bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of PCR-Restriction Fragment Length Polymorphism Analysis To Identify the Main New WorldLeishmaniaSpecies and Analyze Their Taxonomic Properties and Polymorphism by Application of the Assay to Clinical Samples
Authors: Rotureau Brice , Ravel Christophe , Couppié Pierre , Pratlong Francine , Nacher Mathieu , Dedet Jean-Pierre , Carme Bernard
Published: February 2006

At least 13 characterizedLeishmaniaspecies are known to infect humans in South America. Five of these parasites are transmitted in the sylvatic ecotopes of the whole French Guianan territory and responsible for cutaneous leishmaniasis. For the diagnosis of cutaneous leishmaniasis, restriction fragment length polymorphism (RFLP) analyses have shown promising results. Thus, the end of the small subunit and internal transcribed spacer 1 of the rRNA genes were sequenced and targeted by PCR-RFLP analysis in the 10 main New World (NW)Leishmaniaspecies from the two subgenera. Then, the procedure was tested on 40 samples from patients with cutaneous leishmaniasis, and its results were compared with those of conventional methods. (i) The results of this simple genus-specific method were in agreement with those of previous isoenzyme analyses. (ii) This method distinguished the most medically relevantLeishmaniaspecies with only one enzyme (RsaI). (iii) This method could be performed directly on human biopsy specimens (sensitivity of 85.7%). Performing NWLeishmaniaspecies typing rapidly and easily in the field constitutes a very valuable improvement for detection ofLeishmaniaspp. Revealing great diversity with several enzymes, this method could also be useful for taxonomic, ecological, and epidemiological studies in space and time.
Molecular Epidemiology of
Leishmania
(
Viannia
)
guyanensis
in French Guiana
Authors: Rotureau Brice , Ravel Christophe , Nacher Mathieu , Couppié Pierre , Curtet Isabelle , Dedet Jean-Pierre , Carme Bernard
Published: February 2006

Little information is available about the genetic variability of
Leishmania
populations and the possible correlations with ecoepidemiological features of leishmaniases. The present study was carried out in French Guiana, a country where cutaneous leishmaniases (CL) are endemic over the whole territory. The genetic polymorphism of a nuclear sequence encompassing the end of the ribosomal small subunit and the internal transcribed spacer 1 of 265 isolates from patients with CL was examined by restriction fragment length polymorphism analysis. Genotypes based on the fingerprinting phenetic integration were compared to epidemiological, clinical, and geographical data. In agreement with previous reports, five different
Leishmania
species were identified, but
Leishmania
(
Viannia
)
guyanensis
represented 95.8% of the samples. Two distinct
L
. (
V
.)
guyanensis
populations were found to originate in two ecologically characterized regions. Higher lesional parasite densities and the need for additional treatments were significantly linked to genotype group I. Parasites of genotype group II were more likely to cause chronic and disseminated cutaneous forms in patients.
L
. (
V
.)
guyanensis
was previously said not to be very polymorphic; however, the present analysis resulted in a significant degree of discrimination among
L
. (
V
.)
guyanensis
isolates from diverse ecological areas and with different clinical implications.
Sequence Variation of the SeM Gene ofStreptococcus equiAllows Discrimination of the Source of Strangles Outbreaks
Authors: Kelly Charlotte , Bugg Maxine , Robinson Carl , Mitchell Zoe , Davis-Poynter Nick , Newton J. Richard , Jolley Keith A. , Maiden Martin C. J. , Waller Andrew S.
Published: February 2006

Improved understanding of the epidemiology ofStreptococcus equitransmission requires sensitive and portable subtyping methods that can rationally discriminate between strains.S. equiis highly homogeneous and cannot be distinguished by multilocus enzyme electrophoretic or multilocus sequence-typing methods that utilize housekeeping genes. However, on sequence analysis of the N-terminal region of the SeM genes of 60S. equiisolates from 27 strangles outbreaks, we identified 21 DNA codon changes. These resulted in the nonsynonymous substitution of 18 amino acids and allowed the assignment ofS. equistrains to 15 distinct subtypes. Our data suggest the presence of multiple epitopes across this region that are subjected to selective immune pressure (nonsynonymous-synonymous substitution rate [dN/dS] ratio = 3.054), particularly during the establishment of long-termS. equiinfection. We further report the application of SeM gene subtyping as a method to investigate potential cases of disease related to administration of a live attenuatedS. equivaccine. SeM gene subtyping successfully differentiated between the vaccine strain and field strains ofS. equiresponsible for concurrent disease. These results were confirmed by the development and application of a PCR diagnostic test, which identifies thearoApartial gene deletion present in the Equilis StrepE vaccine strain. Although the vaccine strain was found to be responsible for injection site lesions, all seven outbreaks of strangles investigated in recently vaccinated horses were found to be due to concurrent infection with wild-typeS. equiand not due to reversion of the vaccine strain.
Comparison of Physician- and Self-Collected Genital Specimens for Detection of Human Papillomavirus in Men
Authors: Hernandez Brenda Y. , McDuffie K. , Goodman M. T. , Wilkens L. R. , Thompson P. , Zhu X. , Wong W. , Ning L.
Published: February 2006

