bluuebunny/crossref_metadata_2025 huggingface dataset:
Pressure sensitivity kernels applied to time-reversal acoustics
Authors: Raghukumar Kaustubha , Cornuelle Bruce D. , Hodgkiss William S. , Kuperman William A.
Published: July 2008

Sensitivity kernels for receptions of broadband sound transmissions are used to study the effect of the transmitted signal on the sensitivity of the reception to environmental perturbations. A first-order Born approximation is used to obtain the pressure sensitivity of the received signal to small changes in medium sound speed. The pressure perturbation to the received signal caused by medium sound speed changes is expressed as a linear combination of single-frequency sensitivity kernels weighted by the signal in the frequency domain. This formulation can be used to predict the response of a source transmission to sound speed perturbations. The stability of time-reversal is studied and compared to that of a one-way transmission using sensitivity kernels. In the absence of multipath, a reduction in pressure sensitivity using time reversal is only obtained with multiple sources. This can be attributed both to the presence of independent paths and to cancellations that occur due to the overlap of sensitivity kernels for different source-receiver paths. The sensitivity kernel is then optimized to give a new source transmission scheme that takes into account knowledge of the medium statistics and is related to the regularized inverse filter.
Number and duration of echolocation click trains produced by a harbor porpoise (Phocoena phocoena) in relation to target and performance
Authors: Kastelein Ronald A. , Verlaan Mariska , Jennings Nancy
Published: July 2008

Echolocation effort (number and duration of echolocation click trains produced) by a harbor porpoise is described in relation to target presence, strength and distance, and performance of the detection task. The porpoise was presented with two target sizes at five distances (12–20m), or no target, and had to indicate whether it could detect the target. Small, distant targets required long and multiple click trains. Multiple click trains mostly occurred when the small target was far away and not detected, and during target-absent trials in which the animal correctly responded. In target-absent trials, an incorrect response was linked to short click trains. Click train duration probably increased until the animal’s certainty about the target’s presence or absence exceeded a certain level, after which the porpoise responded.
A computational model of human auditory signal processing and perception
Authors: Jepsen Morten L. , Ewert Stephan D. , Dau Torsten
Published: July 2008

A model of computational auditory signal-processing and perception that accounts for various aspects of simultaneous and nonsimultaneous masking in human listeners is presented. The model is based on the modulation filterbank model described by Dau et al. [J. Acoust. Soc. Am. 102, 2892 (1997)] but includes major changes at the peripheral and more central stages of processing. The model contains outer- and middle-ear transformations, a nonlinear basilar-membrane processing stage, a hair-cell transduction stage, a squaring expansion, an adaptation stage, a 150-Hz lowpass modulation filter, a bandpass modulation filterbank, a constant-variance internal noise, and an optimal detector stage. The model was evaluated in experimental conditions that reflect, to a different degree, effects of compression as well as spectral and temporal resolution in auditory processing. The experiments include intensity discrimination with pure tones and broadband noise, tone-in-noise detection, spectral masking with narrow-band signals and maskers, forward masking with tone signals and tone or noise maskers, and amplitude-modulation detection with narrow- and wideband noise carriers. The model can account for most of the key properties of the data and is more powerful than the original model. The model might be useful as a front end in technical applications.
Acoustic and perceptual similarity of Japanese and American English vowels
Authors: Nishi Kanae , Strange Winifred , Akahane-Yamada Reiko , Kubo Rieko , Trent-Brown Sonja A.
Published: July 2008

Acoustic and perceptual similarities between Japanese and American English (AE) vowels were investigated in two studies. In study 1, a series of discriminant analyses were performed to determine acoustic similarities between Japanese and AE vowels, each spoken by four native male speakers using F1, F2, and vocalic duration as input parameters. In study 2, the Japanese vowels were presented to native AE listeners in a perceptual assimilation task, in which the listeners categorized each Japanese vowel token as most similar to an AE category and rated its goodness as an exemplar of the chosen AE category. Results showed that the majority of AE listeners assimilated all Japanese vowels into long AE categories, apparently ignoring temporal differences between 1- and 2-mora Japanese vowels. In addition, not all perceptual assimilation patterns reflected context-specific spectral similarity patterns established by discriminant analysis. It was hypothesized that this incongruity between acoustic and perceptual similarity may be due to differences in distributional characteristics of native and non-native vowel categories that affect the listeners’ perceptual judgments.
Influence of in situ, sound-level calibration on distortion-product otoacoustic emission variability
Authors: Scheperle Rachel A. , Neely Stephen T. , Kopun Judy G. , Gorga Michael P.
Published: July 2008

