bluuebunny/crossref_metadata_2025 huggingface dataset:
TH‐C‐144‐09: Workflow of the in Vivo Range Verification in Proton Therapy
Authors: Samuel D , Testa M , Lee J , Cascio E , de Xivry J Orban , Gottschalk B , Bentefour E , Lu H
Published: July 2013

Purpose: A practical and effective range verification technique for proton treatments is the current need to harness the entire benefits of proton therapy. We developed a new technique to compute the proton beam range in the double scattering mode using the unique time‐dose patterns produced by the steps in the range modulator wheel.We present the integration of the range verification system for treatments of prostate cancer in the AP field configuration with the standard proton therapy workflow. We also present the status of the latest detector design, the various steps of the clinical workflow and the integration of the logical modules for a safe and effective range guided treatment of prostate cancer with AP field. Methods: The method uses a matrix of diodes as dosimeters designed to be inserted in the rectum using a rectal balloon. The diodes measure the time‐dose patterns for a range‐check beam. An analysis routine calculates the WEPL at each diode position and evaluates if the signals are range mixed. The obtained WEPL values are compared with treatment planning for beam range verification and correction and the treatment proceeds. During the treatment, the same detectors are used to monitor the dose to the rectum. The standard workflow for proton therapy is modified to adapt for this range verification procedure by adding the above processes. Results: The validation study on a pelvic phantom proved that the range could be verified with an accuracy of 2 mm with just 0.2 % of the fractionated dose. This workflow enables treatment of prostate cancer albeit sparing the rectum. Conclusion: The range verification system will improve treatment quality for prostate cancers using AP fields. With the results from clinical trials, we hope this simple method will find uses in other proton treatments where a range verification system would be advantageous.
TH‐D‐108‐01: Implementing MR‐Guided Adaptive Brachytherapy for Cervical Cancer
Authors: Craciunescu O , Cai J , Chino J
Published: July 2013

Image‐guidance plays an important role in modern radiation therapy, predominantly in external beam planning and delivery. In recent years, with the advent of high/pulsed dose rate afterloading technology, advanced treatment planning systems, and CT and MRI compatible applicators, image‐guided adaptive brachytherapy treatments (IGABT) are now achievable. With image guidance, the target can be delineated more precisely, resulting in delivering more controlled doses of radiation to the target while sparing surrounding healthy tissue. The whole process requires a committed team of physicians, physicists, nurses, with clear roles and infrastructure needs that will be explained clearly. We are proposing to describe the complex processes of implementing a new IGABT program, drawing from our own group's experience in the Department of Radiation Oncology, Duke University Medical Center. GEC‐ESTRO guidelines, crucial for implementing robust and standardized IGART, will be reviewed. They rely on MRI‐guided planning for cervical cancer. MR imaging has its advantages, but also challenges and limitations (image artifacts and distortion related to magnetic nonlinearity, MR sequence selection, accuracy of 3D applicator reconstruction) that need addressed. Treatment planning flow will be discussed for different scenarios: when both CT and MR images are available vs. MR alone, when solid applicator applicators are available vs. not. Different treatment planning techniques will be presented. Advantages and limitations of our proposed flow will be also addressed.

Learning Objectives:

1. Understand the benefits of IGARBT in general, MR‐based in particular. Understand the GEC‐ESTRO guidelines and resources needed to implement IGARBT based on GEC‐ESTRO. Identify the infrastructure and personnel needed for successful implementation of IGARBT.

2. Learn about the MR imaging sequences needed to image soft tissue and applicators, respectively. Understand the process of applicator reconstruction with and without the use of solid applicators library.

3. Understanding the treatment planning flow: image registration, planning techniques, data reporting, dose summation of brachytherapy fractions and with external beam. Understand potential challenges and barriers in implementing MR‐based IGARBT: Convenient access to MR, time constraints, physician and physicist expertise with MRI, lack of CT/MRI compatible applicators, MR alone planning vs. MR/CT‐based planning.
TH‐E‐105‐01: Next Steps Toward Revising Radiation Protection Regulations
Authors: Flannery C
Published: July 2013

The Nuclear Regulatory Commission (NRC) is continuing the process of engaging stakeholders on issues associated with possible changes to the radiation protection regulations contained in 10 CFR Part 20, and other parts of the NRC regulations, to increase alignment with international recommendations. The Commission is particularly seeking to explore implications, as appropriate and where scientifically justified, of greater alignment with ICRP Publication 103. Other information from national and international sources is also being considered. Given that the NRC regulations provide adequate protection, the discussion has been focusing on discerning the benefits and burdens associated with revising the radiation protection regulatory framework. The NRC staff provided the Commission with recommendations in April, 2012, SECY‐12‐006, and the Commission provided direction to the NRC staff in December, 2012, SRM‐SECY‐12‐0064. Issues of particular interest within the medical community include the use of updated scientific methodologies and terminology, the occupational dose limits including the limits for the lens of the eye, ALARA and alternative approaches to deal with individual protection at or near the current dose limit, use of SI units, and reporting requirements.

Learning Objectives:

1. Participants will become familiar with key radiation protection regulation and guidance changes that are under consideration.

