bluuebunny/crossref_metadata_2025 huggingface dataset:
Propionibacterium acnes
Types I and II Represent Phylogenetically Distinct Groups
Authors: McDowell Andrew , Valanne Susanna , Ramage Gordon , Tunney Michael M. , Glenn Josephine V. , McLorinan Gregory C. , Bhatia Ajay , Maisonneuve Jean-Francois , Lodes Michael , Persing David H. , Patrick Sheila
Published: January 2005

Although two phenotypes of the opportunistic pathogen
Propionibacterium acnes
(types I and II) have been described, epidemiological investigations of their roles in different infections have not been widely reported. Using immunofluorescence microscopy with monoclonal antibodies (MAbs) QUBPa1 and QUBPa2, specific for types I and II, respectively, we investigated the prevalences of the two types among 132
P. acnes
isolates. Analysis of isolates from failed prosthetic hip implants (
n
= 40) revealed approximately equal numbers of type I and II organisms. Isolates from failed prosthetic hip-associated bone (
n
= 6) and tissue (
n
= 38) samples, as well as isolates from acne (
n
= 22), dental infections (
n
= 8), and skin removed during surgical incision (
n
= 18) were predominately of type I. A total of 11 (8%) isolates showed atypical MAb labeling and could not be conclusively identified. Phylogenetic analysis of
P. acnes
by nucleotide sequencing revealed the 16S rRNA gene to be highly conserved between types I and II. In contrast, sequence analysis of
recA
and a putative hemolysin gene (
tly
) revealed significantly greater type-specific polymorphisms that corresponded to phylogenetically distinct cluster groups. All 11 isolates with atypical MAb labeling were identified as type I by sequencing. Within the
recA
and
tly
phylogenetic trees, nine of these isolates formed a cluster distinct from other type I organisms, suggesting a further phylogenetic subdivision within type I. Our study therefore demonstrates that the phenotypic differences between
P. acnes
types I and II reflect deeper differences in their phylogeny. Furthermore, nucleotide sequencing provides an accurate method for identifying the type status of
P. acnes
isolates.
Molecular Phylogenies of
Blastocystis
Isolates from Different Hosts: Implications for Genetic Diversity, Identification of Species, and Zoonosis
Authors: Noël Christophe , Dufernez Fabienne , Gerbod Delphine , Edgcomb Virginia P. , Delgado-Viscogliosi Pilar , Ho Lip-Chuen , Singh Mulkit , Wintjens René , Sogin Mitchell L. , Capron Monique , Pierce Raymond , Zenner Lionel , Viscogliosi Eric
Published: January 2005

Small-subunit (SSU) rRNA gene sequences were obtained by PCR from 12
Blastocystis
isolates from humans, rats, and reptiles for which elongation factor 1α (EF-1α) gene sequences are already available. These new sequences were analyzed by the Bayesian method in a broad phylogeny including, for the first time, all
Blastocystis
sequences available in the databases. Phylogenetic trees identified seven well-resolved groups plus several discrete lineages that could represent newly defined clades. Comparative analysis of SSU rRNA- and EF-1α-based trees obtained by maximum-likelihood methods from a restricted sampling (13 isolates) revealed overall agreement between the two phylogenies. In spite of their morphological similarity, sequence divergence among
Blastocystis
isolates reflected considerable genetic diversity that could be correlated with the existence of potentially ≥12 different species within the genus. Based on this analysis and previous PCR-based genotype classification data, six of these major groups might consist of
Blastocystis
isolates from both humans and other animal hosts, confirming the low host specificity of
Blastocystis
. Our results also strongly suggest the existence of numerous zoonotic isolates with frequent animal-to-human and human-to-animal transmissions and of a large potential reservoir in animals for infections in humans.
Transmission of High-Risk Human Papillomavirus (HPV) between Parents and Infant: a Prospective Study of HPV in Families in Finland
Authors: Rintala Marjut A. M. , Grénman Seija E , Puranen Mirja H. , Isolauri Erika , Ekblad Ulla , Kero Pentti O. , Syrjänen Stina M.
Published: January 2005

The Finnish HPV Family Study is a prospective cohort study assessing the dynamics of human papillomavirus (HPV) transmission between parents and infant. Serial genital and oral scrapings from 76 families, including mother, father, and infant, and semen samples were collected over 2 years of follow-up, analyzed by nested PCR, and confirmed by hybridization with 12 high-risk (HR) HPV types. The most common HPV profile was HR HPV in all family members (29%), followed by HPV-positive mother-infant pairs (26%). HPV-positive father-infant pairs were less frequent (11%), and in six (8%) families, only the infant was HR HPV positive. The prevalence of genital HR HPV in the parents ranged from 13 to 25%, and that of oral HPV ranged from 8 to 34%. In the infants, HPV DNA was detected in 15% of the genital and 10% of the oral samples at birth, reaching peaks of 18 and 21%, respectively, at 6 months, and declining to 10% at 24 months. Persistent HPV in the mother was a risk factor for oral HPV in the infant (odds ratio [OR], 5.69; 95% confidence interval [95% CI], 1.5 to 21.3), while oral HPV in the mother at 6 months was a risk factor for genital HR HPV (OR, 6.38; 95% CI, 1.15 to 35.32). No such independent risk could be attributed to subclinical HPV in the father. Persistent maternal cervical HPV and subclinical oral HPV affect the risk of infant HPV. The age of 6 months is a critical point for the infant to acquire or be free of HR HPV DNA.
Purification of
Enterocytozoon bieneusi
from Stools and Production of Specific Antibodies
Authors: Sheoran Abhineet S. , Feng Xiaochuan , Kitaka Sabrina , Green Linda , Pearson Christine , Didier Elizabeth S. , Chapman Susan , Tumwine James K. , Tzipori Saul
Published: January 2005

