bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational and physicochemical DNA features specific for transcription factor binding sites.
Authors: Ponomarenko J V , Ponomarenko M P , Frolov A S , Vorobyev D G , Overton G C , Kolchanov N A
Published: July 2002

MOTIVATION: A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences. The experimental data make evident an important role of DNA conformational features for site functioning. However, Internet-available tools for revealing conformational and physicochemical DNA features significant for the site functioning and subsequent use of these features for site recognition have not been developed up to now. RESULTS: We suggest an approach for revealing significant conformational and physicochemical properties of functional sites implemented in the database B-DNA-VIDEO. This database is designed to study the sets of various transcription factor binding sites, providing evidence that transcription factor binding sites are characterized by specific sets of significant conformational and physicochemical DNA properties. For a fixed site, by using the B-DNA features selected for this site recognition, the C-program recognizing this site may be generated, control tested and stored in the database B-DNA-VIDEO. Each B-DNA-VIDEO entry links to the Web-applet recognizing the site, whose significant B-DNA features are stored in this entry as the 'site recognition programs'. The pairwise linked entry-applet pairs are compiled within the B-DNA-VIDEO system, which is simultaneously the database and the program tools package applicable immediately for recognizing the sites stored in the database. Indeed, this is the novelty. Hence, B-DNA-VIDEO is the Web resource of both 'searching for static data' and 'active computation' type, that is why it was called an 'activated database'. AVAILABILITY: B-DNA-VIDEO is available at http://wwwmgs.bionet.nsc.ru/systems/BDNAVideo/ and the mirror site at http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.
Domain size distributions can predict domain boundaries
Authors: Wheelan S. J. , Marchler-Bauer A. , Bryant S. H.
Published: July 2002

Motivation: The sizes of protein domains observed in the 3D-structure database follow a surprisingly narrow distribution. Structural domains are furthermore formed from a single-chain continuous segment in over 80% of instances. These observations imply that some choices of domain boundaries on an otherwise uncharacterized sequence are more likely than others, based solely on the size and segment number of predicted domains. This property might be used to guess the locations of protein domain boundaries.

Results: To test this possibility we enumerate putative domain boundaries and calculate their relative likelihood under a probability model that considers only the size and segment number of predicted domains. We ask, in a cross-validated test using sequences with known 3D structure, whether the most likely guesses agree with the observed domain structure. We find that domain boundary predictions are surprisingly successful for sequences up to 400 residues long and that guessing domain boundaries in this way can improve the sensitivity of threading analysis.

Availability: The DGS algorithm, for ‘Domain Guess by Size’, is available as a web service at http://www.ncbi.nlm.nih.gov/dgs. This site also provides the DGS source code.

Contact: bryant@ncbi.nlm.nih.gov

* To whom correspondence should be addressed.
Detection of a surface-exposed PEST like sequence in the
metabotropic glutamate receptor mGluR1 α
Authors: Soloviev M. M.
Published: July 2002

Contact: mikhail.soloviev@pharm.ox.ac.uk
Use of keyword hierarchies to interpret gene expression

patterns
Authors: Masys Daniel R. , Welsh John B. , Lynn Fink J. , Gribskov Michael , Klacansky Igor , Corbeil Jacques
Published: July 2002

Motivation: High-density microarray technology permits the quantitative and simultaneous monitoring of thousands of genes. The interpretation challenge is to extract relevant information from this large amount of data. A growing variety of statistical analysis approaches are available to identify clusters of genes that share common expression characteristics, but provide no information regarding the biological similarities of genes within clusters. The published literature provides a potential source of information to assist in interpretation of clustering results.

Results: We describe a data mining method that uses indexing terms (‘keywords’) from the published literature linked to specific genes to present a view of the conceptual similarity of genes within a cluster or group of interest. The method takes advantage of the hierarchical nature of Medical Subject Headings used to index citations in the MEDLINE database, and the registry numbers applied to enzymes.

Availability: We have created a publicly accessible website that provides this form of gene expression interpretation at http://www.array.ucsd.edu.

Contact: dmasys@ucsd.edu

8 To whom correspondence should be addressed at: University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0602, USA.

7 Present address: Genomics Institute of the Novartis Research Foundation, 3115 Merryfield Row, San Diego, CA 92121, USA.
Antibiotic dosing issues in lower respiratory tract infection: population-derived area under inhibitory curve is predictive of efficacy
Authors: Highet Vicki Sue , Forrest Alan , Ballow Charles H. , Schentag Jerome J.
Published: July 2002

