bluuebunny/crossref_metadata_2025 huggingface dataset:
Slowdown in development of self-assembled InAs∕GaAs(001) dots near the critical thickness
Authors: Hanada Takashi , Totsuka Hirofumi , Hong Soon-Ku , Godo Kenji , Miyajima Kensuke , Goto Takenari , Yao Takafumi
Published: August 2006

By strain relaxation measurements using reflection high-energy electron diffraction, it is observed that development of the self-assembled InAs∕GaAs(001) dots continues after In deposition is stopped just above the critical thickness under As4 atmosphere. Transmission electron microscope and photoluminescence measurements reveal that dot size increases considerably during this postdeposition process. On the other hand, the dot size increases only slightly during the postdeposition if the amount of In is greater than the critical thickness. Energetics within a finite surface area for a dot shows that the energy barrier for the transformation from the metastable InAs wetting layer to the optimum dot on the thinner wetting layer is high and suppresses the transformation near the critical thickness. Development of the dot density is also illustrated by calculating the nucleation rate from the thickness-dependent barrier height.
In situgrowth regime characterization of AlN using reflection high energy electron diffraction
Authors: Burnham Shawn D. , Alan Doolittle W.
Published: August 2006

Methods for characterizing the growth regime of AlN are presented to deal with the unresolved critical issue of in situ growth regime determination during molecular beam epitaxy. Previously, there were no known reports of in situ measurements to determine the growth regime of AlN, making reproducibility difficult. Reflection high energy electron diffraction (RHEED) intensity transitions were observed upon opening and closing Al effusion cells, and three key signatures were identified. First, the time constant of the falling RHEED specular spot intensity upon Al shutter opening was found to vary inversely with the Al flux, providing a means of in situ calibration of Al flux. Second, a RHEED intensity spike or oscillation feature was observed at the onset of Al flux. Third, the behavior of the RHEED intensity rise upon Al shutter closing can be used to identify the Al-rich intermediate and Al-rich droplet regimes. These techniques and observations provide in situ methods of determining the growth regime of AlN, improving reproducibility and control.
Nonequilibrium phases in epitaxial Mn∕GaAs interfacial reactions
Authors: Farrell H. H. , Hilton J. L. , Schultz B. D. , Palmstrøm C. J.
Published: August 2006

Solid-state reactions of Mn thin films on GaAs(001) lead to the formation of epitaxially oriented tetragonal Mn2As near the GaAs substrate and a layer of tetragonal δ-MnGa at the surface at annealing temperatures above 300°C. However, an intermediate structure is first formed that has the composition Mn0.6Ga0.2As0.2 with a repeated distance of about 6.3Å perpendicular to the substrate interface. This intermediate structure is metastable relative to the formation of Mn2As and δ-MnGa but provides pathways for allowing Mn to diffuse toward the substrate and Ga to diffuse toward the surface. First principles, density functional theory calculations were used to study the possible structures of this intermediate material. Both vacancy containing and nonvacancy containing structures were considered. Our results indicate that vacancy containing compounds are the most probable. Furthermore, we propose a mechanism for Mn and Ga diffusions and illustrate how interface compound formation occurs in the Mn∕GaAs reactions.
Growth of a stacked silicon nitride/silicon oxide dielectric on Si(100)
Authors: Bahari A. , Morgen P. , Pedersen K. , Li Z. S.
Published: August 2006

We have recently developed processes to grow ultrathin amorphous silicon oxide and amorphous silicon nitride layers on clean Si(111) and Si(100) surfaces exploring the self-limiting nature of the direct oxidation of Si with O2, and the self-limiting nature of the direct nitridation of Si with atomic N produced by microwave dissociation of N2, at processing temperatures around 500°C. In some of today’s microprocessor devices mixed dielectric systems are used as complementary metal oxide semiconductor gate dielectrics. We demonstrate the use of our processes to produce such systems in various structures, and with maximum control, by exposing oxide to N, or nitride to O2 at 500°C. In addition we produce a stacked layer, consisting of 7–8Å of SiO2 on top of Si(100), with a layer of varying thickness of Si3N4 grown on top of this structure. The growth of Si3N4 occurs at room temperature in this process. Such structures or thermally postprocessed structures thereof should be further examined as potential stacked gate dielectrics in the next generation of Si-based microelectronics.
Study of nanoimprint pattern transfer on hydrogen silsesquioxane
Authors: Chen Sun Zen , Liu Jen Fu , Chen Henry J. H. , Huang Fon Shan
Published: August 2006

The effects of process parameters on pattern embossing into hydrogen silsesquioxane films and the pattern degradation of hydrogen silsesquioxane were investigated. Methylisobutylketone (MIBK) was used to dilute hydrogen silsesquioxane, and NX-1000 (Nanonex) was used to imprint hydrogen silsesquioxane embossed with a Si grating mold at 25°–180°C under 2–2.5MPa. The imprint results were observed by scanning electron microscopy and correlated to the analysis results of Fourier transform infrared spectroscopy (FTIR) and nanoindentation. The FTIR results show that network-type bonding was promoted by dilution with MIBK and increasing baking temperatures from 50°Cto180°C. High-temperature thermal-cycle heat treatment can promote the formation of network bonds, which make hydrogen silsesquioxane film undergo plastic deformation more easily. In contrast, low-temperature thermal-cycle heat treatment can result in hydrogen silsesquioxane having a highly viscous response and high time-dependent deformation behavior. The diluted hydrogen silsesquioxane film under prebaking at 150°C for 3min and imprinting at 180°C for 2min under 2.5MPa resulted in a high-fidelity pattern replication without pattern degradation after aging at room temperature for 20days.
Field and electron trajectory modeling in the vicinity of an emitting tip
Authors: Janik J. , Balon F. , Vinduska P. , Danis T.
Published: August 2006