Standing waves can cause errors during in-the-ear calibration of sound pressure level (SPL), affecting both stimulus magnitude and distortion-product otoacoustic emission (DPOAE) level. Sound intensity level (SIL) and forward pressure level (FPL) are two measurements theoretically unaffected by standing waves. SPL, SIL, and FPL in situ calibrations were compared by determining sensitivity of DPOAE level to probe-insertion depth (deep and “shallow”) for a range of stimulus frequencies (1–8kHz) and levels (20–60dB). Probe-insertion depth was manipulated with the intent to shift the frequencies with standing-wave minima at the emission probe, introducing variability during SPL calibration. The absolute difference in DPOAE level between insertions was evaluated after correcting for an incidental change caused by the effect of ear-canal impedance on the emission traveling from the cochlea. A three-way analysis of variance found significant main effects for stimulus level, stimulus frequency, and calibration method, as well as significant interactions involving calibration method. All calibration methods exhibited changes in DPOAE level due to the insertion depth, especially above 4kHz. However, SPL demonstrated the greatest changes across all stimulus levels for frequencies above 2kHz, suggesting that SIL and FPL provide more consistent measurements of DPOAEs for frequencies susceptible to standing-wave calibration errors.
Theoretical simulation and experimental validation of inverse quasi-one-dimensional steady and unsteady glottal flow models
Authors: Cisonni Julien , Van Hirtum Annemie , Pelorson Xavier , Willems Jan
Published: July 2008

In physical modeling of phonation, the pressure drop along the glottal constriction is classically assessed with the glottal geometry and the subglottal pressure as known input parameters. Application of physical modeling to study phonation abnormalities and pathologies requires input parameters related to in vivo measurable quantities commonly corresponding to the physical model output parameters. Therefore, the current research presents the inversion of some popular simplified flow models in order to estimate the subglottal pressure, the glottal constriction area, or the separation coefficient inherent to the simplified flow modeling for steady and unsteady flow conditions. The inverse models are firstly validated against direct simulations and secondly against in vitro measurements performed for different configurations of rigid vocal fold replicas mounted in a suitable experimental setup. The influence of the pressure corrections related to viscosity and flow unsteadiness on the flow modeling is quantified. The inversion of one-dimensional glottal flow models including the major viscous effects can predict the main flow quantities with respect to the in vitro measurements. However, the inverse model accuracy is strongly dependent on the pertinence of the direct flow modeling. The choice of the separation coefficient is preponderant to obtain pressure predictions relevant to the experimental data.
The effect of multimicrophone noise reduction systems on sound source localization by users of binaural hearing aids
Authors: Van den Bogaert Tim , Doclo Simon , Wouters Jan , Moonen Marc
Published: July 2008

This paper evaluates the influence of three multimicrophone noise reduction algorithms on the ability to localize sound sources. Two recently developed noise reduction techniques for binaural hearing aids were evaluated, namely, the binaural multichannel Wiener filter (MWF) and the binaural multichannel Wiener filter with partial noise estimate (MWF-N), together with a dual-monaural adaptive directional microphone (ADM), which is a widely used noise reduction approach in commercial hearing aids. The influence of the different algorithms on perceived sound source localization and their noise reduction performance was evaluated. It is shown that noise reduction algorithms can have a large influence on localization and that (a) the ADM only preserves localization in the forward direction over azimuths where limited or no noise reduction is obtained; (b) the MWF preserves localization of the target speech component but may distort localization of the noise component. The latter is dependent on signal-to-noise ratio and masking effects; (c) the MWF-N enables correct localization of both the speech and the noise components; (d) the statistical Wiener filter approach introduces a better combination of sound source localization and noise reduction performance than the ADM approach.
Time-frequency analysis and modeling of the backscatter of categorized dolphin echolocation clicks for target discrimination
Authors: Muller Mark W. , Allen John S. , Au Whitlow W. L. , Nachtigall Paul E.
Published: July 2008

A set of dolphin echolocation clicks collected from an Atlantic bottlenose dolphin in Kaneohe Bay, Hawai’i from a previous experiment is examined in terms of their time and frequency characteristics. The center frequency and rms bandwidth are calculated for the clicks and these are clustered into four classes by using a model based on the Bayesian information criterion. The echo signatures are attained from a solid, elastic homogeneous sphere for each class of clicks from an acoustic scattering model. The results from the scattering model are compared to experimental values. The joint time-frequency content of the resulting echo signals is obtained by the reduced interference distribution (RID). The RIDs are plotted and examined for each signal class for four spherical targets of different material compositions. RID correlation values are obtained for a standard target versus comparison targets by using a time-frequency correlator. The results suggest that dolphins may discriminate by auditory inspection of the time-frequency information returned by the targets. The modification of the outgoing clicks and examination of time-frequency target information may be fundamental to a dolphin’s ability to identify and discriminate targets.
Click-evoked potentials in a large marine mammal, the adult male northern elephant seal (Mirounga angustirostris)
Authors: Houser Dorian S. , Crocker Daniel E. , Finneran James J.
Published: July 2008

Auditory evoked potential (AEP) hearing studies in marine mammals should consider an expected size-dependent reduction in AEP amplitude. This study is the first to measure the click-evoked response in a large marine mammal, the adult male elephant seal (Mirounga angustirostris). Click stimuli were presented at peak-peak equivalent sound pressure levels of 117–118dB re: 20μPa. Three positive peaks (P1–P3) and two negative peaks (N4 and N5) were observed in the AEP. Response latencies were longer than previously observed in a 1.8yr old seal and the maximum peak-peak amplitude was comparatively reduced by more than 60%. The inverse relationship between size and AEP amplitude will likely require increased averaging with larger subjects and possibly modifications to electrode placement and design in order to increase the quality of recorded evoked responses.
Temperature effects in ultrasonic Lamb wave structural health monitoring systems
Authors: Lanza di Scalea Francesco , Salamone Salvatore
Published: July 2008

