bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategies to Enhance the Performance of Path‐Based Static Traffic Assignment Algorithms
Authors: Kumar Amit , Peeta Srinivas
Published: November 2013

There are three important stages of path‐based algorithms (PBAs) for solving the static user equilibrium traffic assignment problem (STA): finding shortest paths between various origins and destinations based on the present flow conditions to update the path set, updating path flows based on the move direction of the PBA, and updating the link flows and costs. This article proposes strategies to improve the computational efficiency of these three stages. The first strategy provides a simple method to preclude the through‐routing via the zone centroid and helps to avoid unrealistic flow without affecting the flow update process of a PBA. The second strategy seeks to improve the efficiency of the path flow update process by circumventing unnecessary computation. The third strategy proposes faster link flow and link cost update processes along with a link data structure to support it. The computational experiments using two recently developed PBAs validate the effectiveness of these strategies and help to understand their rationale. The strategies are significant from both theoretical and practical perspectives. From a theoretical viewpoint, they help in designing an efficient execution process for PBAs and provide an improved common platform for comparing their performances. For practice, they can reduce the computational cost in finding the solution of the STA without increasing the complexity of the execution of the algorithm.
Crystal structure of an HD‐GYP domain cyclic‐di‐GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre
Authors: Bellini Dom , Caly Delphine L. , McCarthy Yvonne , Bumann Mario , An Shi‐Qi , Dow J. Maxwell , Ryan Robert P. , Walsh Martin A.
Published: November 2013

Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.
DELLA activity is required for successful pollen development in the Columbia ecotype of Arabidopsis
Authors: Plackett Andrew R. G. , Ferguson Alison C. , Powers Stephen J. , Wanchoo‐Kohli Aakriti , Phillips Andrew L. , Wilson Zoe A. , Hedden Peter , Thomas Stephen G.
Published: November 2013

Excessive gibberellin (GA) signalling, mediated through the DELLA proteins, has a negative impact on plant fertility. Loss of DELLA activity in the monocot rice (Oryza sativa) causes complete male sterility, but not in the dicot model Arabidopsis (Arabidopsis thaliana) ecotype Landsberg erecta (Ler), in which DELLA function has been studied most extensively, leading to the assumption that DELLA activity is not essential for Arabidopsis pollen development. A novel DELLA fertility phenotype was identified in the Columbia (Col‐0) ecotype that necessitates re‐evaluation of the general conclusions drawn from Ler.

Fertility phenotypes were compared between the Col‐0 and Ler ecotypes under conditions of chemical and genetic GA overdose, including mutants in both ecotypes lacking the DELLA paralogues REPRESSOR OF ga1‐3 (RGA) and GA INSENSITIVE (GAI).

Ler displays a less severe fertility phenotype than Col‐0 under GA treatment. Col‐0 rga gai mutants, in contrast with the equivalent Ler phenotype, were entirely male sterile, caused by post‐meiotic defects in pollen development, which were rescued by the reintroduction of DELLA into either the tapetum or developing pollen.

We conclude that DELLA activity is essential for Arabidopsis pollen development. Differences between the fertility responses of Col‐0 and Ler might be caused by differences in downstream signalling pathways or altered DELLA expression.
A Spectroscopic and Theoretical Investigation of a Free‐Base meso‐Trithienylcorrole
Authors: Greco Jordan A. , Rossi Alison , Birge Robert R. , Brückner Christian
Published: November 2013

The unique optical properties of free‐base meso‐tris(5‐methylthien‐2‐yl)corrole were compared to those of the widely investigated meso‐triphenyl‐substituted analogue. A combination of spectroscopic and computational experiments was undertaken to elucidate the relationship between structural features of the neutral, mono‐anionic and mono‐cationic forms of the corroles and their corresponding optical properties. A general bathochromic shift was measured for the thienyl‐substituted corrole. The experimental spectra are supported by excited state calculations. A systematic series of ground state minimizations were performed to determine energy minima for the flexible and solvent‐sensitive molecules. Trithienylcorrole was found to have a more nonplanar macrocycle in conjunction with a high degree of π‐overlap with the meso‐substituents. Both structural features contribute to their bathochromically shifted optical spectra. The configurational character of the thienyl‐substituted corrole is shown to have a larger degree of molecular orbital mixing and doubly excited character, which suggest a more complex electronic structure that does not fully adhere to the Gouterman four‐orbital model. The reactivity of the thienyl groups, particularly with respect to their ability to be (electro)‐polymerized, combined with the tight coupling of the meso‐thienyl groups with the corrole chromophore elucidated in this work, recommends the meso‐thienylcorroles as building blocks in, for instance, organic semiconductor devices.
Role of P‐selectin and P‐selectin glycoprotein ligand‐1 interaction in the induction of tissue factor expression on human platelets after incubation with porcine aortic endothelial cells
Authors: Ezzelarab Mohamed B. , Liu Yueh Wei , Lin Chih Che , Long Cassandra , Ayares David , Dorling Anthony , Cooper David K. C.
Published: November 2013