The aim of this paper is to calculate/simulate electron trajectories in the diode or triode configuration for the cold cathode of a miniature electron gun. An experimental setup with millimeter-scale planar electrodes was prepared to help us estimate the necessary parameters, which were consequently used as the input data for the EGUN software. This software was used to calculate electron trajectories and the beam currents of electron guns and beam optics. This program has an additional subroutine for calculating Fowler-Nordheim emission of the electrons. The calculated results are very promising, giving a parallel or converging beam for the triode configuration. The described method could even be used eventually for simulating micro-emitters for field-emission displays.
1.32
μ
m
InAs∕GaAs quantum-dot resonant-cavity light-emitting diodes grown by metalorganic chemical vapor deposition
Authors: Huang Kun-Fu , Lee Feng-Ming , Hu Chih-Wei , Peng Te-Chin , Wu Meng-Chyi , Lin Chia-Chien , Hsieh Tung-Po , Chyi Jen-Inn
Published: August 2006

The first demonstration of InAs∕GaAs quantum-dot (QD) resonant-cavity light-emitting diode (RCLED) operating at 1.32μm at room temperature is reported. A single-layer InAs QDs inserted in GaAs matrix as the active medium was grown by metalorganic chemical vapor deposition. The bottom and top mirrors of QD RCLEDs were fabricated by employing epitaxial AlGaAs∕GaAs pairs and one dielectric SiO2∕Si3N4 pair as distributed Bragg reflectors (DBRs), respectively. As compared to the nonresonant QD LEDs, the RCLEDs exhibit a forward voltage of 1.13V at 20mA, a peak wavelength of 1.318μm, a narrower full width at half maximum in the electroluminescent spectrum of 14meV at 20mA, a high Q factor of 73.9, a low redshift rate with injection current of 0.033nm∕mA, and a higher light-output power of 28μW at 100mA.
Fabrication and photoluminescence of InGaN-based nanorods fabricated by plasma etching with nanoscale nickel metal islands
Authors: Huang H. W. , Chu J. T. , Hsueh T. H. , Ou-Yang M. C. , Kuo H. C. , Wang S. C.
Published: August 2006

InGaN-based nanorods with a rod density of ∼3.0×1010cm−2 were fabricated from a light-emitting diode structure by an inductively coupled plasma dry-etching with nanoscale nickel metal islands. The nanoscale nickel metal islands were formed from a Ni film by a rapid thermal annealing at 850°C for 1min. The influence of thicknesses of Ni metal film on the diameter and density of nanorods was also investigated. Structural and optical properties of the InGaN-based nanorods were studied with field-emission scanning electron microscopy, transmission electron microscopy, and photoluminescence. The diameters and heights of nanorods were estimated to be 60–100nm and more than 0.28μm, respectively. The emission-peak wavelength of nanorods showed a blueshift of 5.1nm from that of the bulk structure. An enhancement by a factor of five times in photoluminescence intensity of nanorods compared to that of the bulk structure was also observed in this work. The blueshift is attributed to the strain relaxation in the well, quantum-confinement effect, or a combination of the two, which result in the enhancement in emission intensity.
Directed nucleation of ordered nanoparticle arrays on amorphous surfaces
Authors: Coffee Shawn S. , Stanley Scott K. , Ekerdt John G.
Published: August 2006

Germanium nanoparticle nucleation was studied in organized arrays on HfO2 using a SiO2 thin film mask with ∼20–24nm pores and a 6×1010cm−2 pore density. Poly(styrene-b-methyl methacrylate) diblock copolymer was employed to pattern the SiO2 film. Hot wire chemical vapor deposition at 800K produced Ge nanoparticles using 6–19 monolayer Ge exposures. By seeding adatoms on HfO2 at room temperature before growth, nanoparticle density is approximately one particle per pore.
Microwave assisted patterning of vertically aligned carbon nanotubes onto polymer substrates
Authors: Sunden Erik , Moon Jack K. , Wong C. P. , King William P. , Graham Samuel
Published: August 2006

This paper presents a low pressure hot embossing method for transferring patterns of vertically aligned carbon nanotubes into thermoplastic substrates. The procedure utilizes the synthesis of carbon nanotubes in discrete patterns on silicon substrates through the vapor liquid solid growth mechanism. The nanotube pattern and silicon stamp is placed on top of a polycarbonate film and locally heated above the glass transition temperature using microwave processing. The weight of the silicon substrate presses the nanotubes into the polycarbonate, resulting in the complete transfer of vertically aligned patterns. The technique is a rapid processing method, which could be used to integrate aligned nanomaterials with MEMS and flexible electronics that are fabricated on a wide range of thermoplastic polymer materials.
Typing of Human Adenoviruses in Specimens from Immunosuppressed Patients by PCR-Fragment Length Analysis and Real-Time Quantitative PCR
Authors: Ebner Karin , Rauch Margit , Preuner Sandra , Lion Thomas
Published: August 2006