Enterocytozoon bieneusi
is clinically the most significant of the microsporidia in humans, causing chronic diarrhea wasting and cholangitis in individuals with human immunodeficiency virus infection and AIDS. Little progress on this infection has been made because of the inability to propagate
E. bieneusi
in vitro and in vivo, which limits the source of parasite spores to the stools of infected human patients. Given the size and shape of the
E. bieneusi
spores (1.1 to 1.6 by 0.7 to 1.0 μm) and the lack of specific immune reagents, the identification and purification of large quantities of spores from feces are technically challenging. Consequently, diagnosis relies entirely on PCR, a labor-intensive approach that requires highly skilled personnel. We describe a method for the purification of
E. bieneusi
spores from human stools and the production of rabbit-specific antisera. Spores were purified by a combination of isopycnic Percoll gradient centrifugation and continuous sucrose gradient centrifugation. Specific polyclonal antibodies raised in mice and rabbits reacted by indirect immunofluorescence with
E. bieneusi
but not with
Encephalitozoon
spp.,
Candida albicans
,
Staphylococcus aureus
,
Escherichia coli
, or other forms present in human stools.
Real-Time Nucleic Acid Sequence-Based Amplification Is More Convenient than Real-Time PCR for Quantification of
Plasmodium falciparum
Authors: Schneider Petra , Wolters Liselotte , Schoone Gerard , Schallig Henk , Sillekens Peter , Hermsen Rob , Sauerwein Robert
Published: January 2005

Determination of the number of malaria parasites by routine or even expert microscopy is not always sufficiently sensitive for detailed quantitative studies on the population dynamics of
Plasmodium falciparum
, such as intervention or vaccine trials. To circumvent this problem, two more sensitive assays, real-time quantitative nucleic acid sequence-based amplification (QT-NASBA) and real-time quantitative PCR (QT-PCR) were compared for quantification of
P. falciparum
parasites. QT-NASBA was adapted to molecular beacon real-time detection technology, which enables a reduction of the time of analysis and of contamination risk while retaining the specificity and sensitivity of the original assay. Both QT-NASBA and QT-PCR have a sensitivity of 20 parasites/ml of blood, but QT-PCR requires a complicated DNA extraction procedure and the use of 500 μl of venous blood to achieve this sensitivity, compared to 50 μl of finger prick blood for real-time QT-NASBA. Both techniques show a significant correlation to microscopic parasite counts, and the quantification results of the two real-time assays are significantly correlated for in vitro as well as in vivo samples. However, in comparison to real-time QT-PCR, the results of real-time QT-NASBA can be obtained 12 h earlier, with relatively easy RNA extraction and use of finger prick blood samples. The prospective development of multiplex QT-NASBA for detection of various
P. falciparum
developmental stages increases the value of QT-NASBA for malaria studies. Therefore, for studies requiring sensitive and accurate detection of
P. falciparum
parasites in large numbers of samples, the use of real-time QT-NASBA is preferred over that of real-time QT-PCR.
Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis
Authors: Palmer Sarah , Kearney Mary , Maldarelli Frank , Halvas Elias K. , Bixby Christian J. , Bazmi Holly , Rock Diane , Falloon Judith , Davey Richard T. , Dewar Robin L. , Metcalf Julia A. , Hammer Scott , Mellors John W. , Coffin John M.
Published: January 2005

To investigate the extent to which drug resistance mutations are missed by standard genotyping methods, we analyzed the same plasma samples from 26 patients with suspected multidrug-resistant human immunodeficiency virus type 1 by using a newly developed single-genome sequencing technique and compared it to standard genotype analysis. Plasma samples were obtained from patients with prior exposure to at least two antiretroviral drug classes and who were on a failing antiretroviral regimen. Standard genotypes were obtained by reverse transcriptase (RT)-PCR and sequencing of the bulk PCR product. For single-genome sequencing, cDNA derived from plasma RNA was serially diluted to 1 copy per reaction, and a region encompassing p6, protease, and a portion of RT was amplified and sequenced. Sequences from 15 to 46 single viral genomes were obtained from each plasma sample. Drug resistance mutations identified by single-genome sequencing were not detected by standard genotype analysis in 24 of the 26 patients studied. Mutations present in less than 10% of single genomes were almost never detected in standard genotypes (1 of 86). Similarly, mutations present in 10 to 35% of single genomes were detected only 25% of the time in standard genotypes. For example, in one patient, 10 mutations identified by single-genome sequencing and conferring resistance to protease inhibitors (PIs), nucleoside analog reverse transcriptase inhibitors, and nonnucleoside reverse transcriptase inhibitors (NNRTIs) were not detected by standard genotyping methods. Each of these mutations was present in 5 to 20% of the 20 genomes analyzed; 15% of the genomes in this sample contained linked PI mutations, none of which were present in the standard genotype. In another patient sample, 33% of genomes contained five linked NNRTI resistance mutations, none of which were detected by standard genotype analysis. These findings illustrate the inadequacy of the standard genotype for detecting low-frequency drug resistance mutations. In addition to having greater sensitivity, single-genome sequencing identifies linked mutations that confer high-level drug resistance. Such linkage cannot be detected by standard genotype analysis.
Novel Assay Using Total Hepatitis C Virus (HCV) Core Antigen quantification for Diagnosis of HCV Infection in Dialysis Patients
Authors: Fabrizi Fabrizio , Lunghi Giovanna , Aucella Filippo , Mangano Stefano , Barbisoni Francesco , Bisegna Sergio , Vigilante Domenico , Limido Aurelio , Martin Paul
Published: January 2005

