bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of a Ni cap layer on transparent Ni/Au ohmic contacts to p-GaN
Authors: Liu B. , Lambers E. , Alexander W. B. , Holloway P. H.
Published: October 2002

Ohmic contacts to p-GaN were obtained after annealing Ni/Au and Ni/Au/Ni contacts in flowing O2. Both Ni-capped p-GaN/Ni/Au and uncapped Ni/Au contacts were shown to result in specific contact resistance of ∼10−4 Ω cm2. In both cases, transparent NiO and thin, porous Au films were formed. Ni/Au contacts exhibited optical transmittance at λ=450 nm of >85%. Addition of the Ni cap layer was shown to increase the thermal stability of thin Ni/Au ohmic contacts and increase the 450 nm transmittance to 93%, while maintaining a low contact resistance. The ability of the capping layer to produce these improvements was discussed based on a total energy model of thin film morphology.
Plasmon damping in molecular beam epitaxial-grown InAs(100)
Authors: Veal T. D. , Bell G. R. , McConville C. F.
Published: October 2002

High-resolution electron-energy-loss spectroscopy (HREELS) has been used as a noninvasive probe to investigate the plasmon excitations and accumulation layers and determine the nominal electron mobility in the near-surface region of undoped molecular beam epitaxial-grown InAs(100). HREEL spectra were recorded at 300 and 600 K, over a wide range of incident electron energies, to observe the effects of temperature on the electron mobility, carrier concentration, surface state density, accumulation layer profile, and plasmon damping mechanisms. These data have been analyzed using semiclassical dielectric theory with a three-layer model, using a simple Drude dielectric function. A separate wave-vector-dependent Landau damping term was included to allow momentum scattering to be described independently by the usual phenomenological damping term. The probing electron energy and temperature dependence of this momentum damping is used to gauge the relative contributions of surface scattering, ionized impurity scattering, and phonon scattering. By extracting the surface scattering component of the plasmon damping, bulk mobility values have been estimated and are much higher than those determined from the high probing electron energy plasmon damping parameters. The bulk electron mobilities and bulk carrier concentrations are 28 800 cm2 V−1 s−1 and 2×1016 cm−3 at 300 K, respectively, and 12 900 cm2 V−1 s−1 and 2×1017 cm−3 at 600 K.
Triple crystal diffractometry, x-ray standing wave, and transmission electron microscopy investigation of shallow BF2 implantation in Si
Authors: Bocchi C. , Germini F. , Ghezzi G. , Gombia E. , Mosca R. , Nasi L. , Mukhamedzhanov E. Kh. , Privitera V. , Spinella C.
Published: October 2002

Si wafers implanted at 5, 15, and 50 keV with different BF2+ doses and next annealed at 945 °C for 45 s, were studied by means of x-ray triple crystal diffraction, x-ray standing wave, and transmission electron microscopy methods. Due to the implantation energies used, very narrow subsurface regions with a depth ranging from a few tens of nanometers to a few nanometers were damaged. By fitting the diffraction curves and using the information obtained from the photoelectrons emitted by the x-ray standing wave field, it was possible to determine the most appropriate strain and damage profiles versus depth within the disturbed region of the crystal. The above results made it possible to find: (i) the distribution of interstitial ions produced during the implant processes; (ii) the depth of amorphization of the implanted regions at the highest doses; and (iii) the appearance of extended defects (dislocation loops band) at the amorphous/crystal interface during the restoration of the lattice by the annealing process. Transmission electron microscopy investigations and electrochemical capacitance–voltage profiling measurements were made on several annealed samples and the results obtained by the x-ray diffraction and standing wave methods were confirmed.
Thermal effects in atomic-order nitridation of Si by a nitrogen plasma
Authors: Seino Takuya , Muto Daisuke , Matsuura Takashi , Murota Junichi
Published: October 2002

Thermal effects in atomic-order nitridation of Si(100) by an electron-cyclotron-resonance nitrogen plasma were investigated by controlling the Si surface temperature. It is found that the N atom concentration increases linearly and then tends to saturate with increasing plasma exposure time. In the radical reaction limited nitridation, the N atom concentration on the Si surface is normalized by the radical density in the nitrogen plasma, and the nitridation rate does not depend on the Si surface temperature above about −25 °C and decreases with decreasing the temperature below about −25 °C. The saturated N atom concentration is a single atomic layer and more than double atomic layers on the Si surface of about −80 °C and above about −25 °C, respectively. On the other hand, by the contribution of the incident ion, the nitridation of the deeper Si atoms below the surface is enhanced, and the saturated N atom concentration is lower at higher pressure and lower Si surface temperature. Consequently, it is suggested that the nitridation of the deeper Si atoms below the surface is enhanced with increasing ion energy as well as the Si surface temperature.
Formation of InAs/GaAs quantum dots by dewetting during cooling
Authors: Mirin R. P. , Roshko A. , van der Puijl M. , Norman A. G.
Published: October 2002

We describe a method to form InAs quantum dots on GaAs by cooling an InAs film that is deposited at high substrate temperatures. The reflection high-energy electron diffraction pattern taken after deposition of 1.9 monolayers of InAs on (100) GaAs at 540 °C does not display the characteristic spot pattern that is seen when three-dimensional islands form on the surface. The characteristic spot pattern appears when the sample is cooled to about 330 °C, indicating that the three-dimensional islands appear at this temperature. Atomic force microscopy confirms the existence of the islands. An explanation for this behavior based on an increase in intermixing at the InAs/GaAs interface is proposed.
Wafer temperature measurements during dielectric etching in a MERIE etcher
Authors: Gabriel Calvin T.
Published: October 2002