2. Participants will provide feedback on proposed approaches to presenters.

3. Participants will be prepared to facilitate engagement of their facility and colleagues in the ongoing dialogue about changes.
TH‐E‐144‐01: MRI Parallel Imaging
Authors: Yanasak N , Goerner F
Published: July 2013

The term “parallel imaging” in magnetic resonance imaging (or “pMRI”) refers to a broad family of techniques that uses the spatial arrangement of multiple RF coil elements to assist in spatial localization of signal, which reduces the number of phase encoding steps in conventional MRI. The end Result is that image data is acquired within a shorter window of time. This characteristic can be exploited toward a variety of advantages; one can reduce image acquisition time, decrease the time penalty for increased resolution, mitigate image distortion, or lower SAR. Because pMRI can be implemented in most conventional MR sequences, its use is becoming more. Nevertheless, poor understanding and incorrect use of pMRI can lead to images of inadequate quality and inaccurate image quality metrics. Implementations of pMRI vary across vendor platforms, each having its own advantages and pitfalls. pMRI transforms some conventional artifacts into an unfamiliar appearance, and generates new types of artifacts. Critically, signal and noise uniformity across the imaging field of view is perturbed with pMRI, posing new questions for quality assurance (QA) procedures. The presentations in this session will provide a practical overview of pMRI ‐ how it functions and where it can be used effectively — as well as a discussion of considerations relevant to QA of pMRI systems.

Learning Objectives:

1. Understand how pMRI techniques work in general

2. Discern proper (and inappropriate) clinical uses of the technique

3. Conceptualize the new challenges associated with quality assurance for MR systems using pMRI.

4. Appreciate advances in pMRI during the next few years and their associated changes in clinical practice.
TH‐F‐105‐02: Molecular Dynamics Simulation of DNA Damage Induction by Ionizing Radiation
Authors: Abolfath R , Carlson D , Chen Z , Nath R
Published: July 2013

Purpose: To present a multi‐scale simulation of early stage of DNA damage by the indirect action of hydroxyl (OH) free‐radicals generated by electrons and protons in a real‐time animation and to present a comparison of the ratio of the total DNA double strand breaks induced by proton and electron tracks. Methods: The computational method comprises of interfacing Geant4‐DNA Monte Carlo (MC) with ReaxFF molecular dynamics (MD). A clustering method was employed to map the coordinates of OH‐radicals extracted from the ionization track‐structures simulated in 1 cm3 of continuous water onto 1019 of 2.6*2.6*6 nm3 simulation voxels (SV) filled with DNA and water molecules. The MD simulation sampled out of a large population of SVs provides the time evolution and chemical reactions and the energy‐landscape accounted for ensemble of DNAs surrounded by OH and water molecules. Such computational approach allows first principle enumeration of the DNA‐lesions induced by ionizing radiation. Results: We present cascade of chemical reactions between OH‐radicals and DNA induced by beam of electrons and protons. As a Result of ionization of water molecules in the surrounding environment MD simulation reveals broken bonds and identify chemical pathways for carbonyl‐and hydroxyl‐hole formation in the sugar‐moiety rings, nucleotide‐nucleotide hydrogen bond disruption, and nucleotide structural damage. We trace the dynamics of OH and demonstrate the interaction among them and DNA. We find 5% and 20% of the electron and proton track, respectively, populate SVs with at least one pair of ions, capable of forming DSBs. Taking into account the realistic ion distributions, we find that the ratio of the total DNA double strand breaks induced by a single proton and electron track is approximately 4. Conclusion: The first‐generation of hybrid MD‐MC method developed recently in our group allows comparison between the DNA damage induced by beams of electrons and protons.
TH‐F‐105‐04: Development of a Novel High‐Throughput Variable Dose Rate Irradiator for in Vitro Radiobiology Research
Authors: Fowler T , Fulkerson R , Micka J , Kimple R , Bednarz B
Published: July 2013

Purpose : Modern biology research often depends upon high‐throughput assays that are incompatible with traditional irradiation techniques due to dose inhomogeneity and dose rate limitations of the most common irradiator systems. To overcome these limitations, we sought to develop a high‐throughput, variable dose rate irradiator for in vitro radiobiology research. Methods: The Xoft Axxent eBx™ was chosen as the x‐ray source for its ability to vary current up to 300 μA, allowing delivery of a variety of doses over a range of dose rates to be applied to a 96‐well cell culture plate. This system delivers a 50kVp spectrum using standard surface applicators. Field flatness was achieved using a 10‐mm diameter surface applicator equipped with a flattening filter that is used for treating skin cancers. Additional collimation was designed to prevent dose contamination into adjacent wells. Dose uniformity was verified using EBT3 Gafchromic film and analyzed using ImageJ, while dose verification was achieved using TLD‐100 measurements and MCNP5 Monte Carlo simulations. Results : Translation of the well plate across the fixed radiation field is achieved using a precision motor‐driven computer controlled positioning system. An Exradin A20 ion chamber has been incorporated into this system to provide periodic air‐kerma rate verification during the irradiation cycle using newly proposed dosimetry formalism for this source. Ion chamber measurements of air‐kerma rate at the skin applicator exit window indicate achievable dose rates of 6–36 mGy/s while the dose uniformity profile of the 10mm Xoft skin applicator was maintained within 3.2% inside the cell culture well. Conclusions: This work indicates significant potential for the development of a high‐throughput, variable dose rate irradiator for in vitro radiobiology research using the Xoft Axxent eBx™ skin applicator system. This irradiator provides a powerful tool by increasing the efficiency and number of assay techniques available for the radiobiology researcher.
TH‐F‐105‐05: Comparison of Results for RBE‐Weighted Dose From Two RBE Models for Proton Therapy Treatment Plans
Authors: Peeler C , Mirkovic D , Perles L , Titt U , Grosshans D , Mohan R
Published: July 2013