Dialysis patients remain a high-risk group for hepatitis C virus (HCV) infection. The current diagnosis of HCV infection among dialysis patients includes serological assays and nucleic acid amplification technology (NAT) for assessing serum anti-HCV antibody and HCV viremia, respectively. However, current NAT techniques are expensive and labor-intensive and often lack standardization. An assay prototype designed to detect and quantify total HCV core antigen (total HCV core Ag) protein in serum and plasma in the presence or absence of anti-HCV antibodies has been recently developed. A comparison between a total anti-HCV core Ag enzyme-linked immunosorbent assay (ELISA) and a quantitative HCV RNA assay based on reverse transcription-PCR (RT-PCR) (Amplicor HCV Monitor test) was performed using a large (n= 305) cohort of ELISA HCV 3.0 HCV-negative and -positive patients on maintenance dialysis. The concentrations of HCV core Ag and HCV RNA levels (measured by RT-PCR) were significantly correlated (r= 0.471,P= 0.0001) over a wide range of HCV RNA levels and were maintained among different HCV genotypes (HCV genotype 1,r= 0.862,P= 0.0001; HCV genotype 2,r= 0.691,P= 0.0001). We estimated that 1 pg of total HCV core Ag per ml is equivalent to approximately 19.952 IU of HCV RNA per ml, even if the wide range in the ratio of core Ag to HCV RNA (95% confidence intervals, 2.8 × 103to 1.6 × 105IU/ml) precluded definitive conclusions. In summary, total HCV core Ag proved to be useful for performing HCV RNA measurement among dialysis patients in routine laboratories without the need for special equipment or training. The present study supports the use of the total anti-HCV core Ag ELISA for assessing viral load among dialysis patients with HCV infection.
Distribution of Major Genotypes among Methicillin-Resistant
Staphylococcus aureus
Clones in Asian Countries
Authors: Ko Kwan Soo , Lee Ji-Young , Suh Ji Yoeun , Oh Won Sup , Peck Kyong Ran , Lee Nam Yong , Song Jae-Hoon
Published: January 2005

To investigate the evolutionary pattern and genotypic characteristics of methicillin-resistant
Staphylococcus aureus
(MRSA) strains in the Asian region, 74 MRSA strains isolated from 12 Asian countries were analyzed by multilocus sequence typing (MLST) and SCC
mec
typing. Overall, a total of 16 genotypes based on sequence type and SCC
mec
types were identified among MRSA strains from Asian countries. Data revealed two major genotypes of MRSA strains in Asia, with unique geographic distributions. By MLST analysis, all strains from Korea and Japan except one belonged to clonal complex 5 (CC5) while most MRSA isolates from other Asian countries belonged to CC239. SCC
mec
typing showed that most isolates from Korea and Japan were SS
mec
type II whereas SCC
mec
type III (or IIIA) was the most common type in strains from other Asian countries. Our data documented a unique geographic distribution and evolutionary pattern of MRSA clones in Asia.
Controlled Clinical Comparison of Plastic versus Glass Bottles of BacT/ALERT PF Medium for Culturing Blood from Children
Authors: Petti Cathy A. , Mirrett Stanley , Woods Christopher W. , Reller L. Barth
Published: January 2005

The plastic pediatric BacT/ALERT (bioMérieux, Durham, N.C.) PF (PPF) is a new nonvented aerobic culture medium in a clear plastic bottle designed to prevent breakage. We compared the performance of the new PPF bottle to that of the present glass BacT/ALERT PF bottle for the recovery of microorganisms as well as for the time to detection of growth in samples of blood obtained for culture from children. We found that the PPF and PF bottles were comparable for recovery of microorganisms and that the safety advantage of plastic bottles can be achieved without compromising performance.
Clonal Diversity of Metallo-β-Lactamase-Possessing
Pseudomonas aeruginosa
in Geographically Diverse Regions of Japan
Authors: Kimura Soichiro , Alba Jimena , Shiroto Katsuaki , Sano Reiko , Niki Yoshihito , Maesaki Shigefumi , Akizawa Koji , Kaku Mitsuo , Watanuki Yuji , Ishii Yoshikazu , Yamaguchi Keizo
Published: January 2005

The aim of this study was to determine the distribution of metallo-β-lactamase-producing
Pseudomonas aeruginosa
in Japan and to investigate the molecular characteristics of resistance gene cassettes including the gene encoding this enzyme. A total of 594 nonduplicate strains of
P. aeruginosa
isolated from 60 hospitals throughout Japan in 2002 were evaluated. This study indicated that although the prevalence of imipenem-resistant
P. aeruginosa
has not increased compared to that found in previous studies, clonal distribution of the same strain across Japan is evident.
Emerging Incidence of
Enterococcus faecium
among Hospital Isolates (1993 to 2002)
Authors: Treitman Adam N. , Yarnold Paul R. , Warren John , Noskin Gary A.
Published: January 2005

Historically, most clinical microbiology laboratories report that 80 to 90% of enterococci are
Enterococcus faecalis
, whereas
E. faecium
accounts for 5 to 10% of isolates. At our medical center from 1993 to 2002, we evaluated the percentages of
E. faecium
among all enterococcal isolates and the percentages of
E. faecium
isolates that were vancomycin resistant. Over this 10-year period, the percentage of enterococci that were identified as
E. faecium
increased from 12.7 to 22.2% (
P
< 0.001) and the proportion of
E. faecium
that was vancomycin resistant increased from 28.9 to 72.4% (
P
< 0.001). Both the percentage of
E. faecium
among the enterococci and the proportion of vancomycin-resistant
E. faecium
increased significantly over this 10-year period.
Cryptococcus neoformans
Isolates from Transplant Recipients Are Not Selected for Resistance to Calcineurin Inhibitors by Current Immunosuppressive Regimens
Authors: Blankenship Jill R. , Singh Nina , Alexander Barbara D. , Heitman Joseph
Published: January 2005