Using both chemical phase change and wireless thermistor temperature measurement techniques, wafer temperatures were measured during plasma processing in a MERIE dielectric etch tool. An inorganic low-k dielectric etch process was studied first, and many parameters were varied to determine their effect on wafer temperature. Wafer temperature rose rapidly when the plasma was turned on, approaching a stable temperature after about 30 s. When the lower electrode temperature setpoint or the rf power setting was increased, wafer temperature increased linearly. Wafer temperature decreased as backside He cooling pressure was increased. A dual-zone electrostatic chuck allowed separate control of center and edge He pressure, and these pressures were varied individually or together. Temperature measurements indicated that the zones give reasonably independent control of center and edge wafer temperature. Wafer temperature throughout a complete organic low-k dielectric stack etch process was also measured.
Distortion correction for x‐ray image intensifiers: Local unwarping polynomials and RBF neural networks
Authors: Cerveri P. , Forlani C. , Borghese N. A. , Ferrigno G.
Published: October 2002

In this paper we present two novel techniques, namely a local unwarping polynomial (LUP) and a hierarchical radial basis function (HRBF) network, to correct geometric distortions in XRIIimages. The two techniques have been implemented and compared, in terms of residual error measured at control and intermediate points, with local and global methods reported in the previous literature. In particular, LUP rests on a locally optimized 3rd degree polynomial applied within each quadrilateral cell on the rectilinear calibration grid of points. HRBF, based on a feed‐forward neural network paradigm, is constituted by a set of hierarchical layers at increasing cut‐off frequency, each characterized by a set of Gaussian functions. Extensive experiments have been performed both on simulated and real data. In simulation, we tested the effect of pincushion, sigmoidal and local distortions, along with the number of calibration points. Provided that a sufficient number of cells of the calibration grid is available, the obtained accuracy for both LUP and HRBF is comparable to or better than that of global polynomial technique. Tests on real data, carried out by using two different (12 in. and 16 in.) XRIIs, showed that the global polynomial accuracyis slightly worse than that of LUPand HRBFThe effects of the discontinuity at the border of the local areas and the decreased accuracy at intermediate points, typical of local techniques, have been proved to be smoothed for both LUP and HRBF.
Exploring the limits of spatial resolution in radiation dose delivery
Authors: Otto Karl , Clark Brenda G. , Huntzinger Calvin
Published: October 2002

Flexibility and complexity in patient treatment due to advances in radiotherapy techniques necessitates a simple method for evaluating spatial resolution capabilities of the dose delivery device. Our purpose in this investigation is to evaluate a model that describes the ability of a radiation therapy device to deliver a desired dose distribution. The model is based on linear systems theory and is analogous to methods used to describe resolution degradation in imaging systems. A qualitative analysis of spatial resolution degradation using the model is presented in the spatial and spatial frequency domains. The ability of the model to predict the effects of geometric dose conformity to treatment volumes is evaluated by varying multileaf collimator leaf width and magnitude of dose spreading. Dose distributions for three clinical treatment shapes, circular shapes of varying diameter and one intensity modulated shape are used in the evaluation. We show that the model accurately predicts the dependence of dose conformity on these parameters. The spatial resolution capabilities of different radiation therapy devices can be quantified using the model, providing a simple method for comparing different treatment machine characteristics. Also, as different treatment sites have different resolution requirements this model may be used to tailor machine characteristics to the specific site.
Word recognition in competing babble and the effects of age, temporal processing, and absolute sensitivity
Authors: Snell Karen B. , Mapes Frances M. , Hickman Elizabeth D. , Frisina D. Robert
Published: October 2002

This study was designed to clarify whether speech understanding in a fluctuating background is related to temporal processing as measured by the detection of gaps in noise bursts. Fifty adults with normal hearing or mild high-frequency hearing loss served as subjects. Gap detection thresholds were obtained using a three-interval, forced-choice paradigm. A 150-ms noise burst was used as the gap carrier with the gap placed close to carrier onset. A high-frequency masker without a temporal gap was gated on and off with the noise bursts. A continuous white-noise floor was present in the background. Word scores for the subjects were obtained at a presentation level of 55 dB HL in competing babble levels of 50, 55, and 60 dB HL. A repeated measures analysis of covariance of the word scores examined the effects of age, absolute sensitivity, and temporal sensitivity. The results of the analysis indicated that word scores in competing babble decreased significantly with increases in babble level, age, and gap detection thresholds. The effects of absolute sensitivity on word scores in competing babble were not significant. These results suggest that age and temporal processing influence speech understanding in fluctuating backgrounds in adults with normal hearing or mild high-frequency hearing loss.
Acoustic streaming related to minor loss phenomenon in differentially heated elements of thermoacoustic devices
Authors: Mironov Mikhail , Gusev Vitalyi , Auregan Yves , Lotton Pierrick , Bruneau Michel , Piatakov Pavel
Published: October 2002