Purpose: To evaluate the differences between relative biological effectiveness (RBE)‐weighted doses calculated with either the linear quadratic (LQ) or repair‐misrepair‐fixation (RMF) RBE model for intensity modulated proton therapy (IMPT) treatment plans. Methods: The commercial treatment planning system (TPS) used at MD Anderson Cancer Center (MDACC) does not provide the LET information necessary in order to utilize variable RBE models to calculate RBE‐weighted dose for treatment plans. To obtain this information the Monte Carlo code MCNPX was used to recalculate IMPT treatment plans for patients with central nervous system (CNS) disease taken from the TPS and record the track‐averaged LET in each voxel of the dose distribution. The dose‐averaged LET was approximated from the track‐averaged LET by use of an appropriate scaling factor. The Monte Carlo Damage Simulation (MCDS) software was used to parameterize the number of double‐strand breaks generated in cells by protons according to their stopping power. This information, along with relevant biological coefficients, was then used to generate RBE‐weighted dose distributions according to the LQ and RMF RBE models. Plan evaluation metrics, such as a conformality index and heterogeneity index, were used for plan comparison. Results: The LQ RBE model produces higher RBE‐weighted doses, particularly in the target volume, compared to the RMF model. Doses predicted by the RMF model in nearby organs at risk can at times be several Gray lower than those predicted by the LQ model. Both models predict equivalently heterogeneous target dose distributions, while the RMF model predicts more conformal target dose. Conclusion: Calculation of proton treatment plan dose incorporating either the LQ or RMF models of variable RBE produces observable differences in the resultant dose distributions. Further investigation, including utilization of different biological coefficients, is required to determine the implications for all of the associated normal tissues. UTMDACC Sister Institution Network Fund Grant (SINF MDACC‐DKFZ)
Time-frequency integration characteristics of hearing are optimized for perception of speech-like acoustic patterns
Authors: Räsänen Okko , Laine Unto K.
Published: July 2013

Several psychoacoustic phenomena such as loudness perception, absolute thresholds of hearing, and perceptual grouping in time are affected by temporal integration of the signal in the auditory system. Similarly, the frequency resolution of the hearing system, often expressed in terms of critical bands, implies signal integration across neighboring frequencies. Although progress has been made in understanding the neurophysiological mechanisms behind these processes, the underlying reasons for the observed integration characteristics have remained poorly understood. The current work proposes that the temporal and spectral integration are a result of a system optimized for pattern detection from ecologically relevant acoustic inputs. This argument is supported by a simulation where the average time-frequency structure of speech that is derived from a large set of speech signals shows a good match to the time-frequency characteristics of the human auditory system. The results also suggest that the observed integration characteristics are learnable from acoustic inputs of the auditory environment using a Hebbian-like learning rule.
Wideband energy reflectance measurements: Effects of negative middle ear pressure and application of a pressure compensation procedure
Authors: Shaver Mark D. , Sun Xiao-Ming
Published: July 2013

The wideband energy reflectance (ER) technique has become popular as a tool for evaluating middle ear function. Negative middle ear pressure (MEP) is a prevalent form of middle ear dysfunction, which may impact application of ER measurements in differential diagnosis. A negative MEP may be countervailed by application of an equivalent negative ear canal pressure. The present study examined ER in the same ears under normal and experimentally induced negative MEP conditions. Thirty-five subjects produced at least one negative MEP each (−40 to −225 daPa). Negative MEP significantly altered ER in a frequency-specific manner that varied with MEP magnitude. ER increased for low- to mid-frequencies with the largest change (∼0.20 to 0.40) occurring between 1 and 1.5 kHz. ER decreased for frequencies above 3 kHz with the largest change (∼–0.10 to –0.25) observed between 4.5 and 5.5 kHz. Magnitude of changes increased as MEP became more negative, as did the frequencies at which maximum changes occurred, and the frequency at which enhancement transitioned to reduction. Ear canal pressure compensation restored ER to near baseline values. This suggests that the compensation procedure adequately mitigates the effects of negative MEP on ER. Theoretical issues and clinical implications are discussed.
Articulatory overlap as a function of voicing in French and German consonant clusters
Authors: Bombien Lasse , Hoole Philip
Published: July 2013