There is a need to better understand the effect of temperature changes on the response of ultrasonic guided-wave pitch-catch systems used for structural health monitoring. A model is proposed to account for all relevant temperature-dependent parameters of a pitch-catch system on an isotropic plate, including the actuator-plate and plate-sensor interactions through shear-lag behavior, the piezoelectric and dielectric permittivity properties of the transducers, and the Lamb wave dispersion properties of the substrate plate. The model is used to predict the S0 and A0 response spectra in aluminum plates for the temperature range of −40–+60°C, which accounts for normal aircraft operations. The transducers examined are monolithic PZT-5A [PZT denotes Pb(Zr–Ti)O3] patches and flexible macrofiber composite type P1 patches. The study shows substantial changes in Lamb wave amplitude response caused solely by temperature excursions. It is also shown that, for the transducers considered, the response amplitude changes follow two opposite trends below and above ambient temperature (20°C), respectively. These results can provide a basis for the compensation of temperature effects in guided-wave damage detection systems.
Implications of human performance and perception under tonal noise conditions on indoor noise criteria
Authors: Ryherd Erica E. , Wang Lily M.
Published: July 2008

This research investigated differences in task performance and perception under six non-time-varying ventilation-type background noise spectra with differing tonality. The results were related to five indoor noise criteria systems: noise criteria, balanced noise criteria, room criteria, room criteria mark II, and the A-weighted equivalent sound pressure level (LAeq). These criteria systems are commonly used in the U.S. building industry, but concerns exist over whether they are appropriate for all noise situations. Thirty test subjects completed three types of performance tasks (typing, reasoning, and math) and answered questions about their perception of the indoor environment under each noise condition. Results showed that performance scores did not change significantly across the six noise conditions, but there were differences in subjective perception. For example, perception trends for tonality, annoyance, and distraction changed based on the frequency and prominence of discrete tones in noise. However, these perceptual changes were not fully reflected in the criteria level or spectral quality ratings. Additionally, task performance was related to subjective perception but not to criteria level predictions. As a result, the authors suggest that the current criteria should be modified to account for the frequency and prominence of tones in background noise.
Temporal order discrimination of tonal sequences by younger and older adults: The role of duration and rate
Authors: Shrivastav Mini N. , Humes Larry E. , Aylsworth Lacy
Published: July 2008

The effect of tone duration and presentation rate on the discrimination of the temporal order of the middle two tones of a four-tone sequence was investigated in young normal-hearing (YNH) and older hearing-impaired (OHI) listeners. The frequencies and presentation level of the tone sequences were selected to minimize the effect of hearing loss on the performance of the OHI listeners. Tone durations varied from 20to400ms and presentation rates from 2.5to25tones∕s. Two experiments were conducted with anisochronous (nonuniform duration and rate across entire sequence) and isochronous (uniform rate and duration) sequences, respectively. For the YNH listeners, performance for both isochronous and anisochronous sequences was determined primarily by presentation rate such that performance decreased at rates faster than 5tones∕s. For anisochronous tone sequences alone, the effects of rate were more pronounced at short tone durations. For the OHI listeners, both presentation rate and tone duration had an impact on performance for both isochronous and anisochronous sequences such that performance decreased as rate increased above 5tones∕s or duration decreased below 40ms. Temporal masking was offered as an explanation for the interaction of short durations and fast rates on temporal order discrimination for the anisochronous sequences.
Effect of spatial uncertainty of masker on masked detection for nonspeech stimuli
Authors: Fan Wei Li , Streeter Timothy M. , Durlach Nathaniel I.
Published: July 2008

Research on informational masking for nonspeech stimuli has focused on the effects of spectral uncertainty in the masker. In this letter, results are presented from some preliminary probe experiments in which the spectrum of the masker is held fixed but the spatial properties of the masker are randomized. In addition, in some tests, the overall level of the stimulus is randomized. These experiments differ from previous experiments that have measured the effect of spatial uncertainty on masking in that the only attributes (aside from level) that distinguish the target from the masker are the spatial attributes; in all of the tests, the target and masker were statistically identical, statistically independent, narrowband noise signals. In general, the results indicate that detection performance is degraded by spatial uncertainty in the masker but that compared both to the effects of spectral uncertainty and to the effects of overall-level uncertainty, the effects of spatial uncertainty are relatively small.
Temporal coherence of sound transmissions in deep water revisited
Authors: Yang T. C.
Published: July 2008

This paper examines the signal coherence loss due to internal waves in deep water in terms of the signal coherence time and compare to data reported in the literature over the past 35years. The coherence time of the early raylike arrivals was previously modeled by Munk and Zachariasen [“Sound propagation through a fluctuating stratified ocean: Theory and observation,” J. Acoust. Soc. Am. 59, 818–838 (1976)] using the supereikonal approximation and by Dashen et al. [“Path-integral treatment of acoustic mutual coherence functions for arrays in a sound channel,” J. Acoust. Soc. Am. 77, 1716–1722 (1985)] using the path integral approach; a −12 power frequency dependence and a −32 power range dependence were predicted. Recent data in shallow water in downward refractive environments with internal waves suggested that the signal coherence time of the mode arrivals follows a −32 power frequency dependence and a −12 power range dependence. Since the temporal coherence of the acoustic signal is related to the temporal coherence of the internal waves, based on the observation that the (linear) internal waves in deep and shallow waters have a similar frequency spectrum, it is argued that the modelike arrivals in deep water should exhibit a similar frequency dependence in deep and shallow waters. This argument is supported by a brute-force application of the path integral to mode arrivals based on the WKB relation between the ray and mode. It is found that the data are consistent with the −32 power frequency dependence but more data are needed to further test the hypothesis.
Detection of targets colocalized in clutter by big brown bats (Eptesicus fuscus)
Authors: Stamper Sarah A. , Simmons James A. , DeLong Caroline M. , Bragg Rebecca
Published: July 2008

