bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Typing of the Porin Protein of
Neisseria gonorrhoeae
from Clinical Noncultured Samples for Strain Characterization and Identification of Mixed Gonococcal Infections
Authors: Lynn Freyja , Hobbs Marcia M. , Zenilman Jonathan M. , Behets Frieda M. T. F. , Van Damme Kathleen , Rasamindrakotroka Andry , Bash Margaret C. 
Published: January 2005

ABSTRACT

Molecular methods that characterize the
Neisseria gonorrhoeae
porin protein Por are needed to study gonococcal pathogenesis in the natural host and to classify strains from direct clinical samples used with nucleic acid amplification-based tests. We have defined the capabilities of
por
variable region (VR) typing and determined suitable conditions to apply the method to direct clinical specimens. Nested PCR from spiked urine samples detected 1 to 10 copies of template DNA; freezing spiked whole urine greatly reduced the ability to amplify
porB
. In a laboratory model of mixed gonococcal infections, the
por
type of one strain could be determined in the presence of a 100-fold excess of another.
por
VR typing was used to examine clinical samples from women enrolled in studies conducted in Baltimore, Md., and Madagascar.
por
type was determined from 100% of paired cervical swab and wick samples from 20 culture-positive women from Baltimore; results for eight individuals (40%) suggested infection with more than one strain. In frozen urine samples from Madagascar,
porB
was amplified and typed from 60 of 126 samples from ligase chain reaction (LCR)-positive women and 3 samples from LCR-negative women. The
por
VR types of 13 samples (21%) suggested the presence of more than one gonococcal strain. Five
por
types, identified in >45% of women with typed samples, were common to both geographic areas. Molecular typing is an important adjunct to nucleic acid amplification-based diagnostics. Methods that utilize direct clinical samples and can identify mixed infections may contribute significantly to studies of host immunity, gonococcal epidemiology, and pathogenesis.
Latency-Related Gene Encoded by Bovine Herpesvirus 1 Promotes Virus Growth and Reactivation from Latency in Tonsils of Infected Calves
Authors: Perez Sandra , Inman Melissa , Doster Alan , Jones Clinton 
Published: January 2005

ABSTRACTInfection of calves with bovine herpesvirus 1 (BHV-1) results in transient immunosuppression that may lead to bacterium-induced pneumonia and, occasionally, death. Although sensory neurons in the trigeminal ganglia (TG) are the primary site of BHV-1 latency, viral genomes are detected in the tonsils of latently infected calves. Dexamethasone (DEX) consistently induces reactivation from latency, and viral gene expression is detected in TG and tonsils. In sensory neurons of latently infected calves, the latency-related (LR) gene is abundantly expressed and is required for reactivation from latency. In the present study, we compared the abilities of wild-type (wt) BHV-1 and a strain with a mutation in the LR gene (the LR mutant strain) to grow in the tonsils of infected calves and reactivate from latency. Lower levels of the LR mutant virus were detected in the tonsils of acutely infected calves. LR mutant viral DNA was consistently detected by PCR in the tonsils of latently infected calves, suggesting that the establishment of a latent or persistent infection occurred. Although the LR mutant did not reactivate from latency in vivo after DEX treatment, explantation of tonsil tissue from calves latently infected with the LR mutant yielded infectious virus. Relative to wt BHV-1, the LR mutant did not induce explant-induced reactivation as efficiently. These studies indicate that the LR gene promotes virus shedding from tonsil tissue during acute infection and reactivation from latency in tonsil tissue in vivo. We suggest that incorporation of the LR gene mutation into existing modified live vaccines would prevent reactivation from latency in neural and nonneural sites and would thus prevent transmission to other animals.
Multispacer Typing Technique for Sequence-Based Typing ofBartonella quintana
Authors: Foucault C. , La Scola B. , Lindroos H. , Andersson S. G. E. , Raoult D. 
Published: January 2005