Currently, 51 human adenovirus (AdV) serotypes, which are divided into six species (A to F), are known. AdV infections are a major cause of morbidity and mortality in immunosuppressed individuals, particularly in allogeneic stem cell transplant (SCT) recipients. Any AdV species may cause life-threatening disease, but little information is available on the clinical relevance of individual serotypes. The use of serological testing for serotype identification is limited due to the impaired immune response during the posttransplant period. A new molecular approach to serotype identification is presented here that exploits variable regions within the hexon gene. All serotypes belonging to the species A, B, C, E, and F can be determined by fragment length analysis of a single PCR product. For species C, which is the most prevalent in many geographic regions, an alternative technique based on serotype-specific real-time quantitative PCR was established. Of 135 consecutive pediatric patients screened for AdV infections after allogeneic SCT, 40 tested positive. Detailed analysis revealed the presence of 10 different serotypes; serotypes 1 and 2 from species C (C01 and C02) showed the highest prevalence, accounting for 77% of the AdV-positive cases. Representatives of other species were observed less commonly: serotype A12 in 6.5%; serotype A31 in 4.5%; and B03, B16, C05, C06, D19, and F41 in 2%. The approach to rapid molecular serotype analysis presented here provides a basis for detailed studies on adenovirus epidemiology and on the transmission of nosocomial infections. Moreover, in view of the increasing importance of tailored therapy approaches, serotype identification may in the future have implications for the selection of the most appropriate antiviral treatment.
Asymptomatic Norovirus Infection in Mexican Children
Authors: García Coralith , DuPont Herbert L. , Long Kurt Z. , Santos Jose I. , Ko GwangPyo
Published: August 2006

Sixty-three children in periurban Mexico City were examined for the occurrence of asymptomatic norovirus (NoV) infection from June to August 1998. NoV was detected in 48 of 161 stool specimens (29.8%), with 31 children (49.2%) having at least one positive stool. Asymptomatic NoV infection occurred commonly during summertime in a Mexican pediatric population.
Evaluation of the GenoType Mycobacteria Direct Assay for Detection of
Mycobacterium tuberculosis
Complex and Four Atypical Mycobacterial Species in Clinical Samples
Authors: Franco-Álvarez de Luna F. , Ruiz P. , Gutiérrez J. , Casal M.
Published: August 2006

We evaluated GenoType Mycobacteria Direct (GTMD), a novel commercial assay based on nucleic acid sequence-based amplification technology, for the detection of
Mycobacterium tuberculosis
complex,
M. avium
,
M. intracellulare
,
M. kansasii
, and
M. malmoense
directly from clinical specimens. A total of 134 respiratory and extrapulmonary samples from 65 patients were processed. Sensitivity, specificity, positive predictive, and negative predictive values for GTMD were 92, 100, 100, and 77%, respectively. The GMTD technique is useful, reliable, and rapid when used during the normal routine of a clinical laboratory.
Real-Time Quantitative Broad-Range PCR Assay for Detection of the 16S rRNA Gene Followed by Sequencing for Species Identification
Authors: Zucol Franziska , Ammann Roland A. , Berger Christoph , Aebi Christoph , Altwegg Martin , Niggli Felix K. , Nadal David
Published: August 2006

Here we determined the analytical sensitivities of broad-range real-time PCR-based assays employing one of three different genomic DNA extraction protocols in combination with one of three different primer pairs targeting the 16S rRNA gene to detect a panel of 22 bacterial species. DNA extraction protocol III, using lysozyme, lysostaphin, and proteinase K, followed by PCR with the primer pair Bak11W/Bak2, giving amplicons of 796 bp in length, showed the best overall sensitivity, detecting DNA of 82% of the strains investigated at concentrations of ≤10
2
CFU in water per reaction. DNA extraction protocols I and II, using less enzyme treatment, combined with other primer pairs giving shorter amplicons of 466 bp and 342 or 346 bp, respectively, were slightly more sensitive for the detection of gram-negative but less sensitive for the detection of gram-positive bacteria. The obstacle of detecting background DNA in blood samples spiked with bacteria was circumvented by introducing a broad-range hybridization probe, and this preserved the minimal detection limits observed in samples devoid of blood. Finally, sequencing of the amplicons generated using the primer pair Bak11W/Bak2 allowed species identification of the detected bacterial DNA. Thus, broad-spectrum PCR targeting the 16S rRNA gene in the quantitative real-time format can achieve an analytical sensitivity of 1 to 10 CFU per reaction in water, avoid detection of background DNA with the introduction of a broad-range probe, and generate amplicons that allow species identification of the detected bacterial DNA by sequencing. These prerequisites are important for its application to blood-containing patient samples.
Experimental Evaluation of the FluChip Diagnostic Microarray for Influenza Virus Surveillance
Authors: Townsend Michael B. , Dawson Erica D. , Mehlmann Martin , Smagala James A. , Dankbar Daniela M. , Moore Chad L. , Smith Catherine B. , Cox Nancy J. , Kuchta Robert D. , Rowlen Kathy L.
Published: August 2006