The immunosuppressants tacrolimus (FK506) and cyclosporine A inhibit calcineurin and have potent antifungal activity. In this study, 24% of
Cryptococcus neoformans
isolates from solid-organ transplant patients exhibited altered sensitivity to these drugs, which may have an impact on the infectious course but does not appear to be the consequence of immunosuppressive therapy.
Preliminary Evaluation of the API 20NE and RapID NF Plus Systems for Rapid Identification of
Burkholderia pseudomallei
and
B. mallei
Authors: Glass Mindy B. , Popovic Tanja
Published: January 2005

We evaluated the API 20NE and the RapID NF Plus systems with 58
Burkholderia pseudomallei
and 23
B. mallei
strains for identification of these agents, but neither was reliable for confirmatory identification, with only 0 to 60% strains identified accurately. A greater diversity of strains in the system databases would be beneficial.
Analysis of Replication Kinetics of the Human Metapneumovirus in Different Cell Lines by Real-Time PCR
Authors: Deffrasnes Céline , Côté Stéphanie , Boivin Guy
Published: January 2005

Human metapneumovirus (hMPV) is associated with acute respiratory tract disease especially in young children. Using a quantitative real-time TaqMan PCR, we analyzed the replication kinetics of hMPV in different cell lines. Our results indicate that hMPV replicates slightly more efficiently in LLC-MK2 than in Vero cells and poorly in HEp-2 cells.
Discrepancies and Interpretation Problems in Susceptibility Testing of VIM-1-Producing
Klebsiella pneumoniae
Isolates
Authors: Giakkoupi P. , Tzouvelekis L. S. , Daikos G. L. , Miriagou V. , Petrikkos G. , Legakis N. J. , Vatopoulos A. C.
Published: January 2005

Susceptibilities to β-lactam antibiotics of five VIM-1-producing
Klebsiella pneumoniae
isolates were determined by broth microdilution, Etest, disk diffusion, and the automated systems Vitek 2, Phoenix, and MicroScan. Significant discrepancies were observed in the determination of susceptibility to imipenem and meropenem. Interpretation problems by the automated systems were also noted.
Low Proportion of Recent Human Immunodeficiency Virus (HIV) Infections among Newly Diagnosed Cases of HIV Infection as Shown by the Presence of HIV-Specific Antibodies of Low Avidity
Authors: Puchhammer-Stöckl Elisabeth , Schmied Brigitte , Rieger Armin , Sarcletti Mario , Geit Maria , Zangerle Robert , Hofmann Hanns
Published: January 2005

The time between human immunodeficiency virus (HIV) infection and diagnosis is mostly unknown. Two hundred five newly diagnosed patients were investigated for the duration of their HIV infection by avidity testing. Recent HIV infection was identified in 27.3% of the cases. Early diagnosis was achieved significantly less frequently in heterosexually infected persons than in other patients.
Variation of the Polymorphic Region X of the Protein A Gene during Persistent Airway Infection of Cystic Fibrosis Patients Reflects Two Independent Mechanisms of Genetic Change in
Staphylococcus aureus
Authors: Kahl Barbara C. , Mellmann Alexander , Deiwick Susanne , Peters Georg , Harmsen Dag
Published: January 2005

Variation of the polymorphic region of the protein A gene (
spa
) was observed during long-term persistence of
Staphylococcus aureus
in the airways of 10 cystic fibrosis patients and occurred at a rate of one genetic change every 70 months. Independent mutational events were observed eight times in 142 isolates: four deletions, two duplications of repeats, and two point mutations.
Evaluation of an Ultrasensitive p24 Antigen Assay as a Potential Alternative to Human Immunodeficiency Virus Type 1 RNA Viral Load Assay in Resource-Limited Settings
Authors: Respess Richard A. , Cachafeiro Ada , Withum David , Fiscus Susan A. , Newman Daniel , Branson Bernard , Varnier Oliviero E. , Lewis Kim , Dondero Timothy J.
Published: January 2005

An inexpensive enzyme-linked immunosorbent assay method for human immunodeficiency virus type 1 quantitation, ultrasensitive p24 antigen assay (Up24), was compared with RNA viral load assay (VL). Up24 had 100% sensitivity of detection at a viral load of ≥30,000, with sensitivity of 46.4% at a viral load of <30,000 (232 specimens from 65 seropositive subjects). The assay was highly reproducible, with excellent correlation between duplicates and among three laboratories.
Comparison of the Mycoplasma Duo Test with PCR for Detection of
Ureaplasma
Species in Endotracheal Aspirates from Premature Infants
Authors: Cheah Fook-Choe , Anderson Trevor P. , Darlow Brian A. , Murdoch David R.
Published: January 2005

We compared the Mycoplasma Duo kit (Sanofi Diagnostics Pasteur) with PCR for detection of
Ureaplasma
spp. in endotracheal aspirates from 60 premature neonates. The overall agreement between the two tests was 96%. The Mycoplasma Duo assay is a useful alternative to culture and PCR for detection of neonatal
Ureaplasma
infection.
Infant Botulism Acquired from Household Dust Presenting as Sudden Infant Death Syndrome
Authors: Nevas Mari , Lindström Miia , Virtanen Antti , Hielm Sebastian , Kuusi Markku , Arnon Stephen S. , Vuori Erkki , Korkeala Hannu
Published: January 2005