Development of coagulation disorders remains a major challenge in pig‐to‐primate organ xenotransplantation. Our previous studies demonstrated that porcine aortic endothelial cells (pAEC) activate human platelets to express tissue factor (TF). In this study, we investigated the molecular interaction between human platelets and pAEC to identify possible targets for further genetic modification and/or systemic therapy. Human platelets were incubated with pAEC from wild‐type (WT), α1,3‐galactosyltransferase gene‐knockout (GTKO), and GTKO pigs expressing human CD46, after which the platelets were analyzed for TF expression, TF mRNA level and TF function. pAEC were analyzed for von Willebrand factor (vWF) expression and mRNA level as well. Neutralizing antibodies for P‐selectin and P‐selectin glycoprotein ligand‐1 (PSGL‐1) were used to block the molecular interaction between platelets and pAEC. GTKO and GTKO/CD46 pAEC‐activated human platelets to induce human TF activity equivalently to WT pAEC. Simultaneously, after incubation with pAEC, platelets co‐expressed TF and P‐selectin. TF expression was blocked when pAEC and platelets were pre‐incubated with anti‐human P‐selectin or anti‐human PSGL‐1 antibodies, but not by anti‐porcine P‐selectin antibody. Activated pAEC up‐regulated TF on platelets through the interaction of porcine vWF with the human GPIb receptor. Up‐regulation of TF on human platelets by GTKO and GTKO/CD46 pAEC was comparable to that by WT pAEC, which is associated with concomitant expression of P‐selectin and PSGL‐1, forming an auto‐augmented loop of pAEC and platelet activation. Blocking of P‐selectin and PSGL‐1 interaction may be required to prevent up‐regulation of recipient TF in vivo after organ xenotransplantation.
Human cytokines activate JAK–STAT signaling pathway in porcine ocular tissue
Authors: Fasler‐Kan Elizaveta , Barteneva Natasha S. , Ketterer Sylvia , Wunderlich Kerstin , Reschner Anca , Nurzhanova Asil , Flammer Josef , Huwyler Jörg , Meyer Peter
Published: November 2013

Background

The JAK/STAT (Janus Tyrosine Kinase, Signal Transducers and Activators of Transcription) pathway is associated with cytokine or growth factor receptors and it is critical for growth control, developmental regulation and homeostasis. The use of porcine ocular cells as putative xenotransplants appears theoretically possible. The aim of this study was to investigate the response of various porcine ocular cells in vitro to human cytokines in regard to the activation of JAK‐STAT signaling pathways.

Methods

Porcine lens epithelial cells, pigmented iris epithelial cells and pigmented ciliary body cells were used in this study. These cells were isolated from freshly enucleated porcine eyes by enzymatic digestion. Cultured cells between passages 3–8 were used in all experiments. Electromobility shift assay (EMSA), proliferation assay, immunofluorescence staining and flow cytometry were used to evaluate the JAK‐STAT signaling pathway in these cells.

Results

JAK/STAT signaling pathways could be activated in porcine pigmented epithelial ciliary body cells, in pigmented iris epithelial cells and in lens epithelial cells in response to porcine and human interferons and cytokines. All cells showed very strong STAT1 activation upon stimulation with porcine interferon‐gamma. Porcine ocular cells also respond to human cytokines; IFN‐alpha induced strong activation of STAT1 in EMSA, flow cytometry and immunofluorescence experiments whereas activation of STAT3 was less strong in EMSA, but strong in flow cytometry and immunofluorescence. Human recombinant IL‐6 activated STAT3 and human IL‐4 activated STAT6. With the help of immunofluorescence assay and flow cytometry we observed nuclear localization of STAT proteins after activation of porcine ocular cells with cytokines and interferons. Human IFN‐α had an inhibitory effect on porcine ocular cells in proliferation assays.

Conclusion

Our study demonstrated that some types of human cytokines and interferon activate intracellular JAK‐STAT signaling pathways in porcine ocular cells. We hypothesize that direct stimulation of the JAK‐STAT pathway in porcine cells in response to human cytokines will lead to complications or failure, if pig‐to‐human ocular tissue xenotransplantation were to be carried out. For successful xenotransplantation among other obstacles there must be new approaches developed to regulate signaling pathways.
Engineering Drug Delivery Vehicles With Multiphase Microfluidics
Authors: Shum Ho Cheung , Kong Tiantian , Liu Zhou , Song Yang
Published: November 2013

In our work, we propose the use of multiphase microfluidics to prepare drug delivery vehicles with complex structures, such as core-shell capsules, multicompartment microspheres and nonspherical particles; by tailoring the spatial distribution of drugs, unconventional drug release profiles can be achieved. To avoid the use of harmful organic solvents, we introduce the use of aqueous two-phase systems in microfluidics to generate the emulsion templates for making these novel delivery vehicles. By manipulating the interfacial characteristics of the emulsion templates, complex structures with hydrophilic and hydrophobic compartments can be prepared for separate encapsulation and sequential release of both hydrophilic and hydrophobic drugs. We will discuss the fundamental problems that need to be addressed to generate these drug delivery vehicles and highlight their potential by demonstrating their release characteristics.
Multiscale Molecular Dynamics Simulation of Nanobio Membrane in Interaction With Protein
Authors: Maftouni Negin , Amininasab Mehriar , Ejtehadi MohammadReza , Kowsari Farshad
Published: November 2013