It is demonstrated that the differentially heated stack, the heart of all thermoacoustic devices, provides a source of streaming additional to those associated with Reynolds stresses in quasi-unidirectional gas flow. This source of streaming is related to temperature-induced asymmetry in the generation of vortices and turbulence near the stack ends. The asymmetry of the hydrodynamic effects in an otherwise geometrically symmetric stack is due to the temperature difference between stack ends. The proposed mechanism of streaming excitation in annular thermoacoustic devices operates even in the absence of thermo-viscous interaction of sound waves with resonator walls.
Study on the prestressed sandwich piezoelectric ceramic ultrasonic transducer of torsional-flexural composite vibrational mode
Authors: Shuyu Lin
Published: October 2002

Based on the classical torsional and flexural vibrational theory of a slender rod, the prestressed sandwich torsional-flexural composite mode piezoelectric ceramic ultrasonic transducer is studied. This type of transducer consists of the slender metal rods and the longitudinally and tangentially polarized piezoelectric ceramic rings. The resonance frequency equations for the torsional and flexural vibrations in the transducers are derived. The simultaneous resonance of the torsional and flexural vibrations in the transducer is acquired by correcting the length of the metal slender rods resulting from the piezoelectric ceramic elements. The experimental results show that the measured resonance frequencies of the transducers are in good agreement with the computed ones, and the measured resonance frequencies of the torsional and the flexural vibrations in the composite transducers are also in good agreement with each other.
Transition from transient response to steady state for a layered medium
Authors: Liu Shaw-Wen , Ma Chien-Ching
Published: October 2002

The transition from transient response to steady-state for a layered medium subjected to antiplane loadings is studied. The steady-state formula for a layered medium is derived and the solutions for a layered half-space are then expressed explicitly in the form of wave number integrals. The transient response solutions for a layered half-space are obtained by the convolution of time harmonic loading function with transient response formula derived analytically from an effective matrix method. Two layered half-spaces with different ratios of wave velocities in the layer and half-space are considered and investigated by means of extensive numerical results to show their quite different transition behavior. The numerical results indicate that transient responses will approach steady state after certain characteristic times when the transient effects die away. The transition phenomena and characteristic times are investigated in detail through the responses from near field to far field as well as from low frequency to high frequency.
Resonance analysis of a 2D alluvial valley subjected to seismic waves
Authors: Chai Juin-Fu , Teng Tsung-Jen , Yeh Chau-Shioung , Shyu Wen-Shinn
Published: October 2002

The T-matrix formalism and an ultrasonic experiment are developed to study the scattering of in-plane waves for an alluvial valley embedded in a two-dimensional half-space. The solution of the in-plane scattering problem can be determined by the T-matrix method, where the basis functions are defined by the singular solutions of Lamb’s problems with surface loading in both horizontal and vertical directions. In the experiment, a thin steel plate with a semicircular aluminum plate attached on the edge is used to simulate the two-dimensional alluvial valley in the state of plane stress. Based on the spectra of displacement signals measured at the free edge of the scatterer, the resonance frequencies where the peaks appear can be identified. It can be shown that the nondimensional resonance frequency is one of the characteristic properties of the scattering system. Furthermore, it is noted that the nondimensional resonance frequencies measured experimentally are in good agreement with those calculated theoretically.
Applications of the direct Trefftz boundary element method to the free-vibration problem of a membrane
Authors: Chang Jiang Ren , Liu Ru Feng , Yeih Weichung , Kuo Shyh Rong
Published: October 2002

In this paper, the direct Trefftz method is applied to solve the free-vibration problem of a membrane. In the direct Trefftz method, there exists no spurious eigenvalue. However, an ill-posed nature of numerical instability encountered in the direct Trefftz method requires some treatments. The Tikhonov’s regularization method and generalized singular-value decomposition method are used to deal with such an ill-posed problem. Numerical results show the validity of the current approach.
Learning to perceive speech: How fricative perception changes, and how it stays the same
Authors: Nittrouer Susan
Published: October 2002

A part of becoming a mature perceiver involves learning what signal properties provide relevant information about objects and events in the environment. Regarding speech perception, evidence supports the position that allocation of attention to various signal properties changes as children gain experience with their native language, and so learn what information is relevant to recognizing phonetic structure in that language. However, one weakness in that work has been that data have largely come from experiments that all use similarly designed stimuli and show similar age-related differences in labeling. In this study, two perception experiments were conducted that used stimuli designed differently from past experiments, with different predictions. In experiment 1, adults and children (4, 6, and 8 years of age) labeled stimuli with natural /f/ and /θ/ noises and synthetic vocalic portions that had initial formant transitions varying in appropriateness for /f/ or /θ/. The prediction was that similar labeling patterns would be found for all listeners. In experiment 2, adults and children labeled stimuli with initial /s/-like and /∫/-like noises and synthetic vocalic portions that had initial formant transitions varying in appropriateness for /s/ or /∫/. The prediction was that, as found before, children would weight formant transitions more and fricative noises less than adults, but that this age-related difference would elicit different patterns of labeling from those found previously. Results largely matched predictions, and so further evidence was garnered for the position that children learn which properties of the speech signal provide relevant information about phonetic structure in their native language.
Increase in the Asian Southwest Monsoon During the Past Four Centuries
Authors: Anderson David M. , Overpeck Jonathan T. , Gupta Anil K.
Published: October 2002