Echolocating big brown bats (Eptesicus fuscus) frequently catch insects during aerial pursuits in open spaces, but they also capture prey swarming on vegetation, and from substrates. To evaluate perception of targets on cluttered surfaces, big brown bats were trained in a two-alternative forced-choice task to locate a target, varying in height, that was embedded partway in holes (clutter) cut in a foam surface. The holes were colocalized with the possible positions of the target at distances ranging from 25to35cm. For successful perception of the target, the bat had to detect the echoes contributed by the target in the same time window that contained echoes from the clutter. Performance was assessed in terms of target reflective strength relative to clutter strength in the same time window. The bats detected the target whenever the target strength was greater than 1–2dB above the clutter.
Aerodynamic sound generation of flapping wing
Authors: Bae Youngmin , Moon Young J.
Published: July 2008

The unsteady flow and acoustic characteristics of the flapping wing are numerically investigated for a two-dimensional model of Bombus terrestris bumblebee at hovering and forward flight conditions. The Reynolds number Re, based on the maximum translational velocity of the wing and the chord length, is 8800 and the Mach number M is 0.0485. The computational results show that the flapping wing sound is generated by two different sound generation mechanisms. A primary dipole tone is generated at wing beat frequency by the transverse motion of the wing, while other higher frequency dipole tones are produced via vortex edge scattering during a tangential motion. It is also found that the primary tone is directional because of the torsional angle in wing motion. These features are only distinct for hovering, while in forward flight condition, the wing-vortex interaction becomes more prominent due to the free stream effect. Thereby, the sound pressure level spectrum is more broadband at higher frequencies and the frequency compositions become similar in all directions.
Uniformly valid solution for acoustic propagation in weakly tapered circular waveguides: Liquid jet example
Authors: Lonzaga Joel B. , Thiessen David B. , Marston Philip L.
Published: July 2008

The propagation of ultrasound down laminar liquid jets has potential applications to the stimulation of liquid drop production [J. B. Lonzaga, C. F. Osterhoudt, D. B. Thiessen, and P. L. Marston, J. Acoust. Soc. Am. 121, 3323–3330 (2007)] as well as to the coupling of ultrasound to objects through contact with a jet. In normal gravity, a jet issuing from a nozzle becomes tapered as the jet accelerates downward. A uniformly valid solution for the acoustic propagation in a weakly tapered, liquid jet waveguide in air with a turning point is derived using Langer’s transformation and the method of multiple scales. The loss of energy from transmission into the air and from thermal viscous absorption is neglected. A solvability condition is used to obtain the leading-order correction due to the taper of the waveguide. This asymptotic solution is validated using finite-element numerical calculations. The ultrasonic wave amplitude is enhanced in the region of the jet close to the cutoff of the excited mode.
Electronic Publication and the Narrowing of Science and Scholarship
Authors: Evans James A.
Published: July 2008

Online journals promise to serve more information to more dispersed audiences and are more efficiently searched and recalled. But because they are used differently than print—scientists and scholars tend to search electronically and follow hyperlinks rather than browse or peruse—electronically available journals may portend an ironic change for science. Using a database of 34 million articles, their citations (1945 to 2005), and online availability (1998 to 2005), I show that as more journal issues came online, the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles. The forced browsing of print archives may have stretched scientists and scholars to anchor findings deeply into past and present scholarship. Searching online is more efficient and following hyperlinks quickly puts researchers in touch with prevailing opinion, but this may accelerate consensus and narrow the range of findings and ideas built upon.
Observations of Intergranular Stress Corrosion Cracking in a Grain-Mapped Polycrystal
Authors: King A. , Johnson G. , Engelberg D. , Ludwig W. , Marrow J.
Published: July 2008

Nondestructive three-dimensional mapping of grain shape, crystallographic orientation, and grain boundary geometry by diffraction contrast tomography (DCT) provides opportunities for the study of the interaction between intergranular stress corrosion cracking and microstructure. A stress corrosion crack was grown through a volume of sensitized austenitic stainless steel mapped with DCT and observed in situ by synchrotron tomography. Several sensitization-resistant crack-bridging boundaries were identified, and although they have special geometric properties, they are not the twin variant boundaries usually maximized during grain boundary engineering.
The Evolution and Distribution of Species Body Size
Authors: Clauset Aaron , Erwin Douglas H.
Published: July 2008

