bluuebunny/crossref_metadata_2025 huggingface dataset:
Broadband acoustic quantification of stratified turbulence
Authors: Lavery Andone C. , Geyer W. Rockwell , Scully Malcolm E.
Published: July 2013

High-frequency broadband acoustic scattering techniques have enabled the remote, high-resolution imaging and quantification of highly salt-stratified turbulence in an estuary. Turbulent salinity spectra in the stratified shear layer have been measured acoustically and by in situ turbulence sensors. The acoustic frequencies used span 120–600 kHz, which, for the highly stratified and dynamic estuarine environment, correspond to wavenumbers in the viscous-convective subrange (500–2500 m−1). The acoustically measured spectral levels are in close agreement with spectral levels measured with closely co-located micro-conductivity probes. The acoustically measured spectral shapes allow discrimination between scattering dominated by turbulent salinity microstructure and suspended sediments or swim-bladdered fish, the two primary sources of scattering observed in the estuary in addition to turbulent salinity microstructure. The direct comparison of salinity spectra inferred acoustically and by the in situ turbulence sensors provides a test of both the acoustic scattering model and the quantitative skill of acoustical remote sensing of turbulence dissipation in a strongly sheared and salt-stratified estuary.
Computationally robust and noise resistant numerical detector for the detection of atmospheric infrasound
Authors: Lee Dong-Chang , Olson John V. , Szuberla Curt A. L.
Published: July 2013

This work reports on a performance study of two numerical detectors that are particularly useful for infrasound arrays operating under windy conditions. The sum of squares of variance ratios (SSVR1)—proposed for detecting signals with frequency ranging from 1 to 10 Hz—is computed by taking the ratio of the squared sum of eigenvalues to the square of largest eigenvalue of the covariance matrix of the power spectrum. For signals with lower frequency between 0.015 and 0.1 Hz, SSVR2 is developed to reduce the detector's sensitivity to noise. The detectors' performances are graphically compared against the current method, the mean of cross correlation maxima (MCCM), using the receiver operating characteristics curves and three types of atmospheric infrasound, corrupted by Gaussian and Pink noise. The MCCM and SSVR2 detectors were also used to detect microbaroms from the 24 h-long infrasound data. It was found that the two detectors outperform the MCCM detector in both sensitivity and computational efficiency. For mine blasts corrupted by Pink noise (signal-to-noise ratio = −7 dB), the MCCM and SSVR1 detectors yield 62 and 88 % true positives when accepting 20% false positives. For an eight-sensor array, the speed gain is approximately eleven-fold for a 50 s long signal.
Measurements of acoustic environments for urban soundscapes: Choice of homogeneous periods, optimization of durations, and selection of indicators
Authors: Brocolini Laurent , Lavandier Catherine , Quoy Mathias , Ribeiro Carlos
Published: July 2013

In order to minimize the duration of acoustic measurements and to characterize homogeneous areas from a temporal point of view, a series of six location measurements was carried out continuously during three months in Paris. Around fifty thousand samples of 5-min, 10-min, 15-min, 20-min, 30-min, and 1-h duration measurements were extracted for each location. Each sample is characterized by eleven energy indicators and ten event descriptors. In this paper, analysis of a crossroad location is detailed. Through hierarchical ascendant classification and artificial neural networks classification, it is shown that four homogeneous periods can be detected: two during the night, one during the day, and one transition corresponding either to the awakening or to the moment when the city falls asleep. 10-min measurements are necessary to discriminate these time periods at the crossroad location. At the end of the paper, a comparison with the other locations shows that minimum duration states in between 10 and 20 min. The homogeneous periods are connected to the human activities and depend on the location. Energy indicators such as LAeq, LA10, or LA90 and event indicators are necessary to characterize the different clusters.
Predictions of diotic tone-in-noise detection based on a nonlinear optimal combination of energy, envelope, and fine-structure cues
Authors: Mao Junwen , Vosoughi Azadeh , Carney Laurel H.
Published: July 2013

Tone-in-noise detection has been studied for decades; however, it is not completely understood what cue or cues are used by listeners for this task. Model predictions based on energy in the critical band are generally more successful than those based on temporal cues, except when the energy cue is not available. Nevertheless, neither energy nor temporal cues can explain the predictable variance for all listeners. In this study, it was hypothesized that better predictions of listeners' detection performance could be obtained using a nonlinear combination of energy and temporal cues, even when the energy cue was not available. The combination of different cues was achieved using the logarithmic likelihood-ratio test (LRT), an optimal detector in signal detection theory. A nonlinear LRT-based combination of cues was proposed, given that the cues have Gaussian distributions and the covariance matrices of cue values from noise-alone and tone-plus-noise conditions are different. Predictions of listeners' detection performance for three different sets of reproducible noises were computed with the proposed model. Results showed that predictions for hit rates approached the predictable variance for all three datasets, even when an energy cue was not available.
The effect of overall level on sensitivity to interaural differences of time and level at high frequencies
Authors: Dietz Mathias , Bernstein Leslie R. , Trahiotis Constantine , Ewert Stephan D. , Hohmann Volker
Published: July 2013