Climate reconstructions reveal unprecedented warming in the past century; however, little is known about trends in aspects such as the monsoon. We reconstructed the monsoon winds for the past 1000 years using fossilGlobigerina bulloidesabundance in box cores from the Arabian Sea and found that monsoon wind strength increased during the past four centuries as the Northern Hemisphere warmed. We infer that the observed link between Eurasian snow cover and the southwest monsoon persists on a centennial scale. Alternatively, the forcing implicated in the warming trend (volcanic aerosols, solar output, and greenhouse gases) may directly affect the monsoon. Either interpretation is consistent with the hypothesis that the southwest monsoon strength will increase during the coming century as greenhouse gas concentrations continue to rise and northern latitudes continue to warm.
Dipole Moments of Highly Vibrationally Excited Water
Authors: Callegari Andrea , Theulé Patrice , Muenter John S. , Tolchenov Roman N. , Zobov Nikalai F. , Polyansky Oleg L. , Tennyson Jonathan , Rizzo Thomas R.
Published: October 2002

The intensity of water absorption in the region of the solar spectrum plays a dominant role in atmospheric energy balance and hence strongly influences climate. Significant controversy exists over how to model this absorption accurately. We report dipole moment measurements of highly vibrationally excited water, which provide stringent tests of intensities determined by other means. Our measurements and accompanying calculations suggest that the best currently available potential and dipole surfaces do not accurately model intensities in the optical spectrum of water.
Fork Reversal and ssDNA Accumulation at Stalled Replication Forks Owing to Checkpoint Defects
Authors: Sogo José M. , Lopes Massimo , Foiani Marco
Published: October 2002

Checkpoint-mediated control of replicating chromosomes is essential for preventing cancer. In yeast, Rad53 kinase protects stalled replication forks from pathological rearrangements. To characterize the mechanisms controlling fork integrity, we analyzed replication intermediates formed in response to replication blocks using electron microscopy. At the forks, wild-type cells accumulate short single-stranded regions, which likely causes checkpoint activation, whereas
rad53
mutants exhibit extensive single-stranded gaps and hemi-replicated intermediates, consistent with a lagging-strand synthesis defect. Further,
rad53
cells accumulate Holliday junctions through fork reversal. We speculate that, in checkpoint mutants, abnormal replication intermediates begin to form because of uncoordinated replication and are further processed by unscheduled recombination pathways, causing genome instability.
Structure of the Extracellular Region of HER3 Reveals an Interdomain Tether
Authors: Cho Hyun-Soo , Leahy Daniel J.
Published: October 2002

We have determined the 2.6 angstrom crystal structure of the entire extracellular region of human HER3 (ErbB3), a member of the epidermal growth factor receptor (EGFR) family. The structure consists of four domains with structural homology to domains found in the type I insulin-like growth factor receptor. The HER3 structure reveals a contact between domains II and IV that constrains the relative orientations of ligand-binding domains and provides a structural basis for understanding both multiple-affinity forms of EGFRs and conformational changes induced in the receptor by ligand binding during signaling. These results also suggest new therapeutic approaches to modulating the behavior of members of the EGFR family.
Est1p As a Cell Cycle-Regulated Activator of Telomere-Bound Telomerase
Authors: Taggart Andrew K. P. , Teng Shu-Chun , Zakian Virginia A.
Published: October 2002

In
Saccharomyces cerevisiae,
the telomerase components Est2p,
TLC1
RNA, Est1p, and Est3p are thought to form a complex that acts late during chromosome replication (S phase) upon recruitment by Cdc13p, a telomeric DNA binding protein. Consistent with this model, we show that Est1p, Est2p, and Cdc13p are telomere-associated at this time. However, Est2p, but not Est1p, also binds telomeres before late S phase. The
cdc13-2
allele has been proposed to be defective in recruitment, yet Est1p and Est2p telomere association persists in
cdc13-2
cells. These findings suggest a model in which Est1p binds telomeres late in S phase and interacts with Cdc13p to convert inactive, telomere-bound Est2p to an active form.
Checking That Replication Breakdown Is Not Terminal
Authors: Carr Antony M.
Published: October 2002

Two new studies help to clarify the relationship between checkpoint proteins, recombination, and replication fork integrity.
Importance of the Fourth Alpha-Helix within the CAP Homology Domain of Type II Topoisomerase for DNA Cleavage Site Recognition and Quinolone Action
Authors: Strumberg Dirk , Nitiss John L. , Dong Jiaowang , Walker Jerrylaine , Nicklaus Marc C. , Kohn Kurt W. , Heddle Jonathan G. , Maxwell Anthony , Seeber Siegfried , Pommier Yves
Published: October 2002