The distribution of species body size within taxonomic groups exhibits a heavy right tail extending over many orders of magnitude, where most species are much larger than the smallest species. We provide a simple model of cladogenetic diffusion over evolutionary time that omits explicit mechanisms for interspecific competition and other microevolutionary processes, yet fully explains the shape of this distribution. We estimate the model's parameters from fossil data and find that it robustly reproduces the distribution of 4002 mammal species from the late Quaternary. The observed fit suggests that the asymmetric distribution arises from a fundamental trade-off between the short-term selective advantages (Cope's rule) and long-term selective risks of increased species body size in the presence of a taxon-specific lower limit on body size.
Measurement of the Elastic Properties and Intrinsic Strength of Monolayer Graphene
Authors: Lee Changgu , Wei Xiaoding , Kysar Jeffrey W. , Hone James
Published: July 2008

We measured the elastic properties and intrinsic breaking strength of free-standing monolayer graphene membranes by nanoindentation in an atomic force microscope. The force-displacement behavior is interpreted within a framework of nonlinear elastic stress-strain response, and yields second- and third-order elastic stiffnesses of 340 newtons per meter (N m
–1
) and –690 Nm
–1
, respectively. The breaking strength is 42 N m
–1
and represents the intrinsic strength of a defect-free sheet. These quantities correspond to a Young's modulus of
E
= 1.0 terapascals, third-order elastic stiffness of
D
= –2.0 terapascals, and intrinsic strength of σ
int
= 130 gigapascals for bulk graphite. These experiments establish graphene as the strongest material ever measured, and show that atomically perfect nanoscale materials can be mechanically tested to deformations well beyond the linear regime.
Four-jointed Is a Golgi Kinase That Phosphorylates a Subset of Cadherin Domains
Authors: Ishikawa Hiroyuki O. , Takeuchi Hideyuki , Haltiwanger Robert S. , Irvine Kenneth D.
Published: July 2008

The atypical cadherin Fat acts as a receptor for a signaling pathway that regulates growth, gene expression, and planar cell polarity. Genetic studies in
Drosophila
identified the
four-jointed
gene as a regulator of Fat signaling. We show that
four-jointed
encodes a protein kinase that phosphorylates serine or threonine residues within extracellular cadherin domains of Fat and its transmembrane ligand, Dachsous. Four-jointed functions in the Golgi and is the first molecularly defined kinase that phosphorylates protein domains destined to be extracellular. An acidic sequence motif (Asp-Asn-Glu) within Four-jointed was essential for its kinase activity in vitro and for its biological activity in vivo. Our results indicate that Four-jointed regulates Fat signaling by phosphorylating cadherin domains of Fat and Dachsous as they transit through the Golgi.
Outwitting Multidrug Resistance to Antifungals
Authors: Monk Brian C. , Goffeau Andre
Published: July 2008

The economic cost of fungal infection and its mortality associated with multidrug resistance remain unacceptably high. Recent understanding of the transcriptional regulation of plasma membrane efflux pumps of modest specificity provides new avenues for the development of broad-spectrum fungicides. Together with improved diagnosis and indirect intervention via inhibition of the energy supply for drug efflux, we envisage multifunctional azole analogs that inhibit not only ergosterol biosynthesis and drug efflux-pump activity but also activation of the transcriptional machinery that induces drug efflux-pump expression.
Lipoteichoic Acid Synergizes with Glycosphingolipids To Potently Stimulate Secretion of Interleukin-6 from Human Blood Cells
Authors: Meron-Sudai Shiri , Matityahou Ariella , Keisari Yona , Cox Kathleen H. , Hasty David L. , Ofek Itzhak
Published: July 2008

In the present study, we found that lipoteichoic acid (LTA) synergizes with glycosphingolipids to stimulate human blood cells to secrete cytokines. We employed globoside, kerasin, and lactosylceramide as representative neutral glycosphingolipids and mixed gangliosides GM
2
and GM
3
as representative acidic glycosphingolipids. LTA and the glycosphingolipids enhanced cytokine secretion by human whole blood, peripheral blood mononuclear cells, and purified monocytes in a dose-dependent manner. The level of synergy ranged up to ∼10-fold greater than the additive stimulation caused by LTA and glycosphingolipid alone. The greatest synergy was observed with GM
3
. We also found that LTA synergizes with the synthetic bacterial lipopeptide mimic Pam3CysK4. In contrast, the glycosphingolipids suppressed the stimulation caused by Pam3CysK4. The stimulation of human cells requires the simultaneous presence of LTA and the glycosphingolipids and probably requires their physical interactions, as shown by dot blotting and nondenaturing polyacrylamide gel electrophoresis experiments. We hypothesize that the enhanced stimulation is due to heterooligomers that form between LTA and glycosphingolipids at the subcritical micelle concentrations used in these experiments. Previous studies showed that LTA also synergizes with hemoglobin. The data taken together suggest that LTA may be a pathogen-associated molecular pattern, although its full activity requires the presence of a synergistic partner(s).
Validation of Reference Genes in Cervical Cell Samples from Human Papillomavirus-Infected and -Uninfected Women for Quantitative Reverse Transcription-PCR Assays
Authors: Daud Ibrahim I. , Scott Mark E.
Published: July 2008