For high-frequency complex stimuli, detection thresholds for envelope-based interaural time differences (ITDs) decrease with overall level. Substantial heterogeneity is, however, evident among the findings concerning the rate at which thresholds decline with level. This study investigated factors affecting the influence of overall level on threshold ITDs. Thresholds were measured as a function of overall level for 4-kHz-centered “targets” in three experiments focusing, respectively, on stimulus-type (sinusoidally amplitude-modulated or “transposed” tones), modulation frequency, and details concerning low-pass noise used to mask low-frequency distortion products. Results indicated that (1) log-ITD thresholds decreased linearly with overall level; (2) slopes relating log-ITD thresholds to level did not depend significantly on stimulus type; (3) lower modulation frequencies produced greater dependencies of thresholds on overall level than did higher modulation frequencies; (4) the effect of overall level on threshold-ITDs was independent of the interaural configuration and levels of the low-pass noise maskers tested; (5) synchronously gating the low-pass noise and target produced a greater dependency of thresholds on the overall level of the target than did continuous or temporally “fringed” presentation of the noise. A fourth experiment showed that threshold interaural level differences were somewhat less affected by changes in overall level than were threshold ITDs.
Respondents' answers to community attitudinal surveys represent impressions of soundscapes and not merely reactions to the physical noise
Authors: Schomer Paul , Mestre Vincent , Schulte-Fortkamp Brigitte , Boyle James
Published: July 2013

Noise dose as a sole independent variable accounts only for less than half of the variance in community response data. Non-acoustic factors, such as attitude to the noise source identified by Job [(1988). J. Acoust. Soc. Am. 83(3), 991–1001] and others, reduce the unexplained variance. This paper suggests that non-acoustic factors reflect the context in which the sonic environment is perceived; hence, these factors constitute the judgments of a soundscape. Fidell et al. [(2011). J. Acoust. Soc. Am. 130(2), 791–806] show that a “community tolerance level” (CTL) is a one-number, community-specific, independent variable that represents the aggregate influence on annoyance judgments of all non-acoustic influences. Taken together these findings suggest that: (i) CTL is a one-number quantification of a soundscape, and (ii) a soundscape can be quantified by a single, numeric variable. It follows, if one can predict or calculate the single numeric quantification of a soundscape, that number will be the CTL. These results can only be true for a soundscape judged on the basis of annoyance. Virtually no data exist for which the respondents even had the possibility to rate the sonic environment positively, i.e., pleasing, so the application of CTL to soundscapes judged positively is not clear.
Under-ice ambient noise in Eastern Beaufort Sea, Canadian Arctic, and its relation to environmental forcing
Authors: Bazile Kinda G. , Simard Yvan , Gervaise Cédric , Mars Jérome I. , Fortier Louis
Published: July 2013

This paper analyzes an 8-month time series (November 2005 to June 2006) of underwater noise recorded at the mouth of the Amundsen Gulf in the marginal ice zone of the western Canadian Arctic when the area was >90% ice covered. The time-series of the ambient noise component was computed using an algorithm that filtered out transient acoustic events from 7-min hourly recordings of total ocean noise over a [0–4.1] kHz frequency band. Under-ice ambient noise did not respond to thermal changes, but showed consistent correlations with large-scale regional ice drift, wind speed, and measured currents in upper water column. The correlation of ambient noise with ice drift peaked for locations at ranges of ∼300 km off the mouth of the Amundsen Gulf. These locations are within the multi-year ice plume that extends westerly along the coast in the Eastern Beaufort Sea due to the large Beaufort Gyre circulation. These results reveal that ambient noise in Eastern Beaufort Sea in winter is mainly controlled by the same meteorological and oceanographic forcing processes that drive the ice drift and the large-scale circulation in this part of the Arctic Ocean.
Modeling and simulation of a grand piano
Authors: Chabassier Juliette , Chaigne Antoine , Joly Patrick
Published: July 2013

A time-domain global modeling of a grand piano is presented. The string model includes internal losses, stiffness, and geometrical nonlinearity. The hammer-string interaction is governed by a nonlinear dissipative compression force. The soundboard is modeled as a dissipative bidimensional orthotropic Reissner–Mindlin plate where the presence of ribs and bridges is treated as local heterogeneities. The coupling between strings and soundboard at the bridge allows the transmission of both transverse and longitudinal waves to the soundboard. The soundboard is coupled to the acoustic field, whereas all other parts of the structure are supposed to be perfectly rigid. The acoustic field is bounded artificially using perfectly matched layers. The discrete form of the equations is based on original energy preserving schemes. Artificial decoupling is achieved, through the use of Schur complements and Lagrange multipliers, so that each variable of the problem can be updated separately at each time step. The capability of the model is highlighted by series of simulations in the low, medium, and high register, and through comparisons with waveforms recorded on a Steinway D piano. Its ability to account for phantom partials and precursors, consecutive to string nonlinearity and inharmonicity, is particularly emphasized.
Time-angle sensitivity kernels for sound-speed perturbations in a shallow ocean
Authors: Aulanier Florian , Nicolas Barbara , Roux Philippe , Mars Jérôme I.
Published: July 2013