There is currently no consensus regarding the most appropriate methods of sampling for the detection of genital human papillomavirus (HPV) in men. We employed a recently developed collection method involving abrasion and moistened swabbing of the genital skin surface for the detection of HPV in a cohort of 136 university-affiliated males in Hawaii. Genital specimens collected by physicians using this method were compared with self-collected specimens from the same individuals obtained 24 h later. Self-collected specimens yielded a greater proportion of sufficient specimens than physician-collected specimens. HPV detection was comparable in physician- and self-collected specimens; detection was highest in the penile shaft (51.2% and 51.5%, respectively,
P
= 0.96), followed by the scrotum (41.2% and 46.2%,
P
= 0.43), the glans/coronal sulcus (31.9% and 33.1%,
P
= 0.84), and the foreskin (33.3% and 28.6%,
P
= 0.74). Site-specific agreement in HPV detection between paired physician- and self-collected samples ranged from 67.2% (kappa = 0.34) for the penile shaft to 95.0% (kappa = 0.89) for the foreskin. There was a high degree of concordance in HPV genotypes in HPV-positive pairs. The most common type was HPV type 84, which comprised approximately 15% of the specimens. The emery paper-swab method offers an efficient sampling method for genital HPV DNA detection in men that could be used both within and outside of the clinical setting.
Extensive Hospital-Wide Spread of a Multidrug-Resistant
Enterobacter cloacae
Clone, with Late Detection Due to a Variable Antibiogram and Frequent Patient Transfer
Authors: Leverstein-van Hall Maurine A. , Blok Hetty E. M. , Paauw Armand , Fluit Ad C. , Troelstra Annet , Mascini Ellen M. , Bonten Marc J. M. , Verhoef Jan
Published: February 2006

A hospital-wide increase in the number of patients with aminoglycoside-resistant
Enterobacter cloacae
(AREC) isolated from clinical cultures was detected in December 2002 using a classical surveillance system (CSS). CSS refers to a strategy based on the recognition of an increased incidence of a species with a particular antibiogram at certain wards in a limited period. Since clonal spread was suspected, hospital records were reviewed for
E. cloacae
culture-positive patients. Based upon genotyping of 139 clinical
E. cloacae
isolates from 80 patients, it was concluded that 53 patients had had clinical cultures with a single AREC clone since April 2001. Determinants for unnoticed spread were investigated retrospectively, as was the possibility that a computer-assisted surveillance method would have detected this outbreak at an earlier stage. Determinants associated with late detection of clonal spread were the following: (i) the absence of a hospital-wide increase in incidence of
E. cloacae
cases for 1.5 years, (ii) the long time interval between cases, (iii) the hospital-wide occurrence of new cases, due to a high number of patient transfers between wards, (iv) the large variety of clinical sites, and (v) the high variability of antibiograms (
n
= 33). Retrospective application of a recently described computer-assisted surveillance method as well as an “in-house”-developed algorithm resulted in earlier detection of the outbreak of 6 and 12 months, respectively. These findings suggest that computerized tools for surveillance may recognize resistance trends that are too complex to be detected by manual review and indicate the need for prospective evaluation of such algorithms.
Nasopharyngeal versus Oropharyngeal Sampling for Isolation of Potential Respiratory Pathogens in Adults
Authors: Lieberman David , Shleyfer Elena , Castel Hana , Terry Andrei , Harman-Boehm Ilana , Delgado Jorge , Peled Nechama , Lieberman Devora
Published: February 2006

The optimal methodology for the identification of colonization by potential respiratory pathogens (PRP) in adults is not well established. The objectives of the present study were to compare the sensitivities of sampling the nasopharynx and the oropharynx for identification of PRP colonization and to compare the sensitivities of samples from the nasopharynx by swab and by washing for the same purpose. The study included 500 participants with a mean age of 65.1 ± 17.8 years. Of these, 300 patients were hospitalized for acute febrile lower respiratory tract infection and 200 were controls. Each participant was sampled by oropharyngeal swab (OPS), nasopharyngeal swab (NPS), and nasopharyngeal washing (NPW). The samples were tested by conventional bacteriological methods to identify
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
. OPS detected colonization by
S. pneumoniae
in 30% of the subjects compared with 89% by NPS and NPW (
P
< 0.000001). The corresponding rates for
H. influenzae
were 49% and 64%, respectively (no significant difference [NS]), and for
M. catarrhalis
were 72% and 46%, respectively (
P
< 0.0004). NPS identified 61% of the cases of colonization with
S. pneumoniae
, compared with 76% by NPW (NS). The corresponding rates for
H. influenzae
were 31% and 56%, respectively (
P
< 0.04), and for
M. catarrhalis
were 39% and 33%, respectively (NS). We conclude that the sensitivities of nasopharyngeal and oropharyngeal sampling for identification of PRP colonization in adults are different for each of the three bacteria in this category. The combined results of sampling from both sites are necessary to obtain a true picture of the rate of colonization. NPW is superior to NPS.
Triazole Cross-Resistance among
Candida
spp.: Case Report, Occurrence among Bloodstream Isolates, and Implications for Antifungal Therapy
Authors: Magill Shelley S. , Shields Christine , Sears Cynthia L. , Choti Michael , Merz William G.
Published: February 2006