Clostridium botulinum
type B was detected by multiplex PCR in the intestinal contents of a suddenly deceased 11-week-old infant and in vacuum cleaner dust from the patient's household.
C. botulinum
was also isolated from the deceased infant's intestinal contents and from the household dust. The genetic similarity of the two isolates was demonstrated by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA analysis, thereby confirming that dust may act as a vehicle for infant botulism that results in sudden death.
Acute Hemorrhagic Pericarditis in a Child with Pneumonia Due to
Chlamydophila pneumoniae
Authors: Tenenbaum T. , Heusch A. , Henrich B. , MacKenzie C. R. , Schmidt K. G. , Schroten H.
Published: January 2005

Chlamydophila pneumoniae
is mainly responsible for respiratory tract infections but has also been associated with endocarditis and myocarditis. We report a case of pneumonia in a child with hemorrhagic pericardial effusion with a positive result by a new
C. pneumoniae
TaqMan PCR, suggesting a pericardial inflammation directly induced by
C. pneumoniae
.
C. pneumoniae
should be suspected in patients with community-acquired pneumonia and concurrent pericarditis. Empirical treatment with azithromycin seems feasible.
Multiplex PCR-Identified Cutaneous Tuberculosis Evoked by
Mycobacterium bovis
BCG Vaccination in a Healthy Baby
Authors: Okazaki Tatsuma , Ebihara Satoru , Takahashi Hidenori , Asada Masanori , Sato Akimasa , Seki Masaaki , Ohto Hideyasu , Sasaki Hidetada
Published: January 2005

This is the first identified case of
Mycobacterium bovis
bacillus Calmette-Guérin (BCG)-derived cutaneous tuberculosis that localizes at a place different from the vaccination site in hosts without immune deficiency. A healthy baby with a developing abscess is described. A multiplex PCR identified the abscess as originating from
M. bovis
BCG Tokyo 172.
Performance of the New VITEK 2 GP Card for Identification of Medically Relevant Gram-Positive Cocci in a Routine Clinical Laboratory
Authors: Funke Guido , Funke-Kissling Pascale
Published: January 2005

The VITEK 2 gram-positive (GP) identification card (bioMérieux, Marcy l'Etoile, France) has been redesigned to achieve greater accuracy in the identification of gram-positive cocci. A total of 43 biochemical tests, including 17 enzymatic tests, are present in the card and interpreted in a kinetic mode, for up to 8 h. The VITEK 2 database, used in conjunction with the GP identification card, allows the identification of 115 different taxa. A total of 364 strains of GP cocci (217Streptococcaceaestrains and 147Micrococcaceaestrains) belonging to 31 taxa were tested with the new VITEK 2 GP identification card. Of the 364 strains, 105 were taken from routine primary plating media. A total of 344 strains (94.5%) were correctly identified to the species level and 17 strains (4.7%) were identified with low discrimination, requiring additional tests, whereas 1 strain (0.3%) was incorrectly identified and 2 strains (0.5%) remained unidentified. Within 7 h of the start of incubation, more than 90% of all strains were identified. Of the 105 primary cultures, 97% were correctly identified to the species level, 2% were identified with low discrimination, and 1% remained unidentified. Identification performance data were independent of each of the three plating media used. It is concluded that the new VITEK 2 GP identification card provides reliable results for the identification of GP cocci under routine laboratory conditions.
Sensitivities and Specificities of Spoligotyping and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing Methods for Studying Molecular Epidemiology of Tuberculosis
Authors: Scott Allison N. , Menzies Dick , Tannenbaum Terry-Nan , Thibert Louise , Kozak Robert , Joseph Lawrence , Schwartzman Kevin , Behr Marcel A.
Published: January 2005

The development of PCR-based genotyping modalities (spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat [MIRU-VNTR] typing) offers promise for real-time molecular epidemiological studies of tuberculosis (TB). However, the utility of these methods depends on their capacity to appropriately classify isolates. To determine the operating parameters of spoligotyping and MIRU-VNTR typing, we have compared results generated by these newer tests to the standard typing method, IS
6110
restriction fragment length polymorphism, in analyses restricted to high-copy-number IS
6110
isolates. Sensitivities of the newer tests were estimated as the percentages of isolates with identical IS
6110
fingerprints that had identical spoligotypes and MIRU-VNTR types. The specificities of these tests were estimated as the percentages of isolates with unique IS
6110
fingerprints that had unique spoligotypes and MIRU-VNTR types. The sensitivity of MIRU-VNTR typing was 52% (95% confidence interval [CI], 31 to 72%), and the sensitivity of spoligotyping was 83% (95% CI, 63 to 95%). The specificity of MIRU-VNTR typing was 56% (95% CI, 51 to 62%), and the specificity of spoligotyping was 40% (95% CI, 35 to 46%). The proportion of isolates estimated to be due to recent transmission was 4% by identical IS
6110
patterns, 19% by near-identical IS
6110
patterns, 33% by MIRU-VNTR typing, and 53% by spoligotyping. The low calculated specificities of spoligotyping and MIRU-VNTR typing led to misclassification of cases, inflated estimates of TB transmission, and low positive predictive values, suggesting that these techniques have unsuitable operating parameters for population-based molecular epidemiology studies.
Treating competent patients by force: the limits and lessons of Israel’s Patient’s Rights Act: Table 1
Authors: Gross M L
Published: January 2005