The effects of laryngeal specification on the timing of supra-laryngeal articulations have so far received little attention. Previous research has shown that German—but not French—mixed-voicing clusters are produced with less articulatory overlap than phonologically fully voiced clusters. Articulatory and acoustic data of labial and velar stops as simple onsets and in stop + /l/ clusters are examined to probe the causes for this cross-linguistic difference in the light of the different voicing implementations of French and German. The absence of overlap in German mixed-voicing clusters is attributed to the requirement of a time slot for the stop's aspiration phase. Since French does not commonly have aspirated stops, French clusters are expected to pattern with the voiced German clusters. The results confirm that voicing patterns established for simple onsets in the literature in terms of voice onset time of both German and French also obtain in clusters. Furthermore, the data show that contrary to the expectations French clusters pattern with German mixed-voicing clusters. This low degree of overlap in both voiceless and voiced French clusters indicates that overlap is restricted by aerodynamic requirements which result from the implementations of the voicing contrast.
Identification of stimulus cues in narrow-band tone-in-noise detection using sparse observer models
Authors: Schönfelder Vinzenz H. , Wichmann Felix A.
Published: July 2013

The classical psychophysical paradigm of narrow-band tone-in-noise (TiN) detection has been under investigation for more than 70 years, yet no conclusive answer has been given as to which auditory stimulus features listeners rely on. Here, individual observer models were fit to a large trial-by-trial behavioral data set using a modern statistical analysis procedure. Relative perceptual weights were estimated for a set of auditory features including sound energy, representations of the spectra as well as summary statistics of both fine structure and envelope. The fitted models captured the behavior of all listeners on a single-trial level. The estimated perceptual weights were stable across signal levels. They suggest that responses of observers depended on stimulus energy, though that cue was not always dominant, as well as on band-pass detectors applied to the fine structure spectrum. A subset of the observers exhibited an additional dependence on sound envelope which was best captured by two envelope descriptors: average slope and extrema count. For some listeners, a concurrent analysis of sequential dependencies showed interactions between the current and several preceding decisions. There was no unique answer regarding the strategy individual listeners employ during TiN detection, and implications thereof are discussed.
Integrating the energy flux method for reverberation with physics-based seabed scattering models: Modeling and inversion
Authors: Zhou Ji-Xun , Zhang Xue-Zhen
Published: July 2013

During the past 30 years, one of the major accomplishments in ocean acoustics is the improvement of understanding seabed scattering, resulting from a significant effort of both at-sea measurement and theoretical modeling. [Jackson and Richardson: High-Frequency Seafloor Acoustics, 2007]. Benefiting from this accomplishment, this paper integrates the energy flux method for shallow-water (SW) reverberation [Zhou, (Chinese) Acta Acust. 5, 86–99 (1980)] with the physics-based seabed scattering models. This integration directly and intuitively results in general expressions for SW reverberation in the angular and modal domains. The latter expression is the same as the modal reverberation expression derived from the Green's function and boundary perturbation method by Tracey and Schmidt [IEEE J. Ocean. Eng. 22, 317–331(1997)]. The integration also results in a simple relationship between the classic boundary scattering cross sections and the modal scattering matrix in SW waveguides. The bottom roughness spectrum and sediment volume scattering cross section at low grazing angles are inverted in a frequency range of 150–2500 Hz from the wideband long-range reverberation data by using the Biot seabed geoacoustic model. The results may offer some reference data sets for future analysis of the low-frequency seabed scattering mechanisms.
The measurement of ultrasound backscattering from cell pellet biophantoms and tumors ex vivo
Authors: Han Aiguo , Abuhabsah Rami , Miller Rita J. , Sarwate Sandhya , O'Brien William D.
Published: July 2013

Simple scattering media fit scattering model theories much better than more complex scattering media. Tissue is much more complex as an acoustic scattering media and to date there has not been an adequate scattering model that fits it well. Previous studies evaluated the scattering characteristics of simple media (grouping of cells at various number densities) and fit them to the concentric spheres scattering model theory. This study is to increase the complexity of the media to provide insight into the acoustic scattering characteristics of tissue, and specifically two tumor types. Complementing the data from the tumors is 100% volume fraction cell pellets of the same cell lines. Cell pellets and ex vivo tumors are scanned using high-frequency single-element transducers (9–105 MHz), and the attenuation and backscatter coefficient (BSC) are estimated. BSC comparisons are made between cell pellets and tumors. The results show that the 4T1 (ATCC #CRL-2539) cell pellets and tumors have similar BSC characteristics, whereas the MAT (ATCC #CRL-1666) cell pellets and tumors have significantly different BSC characteristics. Factors that yield such differences are explored. Also, the fluid-filled sphere and the concentric spheres models are evaluated against the BSC characteristics, demonstrating that further work is required.
A computational model of auditory attention for use in soundscape research
Authors: Oldoni Damiano , De Coensel Bert , Boes Michiel , Rademaker Michaël , De Baets Bernard , Van Renterghem Timothy , Botteldooren Dick
Published: July 2013

Urban soundscape design involves creating outdoor spaces that are pleasing to the ear. One way to achieve this goal is to add or accentuate sounds that are considered to be desired by most users of the space, such that the desired sounds mask undesired sounds, or at least distract attention away from undesired sounds. In view of removing the need for a listening panel to assess the effectiveness of such soundscape measures, the interest for new models and techniques is growing. In this paper, a model of auditory attention to environmental sound is presented, which balances computational complexity and biological plausibility. Once the model is trained for a particular location, it classifies the sounds that are present in the soundscape and simulates how a typical listener would switch attention over time between different sounds. The model provides an acoustic summary, giving the soundscape designer a quick overview of the typical sounds at a particular location, and allows assessment of the perceptual effect of introducing additional sounds.
Assessment of noise measurements made with a continuous monitoring in time
Authors: Kang Tae-Sun , Lee Lim-Kyu , Kang Sung-Chan , Yoon Chung-Sik , Park Dong-Uk , Kim Rok-Ho
Published: July 2013