Acoustic waves traveling in a shallow-water waveguide produce a set of multiple paths that can be characterized as a geometric approximation by their travel time (TT), direction of arrival (DOA), and direction of departure (DOD). This study introduces the use of the DOA and DOD as additional observables that can be combined to the classical TT to track sound-speed perturbations in an oceanic waveguide. To model the TT, DOA, and DOD variations induced by sound-speed perturbations, the three following steps are used: (1) In the first-order Born approximation, the Fréchet kernel provides a linear link between the signal fluctuations and the sound-speed perturbations; (2) a double-beamforming algorithm is used to transform the signal fluctuations received on two source-receiver arrays in the time, receiver-depth, and source-depth domain into the eigenray equivalent measured in the time, reception-angle and launch angle domain; and finally (3) the TT, DOA, and DOD variations are extracted from the double-beamformed signal variations through a first-order Taylor development. As a result, time-angle sensitivity kernels are defined and used to build a linear relationship between the observable variations and the sound-speed perturbations. This approach is validated with parabolic-equation simulations in a shallow-water ocean context.
Time-domain demonstration of distributed distortion-product otoacoustic emission components
Authors: Martin Glen K. , Stagner Barden B. , Lonsbury-Martin Brenda L.
Published: July 2013

Distortion-product otoacoustic emissions (DPOAEs) were measured in rabbits as time waveforms by employing a phase-rotation technique to cancel all components in the final average, except the 2f1-f2 DPOAE. Subsequent filtering allowed the DPOAE waveform to be clearly visualized in the time domain. In most conditions, f2 was turned off for 6 ms, which produced a gap so that the DPOAE was no longer generated. These procedures allowed the DPOAE onset as well as the decay during the gap to be observed in the time domain. DPOAEs were collected with L1 = L2 = 65-dB sound pressure level primary-tone levels for f2/f1 ratios from 1.25 to 1.01 in 0.02 steps. Findings included the appearance of complex onsets and decays for the DPOAE time waveforms as the f2/f1 ratio was decreased and the DPOAE level was reduced. These complexities were unaffected by interference tones (ITs) near the DPOAE frequency place (fdp), but could be removed by ITs presented above f2, which also increased DPOAE levels. Similar outcomes were observed when DPOAEs were measured at a sharp notch in the DPOAE level as a function of the f2 primary tone frequency, i.e., DP-gram. Both findings were consistent with the hypothesis that the DPOAE-ratio function, and some notches in the DP-gram, are caused by interactions of distributed DPOAE components with unique phases.
Bayesian geoacoustic inversion of single hydrophone light bulb data using warping dispersion analysis
Authors: Bonnel Julien , Dosso Stan E. , Ross Chapman N.
Published: July 2013

This paper presents geoacoustic inversion of a light bulb implosion recorded during the Shallow Water 2006 experiment. The source is low frequency and impulsive, the environment is shallow water, and the acoustic signal is recorded using a single receiver. In this context, propagation is described by modal theory, and inversion is carried out by matching modal dispersion curves in the time-frequency domain. Experimental dispersion curves are estimated using an advanced signal processing method called warping, allowing inversion to be carried out at a relatively short range (≃7 km). Moreover, the inversion itself is performed using Bayesian methodology. This allows inference of the seabed structure from the data, including the number of seabed layers resolved, optimal estimates of the seabed parameters, and quantitative uncertainty estimates. Inversion results of the experimental data are in good agreement with both ground truth and estimates from other experimental data in the same region.
Estimation of seabed shear-wave velocity profiles using shear-wave source data
Authors: Dong Hefeng , Nguyen Thanh-Duong , Duffaut Kenneth
Published: July 2013

This paper estimates seabed shear-wave velocity profiles and their uncertainties using interface-wave dispersion curves extracted from data generated by a shear-wave source. The shear-wave source generated a seismic signature over a frequency range between 2 and 60 Hz and was polarized in both in-line and cross-line orientations. Low-frequency Scholte- and Love-waves were recorded. Dispersion curves of the Scholte- and Love-waves for the fundamental mode and higher-order modes are extracted by three time-frequency analysis methods. Both the vertically and horizontally polarized shear-wave velocity profiles in the sediment are estimated by the Scholte- and Love-wave dispersion curves, respectively. A Bayesian approach is utilized for the inversion. Differential evolution, a global search algorithm is applied to estimate the most-probable shear-velocity models. Marginal posterior probability profiles are computed by Metropolis-Hastings sampling. The estimated vertically and horizontally polarized shear-wave velocity profiles fit well with the core and in situ measurements.
Modal investigation of elastic anisotropy in shallow-water environments: Anisotropy beyond vertical transverse isotropy
Authors: Soukup Darin J. , Odom Robert I. , Park Jeffrey
Published: July 2013

Theoretical and numerical results are presented for modal characteristics of the seismo-acoustic wavefield in anisotropic range-independent media. General anisotropy affects the form of the elastic-stiffness tensor, particle-motion polarization, the frequency and angular dispersion curves, and introduces near-degenerate modes. Horizontally polarized particle motion (SH) cannot be ignored when anisotropy is present for low-frequency modes having significant bottom interaction. The seismo-acoustic wavefield has polarizations in all three coordinate directions even in the absence of any scattering or heterogeneity. Even weak anisotropy may have a significant impact on seismo-acoustic wave propagation. Unlike isotropic and transversely isotropic media with a vertical symmetry axis where acoustic signals comprise P-SV modes alone (in the absence of any scattering), tilted TI media allow both quasi-P-SV and quasi-SH modes to carry seismo-acoustic energy. Discrete modes for an anisotropic medium are best described as generalized P-SV-SH modes with polarizations in all three Cartesian directions. Conversion to SH is a loss that will mimic acoustic attenuation. An in-water explosion will excite quasi-SH.
Effects of low-frequency naval sonar exposure on three species of fish
Authors: Halvorsen Michele B. , Zeddies David G. , Chicoine David , Popper Arthur N.
Published: July 2013