Reference genes for quantitative reverse transcription-PCR (qRT-PCR) studies must be validated for the cell type studied and should be stable between the groups that represent the independent variable in an experimental design. We sought to identify the reference genes in cervical cell specimens showing the most stable expression between human papillomavirus (HPV)-infected and -uninfected women without high-grade cervical intraepithelial neoplasia. Using endocervical cells collected by cytology brush and Sybr green-based qRT-PCR, eight candidate genes were screened for amplification efficiency, specificity, and overall stability (by use of geNorm software). The five most stable genes were then further evaluated both for overall stability (geNorm) and intergroup stability (by use of NormFinder software) in specimens from HPV-negative and HPV-positive women. The combination of the glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) andRPLP0was the most stable overall, with a geNorm stability measure of 0.603. The intergroup analysis showedGAPDHto be the most stable single gene andRPLP0to be second most stable and also showed that these genes represent the most stable two-gene combination, with a NormFinder stability value of 0.130. The fact that these two distinct approaches identified the same pair of genes provides added confidence that, when the focus is on HPV infection, a normalization factor derived from these two genes is likely to be appropriate.
Validation of a Competitive Enzyme-Linked Immunosorbent Assay for Detection ofBabesia bigeminaAntibodies in Cattle
Authors: Goff Will L. , Johnson Wendell C. , Molloy John B. , Jorgensen Wayne K. , Waldron Susan J. , Figueroa Julio V. , Matthee Olivier , Adams D. Scott , McGuire Travis C. , Pino Ignacio , Mosqueda Juan , Palmer Guy H. , Suarez Carlos E. , Knowles Donald P. , McElwain Terry F.
Published: July 2008

A competitive enzyme-linked immunosorbent assay (cELISA) based on a broadly conserved, species-specific, B-cell epitope within the C terminus ofBabesia bigeminarhoptry-associated protein 1a was validated for international use. Receiver operating characteristic analysis revealed 16% inhibition as the threshold for a negative result, with an associated specificity of 98.3% and sensitivity of 94.7%. Increasing the threshold to 21% increased the specificity to 100% but modestly decreased the sensitivity to 87.2%. By using 21% inhibition, the positive predictive values ranged from 90.7% (10% prevalence) to 100% (95% prevalence) and the negative predictive values ranged from 97.0% (10% prevalence) to 48.2% (95% prevalence). The assay was able to detect serum antibody as early as 7 days after intravenous inoculation. The cELISA was distributed to five different laboratories along with a reference set of 100 defined bovine serum samples, including known positive, known negative, and field samples. The pairwise concordance among the five laboratories ranged from 100% to 97%, and all kappa values were above 0.8, indicating a high degree of reliability. Overall, the cELISA appears to have the attributes necessary for international application.
Oral Immunization with RecombinantLactobacillus plantarumInduces a Protective Immune Response in Mice with Lyme Disease
Authors: del Rio Beatriz , Dattwyler Raymond J. , Aroso Miguel , Neves Vera , Meirelles Luciana , Seegers Jos F. M. L. , Gomes-Solecki Maria
Published: July 2008

Mucosal immunization is advantageous over other routes of antigen delivery because it can induce both mucosal and systemic immune responses. Our goal was to develop a mucosal delivery vehicle based on bacteria generally regarded as safe, such asLactobacillusspp. In this study, we used the Lyme disease mouse model as a proof of concept. We demonstrate that an oral vaccine based on live recombinantLactobacillus plantarumprotects mice from tick-transmittedBorrelia burgdorferiinfection. Our method of expressing vaccine antigens inL. plantaruminduces both systemic and mucosal immunity after oral administration. This platform technology can be applied to design oral vaccine delivery vehicles against several microbial pathogens.
Characterization of Vancomycin-Heteroresistant
Staphylococcus aureus
from the Metropolitan Area of Detroit, Michigan, over a 22-Year Period (1986 to 2007)
Authors: Rybak Michael J. , Leonard Steve N. , Rossi Kerri L. , Cheung Chrissy M. , Sadar Helio S. , Jones Ronald N.
Published: July 2008

We screened for heteroresistant, vancomycin-intermediate
Staphylococcus aureus
(hVISA) among clinical isolates of methicillin-resistant
S. aureus
collected from three hospitals (two urban teaching hospitals and one community hospital) in the Detroit metropolitan area over a 22-year period. The Macro Etest method was used to screen all available isolates. Confirmation of hVISA-positive screens were confirmed by population-area under the concentration-time curve (AUC) analysis. A total of 1,499 isolates revealed hVISA/VISA rates of 2.2/0.4% (
n
= 225; 1986 to 1993), 7.6/2.3% (
n
= 356; 1994 to 2002), and 8.3/0.3% (
n
= 917; 2003 to 2007). Population-AUC analysis confirmed 92.6% of the hVISA-positive strains determined by the Macro Etest method. For the isolates with known sources (1,208), the predominant source of hVISA was blood (60%), followed by lung (21%), skin and wound infections (14%), abscess (1%), and other (4%). The percentage of hVISA-positive strains appeared to increase as a function of the vancomycin MIC. Staphylococcal cassette chromosome
mec
(SCC
mec
) typing revealed that the majority (56.9%) of the hVISA strains were SCC
mec
type II and 39.4% were type IV; the majority of these strains were collected from 2000 to 2007. Our data indicate that the prevalence of hVISA may be increasing. Based on the association of vancomycin treatment failure in patients with hVISA, surveillance of hVISA strains is warranted.
Detection and Characterization of Group C Rotaviruses in Asymptomatic Piglets in Ireland
Authors: Collins P. J. , Martella V. , O'Shea H.
Published: July 2008