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of lateral pressure. Our simulations reveal that the insertion of CTX A3 into one monolayer results in an asymmetrical change in the lateral pressure and distribution of surface tension of the individual bilayer leaflets. The relative variation in the surface tension of the two monolayers as a result of a change in the contribution of the various intermolecular forces may be expressed morphologically and lead to deformation of the lipid membrane.
Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Molecular Dynamics
Authors: Bluestein Danny , Soares João S. , Zhang Peng , Gao Chao , Pothapragada Seetha , Zhang Na , Slepian Marvin J. , Deng Yuefan
Published: November 2013

The coagulation cascade of blood may be initiated by flow induced platelet activation, which prompts clot formation in prosthetic cardiovascular devices and arterial disease processes. While platelet activation may be induced by biochemical agonists, shear stresses arising from pathological flow patterns enhance the propensity of platelets to activate and initiate the intrinsic pathway of coagulation, leading to thrombosis. Upon activation platelets undergo complex biochemical and morphological changes: organelles are centralized, membrane glycoproteins undergo conformational changes, and adhesive pseudopods are extended. Activated platelets polymerize fibrinogen into a fibrin network that enmeshes red blood cells. Activated platelets also cross-talk and aggregate to form thrombi. Current numerical simulations to model this complex process mostly treat blood as a continuum and solve the Navier-Stokes equations governing blood flow, coupled with diffusion-convection-reaction equations. It requires various complex constitutive relations or simplifying assumptions, and is limited to μm level scales. However, molecular mechanisms governing platelet shape change upon activation and their effect on rheological properties can be in the nm level scales. To address this challenge, a multiscale approach which departs from continuum approaches, may offer an effective means to bridge the gap between macroscopic flow and cellular scales. Molecular dynamics (MD) and dissipative particle dynamics (DPD) methods have been employed in recent years to simulate complex processes at the molecular scales, and various viscous fluids at low-to-high Reynolds numbers at mesoscopic scales. Such particle methods possess important properties at the mesoscopic scale: complex fluids with heterogeneous particles can be modeled, allowing the simulation of processes which are otherwise very difficult to solve by continuum approaches. It is becoming a powerful tool for simulating complex blood flow, red blood cells interactions, and platelet-mediated thrombosis involving platelet activation, aggregation, and adhesion.
Implementation Issues With Far Field Approximations With Multi-Resolution Biopolymer Simulations
Authors: Laflin Jeremy , Poursina Mohammad , Anderson Kurt , Koerner Daniel
Published: November 2013

Current strategies to simulate the dynamic behavior of large molecular systems involve either computationally expensive fully atomistic models, or lower resolution models that have been coarsened in some manner. Coarsening is nominally accomplished by grouping tightly bonded atoms that have little relative motion. Traditionally this accomplished by treating a region as pseudo-atom and connecting it to other psuedo-atoms to reproduce the system. Alternatively this can be done with a multibody-based approach characterizing the regions as rigid or flexible bodies [1]–[6].
Material Properties of Porcine Corneal Stroma in Unconfined Compression
Authors: Hatami-Marbini Hamed , Etebu Ebitimi
Published: November 2013

The tensile properties of the cornea have been extensively studied while there are fewer studies on its compressive stiffness. The mechanical properties and structure of the cornea like many other connective tissues are derived from the function and properties of their extracellular matrix. The corneal extracellular matrix, stroma, is a polyelectrolyte gel composed of collagenous fibers embedded in an aqueous matrix. The cornea has two different functions: optical and mechanical. It is the main refractive component of the visual system and it is an effective barrier resisting the deformation caused by external and internal stresses. A necessary condition for corneal optical properties and transparency is the maintenance of a pseudo hexagonal arrangement of the collagen fibers inside the extracellular matrix. This regular arrangement is attributed to the interaction of collagen fibers with the proteoglycans. Under physiological conditions, the proteoglycans are ionized and form a hydrated gel in the empty space between the collagen fibrils by attracting the water and solutes. The interaction of the negatively fixed charges of the proteoglycans with themselves and with the free ions inside the interstitial fluid contributes to the corneal swelling pressure and subsequently to its compressive properties.
Predicting Endothelial Cell Phenotypes in Angiogenesis
Authors: Ryan David T. , Hu Jingzhe , Long Byron L. , Qutub Amina A.
Published: November 2013

Controlling endogenous angiogenesis, or the formation of new capillaries, is a potential therapeutic strategy for numerous diseases including cancer, stroke and cardiovascular disease (1–4). These efforts have been met with mixed success in the clinic, partly due to an inadequate understanding, and thus control, of the mechanisms that influence the endothelial cells that form capillaries (1, 3). In order to control angiogenesis in an effort to improve treatment responses, quantitative information about endothelial cell behavior must be used to build accurate models of vascular network formation.