ABSTRACTBartonella quintanais a worldwide fastidious bacterium of the Alphaproteobacteria responsible for bacillary angiomatosis, trench fever, chronic lymphadenopathy, and culture-negative endocarditis. The recent genome sequencing of aB. quintanaisolate allowed us to propose a genome-wide sequence-based typing method. To ensure sequence discrimination based on highly polymorphic areas, we amplified and sequenced 34 spacers in a large collection ofB. quintanaisolates. Six of these exhibited polymorphisms and allowed the characterization of 4 genotypes. However, the strain variants suggested by the noncoding sequences did not correlate with the results of pulsed-field gel electrophoresis (PFGE), which suggested a higher degree of variability. Modification of the PFGE profile of one isolate after nine subcultures confirmed that rearrangement frequencies are high in this species, making PFGE unreliable for epidemiological purposes. The low extent of sequence heterogeneity in the species suggests a recent emergence of this bacterium as a human pathogen. Direct typing of natural samples allowed the identification of a fifth genotype in the DNA extracted from a human body louse collected in Burundi. We have named the typing technique herein described multispacer typing.
Detection of Human Influenza A Viruses by Loop-Mediated Isothermal Amplification
Authors: Poon Leo L. M. , Leung Cynthia S. W. , Chan Kwok H. , Lee Jack H. C. , Yuen Kwok Y. , Guan Yi , Peiris Joseph S. M. 
Published: January 2005

ABSTRACT
Here we describe the use of the loop-mediated isothermal amplification (LAMP) method to detect human influenza viruses (H1 to H3). Our results were correlated 100% with results deduced from routine clinical diagnostic tests. In addition, we also developed a LAMP assay specific for human β-actin cDNA as a quality control test.
Effect of Inoculum Size on Detection of
Candida
Growth by the BACTEC 9240 Automated Blood Culture System Using Aerobic and Anaerobic Media
Authors: George Benjamin J. , Horvath Lynn L. , Hospenthal Duane R. 
Published: January 2005

ABSTRACT

Simulated candidemia was produced with 20
Candida
isolates at three inoculum sizes (100, 10, and 1 CFU/ml of blood). Growth detection was better with larger inocula. The time to growth detection was shorter with larger inocula. Inoculum size does effect
Candida
growth detection and time to detection in BACTEC 9240 automated systems.
Cetyl-Pyridinium Chloride Is Useful for Isolation of
Mycobacterium tuberculosis
from Sputa Subjected to Long-Term Storage
Authors: Pardini Manuela , Varaine Francis , Iona Elisabetta , Arzumanian Erchanik , Checchi Francesco , Oggioni Marco Rinaldo , Orefici Graziella , Fattorini Lanfranco 
Published: January 2005

ABSTRACT

Recovery of
Mycobacterium tuberculosis
from sputa treated with cetyl-pyridinium chloride (CPC) and stored for 20 ± 9 days was significantly higher than that from sputa that were untreated and processed by the
N
-acetyl-
l
-cisteine-NaOH method. Addition of CPC is useful for isolation of
M. tuberculosis
from sputa subjected to long-term storage received from remote areas of the world.
High Prevalence of Respiratory Viral Infections in Patients Hospitalized in an Intensive Care Unit for Acute Respiratory Infections as Detected by Nucleic Acid-Based Assays
Authors: Legoff Jérôme , Guérot Emmanuel , Ndjoyi-Mbiguino Angélique , Matta Mathieu , Si-Mohamed Ali , Gutmann Laurent , Fagon Jean-Yves , Bélec Laurent 
Published: January 2005

ABSTRACT
Forty-seven bronchoalveolar lavages (BAL) were obtained from 41 patients with acute pneumonia attending an intensive care unit. By molecular diagnosis, 30% of total BAL and 63% of bacteria-negative BAL were positive for respiratory viruses. Molecular detection allows for high-rate detection of respiratory viral infections in adult patients suffering from severe pneumonia.
Activities of Available and Investigational Antifungal Agents against
Rhodotorula
Species
Authors: Diekema D. J. , Petroelje B. , Messer S. A. , Hollis R. J. , Pfaller M. A 
Published: January 2005