We report that point mutations causing alteration of the fourth alpha-helix (α4-helix) of the CAP homology domain of eukaryotic (
Saccharomyces cerevisiae
) type II topoisomerases (Ser
740
Trp, Gln
743
Pro, and Thr
744
Pro) change the selection of type II topoisomerase-mediated DNA cleavage sites promoted by Ca
2+
or produced by etoposide, the fluoroquinolone CP-115,953, or mitoxantrone. By contrast, Thr
744
Ala substitution had minimal effect on Ca
2+
- and drug-stimulated DNA cleavage sites, indicating the selectivity of single amino acid substitutions within the α4-helix on type II topoisomerase-mediated DNA cleavage. The equivalent mutation in the gene for
Escherichia coli
gyrase causing Ser
83
Trp also changed the DNA cleavage pattern generated by Ca
2+
or quinolones. Finally, Thr
744
Pro substitution in the yeast type II topoisomerase rendered the enzyme sensitive to antibacterial quinolones. This study shows that the α4-helix within the conserved CAP homology domain of type II topoisomerases is critical for selecting the sites of DNA cleavage. It also demonstrates that selective amino acid residues in the α4-helix are important in determining the activity and possibly the binding of quinolones to the topoisomerase II-DNA complexes.
Oxidative Stress Increases Susceptibility of
Mycobacterium tuberculosis
to Isoniazid
Authors: Bulatovic Vanja M. , Wengenack Nancy L. , Uhl James R. , Hall Leslie , Roberts Glenn D. , Cockerill Franklin R. , Rusnak Frank
Published: October 2002

Isoniazid is a first-line antibiotic used in the treatment of infections caused by
Mycobacterium tuberculosis
. Isoniazid is a prodrug requiring oxidative activation by the catalase-peroxidase hemoprotein, KatG. Resistance to isoniazid can be obtained by point mutations in the
katG
gene, with one of the most common being a threonine-for-serine substitution at position 315 (S315T). The S315T mutation is found in more than 50% of isoniazid-resistant clinical isolates and results in an ≈200-fold increase in the MIC of isoniazid compared to that for
M. tuberculosis
H37Rv. In the present study we investigated the hypothesis that superoxide plays a role in KatG-mediated isoniazid activation. Plumbagin and clofazimine, compounds capable of generating superoxide anion, resulted in a lower MIC of isoniazid for
M. tuberculosis
H37Rv and a strain carrying the S315T mutation. These agents did not cause as great of an increase in isoniazid susceptibility in the mutant strain when the susceptibilities were assessed by using the inhibitory concentration that causes a 50% decrease in growth. These results provide evidence that superoxide can play a role in isoniazid activation. Since clofazimine alone has antitubercular activity, the observation of synergism between clofazimine and isoniazid raises the interesting possibility of using both drugs in combination to treat
M. tuberculosis
infections.
Method for Estimation of Low Outer Membrane Permeability to β-Lactam Antibiotics
Authors: Lakaye Bernard , Dubus Alain , Joris Bernard , Frère Jean-Marie
Published: October 2002

The outer membrane of gram-negative bacteria plays a major role in β-lactam resistance as it slows down antibiotic entry into the periplasm and therefore acts in synergy with β-lactamases and efflux systems. Up to now, the quantitative estimation of low outer membrane permeability by the method of Zimmermann and Rosselet was difficult because of the secreted and cell surface-associated β-lactamases. The method presented here uses the acylation of a highly sensitive periplasmic penicillin-binding protein (PBP) (BlaR-CTD) to assess the rate of β-lactam penetration into the periplasm. The method is dedicated to measurement of low permeability and is only valid when the diffusion rate through the outer membrane is rate limiting. Cytoplasmic membrane associated PBPs do not interfere since they are acylated after the very sensitive BlaR-CTD. This method was used to measure the permeability of β-lactamase-deficient strains of
Enterobacter cloacae
and
Enterobacter aerogenes
to benzylpenicillin, ampicillin, carbenicillin, cefotaxime, aztreonam, and cephacetrile. Except for that of cephacetrile, the permeability coefficients were equal to or below 10
−7
cm/s. For cephacetrile, carbenicillin, and benzylpenicillin, the outer membrane of
E. cloacae
was 20 to 60 times less permeable than that of
Escherichia coli
, whereas for cefotaxime, aztreonam, and ampicillin it was, respectively, 400, 1,000, and 700 times less permeable. The permeability coefficient for aztreonam is the lowest ever measured (
P
= 3.2 × 10
−9
cm/s). Using these values, the MICs for a β-lactamase-overproducing strain of
E. cloacae
were successfully predicted, demonstrating the validity of the method.
Functional Characterization of
Brucella melitensis
NorMI, an Efflux Pump Belonging to the Multidrug and Toxic Compound Extrusion Family
Authors: Braibant Martine , Guilloteau Laurence , Zygmunt Michel S.
Published: October 2002

Two putative proteins (NorMI and NorMII) similar to the multidrug efflux protein NorM of
Vibrio parahaemolyticus
are encoded by the
Brucella melitensis
16 M genome. We show that a drug-hypersusceptible
Escherichia coli
strain overexpressing NorMI displays increased resistance to norfloxacin, ciprofloxacin, gentamicin, tetraphenylphosphonium ion, acriflavine, and berberine. This elevated resistance was proven to be mediated by an energy-dependent efflux mechanism. NorMI belongs to the multidrug and toxic compound extrusion family and is the first multidrug efflux protein identified in
Brucella
spp.
Efficacies of Quinupristin-Dalfopristin Combined with Vancomycin In Vitro and in Experimental Endocarditis Due to Methicillin-Resistant
Staphylococcus aureus
in Relation to Cross-Resistance to Macrolides, Lincosamides, and Streptogramin B- Type Antibiotics
Authors: Pavie Juliette , Lefort Agnès , Zarrouk Virginie , Chau Françoise , Garry Louis , Leclercq Roland , Fantin Bruno
Published: October 2002