Candida
spp. are common causes of bloodstream infections among hospitalized patients. Fluconazole (FLC) remains a first-line therapy for candidemia; and voriconazole (VRC), an expanded-spectrum triazole, was recently approved for the treatment of candidemia in nonneutropenic patients. In vitro studies have suggested that VRC has potent activity against
Candida
spp. with reduced susceptibilities to FLC. We present a case report of invasive candidiasis and candidemia due to a
Candida glabrata
isolate that developed resistance to all currently available triazole antifungals after a course of FLC treatment. This case prompted us to determine the frequency of cross-resistance among bloodstream
Candida
isolates collected during a recent 12-month period at a large, academic medical center. FLC MICs were determined for 125 of 153 isolates (81.7%). Thirty of 125 isolates (24%) were resistant or showed reduced susceptibilites to FLC (MICs ≥ 16 μg/ml). When 28 of these 30 isolates were tested for their VRC susceptibilities, 9 (32%) had MICs that were ≥2 μg/ml. Five of these nine isolates were
C. glabrata
, two isolates were
Candida tropicalis
, one isolate was
Candida albicans
, and one isolate was
Candida parapsilosis
. All five
Candida krusei
isolates tested had VRC MICs ≤0.5 μg/ml. These data have prompted the introduction of reflexive FLC susceptibility testing of first bloodstream
Candida
isolates at our institution. The case report and our data also suggest that VRC should be avoided as initial therapy in unstable patients with invasive candidiasis, particularly in the setting of prior azole exposure. Studies are needed to define the clinical significance of in vitro resistance to the newer antifungal agents.
Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for
hsp65
Gene-Based Identification of
Nocardia
Species
Authors: Rodríguez-Nava Verónica , Couble Andrée , Devulder Gregory , Flandrois Jean-Pierre , Boiron Patrick , Laurent Frédéric
Published: February 2006

Nocardia
identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the
hsp65
gene to differentiate
Nocardia
species, including 36 new species. Our results confirm that
hsp65
PRA must no longer be used for
Nocardia
species identification, as many species have the same restriction pattern. We then compared sequencing-based strategies using an
hsp65
database and a 16S rRNA database and found that the
hsp65
region contained sufficient polymorphisms for comprehensive
Nocardia
species identification.
Recovering Streptococci from the Throat, a Practical Alternative to Direct Plating in Remote Tropical Communities
Authors: McDonald Malcolm , Towers Rebecca , Fagan Peter , McKinnon Melita , Benger Norma , Andrews Ross , Currie Bart J. , Carapetis Jonathan
Published: February 2006

Throat swabs are regarded as the “gold standard” for diagnosing streptococcal pharyngitis and for surveillance research. Culturing throats in remote tropical settings is logistically difficult, and these settings are commonly burdened by high rates of streptococcal disease. The survival of streptococci on swabs may depend on whether they are of “throat” or “skin” type, as determined by
emm
pattern typing. The aims of this study were to compare the recovery rates of beta-hemolytic streptococci (BHS) using three different transport methods and to determine whether the recovery rates correlated with the
emm
pattern type. Monthly duplicate throat swabs were taken from occupants of selected households in three remote Aboriginal communities. Paired swabs were separated and handled in one of three ways: (i) direct inoculation onto culture media with cold-box transport (plated), (ii) sealed in a bag with a silica gel desiccant and cold-box transport (desiccant), and (iii) transport at ambient temperature and humidity (ambient).
emm
pattern typing was done by standard methods. Over 23 months, 4,842 throat swabs were taken, and 4,122 were paired. BHS were recovered on 11.5% of the 4,842 occasions (group A, 4.5%; group C, 1.7%; group G, 5.4%). Results from paired swabs showed the plated method was superior to desiccant and desiccant was better than ambient. Pooled data indicated that plated and desiccant were equivalent, and both were significantly better than ambient. There was no correlation between the
emm
pattern type and recovery of group A streptococci by different methods. In tropical and remote settings, cold-box transport with desiccant and subsequent inoculation of culture plates in the laboratory is a practical alternative to direct plating.
Rapid Susceptibility Testing of Medically Important Zygomycetes by XTT Assay
Authors: Antachopoulos Charalampos , Meletiadis Joseph , Roilides Emmanuel , Sein Tin , Walsh Thomas J.
Published: February 2006

The XTT colorimetric assay quantifies fungal growth by measuring fungal metabolism and has been used successfully for susceptibility testing of
Aspergillus
species after 24 and 48 h of incubation. In the present study using 14 clinical isolates of Zygomycetes (
Rhizopus oryzae
[5 isolates],
Cunninghamella
spp. [3 isolates],
Mucor
spp. [3 isolates], and
Absidia corymbifera
[3 isolates]), significant metabolic activity was demonstrated before visual or spectrophotometric detection of fungal growth by performing the XTT assay as early as 6 h after inoculation. Testing of susceptibility to amphotericin B, posaconazole, and voriconazole was subsequently performed using the XTT method (100 μg/ml XTT, 25 μM menadione) at 6, 8, or 12 h after inoculation and the CLSI (formerly NCCLS) M38-A method with visual and spectrophotometric MIC determinations at 24 h after inoculation. Concentration-effect curves obtained with the use of the
E
max
model (a sigmoid curve with variable slope) were comparable between the early XTT and spectrophotometric readings at 24 h. Complete inhibition of early metabolic activity with the azoles was delayed in comparison to that with amphotericin B. Using appropriate cutoff levels, agreement was demonstrated between the early XTT and 24-h spectrophotometric or visual readings. In particular, for MIC-0 (the lowest drug concentration showing absence of visual growth) of amphotericin B, overall agreement levels were 90 to 93% for the 6-h XTT assay and 100% for the 8- and 12-h time points. For MIC-0 of posaconazole, agreement levels were 86% for the 6-h XTT and 93 to 100% for the 8- and 12-h time points. The overall agreement levels for MIC-0 and MIC-2 (the lowest drug concentration showing prominent reduction of growth compared with the control well) of voriconazole (compared with 24-h spectrophotometric readings) were 93 to 98% for the 8- and 12-h XTT assays. These results support the use of the XTT method for rapid MIC determination for Zygomycetes.
Use of Electrochemical DNA Biosensors for Rapid Molecular Identification of Uropathogens in Clinical Urine Specimens
Authors: Liao Joseph C. , Mastali Mitra , Gau Vincent , Suchard Marc A. , Møller Annette K. , Bruckner David A. , Babbitt Jane T. , Li Yang , Gornbein Jeffrey , Landaw Elliot M. , McCabe Edward R. B. , Churchill Bernard M. , Haake David A.
Published: February 2006