ABSTRACT

Rhodotorula
species are emerging pathogens in immunocompromised patients. We report the in vitro activities of eight antifungals against 64
Rhodotorula
isolates collected in surveillance programs between 1987 and 2003.
Rhodotorula
strains are resistant in vitro to fluconazole (MIC at which 50% of the isolates tested are inhibited [MIC
50
], >128 μg/ml) and caspofungin (MIC
50
, >8 μg/ml). Amphotericin B (MIC
50
,1 μg/ml) and flucytosine (MIC
50
, 0.12 μg/ml) are both active in vitro, and the new and investigational triazoles all have some in vitro activity, with ravuconazole being the most active (MIC
50
, 0.25 μg/ml).
Polymorphism of the Human Immunodeficiency Virus Type 2 (HIV-2) Protease Gene and Selection of Drug Resistance Mutations in HIV-2-Infected Patients Treated with Protease Inhibitors
Authors: Damond F. , Brun-Vezinet F. , Matheron S. , Peytavin G. , Campa P. , Pueyo S. , Mammano F. , Lastere S. , Farfara I. , Simon F. , Chene G. , Descamps D. 
Published: January 2005

ABSTRACT
We described the baseline polymorphism of the human immunodeficiency virus type 2 (HIV-2) protease gene from 94 treatment-naive patients and the longitudinal follow-up of 17 protease inhibitor-treated patients. Compared to the HIV-2 consensus sequences, baseline polymorphism involved 47 positions. Substitutions selected under treatment were observed at positions corresponding to HIV-1 resistance mutations as well as at positions of currently unknown impact on HIV-1.
Variable gp43 Secretion by
Paracoccidioides brasiliensis
Clones Obtained by Two Different Culture Methods
Authors: Berzaghi Rodrigo , Marques da Silva Silvia Helena , Pires de Camargo Zoilo 
Published: January 2005

ABSTRACT

The main objectives of this study were to obtain clones of
Paracoccidioides brasiliensis
by two methods (micromanipulation and plating assay) and to determine if the secretion of the 43-kDa glycoprotein (gp43) is dependent on the clonal culture. The results show that the secretion of gp43 is not dependent on clonal cultures. Clones that originally were secretors of this molecule, after subculturing, lost this characteristic; on the other hand, clones that originally did not secrete gp43 began to secrete gp43 after subculturing.
Comparison of a New Commercial Test, GLABRATA RTT, with a Dipstick Test for Rapid Identification of
Candida glabrata
Authors: Willinger Birgit , Wein Susanne , Hirschl Alexander M. , Rotter Manfred L. , Manafi Mammad 
Published: January 2005

ABSTRACT

This study compares the performance of a 3-h dipstick trehalose test with GLABRATA RTT, a new commercially available 20-min test for the rapid identification of
Candida glabrata
. With the exception of blood agar, GLABRATA RTT gave reliable results with all media tested and was always superior to the dipstick test.
Vibrio fluvialis
Peritonitis in a Patient Receiving Continuous Ambulatory Peritoneal Dialysis
Authors: Ratnaraja Natasha , Blackmore Timothy , Byrne Joan , Shi Shuning 
Published: January 2005

ABSTRACT

We describe a case of peritonitis due to
Vibrio fluvialis
in a patient receiving continuous ambulatory peritoneal dialysis; we believe the case to be associated with the consumption of poorly prepared seafood. This was shown to be an important but rare cause of recurrent infection in our patient.
First Isolation of Metallo-β-Lactamase-Producing Multiresistant
Klebsiella pneumoniae
from a Patient in Brazil
Authors: Lincopan Nilton , McCulloch John Anthony , Reinert Cristina , Cassettari Valéria C. , Gales Ana C. , Mamizuka Elsa M. 
Published: January 2005

ABSTRACT

A multiresistant
Klebsiella pneumoniae
isolate was taken from the blood of a 75-year-old patient with nosocomial pneumonia who developed septic shock and failed therapy with imipenem. The isolate presented an MIC of imipenem of 128 μg/ml, and the production of a metallo-β-lactamase was confirmed by phenotypic and genotypic techniques. We here report, for the first time, the detection of a metalloenzyme (IMP-1)-producing
K. pneumoniae
clinical strain in Latin America. The gene responsible for this phenotype was found to be
bla
IMP-1
, carried in a class 1 integron.
Molecular Epidemiology of Pneumococcal Colonization in Response to Pneumococcal Conjugate Vaccination in Children with Recurrent Acute Otitis Media
Authors: Bogaert D. , Veenhoven R. H. , Sluijter M. , Wannet W. J. W. , Rijkers G. T. , Mitchell T. J. , Clarke S. C. , Goessens W. H. F. , Schilder A. G. , Sanders E. A. M. , de Groot R. , Hermans P. W. M. 
Published: January 2005