Group C rotaviruses are important human enteric pathogens that have also been detected in a variety of mammalian species, including pigs. Group C rotaviruses have been identified in piglets with diarrhea, but their ecology remains to be elucidated. By screening of 292 fecal samples collected from 4- to 5-week-old asymptomatic pigs from four herds in Ireland between 2005 and 2007, 13 (4.4%) samples tested positive by reverse transcription-PCR for group C rotavirus. Group A rotaviruses were also detected in 19 samples but not in conjunction with group C viruses. The gene encoding the major group C neutralization antigen, the outer capsid protein VP7, was sequenced. The majority of the strains were very closely related to each other (>99% amino acid [aa] identity) and were characterized as genogroup G1 since they were genetically related to the prototype porcine strain Cowden (92.6% aa identity). Conversely, two strains (1GA/05/Cork/Ire and 281/07/Dublin/Ire) were characterized as genogroup G6 since they displayed the highest identity (89.2 to 94.0% aa) to porcine G6 strains (43/06-22-like). Unexpectedly, one such G6 strain, 1GA/05/Cork/Ire, lacked the 4-aa insertion in the VP7 variable region VR8 found in all the other G6 group C rotaviruses. This study provides evidence that porcine group C rotavirus may be detected not infrequently in asymptomatic piglets. In addition, it provides evidence that, unlike the human viruses, porcine group C rotaviruses display broad genetic heterogeneity, which may pose a challenge for the development of prophylactic tools.
Genetic Lineages of Community-Associated Methicillin-Resistant
Staphylococcus aureus
in Kuwait Hospitals
Authors: Udo E. E. , O'Brien F. G. , Al-Sweih N. , Noronha Bobby , Matthew B. , Grubb W. B.
Published: July 2008

Twenty-six community-associated methicillin-resistant
Staphylococcus aureus
(CAMSRA) isolates were characterized by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and screened for accessory gene regulator (agr), capsular polysaccharide (cap), and Panton-Valentine leucocidin (PVL) genes. They exhibited five PFGE patterns (types A to E). The majority were PFGE type A (12 isolates) or type B (8 isolates). MLST showed that PFGE type A isolates belonged to sequence type 80 (ST80), while the PFGE type B isolates were ST30. The ST80 and ST30 clones contained agr allotype 3, cap type 8, and PVL. The results showed that two internationally recognized CAMRSA clones are dominant in Kuwait hospitals.
Llama-Derived Single-Chain Antibody Fragments Directed to Rotavirus VP6 Protein Possess Broad Neutralizing Activity In Vitro and Confer Protection against Diarrhea in Mice
Authors: Garaicoechea Lorena , Olichon Aurelien , Marcoppido Gisela , Wigdorovitz Andrés , Mozgovoj Marina , Saif Linda , Surrey Thomas , Parreño Viviana
Published: July 2008

Group A rotavirus is one of the most common causes of severe diarrhea in human infants and newborn animals. Rotavirus virions are triple-layered particles. The outer capsid proteins VP4 and VP7 are highly variable and represent the major neutralizing antigens. The inner capsid protein VP6 is conserved among group A rotaviruses, is highly immunogenic, and is the target antigen of most immunodiagnosis tests. Llama-derived single-chain antibody fragments (VHH) are the smallest molecules with antigen-binding capacity and can therefore be expected to have properties different from conventional antibodies. In this study a library containing the VHH genes of a llama immunized with recombinant inner capsid protein VP6 was generated. Binders directed to VP6, in its native conformation within the viral particle, were selected and characterized. Four selected VHH directed to conformational epitopes of VP6 recognized all human and animal rotavirus strains tested and could be engineered for their use in immunodiagnostic tests for group A rotavirus detection. Three of the four VHH neutralized rotavirus in vivo independently of the strain serotype. Furthermore, this result was confirmed by in vivo partial protection against rotavirus challenge in a neonatal mouse model. The present study demonstrates for the first time a broad neutralization activity of VP6 specific VHH in vitro and in vivo. Neutralizing VHH directed to VP6 promise to become an essential tool for the prevention and treatment of rotavirus diarrhea.
Genomic Analysis Reveals Age-Dependent Innate Immune Responses to Severe Acute Respiratory Syndrome Coronavirus
Authors: Baas Tracey , Roberts Anjeanette , Teal Thomas H. , Vogel Leatrice , Chen Jun , Tumpey Terrence M. , Katze Michael G. , Subbarao Kanta
Published: July 2008

The relationship between immunosenescence and the host response to virus infection is poorly understood at the molecular level. Two different patterns of pulmonary host responses to virus were observed when gene expression profiles from severe acute respiratory syndrome coronavirus (SARS-CoV)-infected young mice that show minimal disease were compared to those from SARS-CoV-infected aged mice that develop pneumonitis. In young mice, genes related to cellular development, cell growth, and cell cycle were downregulated during peak viral replication, and these transcripts returned to basal levels as virus was cleared. In contrast, aged mice had a greater number of upregulated immune response and cell-to-cell signaling genes, and the expression of many genes was sustained even after viral clearance, suggesting an exacerbated host response to virus. Interestingly, in SARS-CoV-infected aged mice, a subset of genes, including Tnfa, Il6, Ccl2, Ccl3, Cxcl10, and Ifng, was induced in a biphasic pattern that correlated with peak viral replication and a subsequent influx of lymphocytes and severe histopathologic changes in the lungs. We provide insight into gene expression profiles and molecular signatures underlying immunosenescence in the context of the host response to viral infection.
The Interaction between Human Papillomavirus Type 16 and FADD Is Mediated by a Novel E6 Binding Domain
Authors: Tungteakkhun Sandy S. , Filippova Maria , Neidigh Jonathan W. , Fodor Nadja , Duerksen-Hughes Penelope J.
Published: July 2008