We describe the first species-specific detection of bacterial pathogens in human clinical fluid samples using a microfabricated electrochemical sensor array. Each of the 16 sensors in the array consisted of three single-layer gold electrodes—working, reference, and auxiliary. Each of the working electrodes contained one representative from a library of capture probes, each specific for a clinically relevant bacterial urinary pathogen. The library included probes for
Escherichia coli
,
Proteus mirabilis
,
Pseudomonas aeruginosa
,
Enterocococcus
spp., and the
Klebsiella-Enterobacter
group. A bacterial 16S rRNA target derived from single-step bacterial lysis was hybridized both to the biotin-modified capture probe on the sensor surface and to a second, fluorescein-modified detector probe. Detection of the target-probe hybrids was achieved through binding of a horseradish peroxidase (HRP)-conjugated anti-fluorescein antibody to the detector probe. Amperometric measurement of the catalyzed HRP reaction was obtained at a fixed potential of −200 mV between the working and reference electrodes. Species-specific detection of as few as 2,600 uropathogenic bacteria in culture, inoculated urine, and clinical urine samples was achieved within 45 min from the beginning of sample processing. In a feasibility study of this amperometric detection system using blinded clinical urine specimens, the sensor array had 100% sensitivity for direct detection of gram-negative bacteria without nucleic acid purification or amplification. Identification was demonstrated for 98% of gram-negative bacteria for which species-specific probes were available. When combined with a microfluidics-based sample preparation module, the integrated system could serve as a point-of-care device for rapid diagnosis of urinary tract infections.
Results of the First World Health Organization International Collaborative Study of Detection of Human Papillomavirus DNA
Authors: Quint Wim G. V. , Pagliusi Sonia R. , Lelie Nico , de Villiers Ethel-Michele , Wheeler Cosette M. ,   the World Health Organization Human Papillomavirus DNA International Collaborative Study Group
Published: February 2006

Twenty-nine laboratories in 12 countries participated in a study to assess the performance of various human papillomavirus (HPV) detection assays through the use of a recombinant HPV DNA standard reagent panel. The panel was designed by a group of HPV experts, and samples were prepared and distributed by the World Health Organization International Laboratory for Standards and Biologicals in The Netherlands. Each panel consisted of 24 coded samples including a dilution series for HPV types 16 and 18, alone or in combination with five other high-risk (HR) HPV types including HPV types 31, 33, 35, 45, and 52, the low-risk HPV type 6, and a negative control. Qualitative assays were generally consistent across laboratories, and most invalid results reflected a lack of HPV test sensitivity. The combined data sets had a proficiency for HPV 16 of 62.5% (15/24) and for HPV 18 of 73.9% (17/23). HPV 31 was the least accurately detected by participating laboratories. Approximately half of participating laboratories failed to detect high concentrations of HPV 31 and, to a lesser extent, to detect HPV types 35, 52, and 6. The panel sample materials offer a source of renewable and reproducible material that could be used in the future development of international standard reagents for calibration of HPV DNA assays and kits.
Performance of MRSA ID, a New Chromogenic Medium for Detection of Methicillin-Resistant
Staphylococcus aureus
Authors: Diederen Bram M. W. , van Leest Marie-Louise , van Duijn Inge , Willemse Piet , van Keulen Peter H. J. , Kluytmans Jan A. J. W.
Published: February 2006

MRSA ID was evaluated for its ability to identify methicillin-resistant
Staphylococcus aureus
. A well-defined collection of staphylococci was used (
n
= 998). The sensitivity after 24 h was 96.4%, increasing to 98.8% after 48 h. The specificity was 98.2% after 24 h and decreased to 89.7% after 48 h.
Identification of
Cpgp40/15
Type Ib as the Predominant Allele in Isolates of
Cryptosporidium
spp. from a Waterborne Outbreak of Gastroenteritis in South Burgundy, France
Authors: Cohen Seth , Dalle Frédéric , Gallay Anne , Di Palma Marc , Bonnin Alain , Ward Honorine D.
Published: February 2006

Cryptosporidium
sp. isolates from a waterborne outbreak of diarrhea in France were analyzed by PCR-restriction fragment length polymorphism analysis and sequencing of the
Cpgp40/15
locus. Ninety-one percent of the isolates were
Cryptosporidium hominis
type Ib. The results of this study and those of studies of other outbreaks suggest that the type Ib allele is the predominant allele associated with waterborne cryptosporidiosis.
Emergence of a Clinical Daptomycin-Resistant
Staphylococcus aureus
Isolate during Treatment of Methicillin-Resistant
Staphylococcus aureus
Bacteremia and Osteomyelitis
Authors: Marty Francisco M. , Yeh Wendy W. , Wennersten Christine B. , Venkataraman Lata , Albano Esperanza , Alyea Edwin P. , Gold Howard S. , Baden Lindsey R. , Pillai Satish K.
Published: February 2006