Global surveillance of influenza is critical for improvements in disease management and is especially important for early detection, rapid intervention, and a possible reduction of the impact of an influenza pandemic. Enhanced surveillance requires rapid, robust, and inexpensive analytical techniques capable of providing a detailed analysis of influenza virus strains. Low-density oligonucleotide microarrays with highly multiplexed “signatures” for influenza viruses offer many of the desired characteristics. However, the high mutability of the influenza virus represents a design challenge. In order for an influenza virus microarray to be of utility, it must provide information for a wide range of viral strains and lineages. The design and characterization of an influenza microarray, the FluChip-55 microarray, for the relatively rapid identification of influenza A virus subtypes H1N1, H3N2, and H5N1 are described here. In this work, a small set of sequences was carefully selected to exhibit broad coverage for the influenza A and B viruses currently circulating in the human population as well as the avian A/H5N1 virus that has become enzootic in poultry in Southeast Asia and that has recently spread to Europe. A complete assay involving extraction and amplification of the viral RNA was developed and tested. In a blind study of 72 influenza virus isolates, RNA from a wide range of influenza A and B viruses was amplified, hybridized, labeled with a fluorophore, and imaged. The entire analysis time was less than 12 h. The combined results for two assays provided the absolutely correct types and subtypes for an average of 72% of the isolates, the correct type and partially correct subtype information for 13% of the isolates, the correct type only for 10% of the isolates, false-negative signals for 4% of the isolates, and false-positive signals for 1% of the isolates. In the overwhelming majority of cases in which incomplete subtyping was observed, the failure was due to the nucleic acid amplification step rather than limitations in the microarray.
Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus
Authors: Mehlmann Martin , Dawson Erica D. , Townsend Michael B. , Smagala James A. , Moore Chad L. , Smith Catherine B. , Cox Nancy J. , Kuchta Robert D. , Rowlen Kathy L.
Published: August 2006

DNA microarrays have proven to be powerful tools for gene expression analyses and are becoming increasingly attractive for diagnostic applications, e.g., for virus identification and subtyping. The selection of appropriate sequences for use on a microarray poses a challenge, particularly for highly mutable organisms such as influenza viruses, human immunodeficiency viruses, and hepatitis C viruses. The goal of this work was to develop an efficient method for mining large databases in order to identify regions of conservation in the influenza virus genome. From these regions of conservation, capture and label sequences capable of discriminating between different viral types and subtypes were selected. The salient features of the method were the use of phylogenetic trees for data reduction and the selection of a relatively small number of capture and label sequences capable of identifying a broad spectrum of influenza viruses. A detailed experimental evaluation of the selected sequences is described in a companion paper. The software is freely available under the General Public License at
http://www.colorado.edu/chemistry/RGHP/software/
.
Analysis of
secA1
Gene Sequences for Identification of
Nocardia
Species
Authors: Conville Patricia S. , Zelazny Adrian M. , Witebsky Frank G.
Published: August 2006

Molecular methodologies, especially 16S rRNA gene sequence analysis, have allowed the recognition of many new species of
Nocardia
and to date have been the most precise methods for identifying isolates reliably to the species level. We describe here a novel method for identifying
Nocardia
isolates by using sequence analysis of a portion of the
secA1
gene. A region of the
secA1
gene of 30 type or reference strains of
Nocardia
species was amplified using
secA1-
specific primers. Sequence analysis of 468 bp allowed clear differentiation of all species, with a range of interspecies similarity of 85.0% to 98.7%. Corresponding 16S rRNA gene sequences of a 1,285-bp region for the same isolates showed a range of interspecies similarity of 94.4 to 99.8%. In addition to the type and reference strains, a 468-bp fragment of the
secA1
gene was sequenced from 40 clinical isolates of 12
Nocardia
species previously identified by 16S rRNA gene sequence analysis. The
secA1
gene sequences of most isolates showed >99.0% similarity to the
secA1
sequences of the type or reference strain to which their identification corresponded, with a range of 95.3 to 100%. Comparison of the deduced 156 amino acid sequences of the SecA1 proteins of the clinical isolates showed between zero and two amino acid residue differences compared to that of the corresponding type or reference strain. Sequencing of the
secA1
gene, and using deduced amino acid sequences of the SecA1 protein, may provide a more discriminative and precise method for the identification of
Nocardia
isolates than 16S rRNA gene sequencing.
Genetic Diversity of PspA Types among Nasopharyngeal Isolates Collected during an Ongoing Surveillance Study of Children in Brazil
Authors: Pimenta Fabiana Cristina , Ribeiro-Dias Fátima , Brandileone Maria Cristina C. , Miyaji Eliane N. , Leite Luciana C. C. , Sgambatti de Andrade Ana Lúcia S.
Published: August 2006

Pneumococcal surface protein A (PspA) has been considered a potential candidate for human vaccines because of its serotype-independent protective immunity. Nasopharyngeal (NP) pneumococcal colonization is highly prevalent in infants and precedes the invasive disease. Thus, prevention of NP colonization may reduce the burden of pneumococcal disease in children. Scarce information focusing on PspA from pneumococcal carriage in humans is available. We examined the genetic diversity of PspA from NP isolates obtained during an ongoing pneumococcal surveillance study with children. PspA families and clades of 183 community-acquired
Streptococcus pneumoniae
NP isolates from healthy children (
n
= 97) and children with respiratory tract infections (
n
= 48), pneumonia (
n
= 33), or meningitis (
n
= 5) were investigated. Overall, 79.8% (
n
= 146) of the pneumococcal isolates were classified as PspA family 1 (35.5%) and family 2 (44.3%), whereas 20.2% of the isolates could not be typed. The distribution of PspA families and clades did not differ significantly according to the clinical status of the children. A dendrogram comparing the genetic relationship between the amino acid sequences of the clade-defining region of PspA from NP strains together with 24 invasive reference strains (GenBank) closely reproduced the profile of the families and clades previously reported for pneumococcal invasive strains. These findings strengthen the idea that the use of PspA as a vaccine antigen may protect children against carriage as well as invasive pneumococcal disease.
Strain-Specific Differences in Two Large
Mycobacterium tuberculosis
Genotype Clusters in Isolates Collected from Homeless Patients in New York City from 2001 to 2004
Authors: Macaraig Michelle , Agerton Tracy , Driver Cynthia R. , Munsiff Sonal S. , Abdelwahab Jalaa' , Park Julie , Kreiswirth Barry , Driscoll Jeffrey , Zhao Benyang
Published: August 2006

