bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of broadband noise on two-tone suppression
Authors: Jesteadt Walt , Weber Daniel L. , Habler Betty L.
Published: October 2005

We measured the forward-masked threshold for a 20-ms, 1000-Hz sinusoidal probe as a function of the levels of a 290-ms, 1000-Hz sinusoidal masker (30–70 dB SPL) and of a 539-Hz sinusoidal suppressor 20–90 dB SPL) presented simultaneously with the masker. At the highest suppressor and musket levels, addition of the suppressor to the masker resulted in a 10-dB reduction in threshold for the probe. These measurements were repeated with a broadband noise (low-pass filtered at 5000 Hz, 20-dB No) presented either during the masker interval or during both the masker and the probe intervals. When added during only the masker interval, the noise had no effect on the probe threshold except in conditions where the noise itself produced more forward masking than either sinusoid. When the noise was presented during both the masker and probe intervals, probe thresholds increased over the level predicted by a simple addition of masker effects. In these “continuous-noise” conditions, adding the suppressor to the masker caused a reduction in probe threshold that was only sightly less than observed in the absence of the noise. We can account for these results by assuming that the nonlinear interaction of the forward masker and the noise occurs after the suppressor has reduced the effective level of the forward masker. [Research supported by NIH and NSF.]
Profile analysis and the critical band
Authors: Green David M. , Kidd Gerald , Mason Christine R.
Published: October 2005

The signal is a 1000-Hz sinusoid added to a complex of several equal amplitude tones. The overall level of the complex varies by + −20 dB within trials of the two-alternative forced-choice task. Thus the detection problem is essentially that of detecting a bump in an otherwise flat spectrum. Consider first the detectability of the signal when added, in phase, to a complex consisting of three components whose frequencies are 725, 1000, and 1380 Hz. Now suppose we add components to this complex by placing additional components above and below our extreme frequencies. The additional components are added so the frequency ratios between sucessive components are all equal. Finally we have nineteen components extending from 200 to 5000 Hz surrounding the 1000-Hz component. The signal is some 10 to 15 dB easier to hear in this multicomponent complex than in the original three component complex. How is this possible since the components nearest to the signal in frequency are at least two critical bands away?. [This work was supported by the NIH.]
A severe departure from Weber's law
Authors: Carlyon Robert P. , Moore Brian C. J.
Published: October 2005

Intensity discrimination for 225-ms sinusoids with frequencies of 500, 4000, and 6500 Hz was measured at 25, 55, and 85 dB SPL both in the presence and absence of band-reject noise centered at the signal frequency. For the lower two frequencies Weber's law, or a near miss to it, was obtained. At 6500 Hz the Weber fraction increased from 25 to 55 dB and decreased again at 85 dB both in the presence and absence of band-reject noise. Removing intensity information conveyed by dynamic responses to stimulus onsets, by masking tone onsets with short burst of bandpass noise, had no effect. Reducing duration to 30 ms greatly increased the deterioration at 55 dB and 6500 Hz, but had little effect at other level/frequency combinations. The results are consistent with a bimodal distribution of thresholds in primary auditory neurons. The absence of a level effect at the lower two frequencies may be explained by phase-locking cues extending the range over which VIIth nerve fibers can signal changes in intensity [Work supported by SERC.]
Spectral-shape discrimination of synthetic plosive bursts
Authors: Farrat C. L. , Reed C. M. , Durlach N. I. , Braida L. D. , Zurek P. M.
Published: October 2005

The objective of this research is to measure the discriminability of speech-like sounds on the basis of spectral shape alone and to relate these measurements to underlying auditory abilities by means of psychoacoustic experiments and quantitative models. Preliminary measurement using normal-hearing listeners have been obtained on: (a) the discriminability of two synthetic plosive bursts (corresponding to /p/ and /t/ bursts in the context C /a/) and (b) the discriminability of incremental changes in the spectral shape os each synthetic stimulus in various frequency regions. Loundness and duration cues were eliminated by roving intensities and equating durations, and the difficulty of the tasks was controlled by adding low-pass noise at various S/N ratios. The talk will include a description of the data and of initial attempts to develop a quantitative theoretical model of spectral shape discrimination. [Work supported by NIH.]
The reflection of acoustic waves from water/composite interfaces
Authors: Nayfeh Adnan H. , Crane Robert L. , Hoppe Wally C.
Published: October 2005

Theoretical and experimental results are presented for the reflection of acoustic waves from liquid-fibrous composite interfaces. For this purpose the composite is oriented such that the fibers are parallel to the propagation directions. Because of the complex microstructure of composites, continuity conditions exist on both the macro and micro scales. On the macro scale the continuity conditions across the fluid-composite interface must be satisfied, while on the micro scale appropriate conditions along the fiber and matrix interface must also be fulfilled. Due to the number and nature of these conditions exact solutions would be exceedingly difficult, if not impossible to obtain. As an alternative we formulate an approximate analysis in which the composite medium is replaced by a homogeneous, yet dispersive medium. In the process of replacing the composite with such a material model, the micro continuity conditions are utilized. The validity of the analytical model is verified by different comparison of the dispersion relations and indirect comparisons of the actual reflected energy with experiments for graphite/epoxy and boron/epoxy composites. Results are found to correlate very well especially at low frequency ranges as is expected from the analytical modeling. [Research of A. H. N. is supported by NSF Grant CME 8021054 and AF Contract F33615-80-C-5015.]
The acoustic resonance modes of two and three layers
Authors: Dreyer John F.
Published: October 2005