The emergence of a clinically daptomycin-resistant
Staphylococcus aureus
isolate occurred during treatment of methicillin-resistant
S. aureus
bacteremia and probable vertebral osteomyelitis. The breakthrough isolate was indistinguishable from pretreatment daptomycin-susceptible isolates by pulsed-field gel electrophoresis. Daptomycin nonsusceptibility was confirmed by MIC and time-kill curve analyses.
Sequence Variability of Human Erythroviruses Present in Bone Marrow of Brazilian Patients with Various Parvovirus B19-Related Hematological Symptoms
Authors: Sanabani Sabri , Neto Walter Kleine , Pereira Juliana , Sabino Ester Cerdeira
Published: February 2006

The presence of erythrovirus infections was investigated by PCR with bone marrow samples of patients with various parvovirus B19-related hematological symptoms. Erythrovirus DNA was found in 17.3% (12/69) of patients. Phylogenetic analysis revealed that five strains cluster with genotype 1, one clusters with genotype 2, and six cluster with genotype 3. Our study is the first to document the presence of the three erythrovirus genotypes in Brazil.
Use of a New Dual-Antigen Enzyme-Linked Immunosorbent Assay To Detect and Characterize the Human Antibody Response to the Human Immunodeficiency Virus Type 2 Envelope gp125 and gp36 Glycoproteins
Authors: Marcelino José Maria , Barroso Helena , Gonçalves Fátima , Silva Sofia Marques , Novo Carlos , Gomes Perpétua , Camacho Ricardo , Taveira Nuno
Published: February 2006

A dual-antigen enzyme-linked immunosorbent assay specific for human immunodeficiency virus type 2 (HIV-2) envelope proteins, ELISA-HIV2, was developed with two new recombinant polypeptides, rpC2-C3 and rgp36, derived from the HIV-2 envelope. The diagnostic performance was determined with HIV-2, HIV-1, and HIV-1/2 samples. Both polypeptides showed 100% specificity. Clinical sensitivity was 100% for rgp36 and 93.4% for rpC2-C3. ELISA-HIV2 may be used for the specific diagnosis and confirmation of HIV-2 infection.
False-Positive Amplified Mycobacterium Tuberculosis Direct Test Results for Samples Containing
Mycobacterium leprae
Authors: Chedore Pam , Broukhanski George , Shainhouse Zev , Jamieson Frances
Published: February 2006

Nucleic acid amplification tests are widely used in mycobacteriology laboratories to rapidly detect
Mycobacterium tuberculosis
complex directly in clinical specimens. A positive result provides an early diagnosis of tuberculosis, allowing initiation of appropriate therapy and public health measures.
Use of Commercially Available Cryogenic Vials for Long-Term Preservation of Dermatophyte Fungi
Authors: Baker M. , Jeffries P.
Published: February 2006

The use of commercially available cryogenic vials (Microbank vials) stored at −70°C for the storage and preservation of dermatophyte fungi was investigated. None of the 200 strains of dermatophytes examined, representing 21 species, showed a loss of viability after they had been stored for periods ranging from 1 week to 2 years at −70°C. All strains showed typical colonial and microscopic morphologies following revival.
High Interlaboratory Reproducibility of DNA Sequence-Based Typing of Bacteria in a Multicenter Study
Authors: Aires-de-Sousa M. , Boye K. , de Lencastre H. , Deplano A. , Enright M. C. , Etienne J. , Friedrich A. , Harmsen D. , Holmes A. , Huijsdens X. W. , Kearns A. M. , Mellmann A. , Meugnier H. , Rasheed J. K. , Spalburg E. , Strommenger B. , Struelens M. J. , Tenover F. C. , Thomas J. , Vogel U. , Westh H. , Xu J. , Witte W.
Published: February 2006

Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the
Staphylococcus aureus
protein A gene (
spa
, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without extensive harmonization of protocols for 30 blind-coded
S. aureus
DNA samples sent to 10 laboratories. Specialized software for automated sequence analysis ensured a common typing nomenclature.
Use of Molecular Beacon Probes for Real-Time PCR Detection of
Plasmodium falciparum
and Other
Plasmodium
Species in Peripheral Blood Specimens
Authors: Elsayed Sameer , Plewes Katherine , Church Deirdre , Chow Barbara , Zhang Kunyan
Published: February 2006

We describe the development and evaluation of a novel pair of real-time, fluorescence-based PCR assays using molecular beacon probes for rapid, sensitive, and specific detection and quantification of
Plasmodium falciparum
and other
Plasmodium
species organisms.
Use of PCR To Demonstrate Presence of Adenovirus Species B, C, or F as Well as Coinfection with Two Adenovirus Species in Children with Flu-Like Symptoms
Authors: Echavarria Marcela , Maldonado Daniela , Elbert Gabriela , Videla Cristina , Rappaport Ruth , Carballal Guadalupe
Published: February 2006

Adenovirus (AdV) respiratory infections have usually been associated with species B, C, and E. In this study, we detected 9.4% of AdVs by PCR in 500 nasal swabs from 319 children with influenza-like symptoms. AdV typing by PCR with specific probes showed species C, B, and F as well as coinfection with two species. Coinfection with two AdV species and the presence of species F in respiratory samples are novel findings that should be further investigated.
Sonication of Explanted Prosthetic Components in Bags for Diagnosis of Prosthetic Joint Infection Is Associated with Risk of Contamination
Authors: Trampuz Andrej , Piper Kerryl E. , Hanssen Arlen D. , Osmon Douglas R. , Cockerill Franklin R. , Steckelberg James M. , Patel Robin
Published: February 2006