We studied two large
Mycobacterium tuberculosis
genotype clusters associated with recent outbreaks in homeless persons to determine factors associated with these tuberculosis (TB) strains. Isolates from all culture-positive TB cases diagnosed from 1 January 2001 to 31 December 2004 were genotyped. Patients whose isolates had identical restriction fragment length polymorphism patterns and spoligotypes were considered clustered. Health department records were reviewed and reinterviews attempted for clustered cases. Patients with the Cs30 and BEs75 strains were compared to other genotypically clustered cases and to each other. The two largest genotype clusters among homeless persons were the Cs30 strain (
n
= 105) and the BEs75 strain (
n
= 47). Fifty-one (49%) patients with the Cs30 strain and 28 (60%) with the BEs75 strain were homeless. Compared to patients with the BEs75 strain, patients with the Cs30 strain were less likely to be respiratory acid-fast bacillus smear positive (51% versus 72%). Furthermore, patients with the BEs75 strain were more likely to be HIV infected (74% versus 42%), which suggests that most patients with this strain advanced to disease after recent infection. Cases in clusters of strains that have been circulating in the community over a long time period, such as the Cs30 strain, require additional investigation to determine whether clustering is a result of recent transmission or reactivation of remote infection.
Role of Metapneumovirus in Viral Respiratory Infections in Young Children
Authors: Ordás José , Boga José Antonio , Alvarez-Argüelles Marta , Villa Laura , Rodríguez-Dehli Cristina , de Oña María , Rodríguez Julián , Melón Santiago
Published: August 2006

The contribution of human metapneumovirus (hMPV) relative to that of other respiratory viruses as a cause of respiratory infections in children less than 1 year old has been evaluated. From October 2003 to April 2004, nasopharyngeal samples from 211 children less than 1 year old were analyzed to detect respiratory viruses. Respiratory syncytial virus (RSV) was the predominant virus isolated (96 children [45.5%]), followed by influenza A virus, parainfluenza virus, adenovirus, cytomegalovirus, and herpes simplex virus type 1, which were only occasionally detected. From January 2004 to April 2004, a nested retrotranscription-PCR, using in-house primers directed to the matrix protein gene of hMPV, was carried out on samples in which no other viruses were detected. hMPV was detected in 18 (16.2%) children, indicating that this virus was the second-most-frequent cause of viral respiratory infections in children less than 1 year old. The rate of hospitalization for RSV- and hMPV-infected children was higher than 75%. While RSV had a peak from December to February, hMPV was increasingly detected from January to April. The mean age of hMPV-infected children (6.44 ± 3.64 [mean ± standard deviation] months) was significantly higher than that of RSV-infected children (3.99 ± 2.96 [mean ± standard deviation] months). On the other hand, 64.3% of the RSV-infected children and 12.5% of the hMPV-infected children showed high levels of C-reactive protein. Although several authors have reported that clinical symptoms of hMPV-positive patients mirrored those of RSV-positive patients, differences between the two viruses can be found.
Prevalence of Antibodies against Herpes Simplex Virus Types 1 and 2 in Children and Young People in an Urban Region in Tanzania
Authors: Kasubi Mabula Joseph , Nilsen Arvid , Marsden Howard S. , Bergström Tomas , Langeland Nina , Haarr Lars
Published: August 2006

Herpes simplex virus type 1 (HSV-1) is transmitted by close contact, both sexual and nonsexual, and infections are acquired during childhood and adolescence. Herpes simplex virus type 2 (HSV-2), however, is thought to be transmitted mainly by sexual contact. Most HSV-2 infections are consequently expected to occur after the onset of sexual activity. Recent reports indicate an increasing prevalence of HSV-2 on the African continent, but most studies have been performed on adult cohorts. In the present study, we collected sera from Tanzanian children and young persons from 1 to 20 years old, with at least 100 individuals in each age group. Antibodies against HSV-1 and HSV-2 were detected by an in-house Western blot method which was shown to perform well in comparison with a commercial Western blot assay. Type-specific antibodies were also analyzed by two noncommercial enzyme-linked immunosorbent assay methods based upon the antigenicities of branched synthetic oligopeptides corresponding to epitopes in glycoprotein G of HSV-1 or HSV-2. The prevalence of HSV-1 antibodies increased gradually from 73% for the age group of 1 to 4 years to 92% for the age group of 17 to 20 years. The prevalence of HSV-2 antibodies was unexpectedly high, as 15% of the children were infected by the age of 8 years, with the incidence increasing gradually to 40% in the age group of 17 to 20 years. The reason for this unexpectedly high frequency is not clear but could suggest that nonsexual transmission of HSV-2 is more common than previously thought. There was no statistically significant association between seropositivities for HSV-2 and human immunodeficiency virus.
Nucleotide Sequencing for Diagnosis of Sinusal Infection by
Schizophyllum commune
, an Uncommon Pathogenic Fungus
Authors: Baron Olivier , Cassaing Sophie , Percodani Josiane , Berry Antoine , Linas Marie-Denise , Fabre Richard , Serrano Elie , Magnaval Jean François
Published: August 2006