Comprehensive equations for the acoustic wave pressure propagation through two and three layers are derived using the exponential method. The two resonant modes for two layers and four for three layers are described. They are expressed relative to φ which = fd 2π/c. The three layer equation consists of eight sinusoidal permutations related with impedances. Their plus or minus combinations control the modes. This equation is verified by test using two layers in water. Under this condition the maximum transmission is obtained when tan φ2 × tan φ3 = 2(Z1)(Z2)/[(Z1)2 + (Z2)2]. The comprehensive three-layer equation is: For three layers A5A1 = 2[[−+++[1+z1z5]cosφ2 cosφ3 cosφ4++−+[z1z4z3z5+z3z4]cosφ2 sinφ3 sinφ4+−++[z1z4z2z5+z2z4]sinφ2 cosφ3 sinφ4+++−[z2z3+z1z3z2z5]sinφ2 sinφ3 cosφ4]2+[+−+−[z4z5+z1z4] cosφ2 cosφ3 sinφ4++++[z1z3+z3z5] cosφ2 sinφ3 cosφ4+−−+[z1z2+z2z5] sinφ2 cosφ3 cosφ4−−++[z2z4z3z5+z1z3z2z4]sinφ2 sinφ3 sinφ4]2]12
Turbulence effects on acoustic wave propagation over a smooth surface
Authors: Clifford Steven F. , Lataitis Richard I.
Published: October 2005

Turbulence produces fluctuations in the observed amplitude and phase of the direct and reflected waves whose sum constitutes the sound field p of an acoustic point source radiating above a smooth boundary. A perturbation approach is used to evaluate the corresponding long-term average of the mean-square pressure field p2. The result is energy conserving and is general enough to allow the insertion of an arbitrary refractive-index correlation function. The effect of turbulence is shown to modify only the interference term of the resulting expression, and can be completely expressed in terms of a relatively simple function of the sum of the direct and reflected wave variances, the wave variance being the sum of the variances corresponding to the amplitude and phase fluctuations, and a quantity describing the lateral correlation between the direct and reflected waves. For certain cases, these results agree well with earlier work by other authors [G. A. Daigle, J. Acoust. Soc. Am. 68, 297–302 (1980)], however, fundamental differences in the propagation models yield significant discrepancies when more detailed comparisons are made.
Attenuation of acoustic waves by suspended particles in a viscous heat-conducting fluid
Authors: Ma Y. , Varadan V. K. , Varadan V. V.
Published: October 2005

The attenuation of acoustic waves by a dense suspension of particles of varying sizes in a viscous, heat-conducting fluid is studied. A self-consistent multiple scattering formalism using the T matrix to characterize the scattering from a single particle including the effects of viscous and thermal absorption is employed along with suitable pair-correlation functions. Results are presented for phase velocity and coherent attenuation as a function of frequency for a wide range of concentrations. A closed form expression for the attenuation of sound in the Rayleigh limit is also given which is useful for marine acoustic remote sensing applications. Numerical results obtained at higher frequency range will be of particular interest in ultrasonic diagnostic techniques.
Omnidirectional and directional sea surface backscattering strength measurements at low frequencies and low grazing angles
Authors: Erskine F. T. , Dundore D. M. , Schifter D. E. , Shaffer J. D.
Published: October 2005

Limited experimental data exists on surface backscattering strengths at low acoustic frequencies (below 300 Hz) and low grazing angles (below 20°) for deep ocean environments. We report here preliminary results of such measurements taken during four days of a sea test in the North Atlantic in September 1980 (sea states varied from 2 to 3). Four sets of approximately 20 small explosive charges (5-lb TNT-equivalent; bubble frequency of 77 Hz) were dropped beneath a towed acoustic array. We measured the direct path surface reverberation by processing the first 3 s of data, for mean grazing angles down to 8°, prior to receipt of the first bottom bounce at 6 s past detonation. The data were averaged over six frequency bands of 20-Hz width from 150 to 270 Hz and were reduced to scattering strengths versus mean grazing angle and frequency by using the NRL reverberation model to remove propagation effects and to compute the grazing angles versus time. Typical omnidirectional surface scattering strengths decrease from −55 to −70 dB for mean grazing angles from 20° to 8° with little (<5 dB) frequency dependence over the measured frequency range. These results are consistent with previously published measurements. Further, the data have been beamformed to examine the azimuthal directionality of the surface backscatter (sea direction varied from 27° to 110° relative to array heading), and preliminary results will be reported. [Data acquisition funded by Defense Mapping Agency; analyses supported by Naval Electronic Systems Command, Code 612.]
Diel variations in volume scattering in the Cariaco Trench
Authors: Love Richard H. , Wilson Marcia A. , Fisher Robert A.
Published: October 2005