A beneficial effect of the combination of quinupristin-dalfopristin and vancomycin was observed against two methicillin-resistant strains of
Staphylococcus aureus
harboring or not harboring the
ermC
gene, which codes for constitutive macrolide, lincosamide, and streptogramin B resistance. The beneficial effect was observed in time-kill studies, in which the drugs were used at inhibitory concentrations, and in a rabbit model of endocarditis, in which the combination was highly bactericidal and more active than monotherapies.
Effect of Lamivudine on Transmission of Human T-Cell Lymphotropic Virus Type 1 to Adult Peripheral Blood Mononuclear Cells In Vitro
Authors: Balestrieri Emanuela , Forte Giancarlo , Matteucci Claudia , Mastino Antonio , Macchi Beatrice
Published: October 2002

The effects of lamivudine (3TC) on in vitro infection of peripheral blood mononuclear cells (PBMC) from healthy donors with human T-cell lymphotropic virus type 1 (HTLV-1) were investigated. Direct measures of viral replication (viral DNA, RNA, and protein) all gave similar, very high 50% inhibitory concentrations in comparison with those previously reported for zidovudine. Nevertheless, 3TC inhibited HTLV-1-driven long-term growth of infected PBMC in vitro at concentrations (6.25 μM) which had poor or no direct antiviral effects, suggesting that another mechanism may be playing a role.
Comparative Evaluation of Disk Diffusion with Microdilution Assay in Susceptibility Testing of Caspofungin against
Aspergillus
and
Fusarium
Isolates
Authors: Arikan Sevtap , Paetznick Victor , Rex John H.
Published: October 2002

We compared the disk diffusion and broth microdilution methods for susceptibility testing of caspofungin against
Aspergillus
(
n
= 78) and
Fusarium
(
n
= 22) isolates. Microdilution testing followed the NCCLS M-38P guidelines but was performed in antibiotic medium 3 supplemented to 2% glucose (AM3). Disk diffusion assays were performed on AM3 agar plates with a 2-μg caspofungin disk. By both methods, caspofungin showed favorable activity against
Aspergillus
isolates and no activity against
Fusarium
isolates. In the disk-based format, intrazonal growth that was not influenced by the drug concentration gradient was consistently observed for all of the
Aspergillus
isolates tested.
Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin
Authors: Reed David W. , Fujita Yoshiko , Delwiche Mark E. , Blackwelder D. Brad , Sheridan Peter P. , Uchida Takashi , Colwell Frederick S.
Published: October 2002

Microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the Nankai Trough near Japan were characterized with cultivation-dependent and -independent techniques. Acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. Lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial subsurface environments at similar depths. Archaeal lipids were more abundant than bacterial lipids. Methane was produced from both acetate and hydrogen in enrichments inoculated with sediment from all depths evaluated, at both 10 and 35°C. Characterization of 16S rRNA genes amplified from the sediments indicated that archaeal clones could be discretely grouped within theEuryarchaeotaandCrenarchaeotadomains. The bacterial clones exhibited greater overall diversity than the archaeal clones, with sequences related to theBacteroidetes,Planctomycetes,Actinobacteria,Proteobacteria, and green nonsulfur groups. The majority of the bacterial clones were either members of a novel lineage or most closely related to uncultured clones. The results of these analyses suggest that the microbial community in this environment is distinct from those in previously characterized methane hydrate-bearing sediments.
Microstructure of Anaerobic Granules Bioaugmented with
Desulfitobacterium frappieri
PCP-1
Authors: Lanthier M. , Tartakovsky B. , Villemur R. , DeLuca G. , Guiot S. R.
Published: October 2002

Oligonucleotide probes were used to study the structure of anaerobic granular biofilm originating from a pentachlorophenol-fed upflow anaerobic sludge bed reactor augmented with
Desulfitobacterium frappieri
PCP-1. Fluorescence in situ hybridization demonstrated successful colonization of anaerobic granules by strain PCP-1. Scattered microcolonies of strain PCP-1 were detected on the biofilm surface after 3 weeks of reactor operation, and a dense outer layer of strain PCP-1 was observed after 9 weeks. Hybridization with probes specific for
Eubacteria
and
Archaea
probes showed that
Eubacteria
predominantly colonized the outer layer, while
Archaea
were observed in the granule interior. Mathematical simulations showed a distribution similar to that observed experimentally when using a specific growth rate of 2.2 day
−1
and a low bacterial diffusion of 10
−7
dm
2
day
−1
. Also, the simulations showed that strain PCP-1 proliferation in the outer biofilm layer provided excellent protection of the biofilm from pentachlorophenol toxicity.
Detection and Differentiation of Chlamydiae by Fluorescence In Situ Hybridization
Authors: Poppert Sven , Essig Andreas , Marre Reinhard , Wagner Michael , Horn Matthias
Published: October 2002