Schizophyllum commune
, a basidiomycete fungus, is a rare cause of mycotic disease. We report here a case of sinusitis in a 35-year-old woman that underscores the value of molecular biology for the diagnosis of this fungal infection.
Comparative Study Using Various Methods for Identification of
Staphylococcus
Species in Clinical Specimens
Authors: Layer F. , Ghebremedhin B. , Moder K.-A. , König W. , König B.
Published: August 2006

Coagulase-negative staphylococci (CNS) play a predominant role in nosocomial infections. Rapid, reliable identification of these organisms is essential for accurate diagnosis and prompt effective treatment of these infections. Quite recently, the VITEK 2 g-positive (gram-positive [GP]) identification card (bioMérieux) has been redesigned for greater accuracy in the identification of gram-positive cocci. We compared the BD Phoenix (Becton Dickinson) and VITEK 2 (bioMérieux) automated microbiology systems, using their respective update version cards, and the API ID32 STAPH test. The glyceraldehyde-3-phosphate dehydrogenase (
gap
) gene-based T-RFLP (terminal restriction fragment length polymorphism) method was used for verifying the results. In total, 86 clinical isolates of CNS and 27 reference strains were analyzed. The results show that for identification of CNS, the automated identification methods using the newest VITEK 2 and BD Phoenix identification cards are comparable. However, API ID32 STAPH revealed more correct results compared to both automated microbiology systems. Despite the increased performance of the phenotypic automated identification systems compared to the former versions, molecular methods, e.g., the
gap
-based T-RFLP method, still show superior accuracy in identifying
Staphylococcus
species other than
Staphylococcus aureus
.
European Multicenter Evaluation of High-Density DNA Probe Arrays for Detection of Hepatitis B Virus Resistance Mutations and Identification of Genotypes
Authors: Tran N. , Berne R. , Chann R. , Gauthier M. , Martin D. , Armand M.-A. , Ollivet A. , Teo C. G. , Ijaz S. , Flichman D. , Brunetto M. , Bielawski K. P. , Pichoud C. , Zoulim F. , Vernet G.
Published: August 2006

Polymorphisms along the hepatitis B virus (HBV) genome have an impact on disease outcome, sensitivity to antiviral treatment, escape from vaccination, and laboratory diagnosis. We have designed a diagnostic tool based on duplex amplification of the whole HBV genome and a high-density DNA chip designed to detect 245 mutations, 20 deletions, and 2 insertions at 151 positions and to determine the genotype of the virus in serum. Assay performances were evaluated with 170 samples, characterized by determination of viral load and sequencing of the Pol, S, and precore genes and the basal core promoter. One hundred fifty-three samples (90%) could be amplified and analyzed by the chip. Only two samples with more than 103genome copies/ml could not be analyzed. Genotype had no impact on analytical sensitivity. Reproducibility studies showed no difference between repeats for codon and genotype determination. Genotype determination by sequencing and the chip were concordant in 148 of 151 samples. Twelve thousand one hundred sixty-one codons were analyzed by both techniques. Only 89.4% could be determined by sequencing, and among the remaining 11,335 codons, 92.8% were identical by sequencing and the chip. Failures to identify an amino acid by the chip were mainly due to reduced hybridization efficiency attributed to unexpected polymorphisms. Optimization of the chip-based reagent for the analysis of the HBV genome is ongoing. This first evaluation showed that DNA chip technology can provide important information in relation to the clinical management of chronic hepatitis B.
Characterization of
Shigella
Strains in Iran by Plasmid Profile Analysis and PCR Amplification of
ipa
Genes
Authors: Farshad Shohreh , Sheikhi Raheleh , Japoni Aziz , Basiri Ezzatollah , Alborzi Abdolvahab
Published: August 2006

To characterize
Shigella
clinical strains, we studied 82
Shigella
strains recovered from 719 stool samples of patients with bloody diarrhea in Shiraz, Iran, over the period from April to October 2003. Serological assay classified the
Shigella
isolates as follows: 61 (74.39%)
Shigella sonnei
isolates, 16 (19.51%)
Shigella flexneri
isolates, 3 (3.65%)
Shigella boydii
isolates, and 2 (2.43%)
Shigella dysenteriae
isolates. In an antibiogram test, all
Shigella
strains were susceptible to ceftazidime, ciprofloxacin, and ceftriaxone. They showed high degrees of sensitivity to nalidixic acid, gentamicin, cephalothin, and amikacin. Approximately 90.24% of the
Shigella
isolates were resistant to co-trimoxazole. The plasmid profile patterns of all strains were determined by a modified alkaline lysis method. The average number of plasmid bands for each strain was 9.5. By plasmid profile analysis we identified 56 genotypes among all isolates and 42, 14, 3, and 2 genotypes among the
S. sonnei
,
S. flexneri
,
S. boydii
, and
S. dysenteriae
strains, respectively. PCR assays showed that all isolates were positive for two virulence genes,
ipaBCD
and
ipaH
. In conclusion, these data mandate local monitoring of drug resistance and its consideration in the empirical therapy of
Shigella
infections. These results also demonstrate that plasmid profile analysis is more reliable than antibiotic susceptibility pattern analysis for the identification of
Shigella
epidemic strains isolated in Iran.
Comparison of the LCx Human Immunodeficiency Virus (HIV) RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan Assays for Quantitation of HIV Type 1 RNA in Plasma
Authors: Foulongne Vincent , Montes Brigitte , Didelot-Rousseau Marie-Noelle , Segondy Michel
Published: August 2006