Acoustic and biological measurements were conducted in the Cariaco Trench in order to investigate diel variations in volume scattering. The Cariaco Trench was chosen because few species of scatterers reside there, due to the presence of anoxic water below about 400 m. This greatly simplifies the interpretation and correlation of acoustic and biological data. Results show that at night all scatterers are in the upper 200 m. Nighttime scattering levels increase markedly for several hours before the predawn downward migration. The downward migrating layer splits in two shortly after dawn, with one port settling just above the anoxic zone. The other part migrates vertically throughout the day, sinking as deep as 900 m, well into anoxic water, before rising again in mid-afternoon. Only two species of fish were caught in a series of trawls between the surface and 900 m: Steindachneria argentea and Bergmaceros ssp. Bregmaceros are the deep migrators and Steindachneria, which feed on Bregrnaceros, stay above the anoxic water. Correlations between scatterers and scattering levels have been made using a model of scattering from swimbladder-bearing fish [R. H. Love, J. Acoust. Soc. Am 64, 571–580(1978)]. [Work supported by NORDA.]
Acoustic and biological measurements in the tongue of the ocean
Authors: Carlton L. F. , Brown C. L.
Published: October 2005

The use of a parametric acoustic source with its narrow beamwidths formed by a relatively small projector, wide frequency bandwidth, and short pulse capability is well suited to the acoustic investigation of biological volume reverberation. This paper describes the results of measurements conducted in September 1982, in the Tongue of the Ocean off Andros Island, Bahamas for the primary purpose of verifying the existence of mid-water scatterers in that area. The characteristics of the parametric sonar system used are presented along with sample echograms made at 14 to 30 kHz that show a deep scattering layer as a function of its diurnal cycles. In addition discrete large echo groups are seen between layers during the day. Echograms of individual targets near the Surface are illustrated to show a comparison between conventional and parametric sources. The volume scattering strengths at 20 kHz with the layer at different water depths were measured and are reported. Additionally, biological samples collected at night from 76- to 152-m depths in the layer are similar to scatterers found elsewhere.
Thin shell theories and acoustic wave scattering by infinitely long cylindrical shells of arbitrary cross section
Authors: Baskar S. , Varadan V. V. , Varadan V. K.
Published: October 2005

The scattering of acoustic waves by an infinitely long cylindrical shell immersed in a fluid is analyzed. A new approach has been proposed using thin shell theory; incorporating the impedance of the shell in the T-matrix formulation. Numerical results are presented for the farfield back scattering amplitude as a function of frequency. Calculations were made for infinitely long circular and elliptic cylindrical shells immersed in water for various shell thicknesses, for waves incident at an arbitrary angle in the plane normal to the axis of the cylinder. The impedance resulting from the use of various shell theory approximations for circular cylindrical shells is presented. Love-Timoshenko and Flugge-Byrne-Lurye theories for circular cylindrical shells have been compared with the full elasticity solution using the separation of variables approach. Comments have been made regarding the range of applicability of various shell theories.
Half-order derivative of sine-wave burst: Applications to scattering, two-dimensional radiation, and photoacoustics
Authors: Marston Philip L.
Published: October 2005

The 12-order time derivative of a function s(t) may be written as (d/dt)1/2s = ∫− ∞t ṡ(τ)[(t − τ)π]−1/2dτ, where it is assumed that ṡ(t) = ds/dt→0 as t→ − ∞. The associated frequency response is evident from the result: (d/dt)1/2 exp(−iωt) = (−iω)1/2 exp(−iωt). This is the response for transmitted-wave glory scattering from a sphere [P. L. Marston et al., J. Acoust. Soc. Am. (in press)] where the enhancement at large ω is due to axial focusing. The distortion of an axially focused sine-wave burst can be predicted by taking s = H(t)sin ωt, where H(t<0) = 0 and H(t⩾0) = 1. The result is (d/dt)1/2s = ω1/2[sin(ωt + 14π) − 21/2g(u)]H(t), where u = (2ωt/π)1/2 and the auxiliary Fresnel-integral function g(u) vanishes as u→∞. This result predicts that the first half-cycle of the scattered burst is reduced in amplitude in comparison to the steady-state value. The result may be extended to finite-length bursts by superposition. It is also applicable to two-dimensional radiation descriptions using the (d/dt)1/2 operator [J. Lighthill, Waves in Fluids (Cambridge U. P., Cambridge, 1978)] and, consequently, to certain photoacoustic sources. [Work supported by ONR.]
Moment method for acoustic scattering problems
Authors: Sonti N. , Varadan V. V. , Varadan V. K.
Published: October 2005

The moment method is utilized to solve the problem of acoustic scattering. Other methods currently used for this class of problems do not give satisfactory results when the scatterer is long and thin. The moment method does not seem to have this limitation. The method is tested for rigid scatterers and for elastic shells of revolution immersed in water. Numerical results are presented for acoustic scattering as a function of frequency and the scattering geometry for both 2-D and 3-D scatterers. The results are critically compared with those obtained by existing methods.
Differential scattering cross sections and the study of resonances for immersed fluid-loaded objects
Authors: Werby M. F. , Hackman R.
Published: October 2005

Form function plots with respect to frequencies for scattering from fluid loaded elastic objects can often be used to locate resonances due to the destructive interference phenomenon which usually produces a null at resonance frequencies. For some cases however, it is not always clear that a null can be associated with a resonance or for that matter that resonances are always associated with nulls in the form function plots. Resonances associated with surface excited waves such as the Rayleigh type will produce bistatic angular distributions that will exhibit standing wave features. These angular distributions will not only serve to establish a resonance but will enable one to characterize the order of the resonance. We present a theoretical study of bistatic angular distributions for scattering from various submerged elastic objects to illustrate their utility in establishing and characterizing resonances.
Scattering from submerged infinite cylindrical elastic thin shells
Authors: Flax L. , Green L. H. , Werby M. F.
Published: October 2005