To address growing concern over the impact of anthropogenic sound on fishes, a series of experiments was conducted that exposed several fish species to high-intensity low-frequency naval sonar. This study extends auditory findings by adding largemouth bass, yellow perch, and channel catfish. No effects on hearing were found in largemouth bass and yellow perch and only small effects in channel catfish (a fish with morphological adaptations for enhanced pressure reception). Together with prior findings, these results suggest limited impact on hearing from high-intensity sonar. Susceptibility may be due to genetic stock, developmental conditions, seasonal variation, and/or buoyancy during exposure.
The effects of lexical neighbors on stop consonant articulation
Authors: Goldrick Matthew , Vaughn Charlotte , Murphy Amanda
Published: July 2013

Lexical neighbors (words sharing phonological structure with a target word) have been shown to influence the expression of phonetic contrasts for vowels and initial voiceless consonants. Focusing on minimal pair neighbors (e.g., bud—but), this research extends this work by examining the production of voiced as well as voiceless stops in both initial and final syllable/word position. The results show minimal pair neighbors can result both in enhancement and reduction of voicing contrasts (in initial vs final position), and differentially affect voiced vs voiceless consonants. These diverse effects of minimal pair neighbors serve to constrain interactive theories of language processing.
Full-scale tests of reflective noise-reducing devices for balconies on high-rise buildings
Authors: Ishizuka Takashi , Fujiwara Kyoji
Published: July 2013

In the present report, the noise-shielding efficiency of balconies with ceiling-mounted reflectors on the façades of high-rise buildings is examined through full-scale field measurements. The reflectors are designed to reflect direct and diffracted waves incident on the balcony ceiling outside the balcony. Field measurements are conducted to investigate the performance of the reflectors on intermediate floors of a high-rise dwelling adjacent to a railway. The reflectors reduce railway noise by approximately 5 dB, in A-weighted sound pressure level, compared to an ordinary balcony. The noise-shielding efficiency of a balcony equipped with reflectors is greater than that of an absorbing balcony.
Applying diffuse ultrasound under dynamic loading to improve closed crack characterization in concrete
Authors: Payan C. , Quiviger A. , Garnier V. , Chaix J. F. , Salin J.
Published: July 2013

Recent studies show the ability of diffuse ultrasound to characterize surface breaking cracks in concrete. However, derived parameters are sensitive to the presence of partially opened zones along the crack whose pattern may differ from one sample to another. The aim of this letter is to study the variation of diffuse ultrasound parameters while the sample is driven by a low frequency bending load which alternatively opens and closes the crack, allowing to access supplementary information about its morphology. The results show the sensitivity of the method for various crack depths and highlight its potential for concrete nondestructive evaluation.
Microcircuits for Hierarchical Elaboration of Object Coding Across Primate Temporal Areas
Authors: Hirabayashi Toshiyuki , Takeuchi Daigo , Tamura Keita , Miyashita Yasushi
Published: July 2013

Hierarchy and Representation

Neuronal representations of objects are elaborated through the hierarchy of occipitotemporal cortical areas, and the recognition of a feature as “novel” is commonly thought to emerge and become prevalent at a cortical area because of local signal processing.

Hirabayashi
et al.

(p.
191
) tested another possibility—that a feature representation becomes prevalent in a given area because a microcircuit creates a small number of precursor representations in a prior area in the cortical hierarchy, and the representations then become prevalent through proliferation in the subsequent area. In support of this notion, critical microcircuits for object association were observed using multiple single-unit recordings in two areas of the macaque temporal cortex.
One-Step Assembly of Coordination Complexes for Versatile Film and Particle Engineering
Authors: Ejima Hirotaka , Richardson Joseph J. , Liang Kang , Best James P. , van Koeverden Martin P. , Such Georgina K. , Cui Jiwei , Caruso Frank
Published: July 2013

Thin adherent films formed from ferric ions and a natural polyphenol, tannic acid, can coat a wide variety of surfaces.

[Also see Perspective by
Bentley and Payne
]
Enhanced Remote Earthquake Triggering at Fluid-Injection Sites in the Midwestern United States
Authors: van der Elst Nicholas J. , Savage Heather M. , Keranen Katie M. , Abers Geoffrey A.
Published: July 2013

Movers and Shakers

We tend to view earthquakes as unpredictable phenomena caused by naturally shifting stresses in Earth's crust. In reality, however, a range of human activity can also induce earthquakes.
Ellsworth
(p.
10.1126/science.1225942
) reviews the current understanding of the causes and mechanics of earthquakes caused by human activity and the means to decrease their associated risk. Notable examples include injection of wastewater into deep formations and emerging technologies related to oil and gas recovery, including hydraulic fracturing. In addition to directly causing increased local seismic activity, activities such as deep fluid injection may have other ramifications related to earthquake occurrence.

Van der Elst
et al.

(p.
164
; see the news story by

Kerr

) demonstrate that in the midwestern United States, some areas with increased human-induced seismicity are also more prone to further earthquakes triggered by the seismic waves from large, remote earthquakes. Improved seismic monitoring and injection data near deep disposal sites will help to identify regions prone to remote triggering and, more broadly, suggest times when activities should, at least temporarily, be put on hold.
Prostate Cancer Takes Nerve
Authors: Isaacs John T.
Published: July 2013

Prostate cancer development and metastasis is driven by invasion of the tumor by the nervous system.

[Also see Research Article by

Magnon
et al.