Competent patients who refuse life saving medical treatment present a dilemma for healthcare professionals. On one hand, respect for autonomy and liberty demand that physicians respect a patient’s decision to refuse treatment. However, it is often apparent that such patients are not fully competent. They may not adequately comprehend the benefits of medical care, be overly anxious about pain, or discount the value of their future state of health. Although most bioethicists are convinced that partial autonomy or marginal competence of this kind demands the same respect as full autonomy, Israeli legislators created a mechanism to allow ethics committees to override patients’ informed refusal and treat them against their will. To do so, three conditions must be satisfied: physicians must make every effort to ensure the patient understands the risks of non-treatment, the treatment physicians propose must offer a realistic chance of significant improvement, and there are reasonable expectations that the patient will consent retroactively. Although not all of these conditions are equally cogent, they offer a way forward to assure care for certain classes of competent patients without abandoning the principle of autonomy altogether. These concerns reach past Israel and should engage healthcare professionals wary that respect for autonomy may sometimes cause avoidable harm.
How physicians face ethical difficulties: a qualitative analysis
Authors: Hurst S A , Hull S C , DuVal G , Danis M
Published: January 2005

Background:Physicians face ethical difficulties daily, yet they seek ethics consultation infrequently. To date, no systematic data have been collected on the strategies they use to resolve such difficulties when they do so without the help of ethics consultation. Thus, our understanding of ethical decision making in day to day medical practice is poor. We report findings from the qualitative analysis of 310 ethically difficult situations described to us by physicians who encountered them in their practice. When facing such situations, the physicians sought to avoid conflict, obtain assistance, and protect the integrity of their conscience and reputation, as well as the integrity of the group of people who participated in the decisions. These goals could conflict with each other, or with ethical goals, in problematic ways. Being aware of these potentially conflicting goals may help physicians to resolve ethical difficulties more effectively. This awareness should also contribute to informing the practice of ethics consultation.

Objective:To identify strategies used by physicians in dealing with ethical difficulties in their practice.

Design, setting, and participants:National survey of internists, oncologists, and intensive care specialists by computer assisted telephone interviews (n =  344, response rate  =  64%). As part of this survey, we asked physicians to tell us about a recent ethical dilemma they had encountered in their medical practice. Transcripts of their open-ended responses were analysed using coding and analytical elements of the grounded theory approach.

Main measurements:Strategies and approaches reported by respondents as part of their account of a recent ethical difficulty they had encountered in their practice.

Results:When faced with ethical difficulties, the physicians avoided conflict and looked for assistance, which contributed to protecting, or attempting to protect, the integrity of their conscience and reputation, as well as the integrity of the group of people who participated in the decisions. These efforts sometimes reinforced ethical goals, such as following patients’ wishes or their best interests, but they sometimes competed with them. The goals of avoiding conflict, obtaining assistance, and protecting the respondent’s integrity and that of the group of decision makers could also compete with each other.

Conclusion:In resolving ethical difficulties in medical practice, internists entertained competing goals that they did not always successfully achieve. Additionally, the means employed were not always the most likely to achieve those aims. Understanding these aspects of ethical decision making in medical practice is important both for physicians themselves as they struggle with ethical difficulties and for the ethics consultants who wish to help them in this process.
Private or intimate relations between doctor and patient: is zero tolerance warranted?
Authors: Spiegel W , Colella T , Lupton P
Published: January 2005

This article reviews and comments on the five categories of arguments used to defend zero tolerance with regard to sexual contacts resulting from the physician-patient relationship as summarised by Cullen. In addition it puts forward a hypothesis—“fear of loss by third party”—as a psychological explanation for the collective insistence on a zero tolerance policy.
HIV prevention research and global inequality: steps towards improved standards of care
Authors: Shapiro K , Benatar S R
Published: January 2005

Intensification of poverty and degradation of health infrastructure over recent decades in countries most affected by HIV/AIDS present formidable challenges to clinical research. This paper addresses theoverallstandard of health care (SOC) that should be provided to research participants in developing countries, rather than the narrow definition of SOC that has characterised the international debate on standards of health care. It argues that contributing to sustainable improvements in health by progressively ratcheting the standard of care upwards for research participants and their communities is an ethical obligation of those in resource-rich countries who sponsor and implement research in poorer ones.
Eliminating the daily life risks standard from the definition of minimal risk
Authors: Resnik D B
Published: January 2005

The phrase “minimal risk,” as defined in the United States’ federal research regulations, is ambiguous and poorly defined. This article argues that most of the ambiguity that one finds in the phrase stems from the “daily life risks” standard in the definition of minimal risk. In this article, the author argues that the daily life risks standard should be dropped and that “minimal risk” should be defined as simply “the probability and magnitude of the harm or discomfort anticipated in research are not greater than those encountered during the performance of routine physical or psychological examinations or tests”.
Rejuvenation of Amal Products Limited
Authors: Kumar Maheshwari Sunil , Kulkarnic Vilas
Published: January 2005

Amal Products Ltd (APL) was a company situated in the southern part of Gujarat manufacturing intermediate dyes and specialty chemicals, mainly for the textile market. The company incurred losses in 1998 due to the recession in the textile industry and fierce competition from Chinese manufacturers as well as local manufacturers who sold their products at much lower rates than APL. In response to the competition APL went for cost reduction and offered voluntary retirement scheme (VRS) to its employees as one of the measures to reduce cost. 51 out of 264 employees opted for VRS. The case explains the process of VRS adopted by the company and how it helped to save costs. It highlights the role of the human resource department in the successful implementation of VRS and the role of line managers. It explains how a VRS should be handled so that the survivors remain productive. It also mentions the role of various stakeholders in the implementation of VRS. The company has reported profits in 2002.
Metabolic effects of insulin on cardiomyocytes from control and diabeticdb/dbmouse hearts
Authors: Carroll Rogayah , Carley Andrew N. , Dyck Jason R. B. , Severson David L.
Published: January 2005