The LCx human immunodeficiency virus (HIV) RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan assays for HIV type 1 (HIV-1) were compared for their abilities to quantitate HIV-1 RNA in plasma. High degrees of correlation and agreement were observed between the assays. Differences in HIV-1 RNA levels according to HIV-1 subtypes did not reach statistical significance.
New
Staphylococcus aureus
Genotyping Method Based on Exotoxin (
set
) Genes
Authors: Aguiar-Alves Fábio , Medeiros Fred , Fernandes Octavio , Gudziki Pereira Rossiane Maria , Perdreau-Remington Françoise , Riley Lee W.
Published: August 2006

A variety of methods for genotyping
Staphylococcus aureus
isolates exists: the two most widely used methods are pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Here, we describe a sequence-based genotyping method based on genes encoding
S. aureus
superantigen-like proteins, which belong to a family of exotoxins called staphylococcal exotoxins. The sequences of PCR-amplified internal fragments of three different
set
genes (
set2
,
set5
, and
set7
) of 61 well-characterized clinical methicillin-resistant
S. aureus
(MRSA) and methicillin-susceptible
S. aureus
(MSSA) isolates and reference strains were compared. Phylogenetic analysis was performed based on single-nucleotide polymorphisms (SNP). The SNP dendrograms of the
set
gene sequences differentiated the 61 isolates into 22 distinct subgroups, designated exotoxin sequence types (ETST), while the standard seven-gene MLST profiles differentiated the same 61 isolates into 19 subgroups. Of the 19 different MLST subgroups, 16 corresponded to 16 distinct ETST groups. However, three MLST subgroups, ST1, ST30, and ST36, were each further separated into more than one ETST subgroup. The exotoxin-based genotyping method was able to discriminate MRSA and MSSA isolates according to their specific epidemiological characteristics. This SNP analysis of the three
set
genes is thus equally or more discriminatory than the seven-gene MLST method, providing a good alternative typing tool for a laboratory that has sequencing capability.
Enhanced Reverse Transcription-PCR Assay for Detection of Norovirus Genogroup I
Authors: Dreier Jens , Störmer Melanie , Mäde Dietrich , Burkhardt Sabine , Kleesiek Knut
Published: August 2006

We have developed a one-tube reverse transcription (RT)-PCR method using the real-time TaqMan PCR system for the detection of norovirus genogroup I (NV GGI). By introduction of a novel probe based on locked nucleic acid technology, we enhanced the sensitivity of the assay compared to those of conventional TaqMan probes. The sensitivity of the NV GGI RT-PCR was determined by probit analysis with defined RNA standards and quantified norovirus isolates to 711 copies/ml (95% detection limit). In order to detect PCR inhibition, we included a heterologous internal control (IC) system based on phage MS2. This internally controlled RT-PCR was tested on different real-time PCR platforms, LightCycler, Rotorgene, Mastercycler EP realplex, and ABI Prism. Compared to the assay without an IC, the duplex RT-PCR exhibited no reduction in sensitivity in clinical samples. In combination with an established NV GGII real-time RT-PCR, we used the novel assay in a routine assay for diagnosis of clinical and food-borne norovirus infection. We applied this novel assay to analyze outbreaks of nonbacterial acute gastroenteritis. Norovirus of GGI was detected in these outbreaks. Sequence and similarity plot analysis of open reading frame 1 (ORF1) and ORF2 showed two genotypes, GGI/2 and GGI/4, in semiclosed communities.
Molecular Identification of
Leuconostoc mesenteroides
as a Cause of Brain Abscess in an Immunocompromised Patient
Authors: Albanese Alessio , Spanu Teresa , Sali Michela , Novegno Federica , D'Inzeo Tiziana , Santangelo Rosaria , Mangiola Annunziato , Anile Carmelo , Fadda Giovanni
Published: August 2006

Leuconostoc
species are emerging pathogens that can cause severe infections, particularly in immunocompromised patients. Using molecular methods, we identified
Leuconostoc mesenteroides
as the cause of a brain abscess which was successfully treated by surgery and antimicrobial treatment. This is the first report of brain abscess caused by this species.
Therapeutic Failures of Antibiotics Used To Treat Macrolide-Susceptible
Streptococcus pyogenes
Infections May Be Due to Biofilm Formation
Authors: Baldassarri Lucilla , Creti Roberta , Recchia Simona , Imperi Monica , Facinelli Bruna , Giovanetti Eleonora , Pataracchia Marco , Alfarone Giovanna , Orefici Graziella
Published: August 2006