]
Meteorite Mystery Edges Closer to an Answer—Or the End of a Field
Authors: Kerr Richard A.
Published: July 2013

Blobs called chondrules in the fabric of rocks from space have long baffled scientists. A new idea may shed light on their origins, but some experts have given up hope.
Isolation of Nontuberculous Mycobacteria (NTM) from Household Water and Shower Aerosols in Patients with Pulmonary Disease Caused by NTM
Authors: Thomson Rachel , Tolson Carla , Carter Robyn , Coulter Chris , Huygens Flavia , Hargreaves Megan
Published: July 2013

It has been postulated that susceptible individuals may acquire infection with nontuberculous mycobacteria (NTM) from water and aerosol exposure. This study examined household water and shower aerosols of patients with NTM pulmonary disease. The mycobacteria isolated from clinical samples from 20 patients included
M. avium
(5 patients),
M. intracellulare
(12 patients),
M. abscessus
(7 patients),
M. gordonae
(1 patient),
M. lentiflavum
(1 patient),
M. fortuitum
(1 patient),
M. peregrinum
(1 patient),
M. chelonae
(1 patient),
M. triplex
(1 patient), and
M. kansasii
(1 patient). One-liter water samples and swabs were collected from all taps, and swimming pools or rainwater tanks. Shower aerosols were sampled using Andersen six-stage cascade impactors. For a subgroup of patients, real-time PCR was performed and high-resolution melt profiles were compared to those of ATCC control strains. Pathogenic mycobacteria were isolated from 19 homes. Species identified in the home matched that found in the patient in seven (35%) cases:
M. abscessus
(3 cases),
M. avium
(1 case),
M. gordonae
(1 case),
M. lentiflavum
(1 case), and
M. kansasii
(1 case). In an additional patient with
M. abscessus
infection, this species was isolated from potable water supplying her home. NTM grown from aerosols included
M. abscessus
(3 homes),
M. gordonae
(2 homes),
M. kansasii
(1 home),
M. fortuitum
complex (4 homes),
M. mucogenicum
(1 home), and
M. wolinskyi
(1 home). NTM causing human disease can be isolated from household water and aerosols. The evidence appears strongest for
M. avium
,
M. kansasii
,
M. lentiflavum
, and
M. abscessus
. Despite a predominance of disease due to
M. intracellulare
, we found no evidence for acquisition of infection from household water for this species.
Genetic Characteristics of CTX-M-Type Extended-Spectrum-β-Lactamase (ESBL)-Producing Enterobacteriaceae Involved in Mastitis Cases on Japanese Dairy Farms, 2007 to 2011
Authors: Ohnishi Mamoru , Okatani Alexandre T. , Harada Kazuki , Sawada Takuo , Marumo Kenji , Murakami Masaru , Sato Reiichiro , Esaki Hidetake , Shimura Keiko , Kato Hajime , Uchida Naoki , Takahashi Toshio
Published: July 2013

Sixty-five CTX-M-2/15/14 extended-spectrum-β-lactamase-producing
Enterobacteriaceae
were isolated from 258,888 mastitic milk samples from Japanese dairy farms between 2007 and 2011. CTX-M-2-producing
Klebsiella pneumoniae
and CTX-M-15-producing
Escherichia coli
were the predominant strains isolated. There was no predominant clonal type, and clonal diversity was found even in strains isolated from a single farm.
A Sensitive Multiplex, Real-Time PCR Assay for Prospective Detection of Shiga Toxin-Producing Escherichia coli from Stool Samples Reveals Similar Incidences but Variable Severities of Non-O157 and O157 Infections in Northern California
Authors: Lefterova Martina I. , Slater Kathleen A. , Budvytiene Indre , Dadone Patricia A. , Banaei Niaz
Published: July 2013

Rapid and accurate detection of Shiga toxin-producing
Escherichia coli
(STEC) of all serotypes from patients with diarrhea is critical for medical management and for the prevention of ongoing transmission. In this prospective study, we assessed the performance of a multiplex, real-time PCR assay targeting
stx
1
and
stx
2
for the detection of O157 and non-O157 STEC in diarrheal stool samples enriched in Gram-negative broth. We show that the assay is 100% sensitive (95% confidence interval [CI], 89.1% to 100%) and 98.5% specific (95% CI, 90.6% to 99.9%) based on a panel of 40 known STEC-positive specimens and 65 known negative specimens. During a 2-year postvalidation period, the assay detected more positive samples from patients in northern California than did culture and PCR testing performed at a public health reference laboratory, with a positive predictive value of 95.6% (95% CI, 87.6% to 99.1%). Serotyping data showed an incidence rate of 51.2% for non-O157 STEC strains, with 5.8% of patients (1/17) with non-O157 strains and 42.9% (6/14) with O157 strains (
P
= 0.03) developing hemolytic-uremic syndrome. The findings from this study underscore the recommendations of the CDC for laboratories to test all diarrheal stool samples from patients with acute community-acquired diarrhea for non-O157 STEC in addition to the O157 serotype by using a sensitive assay. Additionally, a survey of 17 clinical laboratories in northern California demonstrated that nearly 50% did not screen all stool specimens for the presence of Shiga toxins, indicating that many clinical microbiology laboratories still do not routinely screen all stool specimens for the presence of Shiga toxins as recommended in the 2009 CDC guidelines.
Bilateral Conjunctivitis Due to Trichomonas vaginalis without Genital Infection: an Unusual Presentation in an Adult Man
Authors: Abdolrasouli Alireza , Croucher Adam , Roushan Azita , Gaydos Charlotte A.
Published: July 2013