In this paper, we introduce a method to identify and classify endothelial cell responses to angiogenic stimuli through sophisticated image analysis. The presented automated image processing tools and classification framework allow for rapid quantitative investigations of cellular images. Results of our analysis demonstrate that endothelial cells can be grouped into distinct morphological phenotypes as a function of their responses to combinations of angiogenic growth factor stimuli. Information on phenotypic behavior and responses will be applied towards predicting and guiding cell behavior for therapeutic design.
Electroactive, Multi-Component Scaffolds for Skeletal Muscle Regeneration
Authors: McKeon-Fischer K. D. , Flagg D. H. , Rossmeisl J. H. , Whittington A. R. , Freeman J. W.
Published: November 2013

After loss of skeletal muscle function due to traumatic injuries, muscle healing may result in scar tissue formation and reduced function. A restoration method is needed to create a bioartificial muscle that supports cell growth. An electroactive, coaxial electrospun scaffold was created using PCL, MWCNT, and a PAA/PVA hydrogel. This scaffold was conductive and displayed an actuation response when electrically stimulated. Rat primary skeletal muscle cells were biocompatible with the scaffold and displayed multi-nucleated constructs with actin interaction. MWCNT toxicity was tested using a single exposure method on rat primary skeletal muscle cells. A decrease in cellular activity was found on day 14, but a recovering trend was observed on days 21 and 28. Scaffolds were implanted in the quadriceps muscle of rats for in vivo biocompatibility investigation. Muscle cells were found to have attached and infiltrated the PCL-MWCNT-PAA/PVA scaffolds over the 28 day period. Further development of this scaffold would lead to a viable option for a bioartificial muscle as it is biocompatible and may provide some functional movement to the patient.
Effects of coupling, bubble size, and spatial arrangement on chaotic dynamics of microbubble cluster in ultrasonic fields
Authors: Dzaharudin Fatimah , Suslov Sergey A. , Manasseh Richard , Ooi Andrew
Published: November 2013

Microbubble clustering may occur when bubbles become bound to targeted surfaces or are grouped by acoustic radiation forces in medical diagnostic applications. The ability to identify the formation of such clusters from the ultrasound echoes may be of practical use. Nonlinear numerical simulations were performed on clusters of microbubbles modeled by the modified Keller-Miksis equations. Encapsulated bubbles were considered to mimic practical applications but the aim of the study was to examine the effects of inter-bubble spacing and bubble size on the dynamical behavior of the cluster and to see if chaotic or bifurcation characteristics could be helpful in diagnostics. It was found that as microbubbles were clustered closer together, their oscillation amplitude for a given applied ultrasound power was reduced, and for inter-bubble spacing smaller than about ten bubble radii nonlinear subharmonics and ultraharmonics were eliminated. For clustered microbubbles, as for isolated microbubbles, an increase in the applied acoustic power caused bifurcations and transition to chaos. The bifurcations preceding chaotic behavior were identified by Floquet analysis and confirmed to be of the period-doubling type. It was found that as the number of microbubbles in a cluster increased, regularization occurred at lower ultrasound power and more windows of order appeared.
Assessing the coastal occurrence of endangered killer whales using autonomous passive acoustic recorders
Authors: Bradley Hanson M. , Emmons Candice K. , Ward Eric J. , Nystuen Jeffrey A. , Lammers Marc O.
Published: November 2013

Using moored autonomous acoustic recorders to detect and record the vocalizations of social odonotocetes to determine their occurrence patterns is a non-invasive tool in the study of these species in remote locations. Acoustic recorders were deployed in seven locations on the continental shelf of the U.S. west coast from Cape Flattery, WA to Pt. Reyes, CA to detect and record endangered southern resident killer whales between January and June of 2006–2011. Detection rates of these whales were greater in 2009 and 2011 than in 2006–2008, were most common in the month of March, and occurred with the greatest frequency off the Columbia River and Westport, which was likely related to the presence of their most commonly consumed prey, Chinook salmon. The observed patterns of annual and monthly killer whale occurrence may be related to run strength and run timing, respectively, for spring Chinook returning to the Columbia River, the largest run in this region at this time of year. Acoustic recorders provided a unique, long-term, dataset that will be important to inform future consideration of Critical Habitat designation for this U.S. Endangered Species Act listed species.
An asymptotic model in acoustics: Acoustic drift equations
Authors: Vladimirov Vladimir A. , Ilin Konstantin
Published: November 2013

A rigorous asymptotic procedure with the Mach number as a small parameter is used to derive the equations of mean flows which coexist and are affected by the background acoustic waves in the limit of very high Reynolds number.
Compression of head-related transfer function using autoregressive-moving-average models and Legendre polynomials
Authors: Shekarchi Sayedali , Hallam John , Christensen-Dalsgaard Jakob
Published: November 2013