We examine the effects of acoustical scattering from submerged elastic thin shells. The study is performed for a variety of elastic materials for several shell thicknesses. The study will include air-filled, fluid-filled, and solid-filled shells. Comparisons will be made with finite cylinders and the sensitivity of the above variations to resonances will be discussed.
Multi-frequency transmission tomography
Authors: Greenleaf J. F.
Published: October 2005

Multi-frequency signals were transmitted using a plane-wave transducer, through a water immersed phantom consisting of two finger cots, one containing 50% isopropanol alcohol and the other containing normal saline. The scattered ultrasound was received with a small hydrophone and detected with a quadrature detection system. The resulting phase quadrature data were submitted to a reconstruction algorithm which utilized the Rytov approximation to the Helmholtz equation in order to obtain the inverse solution for the distribution of refraction index within the phantom. In one experiment pseudo-random noise was generated by loading a 256 by 8-bit memory with random numbers and then synchronously reading these values through a D/A converter into an EMI power amplifier which drove the plane-wave transducer. The data received from each of 60 angles of view were spectral analyzed and specific frequencies selected for the cw reconstruction algorithm. Multiple frequency reconstructions will be shown as will the effect of frequency on the various underlying assumptions for the approximation. [Supported in part by Grants CA 24085 and NCI and ECS 7296008 from NSF.]
Computational aspects of ultrasound tomography
Authors: Devaney A. J.
Published: October 2005

The filtered backprojection algorithm of x-ray tomography and the filtered backpropagation algorithm developed recently by the author for ultrasound tomography [A. J. Devaney, Ultrason. Imag. 4, 336–350 (1982)] are tested in computer simulations of ultrasound tomography of two-dimensional objects for which the Rytov approximation is valid. It is found that the filtered backprojection algorithm gives unsatisfactory results even for wavelengths much smaller than the smallest scale over which the object varies. The filtered backpropagation algorithm yields, in all cases studied, high quality reconstructions which are simply low-pass filtered versions of the actual object profile. It is shown that the filtered backpropagation algorithm can be approximated by a modified backprojection algorithm having essentially the same computation requirements as filtered backprojection but yielding considerably higher quality object reconstructions.
Single-mode optical fiber sensors for ultrasonic waves in solids
Authors: De Paula R. P. , Ku C. C. , Jarzynski J. , Bucaro J. A. , Cole J. H.
Published: October 2005

Various optical fiber configurations were studied for use as sensors of ultrasonic waves incident at the surface of a solid. These configurations included the fiber sandwiched between the solid and a rigid backing mass, and the fiber sandwiched in a disk of compliant material (silicone rubber). Theoretical models have been derived to represent the experimental configurations used in the laboratory. Experimental and theoretical data are presented on the performance in the frequency range 1–10 MHz, of the above fiber configurations, and a comparison is made with the corresponding performance of a standard piezoelectric ceramic transducer.
Development of a DNA Microarray for Detection and Identification of Fungal Pathogens Involved in Invasive Mycoses
Authors: Leinberger Dirk M. , Schumacher Ulrike , Autenrieth Ingo B. , Bachmann Till T.
Published: October 2005

Invasive fungal infections have emerged as a major cause of morbidity and mortality in immunocompromised patients. Conventional identification of pathogenic fungi in clinical microbiology laboratories is time-consuming and, therefore, often imperfect for the early initiation of an adequate antifungal therapy. We developed a diagnostic microarray for the rapid and simultaneous identification of the 12 most common pathogenic
Candida
and
Aspergillus
species. Oligonucleotide probes were designed by exploiting the sequence variations of the internal transcribed spacer (ITS) regions of the rRNA gene cassette to identify
Candida albicans
,
Candida dubliniensis
,
Candida krusei
,
Candida glabrata
,
Candida tropicalis
,
Candida parapsilosis
,
Candida guilliermondii
,
Candida lusitaniae
,
Aspergillus fumigatus
,
Aspergillus flavus
,
Aspergillus niger
, and
Aspergillus terreus
. By using universal fungal primers (ITS1 and ITS4) directed toward conserved regions of the 18S and 28S rRNA genes, respectively, the fungal ITS target regions could be simultaneously amplified and fluorescently labeled. To establish the system, 12 precharacterized fungal strains were analyzed; and the method was validated by using 21 clinical isolates as blinded samples. As the microarray was able to detect and clearly identify the fungal pathogens within 4 h after DNA extraction, this system offers an interesting potential for clinical microbiology laboratories.
Sequence Diversity in the Glycoprotein B Gene Complicates Real-Time PCR Assays for Detection and Quantification of Cytomegalovirus
Authors: Nye Melinda B. , Leman Adam R. , Meyer Michelle E. , Menegus Marilyn A. , Rothberg Paul G.
Published: October 2005