The World Health Organization has stated that hearing loss is one of the top 10 health problems worldwide and that noise-induced hearing loss is the leading occupational disease. This work evaluated the noise exposure levels of several job categories for 24-h periods over 7 days to determine the contribution of each microenvironment to total noise exposure. The noise exposure levels of 47 individuals were continuously measured using personal noise dosimeters in metropolitan Seoul, Korea. Participants ranged in age from 20 to 50 yr and represented eight occupational groups. Participants were asked to attach the noise dosimeters and complete a time–activity diary 24 h a day for 7 days. The average Leq 24 h,w among these individuals was 74 dBA, which ranged from 64 to 96 dBA. The average Leq 24 h,w was highest for Korean traditional music apprentices, followed by heavy equipment operators, firefighters, service workers, office workers, industrial hygienists, graduate and undergraduate students, and housewives (89, 77, 76, 76, 75, 71, 71, and 71 dBA, respectively, p < 0.001). 38 (80.9%) were exposed to noise levels greater than 70 dBA, which corresponds to the World Health Organization's exposure limit.
Recognition of accented and unaccented speech in different maskers by younger and older listeners
Authors: Gordon-Salant Sandra , Yeni-Komshian Grace H. , Fitzgibbons Peter J. , Cohen Julie I. , Waldroup Christopher
Published: July 2013

This investigation examined the effect of accent of target talkers and background speech maskers on listeners' ability to use cues to separate speech from noise. Differences in accent may create a disparity in the relative timing between signal and background, and such timing cues may be used to separate the target talker from the background speech masker. However, the use of this cue could be reduced for older listeners with temporal processing deficits, especially those with hearing loss. Participants were younger and older listeners with normal hearing and older listeners with hearing loss. Stimuli were IEEE sentences recorded in English by male native speakers of English and Spanish. These sentences were presented in different maskers that included speech-modulated noise and background babbles varying in talker gender and accent. Signal-to-noise ratios corresponding to 50% correct performance were measured. Results indicate that a pronounced Spanish accent limits a listener's ability to take advantage of cues to speech segregation and that a difference in accentedness between the target talker and background masker may be a useful cue for speech segregation. Older hearing-impaired listeners performed poorly in all conditions with the accented talkers.
A precedence effect model to simulate localization dominance using an adaptive, stimulus parameter-based inhibition process
Authors: Braasch Jonas
Published: July 2013

A number of precedence-effect models have been developed to simulate the robust localization performance of humans in reverberant conditions. Although they are able to reduce reverberant information for many conditions, they tend to fail for ongoing stimuli with truncated on/offsets, a condition human listeners master when localizing a sound source in the presence of a reflection, according to a study by Dizon and Colburn [J. Acoust. Soc. Am. 119, 2947–2964 (2006)]. This paper presents a solution for this condition by using an autocorrelation mechanism to estimate the delay and amplitude ratio between the leading and lagging signals. An inverse filter is then used to eliminate the lag signal, before it is localized with a standard localization algorithm. The current algorithm can operate on top of a basic model of the auditory periphery (gammatone filter bank, half-wave rectification) to simulate psychoacoustic data by Braasch et al. [Acoust. Sci. Tech. 24, 293–303 (2003)] and Dizon and Colburn. The model performs robustly with these on/offset truncated and interaural level difference based stimuli and is able to demonstrate the Haas effect.
Effects of secondary loudspeaker properties on broadband feedforward active duct noise control
Authors: Chan Yum-Ji , Huang Lixi , Lam James
Published: July 2013

Dependence of the performance of feedforward active duct noise control on secondary loudspeaker parameters is investigated. Noise reduction performance can be improved if the force factor of the secondary loudspeaker is higher. For example, broadband noise reduction improvement up to 1.6 dB is predicted by increasing the force factor by 50%. In addition, a secondary loudspeaker with a larger force factor was found to have quicker convergence in the adaptive algorithm in experiment. In simulations, noise reduction is improved in using an adaptive algorithm by using a secondary loudspeaker with a heavier moving mass. It is predicted that an extra broadband noise reduction of more than 7 dB can be gained using an adaptive filter if the force factor, moving mass and coil inductance of a commercially available loudspeaker are doubled. Methods to increase the force factor beyond those of commercially available loudspeakers are proposed.
The effect of prosodic weakening on the production and perception of trans-consonantal vowel coarticulation in German
Authors: Harrington Jonathan , Kleber Felicitas , Reubold Ulrich
Published: July 2013