Head-related transfer functions (HRTFs) are generally large datasets, which can be an important constraint for embedded real-time applications. A method is proposed here to reduce redundancy and compress the datasets. In this method, HRTFs are first compressed by conversion into autoregressive-moving-average (ARMA) filters whose coefficients are calculated using Prony's method. Such filters are specified by a few coefficients which can generate the full head-related impulse responses (HRIRs). Next, Legendre polynomials (LPs) are used to compress the ARMA filter coefficients. LPs are derived on the sphere and form an orthonormal basis set for spherical functions. Higher-order LPs capture increasingly fine spatial details. The number of LPs needed to represent an HRTF, therefore, is indicative of its spatial complexity. The results indicate that compression ratios can exceed 98% while maintaining a spectral error of less than 4 dB in the recovered HRTFs.
Inter-speaker articulatory variability during vowel-consonant-vowel sequences in twins and unrelated speakers
Authors: Weirich Melanie , Lancia Leonardo , Brunner Jana
Published: November 2013

The purpose of this study is to examine and compare the amount of inter-speaker variability in the articulation of monozygotic twin pairs (MZ), dizygotic twin pairs (DZ), and pairs of unrelated twins with the goal of examining in greater depth the influence of physiology on articulation. Physiological parameters are assumed to be very similar in MZ twin pairs in contrast to DZ twin pairs or unrelated speakers, and it is hypothesized that the speaker specific shape of articulatory looping trajectories of the tongue is at least partly dependent on biomechanical properties and the speaker's individual physiology. By means of electromagnetic articulography (EMA), inter-speaker variability in the looping trajectories of the tongue back during /VCV/ sequences is analyzed. Results reveal similar looping patterns within MZ twin pairs but in DZ pairs differences in the shape of the loop, the direction of the upward and downward movement, and the amount of horizontal sliding movement at the palate are found.
Infrasonic ray tracing applied to mesoscale atmospheric structures: Refraction by hurricanes
Authors: Bedard Alfred J. , Michael Jones R.
Published: November 2013

A ray-tracing program is used to estimate the refraction of infrasound by the temperature structure of the atmosphere and by hurricanes represented by a Rankine-combined vortex wind plus a temperature perturbation. Refraction by the hurricane winds is significant, giving rise to regions of focusing, defocusing, and virtual sources. The refraction of infrasound by the temperature anomaly associated with a hurricane is small, probably no larger than that from uncertainties in the wind field. The results are pertinent to interpreting ocean wave generated infrasound in the vicinities of tropical cyclones.
Neglect of bandwidth of Odontocetes echo location clicks biases propagation loss and single hydrophone population estimates
Authors: Ainslie Michael A.
Published: November 2013

Passive acoustic monitoring with a single hydrophone has been suggested as a cost-effective method to monitor population density of echolocating marine mammals, by estimating the distance at which the hydrophone is able to intercept the echolocation clicks and distinguish these from the background. To avoid a bias in the estimated population density, this method relies on an unbiased estimate of the detection range and therefore of the propagation loss (PL). When applying this method, it is common practice to estimate PL at the center frequency of a broadband echolocation click and to assume this narrowband PL applies also to the broadband click. For a typical situation this narrowband approximation overestimates PL, underestimates the detection range and consequently overestimates the population density by an amount that for fixed center frequency increases with increasing pulse bandwidth and sonar figure of merit.
Response to “Comment on ‘Resonant acoustic scattering by swimbladder-bearing fish’ ” [J. Acoust. Soc. Am. 64, 571–580 (1978)]
Authors: Love Richard H.
Published: November 2013

In the 1970s a model of resonant scattering from a swimbladder-bearing fish was developed. The fish was modeled as an air bubble, representing a swimbladder, encased in a viscous spherical shell, representing the fish flesh. This model has been used successfully to correlate acoustic scattering data with fish information in a number of ocean locations. Recently, questions have arisen about viscous damping of the flesh and the thickness of the shell [K. Baik, J. Acoust. Soc. Am. 133, 5–8 (2013)]. This Letter responds to those questions and provides practical insight into the model's use.
An axisymmetric boundary element formulation of sound wave propagation in fluids including viscous and thermal losses
Authors: Cutanda-Henríquez Vicente , Juhl Peter Møller
Published: November 2013

The formulation presented in this paper is based on the boundary element method (BEM) and implements Kirchhoff's decomposition into viscous, thermal, and acoustic components, which can be treated independently everywhere in the domain except on the boundaries. The acoustic variables with losses are solved using extended boundary conditions that assume (i) negligible temperature fluctuations at the boundary and (ii) normal and tangential matching of the boundary's particle velocity. The proposed model does not require constructing a special mesh for the viscous and thermal boundary layers as is the case with the existing finite element method (FEM) implementations with losses. The suitability of this approach is demonstrated using an axisymmetrical BEM and two test cases where the numerical results are compared with analytical solutions.
High initial and minimum frequencies of Sotalia guianensis whistles in the southeast and south of Brazil
Authors: Deconto Lucimary S. , Monteiro-Filho Emygdio L. A.
Published: November 2013

