bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACTTo 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACTThe 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

ABSTRACTPolyclonal 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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACTIsolates 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.
A GAME-THEORETIC TREATMENT OF A TIME-DISCRETE EMISSION REDUCTION MODEL
Authors: KRABS WERNER , PICKL STEFAN 
Published: May 2004

We present a game-theoretic treatment of the so-called TEM model which leads to new results in the area of time-discrete dynamical games. The presented TEM-model describes the economical interaction between several actors (players) who intend to minimize their emissions (Ei) caused by technologies (Ti) by means of expenditures of money (Mi) or financial means, respectively. The index stands for the ith player, i=1,…,n. The players are linked by technical cooperations and the market, which expresses itself in the nonlinear time-discrete dynamics of the Technology-Emissions-Means-model, in short: TEM-model. In the sense of environmental protection, the aim is to reach a state which is mentioned in the Kyoto Protocol by choosing the control parameters such that the emissions of each player become minimized. The focal point is the realization of the necessary optimal control parameters via a played cost game, which is determined by the way of cooperation of the actors. In application to the work of G. Leitmann [1974], but not regarding solution sets as feasible sets, the τ-value of S. H. Tijs and T. S. H. Driessen [1986] is taken as a control parameter. This leads to a new class of problems in the area of 1-convex games. We want to solve the problem by a non-cooperative and cooperative treatment. We prove that the core which is gained by cooperation of the players is nonempty and can be used as feasible set for our control problem. With this solution a reasonable model for a Joint-Implementation process is developed, where its necessary fund is represented by the non-empty core of the analyzed game. Steering with parameters of this feasible set, the TEM-model can be regarded as a useful tool to implement and verify a technical Joint-Implementation Program. For the necessary data given to the Clearing House () we are able to compare the numerical results with real world phenomena.
NEW APPROACH TO THE COLLISION AVOIDANCE PROBLEM FOR A SHIP
Authors: MIELE A. , WANG T. 
Published: May 2004

A new algorithm is developed to solve the collision avoidance problem for a host ship subject to kinematic, dynamic, and moment equations and steered via rudder under the assumptions that the rudder angle and rudder angle time rate are subject to upper and lower bounds. The objective of the collision avoidance maneuver is to maximize with respect to the state and control history the timewise minimum distance between a host ship and an intruder ship. Two limiting cases are considered: (i) the intruder ship is uncooperative and keeps its course unchanged during the encounter; (ii) the intruder ship is cooperative. In both cases, a differential game formulation is avoided and the collision avoidance problem is formulated as a maximin problem of optimal control. Four problems are investigated and their solutions compared: Problems P1 and P2 deal with uncooperative collision avoidance, while Problems P3 and P4 deal with cooperative collision avoidance. Numerical results show that the optimal control histories always involve multiple subarcs along which either the rudder angle is kept at one of the extreme positions or the rudder angle time rate is held at one of the extreme values.
Age-Dependent Expression of Advanced Glycation End Product Receptor Genes in the Human Heart
Authors: Casselmann C. , Reimann A. , Friedrich I. , Schubert A. , Silber R.-E. , Simm A. 
Published: May 2004

<i>Background:</i> Advanced glycation end products (AGEs) are formed by the reaction of sugars and NH<sub>2</sub> groups of lysine and arginine residues and have been shown to accumulate in tissues, including the heart, with normal ageing. The interaction of AGEs with their receptors is known to cause changes in cell function, leading, for example, to the production of pro-inflammatory cytokines and free radicals. <i>Objective:</i> This study investigated the gene expression of the five known AGE receptors: AGE-R1, AGE-R2, AGE-R3, the scavenger receptor II, and the receptor for AGEs (RAGE) in human heart tissue. <i>Methods:</i> Tissue samples were taken from the right cardiac auricles from three patient groups: children (2.4 ± 1.1 years), adults (45.3 ± 0.8 years) and elderly subjects (76.4 ± 0.4 years). Analysis of gene expression of the five AGE receptors was performed using the reverse transcription-polymerase chain reaction (RT-PCR) and 18S mRNA levels as loading controls. <i>Results:</i> Our results show an age-dependent upregulation of the genes for AGE-R3 and the scavenger receptor II, but a downregulation for RAGE and no significant differences for AGE-R1 and AGE-R2. <i>Conclusion:</i> This study supports a pathophysiological function for AGE receptors such as AGE-R3 and RAGE in the ageing heart.