The present study considers whether coarticulation in production and its relationship to categorization could provide a synchronic basis for the prevalence of sound change in unstressed syllables. The size of V2-on-V1 coarticulation in the production of /pV1pV2l/ non-words (V1 = /ʊ,ʏ/ and V2 = /e, o/) produced by German speakers and with stress falling either on the first or second syllable was compared with forced-choice perceptual categorization of resynthesized versions of these non-words. In speech production, /ʏ/ but not /ʊ/ was perturbed by anticipatory V2-on-V1 coarticulation. Stress had no influence on coarticulation but caused target undershoot in /ʊ/. The same speakers compensated for coarticulation in perception: however, in the unstressed context the speakers compensated less and their diminished compensatory coarticulation was shown to be linked to /ʊ/-undershoot. Taken together, these results point to a mismatch between coarticulation and categorization that is suggested as a possible source of sound change: whereas de-stressing did not affect V2-on-V1 coarticulation in production, it weakened V2's influence on perceptual /ʊ-ʏ/ categorization. The evidence that this mismatch is indirectly caused by stress-dependent reduction in /ʊ/ that is unrelated to the V2-source of the coarticulation is also consistent with a model of sound change as non-teleological.
Geographic variation of whistles of the striped dolphin (Stenella coeruleoalba) within the Mediterranean Sea
Authors: Azzolin Marta , Papale Elena , Lammers Marc O. , Gannier Alexandre , Giacoma Cristina
Published: July 2013

The striped dolphin is a cosmopolitan species distributed worldwide. Morphological and genetic studies strongly suggest that the Mediterranean and eastern North Atlantic populations are isolated from each other. The Mediterranean population is considered a distinct conservation unit by International Union for the Conservation of Nature experts, classified as “vulnerable.” This study describes the geographical variation of the striped dolphin whistles within the Mediterranean Sea. Recordings were collected from 1996 to 2003 throughout the basin, employing multiple platforms. Thirty-seven independent sightings with acoustic data collection were made, and 599 whistles were extracted and considered for statistical analysis. Whistle analysis enabled the identification of sub-populations of striped dolphins within the Mediterranean Sea. The acoustic diversity observed reflects the genetic differences recently found among striped dolphins inhabiting different Mediterranean regions. The results of this study support the hypothesis that gene flow reduction plays an important role in determining variation in whistle duration and frequency parameters, while ecological and social factors influence parameters of the modulation domains. The ability to acoustically identify distinct geographic sub-populations could provide a useful tool for the management of this protected species.
Directivity control and efficiency of parametric loudspeakers with horns
Authors: Sayin Umut , Guasch Oriol
Published: July 2013

This manuscript presents some recent results on directivity control and efficiency of parametric loudspeakers utilizing horns. Horns act both like an acoustic transformer and a directivity control method. An experimental device has been built and measurements have revealed that the horn has a clear influence on the audible sound levels and directivity of the parametric loudspeakers. When compared with a conventional megaphone, a much more flat frequency response is obtained and the resulting directivity is shown to be almost frequency independent.
Anthropogenic Seismicity Rates and Operational Parameters at the Salton Sea Geothermal Field
Authors: Brodsky Emily E. , Lajoie Lia J.
Published: July 2013

Hot and Bothered

One of the most uncertain aspects of energy production at geothermal fields is the potential for the induction of earthquakes from extraction of hot fluids and injection of wastewater back into the subsurface.
Brodsky and Lajoie
(p.
543
, published online 11 July) compared the historical rates of seismicity—after correcting for the occurrence of aftershocks—to operational parameters at the Salton Sea Geothermal Field in southern California. The net volume of fluid extracted and injected was correlated with recent seismicity. However, since the 1980s, when the first plant came online, the rate of earthquakes induced with additional increments of volume injected has decreased.
Nanoscale Transistors—Just Around the Gate?
Authors: Cress Cory D. , Datta Suman
Published: July 2013

Advanced geometries for gate electrodes that reduce current leakage can decrease the size of high-performance transistors.
LIFE SCIENCE TECHNOLOGIES: Sample-Separation Technologies: Improving Speed and Resolution
Authors: May Mike
Published: July 2013

Many scientific tasks—including studying the composition of blood and sequencing DNA—depend on being able to separate the parts from the whole. Only then can a scientist begin to understand how the pieces build up a process. To separate a sample into its components, scientists have been continually improving traditional approaches as well as developing new ones. In some cases, the improvements speed up separations; in others, advanced techniques provide new forms of separation that improve the efficiency of the processes. Though technologies are growing increasingly sophisticated, they are also becoming easier to use.
Full-Genome Sequence of Bluetongue Virus Serotype 1 (BTV-1) Strain Y863, the First BTV-1 Isolate of Eastern Origin Found in China
Authors: Zhu Jianbo , Yang Heng , Li Huachun , Xiao Lei , Wang Jinpin , Li Nan , Zhang Nianzu
Published: July 2013

The full-genome sequence of the bluetongue virus serotype 1 (BTV-1) strain Y863, the first BTV-1 isolate of Eastern origin found in China, was determined. The virus was isolated from sheep during a severe outbreak of bluetongue in Shizhong County, Yunnan Province, southwest China, in 1979. The total size of the BTV-1 strain Y863 genome is 19,170 bp. Phylogenetic analyses demonstrate that it belongs to the major “Eastern” BTV topotype. The sequence information provided here will help in understanding the geographical origin and spread of this Chinese isolate of BTV-1, as well as aid in its comparison with global isolates of BTV-1 from sheep, cattle, and other host species origins.
Genome Sequence of Streptococcus agalactiae Strain 09mas018883, Isolated from a Swedish Cow
Authors: Zubair S. , de Villiers E. P. , Fuxelius H. H. , Andersson G. , Johansson K.-E. , Bishop R. P. , Bongcam-Rudloff E.
Published: July 2013