Diabetic db/db mice exhibit profound insulin resistance in vivo, but the specific degree of cardiac insensitivity to insulin has not been assessed. Therefore, the effect of insulin on cardiomyocytes from db/db hearts was assessed by measuring two metabolic responses (deoxyglucose uptake and fatty acid oxidation) and the phosphorylation of two enzymes in the insulin-signaling cascade [Akt and AMP-activated protein kinase (AMPK)]. Maximal insulin-stimulated deoxyglucose transport was reduced to 58 and 40% of control in cardiomyocytes from db/db mice at two ages (6 and 12 wk). Insulin-stimulated deoxyglucose uptake was also reduced in myocytes from transgenic db/db mice overexpressing the insulin-sensitive glucose transporter ( db/db-hGLUT4). Treatment of db/db mice for 1 wk with an insulin-sensitizing peroxisome proliferator-activated receptor-γ agonist (COOH) completely normalized insulin-stimulated deoxyglucose uptake. Insulin had no direct effect on palmitate oxidation by either control or db/db cardiomyocytes, but the combination of insulin and glucose reduced palmitate oxidation, likely an indirect effect secondary to increased glucose uptake. Insulin had no effect on AMPK phosphorylation from either control or db/db cardiomyocytes. Insulin increased the phosphorylation of Akt in all cardiomyocyte preparations (control, db/db, COOH-treated db/db) to the same extent. Thus insulin has selective metabolic actions in mouse cardiomyocytes; deoxyglucose uptake and Akt phosphorylation are increased, but fatty acid oxidation and AMPK phosphorylation are unchanged. Insulin resistance in db/db cardiomyocytes is manifested by reduced insulin-stimulated deoxyglucose uptake.
Pioglitazone improves insulin sensitivity through reduction in muscle lipid and redistribution of lipid into adipose tissue
Authors: Rasouli Neda , Raue Ulrika , Miles Leslie M. , Lu Tong , Di Gregorio Gina B. , Elbein Steven C. , Kern Philip A.
Published: January 2005

Patients with insulin resistance often manifest increased intramyocellular lipid (IMCL) along with increased visceral adipose tissue. This study was designed to determine whether the insulin sensitizer drugs pioglitazone and metformin would improve glucose intolerance and insulin sensitivity by decreasing IMCL. In this study, 23 generally healthy subjects with impaired glucose tolerance were randomized to receive either pioglitazone 45 mg/day or metformin 2,000 mg/day for 10 wk. Before and after treatment, we measured insulin sensitivity and abdominal subcutaneous and visceral adipose tissue with CT scanning. In addition, muscle biopsies were performed for measurement of IMCL and muscle oxidative enzymes. After treatment with pioglitazone, 2-h glucose fell from 9.6 mmol/l (172 mg/dl) to 6.1 mmol/l (119 mg/dl), whereas there was no change in 2-h glucose with metformin. With pioglitazone treatment, there was a 65% increase in insulin sensitivity along with a 34% decrease in IMCL (both P ≤ 0.002). This decrease in IMCL was not due to increased muscle lipid oxidation, as there were no changes in muscle lipid oxidative enzymes. However, pioglitazone resulted in a 2.6-kg weight gain along with a significant decrease in the visceral-to-subcutaneous adipose tissue ratio. In contrast, metformin treatment resulted in no change in insulin sensitivity, IMCL, oxidative enzymes, or adipose tissue volumes. Pioglitazone improved glucose tolerance and insulin sensitivity by reducing IMCL. This reduction in IMCL was not due to an increase in muscle lipid oxidation but to a diversion of lipid from ectopic sites into subcutaneous adipose tissue.
Combinatorial control of the bradykinin B2 receptor promoter by p53, CREB, KLF-4, and CBP: implications for terminal nephron differentiation
Authors: Saifudeen Zubaida , Dipp Susana , Fan Hao , El-Dahr Samir S.
Published: January 2005

Despite a wealth of knowledge regarding the early steps of epithelial differentiation, little is known about the mechanisms responsible for terminal nephron differentiation. The bradykinin B2 receptor (B2R) regulates renal function and integrity, and its expression is induced during terminal nephron differentiation. This study investigates the transcriptional regulation of the B2R during kidney development. The rat B2R 5′-flanking region has a highly conserved cis-acting enhancer in the proximal promoter consisting of contiguous binding sites for the transcription factors cAMP response element binding protein (CREB), p53, and Krüppel-like factor (KLF-4). The B2R enhancer drives reporter gene expression in inner medullary collecting duct-3 cells but is considerably weaker in other cell types. Site-directed mutagenesis and expression of dominant negative mutants demonstrated the requirement of CREB DNA binding and Ser-133 phosphorylation for optimal enhancer function. Moreover, helical phasing experiments showed that disruption of the spatial organization of the enhancer inhibits B2R promoter activity. Several lines of evidence indicate that cooperative interactions among the three transcription factors occur in vivo during terminal nephron differentiation: 1) CREB, p53, and KLF-4 are coexpressed in B2R-positive differentiating cells; 2) the maturational expression of B2R correlates with CREB/p53/KLF-4 DNA-binding activity; 3) assembly of CREB, p53, and KLF-4 on chromatin at the endogenous B2R promoter is developmentally regulated and is accompanied by CBP recruitment and histone hyperacetylation; and 4) CREB and p53 occupancy of the B2R enhancer is cooperative. These results demonstrate that combinatorial interactions among the transcription factors, CREB, p53, and KLF-4, and the coactivator CBP, may be critical for the regulation of B2R gene expression during terminal nephron differentiation.
Neural Responses in the Macaque V1 to Bar Stimuli With Various Lengths Presented on the Blind Spot
Authors: Matsumoto Masayuki , Komatsu Hidehiko
Published: January 2005