Real-time quantitative PCR systems (Q-PCR) for the rapid detection and quantification of microorganisms in clinical specimens employ oligodeoxyribonucleotide primers and probes for specificity, which makes them vulnerable to false negatives caused by sequence diversity in the template. Schaade et al. (J. Clin. Microbiol.
39
:3809, 2001) reported a sequence variant (C630T) in the cytomegalovirus (CMV) glycoprotein B (gB) gene that, although detectable in their Q-PCR assay, could not be accurately quantified. In an effort to evaluate the impact of CMV sequence variants in our patient population by use of a similar Q-PCR assay, we surveyed 54 isolates of CMV, each from a different patient. We detected evidence for the C630T variant in 4 of 54 (7.4%) patients. Furthermore, isolates from two additional patients were completely negative in the test. Sequencing of these false-negative isolates revealed multiple mutations within the probe hybridization sites. A Q-PCR that targeted the CMV polymerase gene instead of gB detected all 54 isolates. We suggest that Q-PCR assays for viral load be rigorously tested on large panels of viral isolates to assess the impact of sequence diversity on detection as well as quantification.
Characterization ofMycobacterium capraeIsolates from Europe by Mycobacterial Interspersed Repetitive Unit Genotyping
Authors: Prodinger Wolfgang M. , Brandstätter Anita , Naumann Ludmila , Pacciarini Maria , Kubica Tanja , Boschiroli Maria Laura , Aranaz Alicia , Nagy György , Cvetnic Zeljko , Ocepek Matjaz , Skrypnyk Artem , Erler Wilfried , Niemann Stefan , Pavlik Ivo , Moser Irmgard
Published: October 2005

Mycobacterium caprae, a recently defined member of theMycobacterium tuberculosiscomplex, causes tuberculosis among animals and, to a limited extent, in humans in several European countries. To characterizeM. capraein comparison with otherMycobacterium tuberculosiscomplex members and to evaluate genotyping methods for this species, we analyzed 232M. capraeisolates by mycobacterial interspersed repetitive unit (MIRU) genotyping and by spoligotyping. The isolates originated from 128 distinct epidemiological settings in 10 countries, spanning a period of 25 years. We found 78 different MIRU patterns (53 unique types and 25 clusters with group sizes from 2 to 9) but only 17 spoligotypes, giving Hunter-Gaston discriminatory indices of 0.941 (MIRU typing) and 0.665 (spoligotyping). For a subset of 103M. capraeisolates derived from outbreaks or endemic foci, MIRU genotyping and IS6110restriction fragment length polymorphism were compared and shown to provide similar results. MIRU loci 4, 26, and 31 were most discriminant inM. caprae, followed by loci 10 and 16, a combination which is different than those reported to discriminateM. bovisbest.M. capraeMIRU patterns together with published data were used for phylogenetic inference analysis employing the neighbor-joining method.M. capraeisolates were grouped together, closely related to the branches of classicalM. bovis,M. pinnipedii,M. microti, and ancestralM. tuberculosis, but apart from modernM. tuberculosis.The analysis did not reflect geographic patterns indicative of origin or spread ofM. caprae.Altogether, our data confirmM. capraeas a distinct phylogenetic lineage within theMycobacterium tuberculosiscomplex.
Use of Shell-Vial Cell Culture Assay for Isolation of Bacteria from Clinical Specimens: 13 Years of Experience
Authors: Gouriet Frédérique , Fenollar Florence , Patrice Jean-Yves , Drancourt Michel , Raoult Didier
Published: October 2005

The shell-vial culture assay is performed routinely in our laboratory. Recently we revisited our experience of using the shell-vial culture assay for the isolation of microorganisms from various clinical samples. Over a 13-year period, we have isolated 580 bacterial strains (5%) from 11,083 clinical samples tested. Over the same period, 285 isolates of rickettsiae, bartonellae, or
Coxiella burnetii
were cultured from a total of 7,102 samples tested. These isolates include 55
Rickettsia
sp. isolates, 95
Coxiella burnetii
isolates, and 135
Bartonella
sp. isolates. Based on our experience with the growth of fastidious microorganisms, we have used a centrifugation shell-vial technique called JNSP, for “je ne sais pas” (“I don't know [what I am growing]”) for the isolation of other microorganisms. A total of 173 isolates were cultured from the 3,861 clinical samples tested using the JNSP method. Of these, 40 isolates had not been grown before on usual axenic medium. These include 2
Staphylococcus aureus
isolates, 7 isolates of
Streptococcus
sp. and related genera, 6
Mycobacterium
sp. isolates, 1
Nocardia asteroides
isolate, 1
Actinomyces
sp. isolate, 1
Brucella melitensis
isolate, 2
Francisella tularensis
isolates, 1
Mycoplasma pneumoniae
isolate, and 1
Legionella pneumophila
isolate. Using this protocol, we have also cultured intracellular bacteria such as
Chlamydia trachomatis
and we have performed the first culture and establishment of
Trophyrema whipplei
. Applied in our laboratory, the shell-vial culture generally exhibits a low rate of success. However, in some cases, this technique allowed microbial diagnosis when classical agar procedure and PCR were negative.
Use of Time-Saving Flow Cytometry for Rapid Determination of Resistance of Human Cytomegalovirus to Ganciclovir
Authors: Lee Gyu-Cheol , Lee Dong-Gun , Choi Su-Mi , Yoo Jin-Hong , Park Sun-Hee , Choi Jung-Hyun , Min Woo-Sung , Cho Ok-Hee , Lee Chan-Hee , Shin Wan-Shik
Published: October 2005