Explanted orthopedic implants from 54 patients with aseptic failure and 24 patients with prosthetic knee or hip infection were sonicated in polyethylene bags. The sensitivities of periprosthetic tissue and sonicate fluid cultures for the diagnosis of prosthetic joint infection were 54% and 75%, whereas the specificities were 98% and 87%, respectively. Sonication in bags improved bacterial recovery from the surface of orthopedic implants; however, it lacked specificity, due to bag leakage.
Multilocus Genotyping of
Cryptosporidium
sp. Isolates from Human Immunodeficiency Virus-Infected Individuals in South India
Authors: Muthusamy Dheepa , Rao Sitara S. , Ramani Sasirekha , Monica Bindhu , Banerjee Indrani , Abraham Ooriapadickal C. , Mathai Dilip C. , Primrose Beryl , Muliyil Jayaprakash , Wanke Christine A. , Ward Honorine D. , Kang Gagandeep
Published: February 2006

This study characterized cryptosporidial infections in 48 human immunodeficiency virus-infected individuals in India by multilocus genotyping.
Cryptosporidium hominis
,
C. parvum
,
C. felis
,
C. muris
, and
C. meleagridis
were identified.
Cpgp40/15
PCR-restriction fragment length polymorphism identified six subgenotypes. Cryptosporidial diarrhea was associated with decreased CD4 counts, below 200 (
P
= 0.009), but not high viral loads.
Absence ofHelicobacter pyloriwithin the Oral Cavities of Members of a Healthy South African Community
Authors: Olivier Brenda J. , Bond Robert P. , van Zyl Walda B. , Delport Maraliese , Slavik Tomas , Ziady Christopher , Terhaar sive Droste Jochim S. , Lastovica Albert , van der Merwe Schalk W.
Published: February 2006

Our study aimed to evaluate the oral cavity as a reservoir from whereHelicobacter pylorimay be transmitted. Histology and PCR amplification were performed. Eighty-four percent of the stomach biopsies tested positive; however,H. pyloriwas not detected in dental samples, indicating the absence ofH. pyloriwithin the oral cavity.
Prospective Comparison of a New Chromogenic Medium, MRSA
Select
, to CHROMagar MRSA and Mannitol-Salt Medium Supplemented with Oxacillin or Cefoxitin for Detection of Methicillin-Resistant
Staphylococcus aureus
Authors: Stoakes Luba , Reyes Romina , Daniel Janis , Lennox Gwen , John Michael A. , Lannigan Robert , Hussain Zafar
Published: February 2006

MRSA
Select
agar was compared to CHROMagar, mannitol-salt agar with oxacillin, and mannitol-salt agar with cefoxitin (MSA-CFOX) for the isolation of methicillin-resistant
Staphylococcus aureus
(MRSA). The sensitivities and specificities were 97.3% and 99.8%, 82.9% and 99.1%, 80.2% and 79%, and 99.1% and 84.8%, respectively. MSA-CFOX and MRSA
Select
had a high sensitivity. MRSA
Select
, however, was more specific and proved to be a more reliable and rapid medium for the detection of MRSA.
Detection of Six Copies of the Capsulation b Locus in aHaemophilus influenzaeType b Strain Isolated from a Splenectomized Patient with Fulminant Septic Shock
Authors: Cerquetti Marina , Cardines Rita , Giufrè Maria , Castella Annalisa , Rebora Monica , Mastrantonio Paola , Ciofi degli Atti Marta Luisa
Published: February 2006

We report on the first detection of six copies of the capsulation b locus in aHaemophilus influenzaetype b strain isolated from a splenectomized patient with fulminant septic shock associated with disseminated intravascular coagulation and death. The unusual amplification of the locus might have contributed to the rare and severe clinical presentation.
Etiologic Diagnosis of Adult Bacterial Pneumonia by Culture and PCR Applied to Respiratory Tract Samples
Authors: Strålin Kristoffer , Törnqvist Eva , Kaltoft Margit Staum , Olcén Per , Holmberg Hans
Published: February 2006

Respiratory culture and multiplex PCR for
Streptococcus pneumoniae
,
Haemophilus influenzae
,
Mycoplasma pneumoniae
, and
Chlamydophila pneumoniae
were applied to sputum, nasopharyngeal swabs, and nasopharyngeal aspirates from 235 adult patients with community-acquired pneumonia and 113 controls. Both culture and multiplex PCR performed well with the different samples and appear to be useful as diagnostic tools.
Urosepsis with
Actinobaculum schaalii
and
Aerococcusurinae
Authors: Sturm P. D. J. , Van Eijk J. , Veltman S. , Meuleman E. , Schülin T.
Published: February 2006

Actinobaculum
was isolated from urine only after prolonged incubation in 5%
CO
2
after discrepancy between urine Gram stain and initial
culture results was observed. Additional patients were diagnosed using
this method. The prevalence of
Actinobaculum
species in
urinary tract infections is underestimated since it is not isolated by
routine urine culture procedures.
Treatment Failure Resulting from Resistance of
Staphylococcus aureus
to Daptomycin
Authors: Skiest Daniel J.
Published: February 2006

Daptomycin, a new cyclic lipopeptide, was recently approved for the treatment of infections by gram-positive organisms, including infections with methicillin-resistant
Staphylococcus aureus
(MRSA). A patient infected with infected with MRSA developed resistance to daptomycin after prolonged exposure, which resulted in clinical failure. Clinicians should be aware of the possibility of daptomycin resistance and should consider routine testing for daptomycin susceptibility.
Endocarditis Caused by
Cardiobacterium valvarum
Authors: Bothelo Elisabeth , Gouriet Frédérique , Fournier Pierre-Edouard , Roux Véronique , Habib Gilbert , Thuny Franck , Metras Dominique , Raoult Didier , Casalta Jean-Paul
Published: February 2006