We report an unusual case of extragenital infection with
Trichomonas vaginalis
of the conjunctiva of a 32-year-old man. Only one other similar case has been reported in the English language literature. The present report reinforces the widening pathologic spectrum of trichomonads in humans, especially in the context of emerging extragenital infections.
Negative Regulation of RIG-I-Mediated Innate Antiviral Signaling by SEC14L1
Authors: Li Meng-Tong , Di Wei , Xu Hao , Yang Yong-Kang , Chen Hai-Wei , Zhang Fei-Xiong , Zhai Zhong-He , Chen Dan-Ying
Published: July 2013

Retinoic acid-inducible gene I (RIG-I) is a key sensor for recognizing nucleic acids derived from RNA viruses and triggers beta interferon (IFN-β) production. Because of its important role in antiviral innate immunity, the activity of RIG-I must be tightly controlled. Here, we used yeast two-hybrid screening to identify a SEC14 family member, SEC14L1, as a RIG-I-associated negative regulator. Transfected SEC14L1 interacted with RIG-I, and endogenous SEC14L1 associated with RIG-I in a viral infection-inducible manner. Overexpression of SEC14L1 inhibited transcriptional activity of the IFN-β promoter induced by RIG-I but not TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3). Knockdown of endogenous SEC14L1 in both HEK293T cells and HT1080 cells potentiated RIG-I and Sendai virus-triggered IFN-β production as well as attenuated the replication of Newcastle disease virus. SEC14L1 interacted with the N-terminal domain of RIG-I (RIG-I caspase activation and recruitment domain [RIG-I-CARD]) and competed with VISA/MAVS/IPS-1/Cardif for RIG-I-CARD binding. Domain mapping further indicated that the PRELI-MSF1 and CRAL-TRIO domains but not the GOLD domain of SEC14L1 are required for interaction and inhibitory function. These findings suggest that SEC14L1 functions as a novel negative regulator of RIG-I-mediated antiviral signaling by preventing RIG-I interaction with the downstream effector.
BK Polyomavirus Genotypes Represent Distinct Serotypes with Distinct Entry Tropism
Authors: Pastrana Diana V. , Ray Upasana , Magaldi Thomas G. , Schowalter Rachel M. , Çuburu Nicolas , Buck Christopher B.
Published: July 2013

BK polyomavirus (BKV) causes significant urinary tract pathogenesis in immunosuppressed individuals, including kidney and bone marrow transplant recipients. It is currently unclear whether BKV-neutralizing antibodies can moderate or prevent BKV disease. We developed reporter pseudoviruses based on seven divergent BKV isolates and performed neutralization assays on sera from healthy human subjects. The results demonstrate that BKV genotypes I, II, III, and IV are fully distinct serotypes. While nearly all healthy subjects had BKV genotype I-neutralizing antibodies, a majority of subjects did not detectably neutralize genotype III or IV. Surprisingly, BKV subgenotypes Ib1 and Ib2 can behave as fully distinct serotypes. This difference is governed by as few as two residues adjacent to the cellular glycan receptor-binding site on the virion surface. Serological analysis of mice given virus-like particle (VLP)-based BKV vaccines confirmed these findings. Mice administered a multivalent VLP vaccine showed high-titer serum antibody responses that potently cross-neutralized all tested BKV genotypes. Interestingly, each of the neutralization serotypes bound a distinct spectrum of cell surface receptors, suggesting a possible connection between escape from recognition by neutralizing antibodies and cellular attachment mechanisms. The finding implies that different BKV genotypes have different cellular tropisms and pathogenic potentials
in vivo
. Individuals who are infected with one BKV serotype may remain humorally vulnerable to other BKV serotypes after implementation of T cell immunosuppression. Thus, prevaccinating organ transplant recipients with a multivalent BKV VLP vaccine might reduce the risk of developing posttransplant BKV disease.
The Avian XPR1 Gammaretrovirus Receptor Is under Positive Selection and Is Disabled in Bird Species in Contact with Virus-Infected Wild Mice
Authors: Martin Carrie , Buckler-White Alicia , Wollenberg Kurt , Kozak Christine A.
Published: July 2013

Xenotropic mouse leukemia viruses (X-MLVs) are broadly infectious for mammals except most of the classical strains of laboratory mice. These gammaretroviruses rely on the XPR1 receptor for entry, and the unique resistance of laboratory mice is due to two mutations in different putative XPR1 extracellular loops. Cells from avian species differ in susceptibility to X-MLVs, and 2 replacement mutations in the virus-resistant chicken XPR1 (K496Q and Q579E) distinguish it from the more permissive duck and quail receptors. These substitutions align with the two mutations that disable the laboratory mouse XPR1. Mutagenesis of the chicken and duck genes confirms that residues at both sites are critical for virus entry. Among 32 avian species, the 2 disabling
XPR1
mutations are found together only in the chicken, an omnivorous, ground-dwelling fowl that was domesticated in India and/or Southeast Asia, which is also where X-MLV-infected house mice evolved. The receptor-disabling mutations are also present separately in 5 additional fowl and raptor species, all of which are native to areas of Asia populated by the virus-infected subspecies
Mus musculus castaneus
. Phylogenetic analysis showed that the avian XPR1 gene is under positive selection at sites implicated in receptor function, suggesting a defensive role for XPR1 in the avian lineage. Contact between bird species and virus-infected mice may thus have favored selection of mouse virus-resistant receptor orthologs in the birds, and our data suggest that similar receptor-disabling mutations were fixed in mammalian and avian species exposed to similar virus challenges.
The Amphipathic Helix of Influenza A Virus M2 Protein Is Required for Filamentous Bud Formation and Scission of Filamentous and Spherical Particles
Authors: Roberts Kari L. , Leser George P. , Ma Chunlong , Lamb Robert A.
Published: July 2013