There are two ways to assess the susceptibility of human cytomegalovirus (HCMV) to ganciclovir (GCV): one is a genotypic test that detects resistance-related mutations and the other is a phenotypic test that actually assesses susceptibility. The advantages of genotyping the UL97 gene are its rapidity and accuracy. However, to detect novel mutations or mutations affecting the UL54 DNA polymerase, a phenotypic test such as the plaque reduction assay (PRA) is also required. To avoid the shortcomings of PRA such as its time-consuming nature and labor-intensiveness, we developed a time-saving fluorescence-activated cell sorting (TS-FACS) technique. We obtained a GCV 50% inhibitory concentration (IC
50
) from five clinical isolates and an HCMV laboratory strain (AD169) and compared the results with those from the PRA. The laboratory strain and three clinical isolates were sensitive to GCV. Although there was a minor discrepancy in the case of one of the three isolates, the GCV IC
50
values obtained by TS-FACS analysis correlated well with the results of the PRA. The remaining two isolates were resistant to GCV; one was GCV resistant due to the mutation M460V, and the GCV IC
50
results obtained by TS-FACS analysis and by PRA were also comparable. The advantages of TS-FACS analysis are the shorter time required, the possibility of automation, and its comparability to PRA, considered the gold standard. Thus, TS-FACS analysis may be useful as an alternative to PRA in the clinic.
Phylogenetic Characterization of Canine Distemper Viruses Detected in Naturally Infected Dogs in North America
Authors: Pardo Ingrid D. R. , Johnson Gayle C. , Kleiboeker Steven B.
Published: October 2005

In 2004, six puppies and one adult dog from a total of four premises were subjected to necropsy evaluation. For five of the seven dogs, disease caused by canine distemper virus (CDV) infection was suspected based on clinical signs. In all of the dogs, a diagnosis of CDV infection was established by the presence of compatible gross and histologic lesions, immunohistochemical labeling for CDV antigen, and detection of CDV RNA by reverse transcription-PCR. To further characterize the CDV strains detected in the four cases, complete gene sequences were determined for the hemagglutinin (H) and fusion (F) protein genes, while partial gene sequencing was performed for the phosphoprotein gene. A total of 4,508 bases were sequenced for the CDV strains detected from each of the four cases. Two cases were found to have identical sequences except for 2 bases in the intergenic region of the F and H genes. Phylogenetic analysis strongly suggested an evolutionary relationship between sequences detected in these two cases and those of phocine distemper virus 2 and two other strains of CDV not previously detected in the continental United States. Clear phylogenetic relationships were not established for viruses detected in the two additional cases; however, one strain showed similarity to CDV strains detected in a panda from China. Importantly, the three CDV strains detected were demonstrated to be genetically distinct from known vaccine strains and strains previously reported in the continental United States.
Novel Multiplex PCR Assay for Characterization and Concomitant Subtyping of Staphylococcal Cassette ChromosomemecTypes I to V in Methicillin-ResistantStaphylococcus aureus
Authors: Zhang Kunyan , McClure Jo-Ann , Elsayed Sameer , Louie Thomas , Conly John M.
Published: October 2005

Staphylococcal cassette chromosomemec(SCCmec) typing is essential for understanding the molecular epidemiology of methicillin-resistantStaphylococcus aureus(MRSA). SCCmecelements are currently classified into types I to V based on the nature of themecandccrgene complexes, and are further classified into subtypes according to their junkyard region DNA segments. Previously described traditional SCCmecPCR typing schemes require multiple primer sets and PCR experiments, while a previously published multiplex PCR assay is limited in its ability to detect recently discovered types and subtypes such as SCCmectype V and subtypes IVa, b, c, and d. We designed new sets of SCCmectype- and subtype-unique and specific primers and developed a novel multiplex PCR assay allowing for concomitant detection of the methicillin resistance (mecAgene) (also serving as an internal control) to facilitate detection and classification of all currently described SCCmectypes and subtypes I, II, III, IVa, b, c, d, and V. Our assay demonstrated 100% sensitivity and specificity in accurately characterizing 54 MRSA strains belonging to the various known SCCmectypes and subtypes, when compared with previously described typing methods. Further application of our assay in 453 randomly selected local clinical isolates confirmed its feasibility and practicality. This novel assay offers a rapid, simple, and feasible method for SCCmectyping of MRSA, and may serve as a useful tool for clinicians and epidemiologists in their efforts to prevent and control infections caused by this organism.
Diagnosis of Cerebral Toxoplasmosis in AIDS Patients in Brazil: Importance of Molecular and Immunological Methods Using Peripheral Blood Samples
Authors: Colombo Fabio A. , Vidal José E. , Oliveira Augusto C. Penalva de , Hernandez Adrián V. , Bonasser-Filho Francisco , Nogueira Roberta S. , Focaccia Roberto , Pereira-Chioccola Vera Lucia
Published: October 2005

Cerebral toxoplasmosis is the most common cerebral focal lesion in AIDS and still accounts for high morbidity and mortality in Brazil. Its occurrence is more frequent in patients with low CD4+T-cell counts. It is directly related to the prevalence of anti-Toxoplasma gondiiantibodies in the population. Therefore, it is important to evaluate sensitive, less invasive, and rapid diagnostic tests. We evaluated the value of PCR using peripheral blood samples on the diagnosis of cerebral toxoplasmosis and whether its association with immunological assays can contribute to a timely diagnosis. We prospectively analyzed blood samples from 192 AIDS patients divided into two groups. The first group was composed of samples from 64 patients with cerebral toxoplasmosis diagnosed by clinical and radiological features. The second group was composed of samples from 128 patients with other opportunistic diseases. Blood collection from patients with cerebral toxoplasmosis was done before or on the third day of anti-toxoplasma therapy. PCR forT. gondii, indirect immunofluorescence, enzyme-linked immunosorbent assay, and an avidity test for toxoplasmosis were performed on all samples. The PCR sensitivity and specificity for diagnosis of cerebral toxoplasmosis in blood were 80% and 98%, respectively. Patients with cerebral toxoplasmosis (89%) presented higher titers of anti-T. gondiiIgG antibodies than patients with other diseases (57%) (P< 0.001). These findings suggest the clinical value of the use of both PCR and high titers of anti-T. gondiiIgG antibodies for the diagnosis of cerebral toxoplasmosis. This strategy may prevent more invasive approaches.
Clinical and Molecular Analysis of Extended-Spectrum β-Lactamase-Producing Enterobacteria in the Community Setting
Authors: Arpin Corinne , Dubois Véronique , Maugein Jeanne , Jullin Jacqueline , Dutilh Brigitte , Brochet Jean-Philippe , Larribet Gilberte , Fischer Isabelle , Quentin Claudine
Published: October 2005