A fastidious, gram-negative bacterium was isolated from the blood of a 51-year-old man who had acute infectious endocarditis (IE). Characterization of the organism through phenotypic and genotypic analyses revealed the causative role of
Cardiobacterium valvarum
. This is the third reported case of IE caused by
C. valvarum
.
Unilateral Empyema as a Complication of Infectious Mononucleosis: a Pathogenic Variant of Lemierre’s Syndrome
Authors: Matten Eric C. , Grecu Loreta
Published: February 2006

We present a case of a healthy 19-year-old female who developed infectious mononucleosis complicated by unilateral empyema.
Group O Human Immunodeficiency Virus Type 1 Infection That Escaped Detection in Two Immmunoassays
Authors: Zouhair Said , Roussin-Bretagne Sylvie , Moreau Alain , Brunet Sylvie , Laperche Syria , Maniez Michèle , Barin Francis , Harzic Martine
Published: February 2006

We report a case of human immunodeficiency virus type 1 group O infection not detected by two highly sensitive immunoassays. The sera were strongly reactive to the V3 peptide of group O but not to the gp41 immunodominant epitope. Gp41 was sequenced, confirming that this virus belonged to group O.
Neonatal Mortality in Puppies Due to Bacteremia byStreptococcus dysgalactiaesubsp.dysgalactiae
Authors: Vela Ana I. , Falsen Enevold , Simarro Isabel , Rollan Eduardo , Collins Matthew D. , Domínguez Lucas , Fernandez-Garayzabal Jose F.
Published: February 2006

We report a case of bacteremia in puppies caused byStreptococcus dysgalactiaesubsp.dysgalactiae.Identification was achieved by phenotypic and molecular genetic methods. This is the first report of the recovery ofS. dysgalactiaesubsp.dysgalactiaefrom dogs.
Response of a bridge to a moving vehicle load
Authors: Lin J H
Published: February 2006

The determination of the statistical characteristics of bridge deflections due to a load of a vehicle moving across the span of a bridge is frequently a problem of great interest for bridge engineers. Developed herein is a spectral approach for evaluating the variation of bridge deflections due to a vehicle moving at constant speed along a rough bridge surface. Based on the above-mentioned approach, this study presents a closed-form solution for variances of bridge deflections. An example of application of the solution to the estimation of variances of bridge deflections is also presented. The effects of pavement type, vehicle speed, and bridge span on standard deviation of bridge deflections are investigated. The results of numerical examples show that if the effect of engine motions on vehicle vibrations is disregarded, the standard deviation of bridge deflections is proportional to the square root of the pavement roughness coefficient a for a specified vehicle speed.Key words: moving load, bridge deflection, pavement roughness.
NON-ABELIAN GAUGE SYMMETRIES INDUCED BY THE UNOBSERVABILITY OF EXTRA DIMENSIONS IN A KALUZA–KLEIN APPROACH
Authors: CIANFRANI FRANCESCO , MONTANI GIOVANNI
Published: February 2006

In this work we deal with the extension of the Kaluza–Klein approach to a non-Abelian gauge theory; we show how we need to consider the link between the n-dimensional model and a four-dimensional observer physics, in order to reproduce field equations and gauge transformations in the four-dimensional picture. More precisely, in field equations any dependence on extra coordinates is canceled out by an integration, as consequence of the unobservability of extra dimensions. Thus, by virtue of this extra dimension unobservability, we are able to recast the multidimensional Einstein equations into the four-dimensional Einstein–Yang–Mills ones, as well as all the right gauge transformations of fields are induced. The same analysis is performed for the Dirac equation describing the dynamics of the matter fields and, again, the gauge coupling with Yang–Mills fields are inferred from the multidimensional free fields theory, together with the proper spinors transformations.
MULTIPLIERS OF HOMOCLINIC TANGENCIES AND A THEOREM OF GONCHENKO AND SHILNIKOV ON AREA PRESERVING MAPS
Authors: AFRAIMOVICH VALENTIN , YOUNG TODD
Published: February 2006

We investigate differential invariants for homoclinic tangencies and discuss the role of these invariants in the Hausdorff dimension of invariant sets associated with the tangency and its unfoldings. Further, we give a streamlined proof of a theorem of Goncheko and Shilnikov on the case of a tangency in an area preserving map. Specifically, the invariants determine whether or not a hyperbolic invariant set is formed near the tangency.
ABSENCE OF THE LOCAL EXISTENCE THEOREM IN THE CRITICAL SPACE FOR THE $3\mathcal{D}$-NAVIER–STOKES SYSTEM
Authors: SINAI YAKOV
Published: February 2006

We consider the [Formula: see text]-Navier–Stokes System (NSS) on R3 without external forcing. After Fourier transform we get a nonlocal nonlinear integral equation equivalent to NSS. For one-parameter families of initial conditions A · c(0)(k)/|k|2 in the case of small |A| the NSS has a unique global solution. We argue that for large A NSS has no local solutions with these initial conditions.
THREE ADDITIONS TO PASSIVE DYNAMIC WALKING: ACTUATION, AN UPPER BODY, AND 3D STABILITY
Authors: WISSE MARTIJN
Published: February 2006