ABSTRACT
A randomized double-blind trial with a 7-valent pneumococcal conjugate vaccine was conducted in The Netherlands among 383 children, aged 1 to 7 years, with a history of recurrent acute otitis media. No effect of vaccination on the pneumococcal colonization rate was found. However, a shift in serotype distribution was clearly observed (R. Veenhoven et al., Lancet 361:2189-2195, 2003). We investigated the molecular epidemiology of 921 pneumococcal isolates retrieved from both the pneumococcal vaccine (PV) and control vaccine (CV) groups during the vaccination study. Within individuals a high turnover rate of pneumococcal restriction fragment end labeling genotypes, which was unaffected by vaccination, was observed. Comparison of the genetic structures before and after completion of the vaccination scheme revealed that, despite a shift in serotypes, there was clustering of 70% of the pneumococcal populations. The remaining isolates (30%) were equally observed in the PV and CV groups. In addition, the degree of genetic clustering was unaffected by vaccination. However, within the population genetic structure, nonvaccine serotype clusters with the serotypes 11, 15, and 23B became predominant over vaccine-type clusters after vaccination. Finally, overall pneumococcal resistance was low (14%), and, albeit not significant, a reduction in pneumococcal resistance as a result of pneumococcal vaccination was observed. Molecular surveillance of colonization in Dutch children shows no effect of pneumococcal conjugate vaccination on the degree of genetic clustering and the genetic structure of the pneumococcal population. However, within the genetic pneumococcal population structure, a clear shift toward nonvaccine serotype clusters was observed.
Distribution of the Beijing Family Genotypes of
Mycobacterium tuberculosis
in Taiwan
Authors: Jou Ruwen , Chiang Chen-Yuan , Huang Wei-Lun 
Published: January 2005

ABSTRACT

To investigate the distribution of the Beijing family genotypes of
Mycobacterium tuberculosis
in Taiwan, we collected 421
M. tuberculosis
complex clinical isolates at random from four geographic regions of Taiwan and analyzed them by spacer oligonucleotide typing (spoligotyping) in 2003. We found 113 resolved spoligotypes, among which we identified 28 (24.8%) clusters. One hundred eighty-seven (44.4%) isolates were Beijing family genotypes and consisted of 172 (40.9%) characteristic Beijing genotypes and 15 (3.6%) Beijing-like ones. We also found that substantially larger proportions of tuberculosis patients were infected with Beijing family genotypes in the northern (51.6%) and eastern (46.2%) regions of Taiwan, while 31.6 and 28.0% of the tuberculosis patients in the central and southern regions, respectively, were infected with these genotypes. The proportion of Beijing genotype isolates was the highest in patients below the age of 24 years (61.5%), the second highest in elderly patients over age 65 years (46.8%), and the lowest in middle-age patients between the ages of 45 and 54 years (34.0%). Geographic location and age were found by multivariate analysis to be associated with Beijing family genotypes. Antituberculosis drug resistance was found more often in Beijing family genotype strains (46.4%) than in non-Beijing family genotype strains (34.3%), with more Beijing family genotype strains being resistant to ethambutol and isoniazid. These findings suggest that
M. tuberculosis
Beijing family genotypes have been dominant for several decades and that they are the cause of a significant proportion of the recent transmissions of tuberculosis in Taiwan.
Informed consent should be obtained from patients to use products (skin substitutes) and dressings containing biological material
Authors: Enoch S , Shaaban H , Dunn K W 
Published: January 2005