During a previous survey, five extended-spectrum β-lactamase (ESBL)-producing enterobacteria (ESBLE) (two
Enterobacter aerogenes
isolates expressing TEM-24b, two
Escherichia coli
isolates expressing TEM-21 or TEM-24b, and one
Klebsiella pneumoniae
isolate expressing SHV-4/TEM-15) responsible for urinary tract infections (UTIs) were found among 1,584 strains collected from community patients. The aim of the present study was to elucidate the route of emergence of these typically nosocomial organisms in the community. Thus, the files of the five patients were analyzed over at least a decade, and potentially related ESBLE from hospitals or clinics were examined. Their enzymes were characterized at a molecular level, and the strains were typed by amplified-primed PCR, enterobacterial repetitive intergenic consensus PCR, and restriction plasmid profile. All patients (C1 to C5) had risk factors for ESBLE acquisition, including past history of hospitalization (2.5 to 23 months before). Four (C1 and C3 to C5) had previously received antibiotics (concomitantly to 35 months earlier), two (C1 and C3) had indwelling urinary catheters and recurrent UTIs, and three (C2, C3, and C5) formerly experienced ESBLE-induced UTIs (2 to 11 months before). The same ESBLE and/or an identical or similar ESBL-encoding plasmid was identified in the hospital ward (C1 to C4) or in a clinic (C5) where the patients had previously resided. Patients C1 and C4, infected with different ESBLE carrying a closely related plasmid, were hospitalized in the same unit. Persistence of ESBLE over at least a 5-year period was demonstrated for patient C3. Thus, community-acquired UTIs in these patients likely resulted from nosocomially acquired ESBLE or an ESBL-encoding plasmid followed by a prolonged digestive carriage.
Real-Time Reverse Transcription PCR for Detection and Quantitative Analysis of Equine Influenza Virus
Authors: Quinlivan Michelle , Dempsey Eugene , Ryan Fergus , Arkins Sean , Cullinane Ann
Published: October 2005

Equine influenza is a cause of epizootic respiratory disease of the equine. The detection of equine influenza virus using real-time Light Cycler reverse transcription (RT)-PCR technology was evaluated over two influenza seasons with the analysis of 171 samples submitted for viral respiratory disease. Increased sensitivity was found in overall viral detection with this system compared to Directigen Flu A and virus isolation, which were 40% and 23%, respectively, that of the RT-PCR. The assay was also evaluated as a viable replacement for the more traditional methods of quantifying equine influenza virus, 50% egg infectious dose and 50% tissue culture infectious dose. There was a significant positive correlation (P< 0.05) between the quantitative RT-PCR and both of these assays.
Validation of a Rapid and Reliable Test for Diagnosis of Chagas' Disease by Detection of
Trypanosoma cruzi
-Specific Antibodies in Blood of Donors and Patients in Central America
Authors: Ponce Carlos , Ponce Elisa , Vinelli Elizabeth , Montoya Alberto , de Aguilar Vilma , Gonzalez Antonio , Zingales Bianca , Rangel-Aldao Rafael , Levin Mariano J. , Esfandiari Javan , Umezawa Eufrosina S. , Luquetti Alejandro O. , da Silveira José Franco
Published: October 2005

In this study we compared the performance of the Chagas Stat-Pak rapid immunochromatographic test with a standard enzyme-linked immunosorbent assay (ELISA) in the serodiagnosis of Chagas' disease in Central America. Out of 3,400 blood donor samples, 156 (4.6%) were positive in both assays. Three sera out of 2,084 samples from reference laboratories were negative with the rapid test but positive with the ELISA (99.8% agreement). Agreement of 100% between the two tests was observed with 339 additional sera from patients with cardiopathies and 175 sera from potential blood donors in emergency surgical cases occurring on weekends or at night. In conclusion, Chagas Stat-Pak showed 99.6% and 99.9% sensitivity and specificity, respectively, when assayed with 5,998 serum samples. It is a sensitive and specific alternative to the ELISA, as required in medical emergencies and blood screenings in Central America.
Antibiotic Susceptibilities of
Pseudomonas aeruginosa
Isolates Derived from Patients with Cystic Fibrosis under Aerobic, Anaerobic, and Biofilm Conditions
Authors: Hill Dominic , Rose Barbara , Pajkos Aniko , Robinson Michael , Bye Peter , Bell Scott , Elkins Mark , Thompson Barbara , MacLeod Colin , Aaron Shawn D. , Harbour Colin
Published: October 2005