We announce the complete genome sequence of
Streptococcus agalactiae
strain 09mas018883, isolated from the milk of a cow with clinical mastitis. The availability of this genome may allow identification of candidate genes, leading to discovery of antigens that might form the basis for development of a vaccine as an alternative means of mastitis control.
Draft Genome Sequence of the Lignocellulose Decomposer Thermobifida fusca Strain TM51
Authors: Tóth Ákos , Barna Terézia , Nagy István , Horváth Balázs , Nagy István , Táncsics András , Kriszt Balázs , Baka Erzsébet , Fekete Csaba , Kukolya József
Published: July 2013

Here, we present the complete genome sequence of
Thermobifida fusca
strain TM51, which was isolated from the hot upper layer of a compost pile in Hungary.
T. fusca
TM51 is a thermotolerant, aerobic actinomycete with outstanding lignocellulose-decomposing activity.
Contribution of Myocyte Enhancer Factor 2 Family Transcription Factors to BZLF1 Expression in Epstein-Barr Virus Reactivation from Latency
Authors: Murata Takayuki , Narita Yohei , Sugimoto Atsuko , Kawashima Daisuke , Kanda Teru , Tsurumi Tatsuya
Published: July 2013

Reactivation of Epstein-Barr virus (EBV) from latency is dependent on expression of the viral transactivator BZLF1 protein, whose promoter (Zp) normally exhibits only low basal activity but is activated in response to chemical or biological inducers. Using a reporter assay system, we screened for factors that can activate Zp and isolated genes, including those encoding MEF2B, KLF4, and some cellular b-Zip family transcription factors. After confirming their importance and functional binding sites in reporter assays, we prepared recombinant EBV-BAC, in which the binding sites were mutated. Interestingly, the MEF2 mutant virus produced very low levels of BRLF1, another transactivator of EBV, in addition to BZLF1 in HEK293 cells. The virus failed to induce a subset of early genes, such as that encoding BALF5, upon lytic induction, and accordingly, could not replicate to produce progeny viruses in HEK293 cells, but this restriction could be completely lifted by exogenous supply of BRLF1, together with BZLF1. In B cells, induction of BZLF1 by chemical inducers was inhibited by point mutations in the ZII or the three SP1/KLF binding sites of EBV-BAC Zp, while leaky BZLF1 expression was less affected. Mutation of MEF2 sites severely impaired both spontaneous and induced expression of not only BZLF1, but also BRLF1 in comparison to wild-type or revertant virus cases. We also observed that MEF2 mutant EBV featured relatively high repressive histone methylation, such as H3K27me3, but CpG DNA methylation levels were comparable around Zp and the BRLF1 promoter (Rp). These findings shed light on BZLF1 expression and EBV reactivation from latency.
Heterogeneous Nuclear Ribonucleoprotein K Supports Vesicular Stomatitis Virus Replication by Regulating Cell Survival and Cellular Gene Expression
Authors: Dinh Phat X. , Das Anshuman , Franco Rodrigo , Pattnaik Asit K.
Published: July 2013

The heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a member of the family of hnRNPs and was recently shown in a genome-wide small interfering RNA (siRNA) screen to support vesicular stomatitis virus (VSV) growth. To decipher the role of hnRNP K in VSV infection, we conducted studies which suggest that the protein is required for VSV spreading. Virus binding to cells, entry, and nucleocapsid uncoating steps were not adversely affected in the absence of hnRNP K, whereas viral genome transcription and replication were reduced slightly. These results indicate that hnRNP K is likely involved in virus assembly and/or release from infected cells. Further studies showed that hnRNP K suppresses apoptosis of virus-infected cells, resulting in increased cell survival during VSV infection. The increased survival of the infected cells was found to be due to the suppression of proapoptotic proteins such as Bcl-X
S
and Bik in a cell-type-dependent manner. Additionally, depletion of hnRNP K resulted in not only significantly increased levels of T-cell-restricted intracellular antigen 1 (TIA1) but also switching of the expression of the two isoforms of the protein (TIA1a and TIA1b), both of which inhibited VSV replication. hnRNP K was also found to support expression of several cellular proteins known to be required for VSV infection. Overall, our studies demonstrate hnRNP K to be a multifunctional protein that supports VSV infection via its role(s) in suppressing apoptosis of infected cells, inhibiting the expression of antiviral proteins, and maintaining the expression of proteins required for the virus.
The Respiratory Syncytial Virus Fusion Protein and Neutrophils Mediate the Airway Mucin Response to Pathogenic Respiratory Syncytial Virus Infection
Authors: Stokes Kate L. , Currier Michael G. , Sakamoto Kaori , Lee Sujin , Collins Peter L. , Plemper Richard K. , Moore Martin L.
Published: July 2013