Chlamydiae are important pathogens of humans and animals but diagnosis of chlamydial infections is still hampered by inadequate detection methods. Fluorescence in situ hybridization (FISH) using rRNA-targeted oligonucleotide probes is widely used for the investigation of uncultured bacteria in complex microbial communities and has recently also been shown to be a valuable tool for the rapid detection of various bacterial pathogens in clinical specimens. Here we report on the development and evaluation of a hierarchic probe set for the specific detection and differentiation of chlamydiae, particularly
C. pneumoniae
,
C. trachomatis
,
C. psittaci
, and the recently described chlamydia-like bacteria comprising the novel genera
Neochlamydia
and
Parachlamydia
. The specificity of the nine newly developed probes was successfully demonstrated by in situ hybridization of experimentally infected amoebae and HeLa 229 cells, including HeLa 229 cells coinfected with
C. pneumoniae
and
C. trachomatis
. FISH reliably stained chlamydial inclusions as early as 12 h postinfection. The sensitivity of FISH was further confirmed by combination with direct fluorescence antibody staining. In contrast to previously established detection methods for chlamydiae, FISH was not susceptible to false-positive results and allows the detection of all recognized chlamydiae in one single step.
Noninvasive Measurement of Bacterial Intracellular pH on a Single-Cell Level with Green Fluorescent Protein and Fluorescence Ratio Imaging Microscopy
Authors: Olsen Katja N. , Budde Birgitte B. , Siegumfeldt Henrik , Rechinger K. Björn , Jakobsen Mogens , Ingmer Hanne
Published: October 2002

We show that a pH-sensitive derivative of the green fluorescent protein, designated ratiometric GFP, can be used to measure intracellular pH (pH
i
) in both gram-positive and gram-negative bacterial cells. In cells expressing ratiometric GFP, the excitation ratio (fluorescence intensity at 410 and 430 nm) is correlated to the pH
i
, allowing fast and noninvasive determination of pH
i
that is ideally suited for direct analysis of individual bacterial cells present in complex environments.
virB-Mediated Survival ofBrucella abortusin Mice and Macrophages Is Independent of a Functional Inducible Nitric Oxide Synthase or NADPH Oxidase in Macrophages
Authors: Sun Yao-Hui , den Hartigh Andreas B. , Santos Renato de Lima , Adams L. Garry , Tsolis Renée M.
Published: October 2002

TheBrucella abortus virBlocus is required for establishing chronic infection in the mouse. Using in vitro and in vivo models, we investigated whethervirBis involved in evasion of the bactericidal activity of NADPH oxidase and the inducible nitric oxide synthase (iNOS) in macrophages. Elimination of NADPH oxidase or iNOS activity in macrophages in vitro increased recovery of wild-typeB. abortusbut not recovery of avirBmutant. In mice lacking either NADPH oxidase or iNOS, however,B. abortusinfected and persisted to the same extent as it did in congenic C57BL/6 mice up until 60 days postinfection, suggesting that these host defense mechanisms are not critical for limiting bacterial growth in the mouse. AvirBmutant did not exhibit increased survival in either of the knockout mouse strains, indicating that this locus does not contribute to evasion of nitrosative or oxidative killing mechanisms in vivo.
Induction of the Gene Encoding Macrophage Chemoattractant Protein 1 byOrientia tsutsugamushiin Human Endothelial Cells Involves Activation of Transcription Factor Activator Protein 1
Authors: Cho Nam-Hyuk , Seong Seung-Yong , Huh Myung-Sook , Kim Na-Hyun , Choi Myung-sik , Kim Ik-sang
Published: October 2002

Human macrophage chemoattractant protein 1 (MCP-1) is a potent mediator of macrophage migration and therefore plays an essential role in early events of inflammation. In endothelial cells, at least three independent pathways regulate MCP-1 expression by NF-κB and AP-1.Orientia tsutsugamushicauses vasculitis in humans by replicating inside macrophages and endothelial cells. In the present study, we investigated thecis-acting andtrans-acting elements involved inO. tsutsugamushi-induced MCP-1 gene expression in human umbilical vein endothelial cells (HUVEC). Although NF-κB activation was observed in HUVEC infected withO. tsutsugamushi, inhibition of NF-κB activation did not affect the MCP-1 expression. However, treatment of HUVEC with extracellular signal-regulated kinase (ERK) kinase inhibitor or p38 mitogen-activated protein kinase (MAPK) inhibitor suppressed expression of MCP-1 mRNA concomitant with downregulation of activator protein 1 (AP-1) activation. Deletion of triphorbol acetate response elements (TRE) at position −69 to −63 of MCP-1 gene abolished inducible promoter activity. Deletion of TRE at position −69 to −63−96 to −90 or deletion of NF-κB-binding site at position −69 to −63−88 to −79 did not affect the inducibility of promoter. Site-directed mutagenesis of the NF-κB binding sites at positions −2640 to −2632, −2612 to −2603 in the enhancer region, or the AP-1 biding site at position −2276 to −2270 decreased the inducible activity of the promoter. Taken together, AP-1 activation by both the ERK pathway and the p38 MAPK pathway as well as their binding to TRE at position −69 to −63 in proximal promoter and TRE at position −2276 to −2270 in enhancer region is altogether essential in induction of MCP-1 mRNA in HUVEC infected withO. tsutsugamushi. Although NF-κB activation is not essential per se, the κB site in the enhancer region is important in MCP-1 induction of HUVEC. This discrepancy in the involvement of the NF-κB may be due to the function of chromatin structures and other transcription cofactors in the regulation of MCP-1 gene expression in response toO. tsutsugamushiinfectioin.
Effect of Vaccination with Carrier Protein on Response to Meningococcal C Conjugate Vaccines and Value of Different Immunoassays as Predictors of Protection
Authors: Burrage Moya , Robinson Andrew , Borrow Ray , Andrews Nick , Southern Joanna , Findlow Jamie , Martin Sarah , Thornton Carol , Goldblatt David , Corbel Michael , Sesardic Dorothea , Cartwight Keith , Richmond Peter , Miller Elizabeth
Published: October 2002