Influenza virus assembles and buds at the infected-cell plasma membrane. This involves extrusion of the plasma membrane followed by scission of the bud, resulting in severing the nascent virion from its former host. The influenza virus M2 ion channel protein contains in its cytoplasmic tail a membrane-proximal amphipathic helix that facilitates the scission process and is also required for filamentous particle formation. Mutation of five conserved hydrophobic residues to alanines within the amphipathic helix (M2 five-point mutant, or 5PM) reduced scission and also filament formation, whereas single mutations had no apparent phenotype. Here, we show that any two of these five residues mutated together to alanines result in virus debilitated for growth and filament formation in a manner similar to 5PM. Growth kinetics of the M2 mutants are approximately 2 logs lower than the wild-type level, and plaque diameter was significantly reduced. When the 5PM and a representative double mutant (I51A-Y52A) were introduced into A/WSN/33 M2, a strain that produces spherical particles, similar debilitation in viral growth occurred. Electron microscopy showed that with the 5PM and the I51A-Y52A A/Udorn/72 and WSN viruses, scission failed, and emerging virus particles exhibited a “beads-on-a-string” morphology. The major spike glycoprotein hemagglutinin is localized within lipid rafts in virus-infected cells, whereas M2 is associated at the periphery of rafts. Mutant M2s were more widely dispersed, and their abundance at the raft periphery was reduced, suggesting that the M2 amphipathic helix is required for proper localization in the host membrane and that this has implications for budding and scission.
Mutations in the Cytoplasmic Domain of the Newcastle Disease Virus Fusion Protein Confer Hyperfusogenic Phenotypes Modulating Viral Replication and Pathogenicity
Authors: Samal Sweety , Khattar Sunil K. , Paldurai Anandan , Palaniyandi Senthilkumar , Zhu Xiaoping , Collins Peter L. , Samal Siba K.
Published: July 2013

The Newcastle disease virus (NDV) fusion protein (F) mediates fusion of viral and host cell membranes and is a major determinant of NDV pathogenicity. In the present study, we demonstrate the effects of functional properties of F cytoplasmic tail (CT) amino acids on virus replication and pathogenesis. Out of a series of C-terminal deletions in the CT, we were able to rescue mutant viruses lacking two or four residues (rΔ2 and rΔ4). We further rescued viral mutants with individual amino acid substitutions at each of these four terminal residues (rM553A, rK552A, rT551A, and rT550A). In addition, the NDV F CT has two conserved tyrosine residues (Y524 and Y527) and a dileucine motif (LL536-537). In other paramyxoviruses, these residues were shown to affect fusion activity and are central elements in basolateral targeting. The deletion of 2 and 4 CT amino acids and single tyrosine substitution resulted in hyperfusogenic phenotypes and increased viral replication and pathogenesis. We further found that in rY524A and rY527A viruses, disruption of the targeting signals did not reduce the expression on the apical or basolateral surface in polarized Madin-Darby canine kidney cells, whereas in double tyrosine mutant, it was reduced on both the apical and basolateral surfaces. Interestingly, in rL536A and rL537A mutants, the F protein expression was more on the apical than on the basolateral surface, and this effect was more pronounced in the rL537A mutant. We conclude that these wild-type residues in the NDV F CT have an effect on regulating F protein biological functions and thus modulating viral replication and pathogenesis.
Surgical management of iatrogenic perforation in maxillary central incisor using mineral trioxide aggregate
Authors: Nagpal Rajni , Manuja Naveen , Pandit I K , Rallan Mandeep
Published: July 2013

Root perforations are undesired complications of endodontic treatment. The repair of root perforation can be accomplished using different materials and techniques. Mineral trioxide aggregate (MTA) is widely used to seal perforations because of its biocompatibility and sealability. This article describes a case report where an iatrogenic root perforation was repaired successfully with MTA in maxillary right central incisor of a 13-year-old boy.
The size and distribution of key populations at greater risk of HIV in Pakistan: implications for resource allocation for scaling up HIV prevention programmes
Authors: Emmanuel Faran , Thompson Laura H , Salim Momina , Akhtar Naeem , Reza Tahira E , Hafeez Hajra , Ahmed Sajid , Blanchard James F
Published: July 2013

Background

With competing interests, limited funding and a socially conservative context, there are many barriers to implementing evidence-informed HIV prevention programmes for sex workers and injection drug users in Pakistan. Meanwhile, the HIV prevalence is increasing among these populations across Pakistan. We sought to propose and describe an approach to resource allocation which would maximise the impact and allocative efficiency of HIV prevention programmes.

Methods

Programme performance reports were used to assess current resource allocation. Population size estimates derived from mapping conducted in 2011 among injection drug users andhijra, male and female sex workers and programme costs per person documented from programmes in the province of Sindh and also in India were used to estimate the cost to deliver services to 80% of these key population members across Pakistan. Cities were prioritised according to key population size.