Although there is no retinal input within the blind spot, it is filled with the same visual attributes as its surround. Earlier studies showed that neural responses are evoked at the retinotopic representation of the blind spot in the primary visual cortex (V1) when perceptual filling-in of a surface or completion of a bar occurs. To determine whether these neural responses correlate with perception, we recorded from V1 neurons whose receptive fields overlapped the blind spot. Bar stimuli of various lengths were presented at the blind spots of monkeys while they performed a fixation task. One end of the bar was fixed at a position outside the blind spot, and the position of the other end was varied. Perceived bar length was measured using a similar set of bar stimuli in human subjects. As long as one end of the bar was inside the blind spot, the perceived bar length remained constant, and when the bar exceeded the blind spot, perceptual completion occurred, and the perceived bar length increased substantially. Some V1 neurons of the monkey exhibited a significant increase in their activity when the bar exceeded the blind spot, even though the amount of the retinal stimulation increased only slightly. These response increases coincided with perceptual completion observed in human subjects and were much larger than would be expected from simple spatial summation and could not be explained by contextual modulation. We conclude that the completed bar appearing on the part of the receptive field embedded within the blind spot gave rise to the observed increase in neuronal activity.
Characterization of Upper-Troposphere Water Vapor Measurements during AFWEX Using LASE
Authors: Ferrare R. A. , Browell E. V. , Ismail S. , Kooi S. A. , Brasseur L. H. , Brackett V. G. , Clayton M. B. , Barrick J. D. W. , Diskin G. S. , Goldsmith J. E. M. , Lesht B. M. , Podolske J. R. , Sachse G. W. , Schmidlin F. J. , Turner D. D. , Whiteman D. N. , Tobin D. , Miloshevich L. M. , Revercomb H. E. , Demoz B. B. , Di Girolamo P.
Published: January 2005

Water vapor mass mixing ratio profiles from NASA's Lidar Atmospheric Sensing Experiment (LASE) system acquired during the Atmospheric Radiation Measurement (ARM)–First International Satellite Cloud Climatology Project (ISCCP) Regional Experiment (FIRE) Water Vapor Experiment (AFWEX) are used as a reference to characterize upper-troposphere water vapor (UTWV) measured by ground-based Raman lidars, radiosondes, and in situ aircraft sensors over the Department of Energy (DOE) ARM Southern Great Plains (SGP) site in northern Oklahoma. LASE was deployed from the NASA DC-8 aircraft and measured water vapor over the ARM SGP Central Facility (CF) site during seven flights between 27 November and 10 December 2000. Initially, the DOE ARM SGP Cloud and Radiation Testbed (CART) Raman lidar (CARL) UTWV profiles were about 5%–7% wetter than LASE in the upper troposphere, and the Vaisala RS80-H radiosonde profiles were about 10% drier than LASE between 8 and 12 km. Scaling the Vaisala water vapor profiles to match the precipitable water vapor (PWV) measured by the ARM SGP microwave radiometer (MWR) did not change these results significantly. By accounting for an overlap correction of the CARL water vapor profiles and by employing schemes designed to correct the Vaisala RS80-H calibration method and account for the time response of the Vaisala RS80-H water vapor sensor, the average differences between the CARL and Vaisala radiosonde upper-troposphere water vapor profiles are reduced to about 5%, which is within the ARM goal of mean differences of less than 10%. The LASE and DC-8 in situ diode laser hygrometer (DLH) UTWV measurements generally agreed to within about 3%–4%. The DC-8 in situ frost point cryogenic hygrometer and Snow White chilled-mirror measurements were drier than the LASE, Raman lidars, and corrected Vaisala RS80H measurements by about 10%–25% and 10%–15%, respectively. Sippican (formerly VIZ Manufacturing) carbon hygristor radiosondes exhibited large variabilities and poor agreement with the other measurements. PWV derived from the LASE profiles agreed to within about 3% on average with PWV derived from the ARM SGP microwave radiometer. The agreement between the LASE and MWR PWV and the LASE and CARL UTWV measurements supports the hypotheses that MWR measurements of the 22-GHz water vapor line can accurately constrain the total water vapor amount and that the CART Raman lidar, when calibrated using the MWR PWV, can provide an accurate, stable reference for characterizing upper-troposphere water vapor.
The Dispersion Relation of Short Wind Waves from Space–Time Wave Measurements*
Authors: Wang David W. , Hwang Paul A.
Published: January 2005

To study the dispersion relation of short wind waves, a linear wave gauge array (WGA) is configured and mounted on a wave-following buoy to conduct in situ space–time measurements of short gravity waves. Results from two field deployments of the WGA buoy in growing seas are presented. The two-dimensional (2D) wavenumber–frequency spectra derived from the space–time measurements provide a direct examination on the relation of wave frequency and wavenumber of short waves in the along-wind direction. Both wavenumber-based and frequency-based phase velocities are extracted from the 2D spectra. The effect of higher harmonics resulting from the Fourier decomposition of nonlinear wave profiles is more prominent to the frequency-based phase velocity than the wavenumber-based phase velocity. The wavenumber-based phase velocity is consistent with that according to the linear dispersion relation, while the frequency-based phase velocity becomes larger due to the higher harmonics.