Recent studies have determined that
Pseudomonas aeruginosa
can live in a biofilm mode within hypoxic mucus in the airways of patients with cystic fibrosis (CF).
P. aeruginosa
grown under anaerobic and biofilm conditions may better approximate in vivo growth conditions in the CF airways, and combination antibiotic susceptibility testing of anaerobically and biofilm-grown isolates may be more relevant than traditional susceptibility testing under planktonic aerobic conditions. We tested 16 multidrug-resistant isolates of
P. aeruginosa
derived from CF patients using multiple combination bactericidal testing to compare the efficacies of double and triple antibiotic combinations against the isolates grown under traditional aerobic planktonic conditions, in planktonic anaerobic conditions, and in biofilm mode. Both anaerobically grown and biofilm-grown bacteria were significantly less susceptible (
P
< 0.01) to single and combination antibiotics than corresponding aerobic planktonically grown isolates. Furthermore, the antibiotic combinations that were bactericidal under anaerobic conditions were often different from those that were bactericidal against the same organisms grown as biofilms. The most effective combinations under all conditions were colistin (tested at concentrations suitable for nebulization) either alone or in combination with tobramycin (10 μg ml
−1
), followed by meropenem combined with tobramycin or ciprofloxacin. The findings of this study illustrate that antibiotic sensitivities are dependent on culture conditions and highlight the complexities of choosing appropriate combination therapy for multidrug-resistant
P. aeruginosa
in the CF lung.
Transmission of
Burkholderia cepacia
Complex: Evidence for New Epidemic Clones Infecting Cystic Fibrosis Patients in Italy
Authors: Campana S. , Taccetti G. , Ravenni N. , Favari F. , Cariani L. , Sciacca A. , Savoia D. , Collura A. , Fiscarelli E. , De Intinis G. , Busetti M. , Cipolloni A. , d'Aprile A. , Provenzano E. , Collebrusco I. , Frontini P. , Stassi G. , Trancassini M. , Tovagliari D. , Lavitola A. , Doherty C. J. , Coenye T. , Govan J. R. W. , Vandamme P.
Published: October 2005

To analyze national prevalence, genomovar distribution, and epidemiology of the
Burkholderia cepacia
complex in Italy, 225 putative
B. cepacia
complex isolates were obtained from 225 cystic fibrosis (CF) patients attending 18 CF centers. The genomovar status of these isolates was determined by a polyphasic approach, which included whole-cell protein electrophoresis and
recA
restriction fragment length polymorphism (RFLP) analysis. Two approaches were used to genotype
B. cepacia
complex isolates: BOX-PCR fingerprinting and pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments. A total of 208 (92%) of 225 isolates belonged to the
B. cepacia
complex, with
Burkholderia cenocepacia
as the most prevalent species (61.1%). Clones delineated by PFGE were predominantly linked to a single center; in contrast, BOX-PCR clones were composed of isolates collected either from the same center or from different CF centers and comprised multiple PFGE clusters. Three BOX-PCR clones appeared of special interest. One clone was composed of 17
B. cenocepacia
isolates belonging to
recA
RFLP type H. These isolates were collected from six centers and represented three PFGE clusters. The presence of insertion sequence IS
1363
in all isolates and the comparison with PHDC reference isolates identified this clone as PHDC, an epidemic clone prominent in North American CF patients. The second clone included 22 isolates from eight centers and belonged to
recA
RFLP type AT. The genomovar status of strains with the latter RFLP type is not known. Most of these isolates belonged to four different PFGE clusters. Finally, a third clone comprised nine
B. pyrrocinia
isolates belonging to
recA
RFLP type Se13. They represented three PFGE clusters and were collected in three CF centers.
Comparison of Genetic Backgrounds of Methicillin-Resistant and -Susceptible
Staphylococcus aureus
Isolates from Portuguese Hospitals and the Community
Authors: de Sousa M. Aires , Conceição T. , Simas C. , de Lencastre H.
Published: October 2005

In order to understand the origins of the dominant methicillin-resistant
Staphylococcus aureus
(MRSA) clones in Portuguese hospitals, we compared the genetic backgrounds of nosocomial MRSA with methicillin-susceptible
S. aureus
(MSSA) isolates from the same hospitals (
n
= 155) and from the community (
n
= 157) where they were located. Pulsed-field gel electrophoresis,
spa
typing, multilocus sequence typing, and
agr
type analysis revealed that the genetic backgrounds correspondent to the dominant MRSA clones in Portuguese hospitals during the last 15 years (Iberian ST247, Brazilian ST239, and EMRSA-15 ST22) were scarcely or not found among the present MSSA collection. The four major MSSA clones encountered (A-ST30, B-ST34, C-ST5, and H-ST45) correspond, or are very similar, to the background of other international MRSA pandemic clones, i.e., EMRSA-16, New York/Japan, Pediatric, and Berlin clones. However, with the exception of the Pediatric clone, none of these MRSA clones has been detected in Portugal. Our findings suggest the three major MRSA clones identified in Portuguese hospitals have not originated from the introduction of SCC
mec
into dominant MSSA backgrounds present in the Portuguese nosocomial or community environment but were probably imported from abroad. In contrast, the MRSA Pediatric clone might have originated in our country by the acquisition of SCC
mec
type IV into MSSA clone C. Furthermore, we provide evidence that the introduction of SCC
mec
into sensitive clones is most likely a relatively infrequent event that seems to depend not exclusively on the presence of a successful MSSA lineage.