One of the main challenges in the design of human-like walking robots (useful for service or entertainment applications as well as the study of human locomotion) is to obtain dynamic locomotion, as opposed to the static form of locomotion demonstrated by most of the current prototypes. A promising concept is the idea of passive dynamic walking; even completely unactuated and uncontrolled mechanisms can perform a stable gait when walking down a shallow slope. This concept enables the construction of dynamically walking prototypes that are simpler yet more natural in their motions than the static bipeds. This paper presents three additions to the concept of passive dynamic walking. First, hip actuation is added to increase the fore-aft stability and to provide power to the system, removing the need for a downhill floor. Second, a bisecting hip mechanism is introduced to allow the addition of a passive upper body without compromising the simplicity, efficiency and naturalness of the concept of passive dynamic walking. Third, skateboard-like ankle joints are implemented to provide 3D stability. These ankles couple the unstable sideways lean motion to yaw (steering), a kinematic coupling which provides sideways stability when walking with sufficient forward velocity. The three additions are investigated both with elementary simulation models and with prototype experiments. All three prototypes demonstrate an uncannily natural and stable gait while requiring only two foot switches and three on/off actuators.
Sound science
Authors: Kramer Gregory , Walker Bruce N.
Published: February 2006

This special issue of
ACM Transactions on Applied Perception
is intended to commemorate the tenth International Conference on Auditory Display (ICAD) and to serve as an introduction and overview of the field of auditory displays. This paper discusses the goals of the issue and describes the paper selection process. The selected papers are also introduced, with their connections to each other, their place in ICAD, and their relevance to other fields briefly highlighted.
Reflections on sonic browsing
Authors: Fernström Mikael
Published: February 2006

In the original Fernström and McNamara paper at ICAD 1998, we described our work on a novel user interface for sonic browsing of music collections. In this commentary, we reflect upon the continued research in this area and how our interactive sonification approach has come to be used also for browsing collections of everyday sounds and for perception experiments.
A framework for information technology outsourcing risk management
Authors: Aubert Benoit A. , Patry Michel , Rivard Suzanne
Published: February 2006

This paper takes stock from several studies on Information Technology outsourcing risk. A definition of risk is offered, and an illustration from five case studies is used to show how risk can be managed. Results show that an active risk management approach can reduce risk exposure substantially while enabling the organizations to still reap the benefits associated with outsourcing.
Information Extraction
Authors: McCallum Andrew
Published: February 2006

In 2001 the U.S. Department of Labor was tasked with building a Web site that would help people find continuing education opportunities at community colleges, universities, and organizations across the country. The department wanted its Web site to support fielded Boolean searches over locations, dates, times, prerequisites, instructors, topic areas, and course descriptions. Ultimately it was also interested in mining its new database for patterns and educational trends. This was a major data-integration project, aiming to automatically gather detailed, structured information from tens of thousands of individual institutions every three months.
Linguistic continuity in software engineering
Authors: Riehle Richard
Published: February 2006

Many different concerns contribute to the complexity of software development. Some of these concerns are easy to spot. Others are right in front of us all along but not explicitly identified in a way that makes them intellectually accessible. We describe an idea that has always been in the background of awareness for programmers and software designers, but which seldom gets sufficient acknowledgement to be written about on its own. We call this linguistic [dis]continuity.
Automatically generating refactorings to support API evolution
Authors: Perkins Jeff H.
Published: February 2006

When library APIs change, client code should change in response, in order to avoid erroneous behavior, compilation failures, or warnings. Previous research has introduced techniques for generating such client refactorings. This paper improves on the previous work by proposing a novel, lightweight technique that takes advantage of information that programmers can insert in the code rather than forcing them to use a different tool to re-express it. The key idea is to replace calls to deprecated methods by their bodies, where those bodies consist of the appropriate replacement code. This approach has several benefits. It requires no change in library development practice, since programmers already adjust method bodies and/or write example code, and there are no new tools or languages to learn. It does not require distribution of new artifacts, and a tool to apply it can be lightweight. We evaluated the applicability of our approach on a number of libraries and found it to to be applicable in more than 75% of the cases.
Some comments on comments
Authors: Sachs Jon
Published: February 2006

My objective here is to set out some (hopefully enlightening) opinions on the writing of comments in computer programs. Programmers probably spend more time writing and reading comments than any other kind of documentation. Thus it is strange that little attention has been given to the problem of making comments as useful as possible.
Automated documentation
Authors: Goetz Martin A.
Published: February 2006

The problem of developing and maintaining adequate documentation for computerized user applications is certainly not being addressed properly at most installations. Documentation is needed at the module, program, and system levels, at the user levels, and at the operations level.
The internet AS-level topology
Authors: Mahadevan Priya , Krioukov Dmitri , Fomenkov Marina , Dimitropoulos Xenofontas , claffy k c , Vahdat Amin
Published: February 2006

We calculate an extensive set of characteristics for Internet AS topologies extracted from the three data sources most frequently used by the research community: traceroutes, BGP, and WHOIS. We discover that traceroute and BGP topologies are similar to one another but differ substantially from the WHOIS topology. Among the widely considered metrics, we find that the
joint degree distribution
appears to fundamentally characterize Internet AS topologies as well as narrowly define values for other important metrics. We discuss the interplay between the specifics of the three data collection mechanisms and the resulting topology views. In particular, we how how the data collection peculiarities explain differences in the resulting joint degree distributions of the respective topologies. Finally, we release to the community the input topology datasets, along with the scripts and output of our calculations. This supplement hould enable researchers to validate their models against real data and to make more informed election of topology data sources for their specific needs