In order to plan for the wide-scale introduction of meningococcal C conjugate (MCC) vaccine for United Kingdom children up to 18 years old, phase II trials were undertaken to investigate whether there was any interaction between MCC vaccines conjugated to tetanus toxoid (TT) or a derivative of diphtheria toxin (CRM
197
) and diphtheria-tetanus vaccines given for boosting at school entry or leaving. Children (
n
= 1,766) received a diphtheria-tetanus booster either 1 month before, 1 month after, or concurrently with one of three MCC vaccines conjugated to CRM
197
or TT. All of the MCC vaccines induced high antibody responses to the serogroup C polysaccharide that were indicative of protection. The immune response to the MCC-TT vaccine was reduced as a result of prior immunization with a tetanus-containing vaccine, but antibody levels were still well above the lower threshold for protection. Prior or simultaneous administration of a diphtheria-containing vaccine did not affect the response to MCC-CRM
197
vaccines. The immune responses to the carrier proteins were similar to those induced by a comparable dose of diphtheria or tetanus vaccine. The results also demonstrate that, for these conjugate vaccines in these age groups, both standard enzyme-linked immunosorbent assays and those that measure high-avidity antibodies to meningococcal C polysaccharide correlated equally well with assays that measure serum bactericidal antibodies, the established serological correlate of protection for MCC vaccines.
Identification and Characterization of aBrucella abortusATP-Binding Cassette Transporter Homolog toRhizobium melilotiExsA and Its Role in Virulence and Protection in Mice
Authors: Rosinha G. M. S. , Freitas Daniela A. , Miyoshi Anderson , Azevedo Vasco , Campos Eleonora , Cravero Silvio L. , Rossetti Osvaldo , Splitter Gary , Oliveira S. C.
Published: October 2002

Brucella abortusis a facultative intracellular bacterial pathogen that causes abortion in domestic animals and undulant fever in humans. The mechanism of virulence ofBrucellaspp. is not fully understood yet. Furthermore, genes that allowBrucellato reach the intracellular niche and to interact with host cells need to be identified. Using the genomic survey sequence (GSS) approach, we identified the gene encoding an ATP-binding cassette (ABC) transporter ofB. abortusstrain S2308. The deduced amino acid sequence encoded by this gene exhibited 69 and 67% identity with the sequences of the ABC transporters encoded by theexsAgenes ofRhizobium melilotiandMesorhizobium loti, respectively. Additionally,B. abortusExsA, likeR. melilotiandM. lotiExsA, possesses ATP-binding motifs and the ABC signature domain features of a typical ABC transporter. Furthermore, ortholog group analysis placedB. abortusExsA in ortholog group 6 of ABC transporters more likely to be involved in bacterial pathogenesis. InR. meliloti, ExsA is an exopolysaccharide transporter essential for alfalfa root nodule invasion and establishment of infection. To test the role of ExsA inBrucellapathogenesis, anexsAdeletion mutant was constructed. Replacement of the wild-typeexsAby recombination was demonstrated by Southern blot analysis ofBrucellagenomic DNA. Decreased survival in mice of theBrucella ΔexsAmutant compared to the survival of parental strain S2308 demonstrated that ExsA is critical for full bacterial virulence. Additionally, theB. abortus exsAdeletion mutant was used as a live vaccine. Challenge experiments revealed that theexsAmutant strain induced superior protective immunity in BALB/c mice compared to the protective immunity induced by strain S19 or RB51.
Genomic Analysis ofClostridium perfringensBacteriophage φ3626, Which Integrates intoguaAand Possibly Affects Sporulation
Authors: Zimmer Markus , Scherer Siegfried , Loessner Martin J.
Published: October 2002

Two temperate viruses, φ3626 and φ8533, have been isolated from lysogenicClostridium perfringensstrains. Phage φ3626 was chosen for detailed analysis and was inspected by electron microscopy, protein profiling, and host range determination. For the first time, the nucleotide sequence of a bacteriophage infectingClostridiumspecies was determined. The virus belongs to theSiphoviridaefamily of the tailed phages, the orderCaudovirales. Its genome consists of a linear double-stranded DNA molecule of 33,507 nucleotides, with invariable 3′-protruding cohesive ends of nine residues. Fifty open reading frames were identified, which are organized in three major life cycle-specific gene clusters. The genes required for lytic development show an opposite orientation and arrangement compared to the lysogeny control region. A function could be assigned to 19 gene products, based upon bioinformatic analyses, N-terminal amino acid sequencing, or experimental evidence. These include DNA-packaging proteins, structural components, a dual lysis system, a putative lysogeny switch, and proteins that are involved in replication, recombination, and modification of phage DNA. The presence of genes encoding a putative sigma factor related to sporulation-dependent sigma factors and a putative sporulation-dependent transcription regulator suggests a possible interaction of φ3626 with onset of sporulation inC. perfringens. We found that the φ3626 attachment siteattPlies in a noncoding region immediately downstream ofint. Integration of the viral genome occurs into the bacterial attachment siteattB, which is located within the 3′ end of aguaAhomologue. This essential housekeeping gene is functionally independent of the integration status, due to reconstitution of its terminal codons by phage sequence.