Recent studies have proposed latitudinal variations for the whistles of Sotalia guianensis, since parameters of frequency increase from the southernmost distribution of the species (State of Santa Catarina, Brazil) toward the North. The last study on the whistles of S. guianensis, conducted in Costa Rica, confirmed the geographical variation of whistles, regardless of frequency responses used in the samples. Initial and minimum frequencies of whistles of the Costa Rican populations were higher than were the frequencies of Brazilian populations. In this current study, the whistles of S. guianensis were recorded with a sampling frequency of 48 kHz, the highest frequency band used in Brazilian studies. The initial and minimum frequency of whistles recorded and analyzed were similar to parameters of Costa Rican populations and show little or no difference when compared to the average of each study. Therefore, whistle frequency variables do not increase with latitude. It is likely that variations in acoustic parameters S. guianensis are mainly linked to environmental characteristics of the habitats in which the populations occur. Thus, the repertoire sound S. guianensis appears linked to similar environments with similar physical characteristics and not linked to population characteristics (dialects).
Acoustic waveguiding by pliable conduits with axial cross sections as linear waveguides in two-dimensional sonic crystals
Authors: Cicek Ahmet , Adem Kaya Olgun , Ulug Bulent
Published: November 2013

Pliable conduits composed of periodically arranged concentric aluminum tori in air, with their axial cross sections acting as linear waveguides in two-dimensional sonic crystals, are numerically shown to guide acoustic waves in three dimensions in a flexible manner. Waveguide band structures are obtained by exploiting axial symmetry in a super-cell approach through two-dimensional finite-element simulations under the periodic boundary conditions. One isolated band having a bandwidth of 19.66% or 10.10% is observed for each guide, whose cross section is either in square or triangular geometry, respectively. Corresponding mode profiles indicate efficient guiding, as the acoustic energy is mainly concentrated in the hollow-core region of the guides. Transmittance spectra calculated through finite-element simulations are in agreement with the computed guiding bands. Transmittance along the waveguides with square and triangular axial cross sections around mid-band frequencies of their guiding bands varies slightly from −6.05 and −6.65 dB to −5.98 and −8.86 dB, respectively, as the guide length is increased from 10 to 200 periods. Efficient guiding across the smooth bends over circular arcs up to 90 deg is also demonstrated through three-dimensional finite-element method simulations.
A simple electrical lumped-element model simulates intra-cochlear sound pressures and cochlear impedance below 2 kHz
Authors: Marquardt Torsten , Hensel Johannes
Published: November 2013

Low-frequency sounds displace large parts of the basilar membrane (BM) and can have a modulating and possibly disturbing effect on hearing at other frequencies. A better understanding of the transfer of such sounds onto the BM is therefore desirable. Lumped-element models have previously been employed to determine the low-frequency acoustic properties of the cochlea. Although helpful in illustrating schematically the role of the helicotrema, BM compliance, and the round window on low-frequency hearing, these models, when applied quantitatively, have not been able to explain experimental data in detail. Building on these models, an extended electrical analog requires just 13 lumped elements to capture, in surprising detail, the physiologically determined frequency-dependence of intra-cochlear pressure and cochlear impedance between 10 Hz and 2 kHz. The model's verification is based on data from cat, guinea pig, and humans, who differ principally in their low-frequency cochlear acoustics. The modeling data suggest that damping within the helicotrema plays a less prominent role than previously assumed. A resonance feature, which is often observed experimentally near 150 Hz in these animals and near 50 Hz in humans, is presumably a phenomenon local to the apex and not the result of a standing wave between stapes and helicotrema.
Offshore killer whale tracking using multiple hydrophone arrays
Authors: Gassmann Martin , Elizabeth Henderson E. , Wiggins Sean M. , Roch Marie A. , Hildebrand John A.
Published: November 2013

To study delphinid near surface movements and behavior, two L-shaped hydrophone arrays and one vertical hydrophone line array were deployed at shallow depths (<125 m) from the floating instrument platform R/P FLIP, moored northwest of San Clemente Island in the Southern California Bight. A three-dimensional propagation-model based passive acoustic tracking method was developed and used to track a group of five offshore killer whales (Orcinus orca) using their emitted clicks. In addition, killer whale pulsed calls and high-frequency modulated (HFM) signals were localized using other standard techniques. Based on these tracks sound source levels for the killer whales were estimated. The peak to peak source levels for echolocation clicks vary between 170–205 dB re 1 μPa @ 1 m, for HFM calls between 185–193 dB re 1 μPa @ 1 m, and for pulsed calls between 146–158 dB re 1 μPa @ 1 m.
Influence of “omnidirectional” loudspeaker directivity on measured room impulse responses
Authors: Knüttel Tobias , Witew Ingo B. , Vorländer Michael
Published: November 2013