Background:Biological products (tissue engineered skin, allograft and xenograft, and biological dressings) are widely used in the treatment of burns, chronic wounds, and other forms of acute injury. However, the religious and ethical issues, including consent, arising from their use have never been addressed in the medical literature.Aims:This study was aimed to ascertain the views of religious leaders about the acceptability of biological products and to evaluate awareness among healthcare professionals about their constituents.Methods:The religious groups that make up about 75% of the United Kingdom population were identified and a questionnaire on 11 biological products was sent to its leaders. Another questionnaire concerning 17 products (11 biological and 6 synthetic dressings) was sent to 100 healthcare professionals working in seven specialist units in the UK.Results:All religious leaders (100% response rate) replied, some after consultation with international bodies. Among them, 77% said that patients should be informed of the constituents of the biological products and consent obtained. Some leaders expressed concerns about particular products including the transmission of viral and prion diseases, cruelty to animals, and material derived from neonates. None of the healthcare professionals (73% response rate) surveyed knew the constituents of all the products correctly.Conclusion:Ignoring religious sensitivities and neglecting consent in the usage of biological products could have very serious implications, including litigation. Hospitals and manufacturers should take immediate measures to enlighten healthcare professionals of the constituents of these products so that they can obtain informed consent from patients.
Atmospheric Emitted Radiance Interferometer. Part I: Instrument Design
Authors: Knuteson R. O. , Revercomb H. E. , Best F. A. , Ciganovich N. C. , Dedecker R. G. , Dirkx T. P. , Ellington S. C. , Feltz W. F. , Garcia R. K. , Howell H. B. , Smith W. L. , Short J. F. , Tobin D. C. 
Published: January 2005

Abstract
A ground-based Fourier transform spectrometer has been developed to measure the atmospheric downwelling infrared radiance spectrum at the earth's surface with high absolute accuracy. The Atmospheric Emitted Radiance Interferometer (AERI) instrument was designed and fabricated by the University of Wisconsin Space Science and Engineering Center (UW-SSEC) for the Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Program. This paper emphasizes the key features of the UW-SSEC instrument design that contribute to meeting the AERI instrument requirements for the ARM Program. These features include a highly accurate radiometric calibration system, an instrument controller that provides continuous and autonomous operation, an extensive data acquisition system for monitoring calibration temperatures and instrument health, and a real-time data processing system. In particular, focus is placed on design issues crucial to meeting the ARM requirements for radiometric calibration, spectral calibration, noise performance, and operational reliability. The detailed performance characteristics of the AERI instruments built for the ARM Program are described in a companion paper.
Atmospheric Emitted Radiance Interferometer. Part II: Instrument Performance
Authors: Knuteson R. O. , Revercomb H. E. , Best F. A. , Ciganovich N. C. , Dedecker R. G. , Dirkx T. P. , Ellington S. C. , Feltz W. F. , Garcia R. K. , Howell H. B. , Smith W. L. , Short J. F. , Tobin D. C. 
Published: January 2005

Abstract
The Atmospheric Emitted Radiance Interferometer (AERI) instrument was developed for the Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Program by the University of Wisconsin Space Science and Engineering Center (UW-SSEC). The infrared emission spectra measured by the instrument have the sensitivity and absolute accuracy needed for atmospheric remote sensing and climate studies. The instrument design is described in a companion paper. This paper describes in detail the measured performance characteristics of the AERI instruments built for the ARM Program. In particular, the AERI systems achieve an absolute radiometric calibration of better than 1% (3σ) of ambient radiance, with a reproducibility of better than 0.2%. The knowledge of the AERI spectral calibration is better than 1.5 ppm (1σ) in the wavenumber range 400– 3000 cm−1.
Gas Exchange and Bubble-Induced Supersaturation in a Wind-Wave Tank
Authors: Bowyer Peter , Woolf David 
Published: January 2005

Abstract
Gas exchange and bubble-induced supersaturation were measured in a wind-wave tank using total gas saturation meters. The water in the tank was subjected to bubbling using a large number of frits at a depth of 0.6 m.
A simple linear model of bubble-mediated gas exchange implies that this should force an equilibrium supersaturation of 3%. This is confirmed by experiment, but a small additional steady-state supersaturation is also forced by warming. The total steady-state supersaturation is approached asymptotically.
When the bubblers were switched off, the total gas pressure approached a new steady state at much lower supersaturation, at a rate that depended on the state of the wind and waves in the tank. The rates of approach on the various equilibria enabled the gas flux across the surface of the bubbles or across the air–water interface to be calculated.
In addition a series of experiments was conducted where the water was subjected to bubbling in the presence of wind or wind and paddle waves: in this case gas invasion from the bubbles was balanced by gas evasion near or at the surface resulting in an equilibrium at &lt;3% and enabling the relative strength of the invasion and evasion to be estimated.
Gas concentrations could be measured in a rapid, automated manner using simple apparatus. To derive gas fluxes, corrections for changes in water temperature and fluctuations in air pressure are necessary, and these are quantified. In addition, transient fluctuations in gas concentration at the start of bubbling periods allowed mixing within the tank to be observed.