonella
, 7 of which are involved in an increasing variety of human diseases. Development of molecular tools for detection, identification, and subtyping of strains and isolates has promoted research on
Bartonella
spp. We amplified and sequenced the portion of the
ftsZ
gene encoding the N-terminal region of the cell division protein for 13
Bartonella
species:
Bartonella alsatica
,
B. birtlesii
,
B. doshiae
,
B. elizabethae
,
B. grahami
,
B. koehlerae
,
B. schoenbuchensis
,
B. taylorii
,
B. tribocorum
,
Bartonella vinsonii
subsp.
arupensis
,
Bartonella vinsonii
subsp.
berkhoffii
,
Bartonella vinsonii
subsp.
vinsonii
, and
B. bovis
Bermond et al.(“
B. weissii
”). Phylogenetically derived trees revealed four statistically supported groups, indicating that sequencing of the
ftsZ
gene is a useful tool for identifying evolutionary relationships among
Bartonella
species. Furthermore, we amplified and sequenced the portion of the
ftsZ
gene encoding the C-terminal region of the protein for 4
B. bacilliformis
isolates, 14
B. clarridgeiae
isolates, 14
B. quintana
isolates, and 30
B. henselae
isolates that were obtained from different geographic regions, hosts, and clinical specimens.
B. clarridgeiae
and
B. quintana
sequences were highly conserved, while those of the four
B. bacilliformis
isolates differed from the type strain at 5 positions. Among
B. henselae
strains isolated from cats and patients, only two genotypes were detected: Houston and Marseille. Among 80 clinical samples we detected
Bartonella
spp. in 35 (43.75%) and found the assay to be comparable to that of a combined intergenic-spacer-region- and
pap31
-based PCR assay. Our results show the usefulness of the portion of the
ftsZ
gene encoding the C-terminal region for diagnosis of
Bartonella
infections. More samples should be tested to study its usefulness for epidemiological investigations.
Molecular Follow-Up of
Salmonella enterica
subsp.
enterica
Serovar Agona Infection in Cattle and Humans
Authors: Lindqvist Nanna , Siitonen Anja , Pelkonen Sinikka
Published: September 2002

Salmonella enterica
subsp.
enterica
serovar Agona was not frequently encountered in Finland until an increase in rates of isolation among animal and feed was seen in 1994. A small outbreak among cattle farms in the regions of Oulu and Vaasa in northwestern Finland in 1994-1995 included eight farms. After the outbreak, an increase in the number of serovar Agona infections in humans was seen in 1999: the number of annual microbiologically confirmed cases in humans increased from about 10 from 1990 to 1998 to 84 in 1999, including an outbreak in which more than 50 people were infected. To gather epidemiological data on serovar Agona and to trace the origin of the human infections, 110 serovar Agona isolates isolated from animal, feed, and other sources as well as from humans with cases of salmonellosis of domestic and foreign origin, which were recovered from 1984 to 1999, were analyzed for their pulsed-field gel electrophoresis (PFGE), plasmid, and IS
200
profiles and antibiograms. Of these typing methods, PFGE with restriction endonucleases
Xba
I,
Bln
I,
Not
I, and
Spe
I was the most useful. The PFGE profile of the strain causing an outbreak among cattle in Finland in 1994-1995 was not seen previously. The strain with this profile was later only sporadically found in human infections. The profile of the strain causing the human outbreak in 1999 was not found among isolates from cattle or any other sources. Molecular typing was valuable in showing that although the outbreaks in cattle and humans seemed to be related regionally, they were not related otherwise.
Plasma RNA Viral Load in Human Immunodeficiency Virus Type 2 Subtype A and Subtype B Infections
Authors: Damond Florence , Gueudin Marie , Pueyo Sophie , Farfara Isabelle , Robertson David L. , Descamps Diane , Chène Geneviève , Matheron Sophie , Campa Pauline , Brun-Vézinet Françoise , Simon François
Published: September 2002

Human immunodeficiency virus type 2 (HIV-2) is much less pathogenic than HIV-1, and HIV-2 infection is associated with plasma viral loads significantly lower than those found in HIV-1 infection. We have developed a real-time quantitative PCR method for measuring the HIV-2 RNA load that covers the range of genetic diversity of HIV-2 isolates and that detects extremely low viral loads. Samples from 49 patients were studied. Proviral DNA was first detected and quantified. The strains that were detected were then genotyped: 21 patients were infected with HIV-2 subtype A and 15 patients were infected with HIV-2 subtype B; 1 patient was infected with a highly divergent strain.
Env
PCR failed for the remaining 12 patients, so subtypes could not be determined. For viral RNA quantification, a stock of HIV-2 strain NIHZ, which was counted by electron microscopy, was used as the standard. Several primer sets targeting the highly conserved
gag
region were evaluated. Various primer combinations failed to amplify subtype B strains. With the final primer pair selected, which detected both subtype A and subtype B strains, the sensitivity of the assay was 100% at a viral load of 250 copies/ml and 66% at a viral load of 125 copies/ml. We found a correlation between the CD4
+
-cell count, the clinical stage, and the plasma HIV-2 RNA level. The median plasma HIV-2 RNA value for the 33 asymptomatic patients was 2.14 log
10
, whereas it was 3.1 log
10
for the 16 patients with AIDS (
P
< 0.01). Proviral DNA was detectable in 18 symptom-free patients with high CD4
+
-cell counts, in whom viral RNA was undetectable.