Results

To achieve 80% population coverage, HIV prevention programmes should be implemented in 10 major cities across Pakistan for a total annual operating cost of approximately US$3.5 million, which is much less than current annual expenditures. The total cost varies according to the local needs and the purchasing power of the local currency.

Conclusions

By prioritising key populations at greatest risk of HIV in cities with the largest populations and limited resources, may be most effectively harnessed to quell the spread of HIV in Pakistan.
Case study of copper poisoning in a British dairy herd
Authors: Bidewell C. A. , Drew J. R. , Payne J. H. , Sayers A. R. , Higgins R. J. , Livesey C. T.
Published: July 2013

Following the initial diagnosis of chronic copper poisoning (CCP), the copper (Cu) status of a British dairy herd was investigated. Eight fatal cases of CCP were identified over a 17‐month period, from December 1999 to May 2001, involving seven Jersey cows and one Holstein‐Friesian; seven cows were dry when CCP occurred. Case diagnostic criteria were necrotising hepatopathy associated with abnormally high liver and kidney Cu concentrations. Analysis of the ration for the high‐yielding Jersey cow group revealed about 50 mg Cu/kg dry matter intake (DMI). Risk factors predisposing to fatal CCP were Jersey breed, previous high yield, first two weeks of the dry period and moderately high dietary Cu (greater than 40 mg Cu/kg DMI).
Three cases of Parafilaria bovicola infection in Belgium, and a few recent epidemiological observations on this emergent disease
Authors: Caron Y. , Groignet S. , Saegerman C. , Losson B. J.
Published: July 2013

Parafilariosis is a vectorborne parasitic disease caused by the development of the nematode Parafilaria bovicola in the subcutaneous and intermuscular connective tissues of cattle. On February 28, 2012, the so‐called bleeding spots were observed in two heifers and one bull in a cattle herd close to Namur (Belgium). The animals had been treated in December with an injectable ivermectin/closantel solution (Closamectin pour‐on, Norbrook Lab) at the recommended dosage. Samples of serohaemorrhagic exudate and blood, as well as skin biopsies, were collected. Embryonated eggs of P bovicola in the serohaemorrhagic exudate and high levels of creatine phosphokinase were detected. Clinically affected animals were treated with injectable ivermectin (Ivomec, Merial) at 200 μg/kg. Two epidemiological phone surveys were carried out in the south of Belgium (Wallonia) in order to estimate the geographical distribution of this condition since it was first described and published in 2009. A standardised questionnaire was used and the results were analysed. Most outbreaks were recorded in the provinces of Liege and Luxembourg. The initial source of infection is still unknown, but this parasitic infection is clearly spreading from the initial Belgian outbreak site.
Arrhythmogenic right ventricular cardiomyopathy as a cause of unexpected cardiac death in two horses
Authors: Freel K. M. , Morrison L. R. , Thompson H. , Else R. W.
Published: July 2013

Postmortem and histological examination of the hearts from two horses, a five‐yearold Clydesdale gelding and a 15‐year‐old cob gelding, revealed changes characteristic of arrhythmogenic right ventricular cardiomyopathy. In both cases, on gross examination, the right ventricular endocardium and interventricular septum were almost entirely replaced with a gelatinous yellow fibroareolar tissue. This tissue was histologically a combination of fibrous and adipose tissue that had replaced the normal myofibres and disrupted the Purkinje fibres.
EFFECTS OF COPPER DOPING ON DIELECTRIC AND A.C. CONDUCTIVITY IN LAYERED SODIUM TRI-TITANATE CERAMIC
Authors: SHRIPAL  , DWIVEDI SHAILJA , SINGH RAKESH , TANDON R. P.
Published: July 2013

Electron paramagnetic resonance (EPR) spectra of 0.01, 0.1 and 1.0 molar percentage (mp) of CuO doped derivatives of layered Na 2 Ti 3 O 7 ceramic have been reported. The results show that copper substitutes as Cu 2+ at Ti 4+ octahedral sites. From the dependence of loss tangent ( tan δ) and the relative permittivity (ε′) on temperature and frequency, it is concluded that all the derivatives are of polar nature. The relaxation peaks at lower temperatures have been attributed to the presence of different types of dipoles, whereas peaks in the higher temperature region indicate possible ferroelectric phase transition. The dependence of conductivity on temperature show that electron hopping (polaron) conduction exists in a wide span of temperature range. However, the associated interlayer ionic conduction exists in a small temperature range. Interlayer alkali ion hopping mechanism of conduction has been proposed toward higher temperatures. The conductivity versus frequency plots reveal that the polaron conduction plays a prominent role toward the lower temperature side that diminishes with the rise in temperature. The most probable relaxation times for 0.01 and 0.1 mp CuO doped derivatives are almost same but it records an increased value for 1.0 mp doped material. This again attributes to the possible change in the symmetry of copper environment.
INFORMATION ENTROPY AND SPIN-SQUEEZING IN ATOMIC THREE-LEVEL SYSTEMS
Authors: REBOIRO M. , CIVITARESE O. , TIELAS D.
Published: July 2013

We consider the problem of an atomic three-level system in interaction with a radiation field. The time evolution of the system, in atomic ladder and Λ configurations, is solved exactly assuming a coherent-state as the initial atomic state. We calculate the atomic spin-squeezing, the atomic entropy-squeezing, and their variances. We show that the spin-squeezing and the entropy-squeezing exhibit similar time dependence.