Measured room impulse responses (RIR) strongly depend on the directivity of the sound source used for the measurement. An analysis method is presented that is capable of pinpointing the influence of the loudspeaker's directivity on a set of RIRs. Taking into account the rotational symmetries of a dodecahedron loudspeaker, it detects the effects that the changing directional pattern induces in the RIR. The analysis of RIRs measured in completely different acoustical environments reveals that the influence of the loudspeaker's directivity can still be observed in the very late part of the RIR—even in very reverberant rooms. These results are presented and the consistency with general room acoustical theory is revised and discussed.
Nonlinear derating of high-intensity focused ultrasound beams using Gaussian modal sums
Authors: Ahmad Reza Dibaji Seyed , Banerjee Rupak K. , Soneson Joshua E. , Myers Matthew R.
Published: November 2013

A method is introduced for using measurements made in water of the nonlinear acoustic pressure field produced by a high-intensity focused ultrasound transducer to compute the acoustic pressure and temperature rise in a tissue medium. The acoustic pressure harmonics generated by nonlinear propagation are represented as a sum of modes having a Gaussian functional dependence in the radial direction. While the method is derived in the context of Gaussian beams, final results are applicable to general transducer profiles. The focal acoustic pressure is obtained by solving an evolution equation in the axial variable. The nonlinear term in the evolution equation for tissue is modeled using modal amplitudes measured in water and suitably reduced using a combination of “source derating” (experiments in water performed at a lower source acoustic pressure than in tissue) and “endpoint derating” (amplitudes reduced at the target location). Numerical experiments showed that, with proper combinations of source derating and endpoint derating, direct simulations of acoustic pressure and temperature in tissue could be reproduced by derating within 5% error. Advantages of the derating approach presented include applicability over a wide range of gains, ease of computation (a single numerical quadrature is required), and readily obtained temperature estimates from the water measurements.
Defining the coupling coefficient for electrodynamic transducers
Authors: Cheng Shuo , Arnold David P.
Published: November 2013

This paper provides a simple, practical definition of the coupling coefficient for electrodynamic transducers. Comparing to efforts made in previous works that assumed a lossless spring-inductor model, the definition presented here is based on a lossy mass-inductor model. Time-harmonic analysis is used to model the energy flow in the transducer. Both energy storage and energy dissipation are included in the electrodynamic coupling coefficient definition. An in-depth discussion is provided to explain and justify the derivation and overall methodology. This definition is expected to provide a useful and practical measure of the electromechanical energy conversion performance of electrodynamic transducers, both actuators and generators.
ACOUSTICAL STANDARDS NEWS
Authors: Blaeser Susan B. , Schomer Paul D.
Published: November 2013

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes catalogs of Acoustical Standards, both National and International. To receive copies of the latest Standards catalogs, please contact Susan B. Blaeser.

Comments are welcomed on all material in Acoustical Standards News.

This Acoustical Standards News section in JASA, as well as the National and International Catalogs of Acoustical Standards, and other information on the Standards Program of the Acoustical Society of America, are available via the ASA home page: http://acousticalsociety.org.
Headphone- and loudspeaker-based concert hall auralizations and their effects on listeners' judgments
Authors: Clapp Samuel , Guthrie Anne E. , Braasch Jonas , Xiang Ning
Published: November 2013

Room impulse responses were measured in a wide variety of concert and recital halls throughout New York State using a spherical microphone array and dummy head as receivers. These measurements were used to create auralizations for second-order ambisonic playback via a loudspeaker array and headphone playback, respectively. The playback methods were first evaluated objectively to determine how accurately they could reproduce the measured soundfields with respect to spatial cues. Subjects were then recruited for listening tests conducted with both reproduction methods and asked to evaluate the different spaces based on specific parameters and overall subjective preference. The results were examined in order to determine the degree to which judgments of the different parameters were affected by the playback method.
How room acoustics impact speech comprehension by listeners with varying English proficiency levels
Authors: Peng Zhao , Steinbach Adam M. , Hanna Kristin E. , Wang Lily M.
Published: November 2013

The authors previously reported the preliminary results from an investigation on effects of reverberation and noise on speech comprehension by native and non-native English-speaking listeners at ICA, Montreal. The results showed significant main effects of reverberation time (from 0.4 to 1.2 s) and background noise level (three settings of RC-30, 40, and 50). Non-native listeners performed significantly worse than natives on speech comprehension in general. Furthermore, the negative effect of reverberation was more detrimental for non-native than for native English-speaking listeners. However, the preliminary analyses have not yet accounted for effects of English proficiency on speech comprehension in addition to the room acoustic environments tested. All test participants were screened for three measures of English proficiency (listening span, oral comprehension, and verbal abilities). Non-native listeners as a group scored lower on all three proficiency measures than native English-speaking listeners. In this paper, English proficiency is investigated as confounding factor affecting speech comprehension performance alongside noise and reverberation. The results help to further the understanding of how room acoustics impacts speech comprehension by listeners, native and non-native English-speaking, with varying English proficiency levels. [Work supported by a UNL Durham School Seed Grant and the Paul S. Veneklasen Research Foundation.]
Localization of humpback whale signals with two directional frequency analysis and recording sonobouys
Authors: Rudd Alexis B. , Au Whitlow , Nosal Eva Marie , Murphey Seibert
Published: November 2013