Streptococcus pyogenes
infections often fail to respond to antibiotic therapy, leading to persistent throat carriage and recurrent infections. Such failures cannot always be explained by the occurrence of antibiotic resistance determinants, and it has been suggested that
S. pyogenes
may enter epithelial cells to escape antibiotic treatment. We investigated 289
S. pyogenes
strains isolated from different clinical sources to evaluate their ability to form biofilm as an alternative method to escape antibiotic treatment and host defenses. Up to 90% of
S. pyogenes
isolates, from both invasive and noninvasive infections, were able to form biofilm. Specific
emm
types, such as
emm
6, appeared to be more likely to produce biofilm, although variations within strains belonging to the same type might suggest biofilm formation to be a trait of individual strains rather than a general attribute of a serotype. Interestingly, erythromycin-susceptible isolates formed a significantly thicker biofilm than resistant isolates (
P
< 0.05). Among resistant strains, those carrying the
erm
class determinants formed a less organized biofilm than the
mef
(A)-positive strains. Also,
prtF1
appeared to be negatively associated with the ability to form biofilm (
P
< 0.01). Preliminary data on a selection of strains indicated that biofilm-forming isolates entered epithelial cells with significantly lower efficiency than biofilm-negative strains. We suggest that
prtF1
-negative macrolide-susceptible or
mef
(A)-carrying isolates, which are poorly equipped to enter cells, may use biofilm to escape antimicrobial treatments and survive within the host. In this view, biofilm formation by
S. pyogenes
could be responsible for unexplained treatment failures and recurrences due to susceptible microorganisms.
First Report of Bacteremia by
Asaia bogorensis
, in a Patient with a History of Intravenous-Drug Abuse
Authors: Tuuminen Tamara , Heinäsmäki Terhi , Kerttula Tuija
Published: August 2006

We report the first documented case of bacteremia caused by
Asaia bogorensis
in a young patient with a history of intravenous-drug abuse.
A. bogorensis
was identified by sequencing the 16S rRNA gene. The isolate was exceptionally resistant to almost all antibiotics that are routinely tested for gram-negative rods but was susceptible to netilmicin, gentamicin, and doxycycline.
Azole Resistance of
Candida glabrata
in a Case of Recurrent Fungemia
Authors: Posteraro Brunella , Tumbarello Mario , La Sorda Marilena , Spanu Teresa , Trecarichi Enrico Maria , De Bernardis Flavia , Scoppettuolo Giancarlo , Sanguinetti Maurizio , Fadda Giovanni
Published: August 2006

We describe a case of recurrent
Candida glabrata
fungemia that became unresponsive to fluconazole treatment. Posttreatment isolates from blood and vaginal cultures of the immunocompetent patient were azole resistant and exhibited upregulated expression of
CgCDR1
/
CgCDR2
efflux pumps compared to the original isolates. Amphotericin B therapy eradicated the infection.
Use of an Immunochromatographic Dipstick Test for Rapid Detection of
Trypanosoma cruzi
in Sera from Animal Reservoir Hosts
Authors: Cardinal Marta V. , Reithinger Richard , Gürtler Ricardo E.
Published: August 2006

We evaluated an immunochromatographic dipstick test to detect
Trypanosoma cruzi
in canine serum samples from areas of endemicity (
n
= 141) and nonendemicity (
n
= 28) for Chagas' disease with known serological and xenodiagnostic test results. The dipstick test had a specificity of at least 94% and a sensitivity of at least 96%. The dipstick tested could become the first choice for screening purposes in disease surveillance or intervention programs.
Synergistes
Group Organisms of Human Origin
Authors: Horz Hans-Peter , Citron Diane M. , Warren Yumi A. , Goldstein Ellie J. C. , Conrads Georg
Published: August 2006

The bacterial division
Synergistes
represents a poorly characterized phylotype of which only a few isolates have been cultured, primarily from natural environments. Recent detection of
Synergistes
-like sequence types in periodontal pockets and caries lesions of humans prompted us to search the R. M. Alden culture collection (Santa Monica, Calif.) for biochemically unidentifiable, slow-growing, obligately anaerobic gram-negative bacilli. Here we report on five clinical isolates cultured from peritoneal fluid and two isolates from soft-tissue infections that together constitute three separate evolutionary lineages within the phylogenetic radiation of the division
Synergistes
. One of these clusters was formed by the peritoneal isolates and had an 85% similarity to
Synergistes jonesii
, the first described
Synergistes
species, which was isolated from the rumen of a goat. The isolates from soft-tissue infections, on the other hand, formed two distinct lineages moderately related to each other with a similarity of approximately 78%. In addition, by using a newly designed 16S rRNA gene-based PCR assay with intended target specificity for
Synergistes
, we found that the dominant phylotype from a fecal sample was nearly identical to that of the strains obtained from peritonitis. Conversely, sequence types detected in periodontal pockets formed a separate cluster that shared a similarity of only 80% with the soft-tissue isolates. These findings suggest a high diversity of medically important
Synergistes
clades that apparently are unique to individual ecological niches in the human body. In conclusion, we now have available the first characterized human isolates of the division
Synergistes
which are colonizing, and probably infecting, several sites in the human body.
Short-Sequence-Repeat Analysis ofMycobacterium aviumsubsp.paratuberculosisandMycobacterium aviumsubsp.aviumIsolates Collected from Animals Throughout the United States Reveals Both Stability of Loci and Extensive Diversity
Authors: Harris N. Beth , Payeur Janet B. , Kapur Vivek , Sreevatsan Srinand
Published: August 2006

We analyzed the multilocus short sequence repeats (SSRs) of 211 and 56 isolates ofMycobacterium aviumsubsp.paratuberculosisandM. aviumsubsp.avium, respectively. TheM. aviumsubsp.paratuberculosisisolates could be differentiated into 61 genotypes. TheM. aviumsubsp.aviumisolates showed limited diversity. These SSRs are stable and suitable for studying the molecular epidemiology ofM. aviumsubsp.paratuberculosis.