High-risk strains of human papillomavirus, such as types 16 and 18, have been etiologically linked to cervical cancer. Most cervical cancer tissues are positive for both the E6 and E7 oncoproteins, since it is their cooperation that results in successful transformation and immortalization of infected cells. We have reported that E6 binds to tumor necrosis factor receptor 1 and to Fas-associated death domain (FADD) and, in doing so, prevents E6-expressing cells from responding to apoptotic stimuli. The binding site of E6 to FADD localizes to the first 23 amino acids of FADD and has now been further characterized by the use of deletion and site-directed mutants of FADD in pull-down and functional assays. The results from these experiments revealed that mutations of serine 16, serine 18, and leucine 20 obstruct FADD binding to E6, suggesting that these residues are part of the E6 binding domain on FADD. Because FADD does not contain the two previously identified E6 binding motifs, the LxxφLsh motif, and the PDZ motif, a novel binding domain for E6 has been identified on FADD. Furthermore, peptides that correspond to this region can block E6/FADD binding in vitro and can resensitize E6-expressing cells to apoptotic stimuli in vivo. These results demonstrate the existence of a novel E6 binding domain.
The Crystal Structure of Coxsackievirus B3 RNA-Dependent RNA Polymerase in Complex with Its Protein Primer VPg Confirms the Existence of a Second VPg Binding Site on
Picornaviridae
Polymerases
Authors: Gruez Arnaud , Selisko Barbara , Roberts Michael , Bricogne Gérard , Bussetta Cécile , Jabafi Ilham , Coutard Bruno , De Palma Armando M. , Neyts Johan , Canard Bruno
Published: July 2008

The RNA-dependent RNA polymerase (RdRp) is a central piece in the replication machinery of RNA viruses. In picornaviruses this essential RdRp activity also uridylates the VPg peptide, which then serves as a primer for RNA synthesis. Previous genetic, binding, and biochemical data have identified a VPg binding site on poliovirus RdRp and have shown that is was implicated in VPg uridylation. More recent structural studies have identified a topologically distinct site on the closely related foot-and-mouth disease virus RdRp supposed to be the actual VPg-primer-binding site. Here, we report the crystal structure at 2.5-Å resolution of active coxsackievirus B3 RdRp (also named 3D
pol
) in a complex with VPg and a pyrophosphate. The pyrophosphate is situated in the active-site cavity, occupying a putative binding site either for the coproduct of the reaction or an incoming NTP. VPg is bound at the base of the thumb subdomain, providing first structural evidence for the VPg binding site previously identified by genetic and biochemical methods. The binding mode of VPg to CVB3 3D
pol
at this site excludes its uridylation by the carrier 3D
pol
. We suggest that VPg at this position is either uridylated by another 3D
pol
molecule or that it plays a stabilizing role within the uridylation complex. The CVB3 3D
pol
/VPg complex structure is expected to contribute to the understanding of the multicomponent VPg-uridylation complex essential for the initiation of genome replication of picornaviruses.
ERK1/2-Mediated Phosphorylation of Small Hepatitis Delta Antigen at Serine 177 Enhances Hepatitis Delta Virus Antigenomic RNA Replication
Authors: Chen Yen-Shun , Huang Wen-Hung , Hong Shiao-Ya , Tsay Yeou-Guang , Chen Pei-Jer
Published: July 2008

The small hepatitis delta virus (HDV) antigen (SHDAg) plays an essential role in HDV RNA double-rolling-circle replication. Several posttranslational modifications (PTMs) of HDAgs, including phosphorylation, acetylation, and methylation, have been characterized. Among the PTMs, the serine 177 residue of SHDAg is a phosphorylation site, and its mutation preferentially abolishes HDV RNA replication from antigenomic RNA to genomic RNA. Using coimmunoprecipitation analysis, the cellular kinases extracellular signal-related kinases 1 and 2 (ERK1/2) are found to be associated with the Flag-tagged SHDAg mutant (Ser-177 replaced with Cys-177). In an in vitro kinase assay, serine 177 of SHDAg was phosphorylated directly by either Flag-ERK1 or Flag-ERK2. Activation of endogenous ERK1/2 by a constitutively active MEK1 (hemagglutinin-AcMEK1) increased phosphorylation of SHDAg at Ser-177; this phosphorylation was confirmed by immunoblotting using an antibody against phosphorylated S177 and mass spectrometric analysis. Interestingly, we found an increase in the HDV replication from antigenomic RNA to genomic RNA but not in that from genomic RNA to antigenomic RNA. The Ser-177 residue was critical for SHDAg interaction with RNA polymerase II (RNAPII), the enzyme proposed to regulate antigenomic RNA replication. These results demonstrate the role of ERK1/2-mediated Ser-177 phosphorylation in modulating HDV antigenomic RNA replication, possibly through RNAPII regulation. The results may shed light on the mechanisms of HDV RNA replication.