For many years, the navy has used directional frequency analysis and recording (DIFAR) sonobouys to record and track ships. DIFAR sonobouys compute acoustic particle velocity for two bimodal perpendicular hydrophone elements, which, with a magnetic compass, gives a directional bearing to the sound recorded on a third omnidirectional hydrophone. Use of DIFAR represents an easily deployable alternative method to standard time-difference of arrival localization with towed or bottom-mounted hydrophone arrays. In this study, we used two tethered DIFAR sonobouys to record and track playbacks of humpback whale song. GPS positions of playbacks were recorded. Digital signals were recorded at the sonobouy before multiplexing. Song units were recorded on both sonobouys, and then matched between sonobouys using time from the sonobouy GPS. To localize the signals, azimuths from the DIFAR sonobouys were combined with the time difference of arrival parabola to create a three-dimensional likelihood surface that gives the probabilities that a signal originated at a specific point in space. The locations with maximum likelihood were used to estimate source level of whale calls, and singing whales were tracked over time. Comparisons will be made between DIFAR methods and GPS locations from the playback boat, to ground-truth this localization methodology.
The acoustic presence of sperm whales (Physeter macrocephalus) at Ocean Station PAPA in the Gulf of Alaska 2007–2012
Authors: Diogou Nikoletta , Klinck Holger , Nystuen Jeffrey A.
Published: November 2013

Sperm whale (Physeter macrocephalus) populations were severely depleted by commercial whaling worldwide in the 18th through the 20th century. Consequently, in 1970, this species was listed in the United States as an endangered species. To date, accurate information on the abundance and distribution of sperm whales in offshore areas of the North Pacific are scant. Sperm whales regularly produce high intensity sounds for navigation, prey detection, and communication. Thus, this species can be very effectively monitored using passive acoustic techniques especially in remote and inaccessible locations such as the Gulf of Alaska (GOA). In this study, a Passive Aquatic Listener (PAL) was deployed at Ocean Station PAPA (50°N, 145°W) in the GOA between 2007 and 2012 to monitor the seasonal occurrence of sperm whales in the area. Preliminary results indicate that within the 5-year deployment period sperm whales were acoustically present year round and that the number of acoustic sperm whale detections showed a seasonal trend with slightly higher numbers during the summer months. We are currently investigating the linkage between the occurrence of sperm whales and environmental conditions (e.g., Pacific Decadal Oscillation index) in the study area. [Funding from the Office of Naval Research.]
Measurement of hydrothermal heat flux using a sonar deployed on the Canadian Neptune cabled observatory
Authors: Xu Guangyu , Rona Peter A. , Bemis Karen G. , Jackson Darrell R.
Published: November 2013

The Cabled Observatory Vent Imaging Sonar (COVIS) was deployed at the Main Endeavour Field node of the Canadian NEPTUNE cabled observatory in September 2010 and has acquired long time series on plume and diffuse hydrothermal flows. This talk will focus on recent efforts by the Rutgers-APL collaboration to invert sonar data to determine heat flux from the Grotto plume complex. Inversion employs plume theory to relate velocity as determined by Doppler shift to buoyancy flux, hence heat flux. The primary uncertainties have to do with plume bending due to ambient current and short sampling times relative to dynamic changes in plume shape. These uncertainties have been quantified by means of special high-statistics experiments using COVIS. Time series for heat flux will be compared with ground truth obtained by thermometry using an ROV. [Work supported by NSF Grants OCE-0824612 and OCE-0825088.]
The mechanical index and bubbles in tissue, an evidentiary review
Authors: Church Charles C.
Published: November 2013

The mechanical index (MI) quantifies the likelihood that diagnostic ultrasound will produce an adverse biological effect by a non-thermal mechanism. The current formulation of the MI is based on inertial cavitation thresholds in water and blood as calculated for a pulse duration of one period. However, tissue is not a liquid but a viscoelastic solid, and imaging pulses may be much longer. The importance of these differences has been quantified using the Gilmore equation for water and blood and a form of the Keller-Miksis equation modified for soft tissue. It is shown that the threshold for cavitation is higher in soft tissues, and much higher in muscle, than in blood. Experimentally determined thresholds in tissue lie above these theoretical results by up to an order of magnitude. This suggests that use of the MI as part of the FDA 501(k) approval process may unnecessarily restrict the outputs of diagnostic ultrasound machines. Additionally, a simple analysis of another potential mechanism for biological effects, radiation force, indicates that the very form of the MI does not include all non-thermal mechanisms but, perhaps, only one. These results cast doubt on the value of the MI as a reliable means of assessing patient safety.