Respiratory syncytial virus (RSV) is the leading cause of death due to a viral etiology in infants. RSV disease is characterized by epithelial desquamation, neutrophilic bronchiolitis and pneumonia, and obstructive pulmonary mucus. It has been shown that infection of BALB/cJ mice with RSV clinical isolate A2001/2-20 (2-20) results in a higher early viral load, greater airway necrosis, and higher levels of interleukin-13 (IL-13) and airway mucin expression than infection with RSV laboratory strain A2. We hypothesized that the fusion (F) protein of RSV 2-20 is a mucus-inducing viral factor.In vitro, the fusion activity of 2-20 F but not that of A2 F was enhanced by expression of RSV G. We generated a recombinant F-chimeric RSV by replacing the F gene of A2 with the F gene of 2-20, generating A2–2-20F. Similar to the results obtained with the parent 2-20 strain, infection of BALB/cJ mice with A2–2-20F resulted in a higher early viral load and higher levels of subsequent pulmonary mucin expression than infection with the A2 strain. A2–2-20F infection induced greater necrotic airway damage and neutrophil infiltration than A2 infection. We hypothesized that the neutrophil response to A2–2-20F infection is involved in mucin expression. Antibody-mediated depletion of neutrophils in RSV-infected mice resulted in lower tumor necrosis factor alpha levels, fewer IL-13-expressing CD4 T cells, and less airway mucin production in the lung. Our data are consistent with a model in which the F and attachment (G) glycoprotein functional interaction leads to enhanced fusion and F is a key factor in airway epithelium infection, pathogenesis, and subsequent airway mucin expression.
An Eight-Segment Swine Influenza Virus Harboring H1 and H3 Hemagglutinins Is Attenuated and Protective against H1N1 and H3N2 Subtypes in Pigs
Authors: Masic Aleksandar , Pyo Hyun-Mi , Babiuk Shawn , Zhou Yan
Published: July 2013

Swine influenza virus (SIV) infections continue to cause production losses in the agricultural industry in addition to being a human public health concern. The primary method of controlling SIV is through vaccination. The killed SIV vaccines currently in use must be closely matched to the challenge virus, and their protective efficacy is limited. Live attenuated influenza vaccines (LAIV) provide strong, long-lived cell-mediated and humoral immunity against different influenza virus subtypes with no need for antigen matching. Here we report the generation of a new potential LAIV, an eight-segment SIV harboring two different SIV hemagglutinins (HAs), H1 and H3, in the genetic background of H1N1 SIV. This mutant SIV was generated by fusing the H3 HA ectodomain from A/Swine/Texas/4199-2/98 (H3N2) to the cytoplasmic tail, transmembrane domain, and stalk region of neuraminidase (NA) from A/Swine/Saskatchewan/18789/02 (H1N1) SIV. While this H1-H3 chimeric SIV, when propagated
in vitro
in the presence of exogenous neuraminidase, showed kinetics and growth properties similar to those of the parental wild-type virus,
in vivo
it was highly attenuated in pigs, demonstrating a great potential for serving as a dual LAIV. Furthermore, vaccination with the H1-H3 virus elicited robust immune responses, which conferred complete protection against infections with both H1 and H3 SIV subtypes in pigs.
The Effect of the PB2 Mutation 627K on Highly Pathogenic H5N1 Avian Influenza Virus Is Dependent on the Virus Lineage
Authors: Long Jason S. , Howard Wendy A. , Núñez Alejandro , Moncorgé Olivier , Lycett Samantha , Banks Jill , Barclay Wendy S.
Published: July 2013

Clade 2.2 Eurasian-lineage H5N1 highly pathogenic avian influenza viruses (HPAIVs) were first detected in Qinghai Lake, China, in 2005 and subsequently spread through Asia, Europe, and Africa. Importantly, these viruses carried a lysine at amino acid position 627 of the PB2 protein (PB2 627K), a known mammalian adaptation motif. Previous avian influenza virus isolates have carried glutamic acid in this position (PB2 627E), commonly described to restrict virus polymerase function in the mammalian host. We sought to examine the effect of PB2 627K on viral maintenance in the avian reservoir. Viruses constructed by reverse genetics were engineered to contain converse PB2 627K/E mutations in a Eurasian H5N1 virus (A/turkey/Turkey/5/2005 [Ty/05]) and, for comparison, a historical pre-Asian H5N1 HPAIV that naturally bears PB2 627E (A/turkey/England/50-92/1991 [50-92]). The 50-92 PB2 627K was genetically unstable during virus propagation, resulting in reversion to PB2 627E or the accumulation of the additional mutation PB2 628R and/or a synonymous mutation from an A to a G nucleotide at nucleotide position 1869 (PB2 A1869G). Intriguingly, PB2 628R and/or A1869G appeared to improve the genetic stability of 50-92 PB2 627K. However, the replication of 50-92 PB2 627K in conjunction with these stabilizing mutations was significantly restricted in experimentally infected chickens, where reversion to PB2 627E occurred. In contrast, no significant effects on viral fitness were observed for Ty/05 PB2 627E or 627K in
in vitro
or
in vivo
experiments. Our observations suggest that PB2 627K is supported in Eurasian-lineage viruses; in contrast, PB2 627K carries a significant fitness cost in the historical pre-Asian 50-92 virus.