Several lower respiratory tract infection (LRTI) trials have documented a correlation between clinical response and area under the inhibitory curve (24 h AUC/MIC; AUIC). The AUIC values in these studies were based on measured MICs and measured serum concentrations. This study evaluates AUIC estimates made using population pharmacokinetic parameters, and MICs from an automated microbiological susceptibility testing system. A computer database review over 2 years yielded 81 patients at Millard Fillmore Hospital with a culture-documented Gram-negative LRTI who had been treated with piperacillin and an aminoglycoside, ceftazidime, ciprofloxacin or imipenem. Their AUIC values were estimated using renal function, drug dosages and MIC values. Outcome groups (clinical and microbiological cures and failures) were related to the AUIC values using Kruskal–Wallis ANOVA, linear regression and classification and regression tree (CART) analysis. A significant breakpoint for clinical cures was an AUIC value at least 72 SIT −1⋅24 h (inverse serum inhibitory titre integrated over time). All antibiotics performed significantly better above this value than below it. Clinical cure was well described by a Hill-type equation. Within the piperacillin/aminoglycoside regimen, most of the activity came from the piperacillin, which had a higher overall AUIC value than the aminoglycoside. AUIC estimations based upon MIC values derived from the automated susceptibility testing method differed from NCCLS breakpoint data and from tube dilution derived values in this hospital by as much as three tube dilutions. These automated methods probably overestimated the MIC values of extremely susceptible organisms. The lack of precise MIC estimates in automated clinical microbiology methods impairs the use of AUIC to prospectively optimize microbiological outcome. Even ignoring this limitation and using the values as they are reported, the results of this analysis suggest that AUIC targets between 72 and 275 SIT −1⋅24 h are useful in predicting clinical outcome.
Progesterone facilitates chromosome instability (aneuploidy) in p53 null
Authors: Goepfert T. M. , McCarthy M. , Kittrell F. S. , Stephens C. , Ullrich R. L. , Brinkley B. R. , Medina D.
Published: July 2002

ABSTRACT Mammary epithelial cells from p53 null mice have been shown recently to exhibit an increased risk for tumor development. Hormonal stimulation markedly increased tumor development in p53 null mammary cells. Here we demonstrate that mammary tumors arising in p53 null mammary cells are highly aneuploid, with greater than 70% of the tumor cells containing altered chromosome number and a mean chromosome number of 56. Normal mammary cells of p53 null genotype and aged less than 14 wk do not exhibit aneuploidy in primary cell culture. Significantly, the hormone progesterone, but not estrogen, increases the incidence of aneuploidy in morphologically normal p53 null mammary epithelial cells. Such cells exhibited 40% aneuploidy and a mean chromosome number of 54. The increase in aneuploidy measured in p53 null tumor cells or hormonally stimulated normal p53 null cells was not accompanied by centrosome amplification. These results suggest that normal levels of progesterone can facilitate chromosomal instability in the absence of the tumor suppressor gene, p53. The results support the emerging hypothesis based both on human epidemiological and animal model studies that progesterone markedly enhances mammary tumorigenesis.—Goepfert, T. M., McCarthy, M., Kittrell, F. S., Stephens, C., Ullrich, R. L., Brinkley, B. R., Medina, D. Progesterone facilitates chromosome instability (aneuploidy) in p53 null normal mammary epithelial cells. FASEB J. 14, 2221‐2229 (2000)
Processing of ARIA and release from isolated nerve terminals
Authors: Han Bomie , Fischbach Gerald D.
Published: July 2002

The neuromuscular junction is a specialized synapse in that every action potential in the presynaptic nerve terminal results in an action potential in the postsynaptic membrane, unlike most interneuronal synapses where a single presynaptic input makes only a small contribution to the population postsynaptic response. The postsynaptic membrane at the neuromuscular junction contains a high density of neurotransmitter (acetylcholine) receptors and a high density of voltage–gated Na+channels. Thus, the large acetylcholine activated current occurs at the same site where the threshold for action potential generation is low. Acetylcholine receptor inducing activity (ARIA), a 42 kD protein, that stimulates synthesis of acetylcholine receptors and voltage–gated Na+channels in cultured myotubes, probably plays the same roles at developing and mature motor endplatesin vivo. ARIA is synthesized as part of a larger, transmembrane, precursor protein called proARIA. Delivery of ARIA from motor neuron cell bodies in the spinal cord to the target endplates involves several steps, including proteolytic cleavage of proARIA. ARIA is also expressed in the central nervous system and it is abundant in the molecular layer of the cerebellum. In this paper we describe our first experiments on the processing and release of ARIA from subcellular fractions containing synaptosomes from the chick cerebellum as a model system.
Quantitative analysis of the CD8+T–cell response to readily eliminated and persistent viruses
Authors: Doherty P. C. , Riberdy J. M. , Belz G. T.
Published: July 2002

The recent development of techniques for the direct staining of peptide–specific CD8+T cells has revolutionized the analysis of cell–mediated immunity (CMI) in virus infections. This approach has been used to quantify the acute and long–term consequences of infecting laboratory mice with the readily eliminated influenza A viruses (fluA) and a persistent γherpesvirus (γHV). It is now, for the first time, possible to work with real numbers in the analysis of CD8+T CMI, and to define various characteristics of the responding lymphocytes both by direct flow cytometric analysis and by sorting for furtherin vitromanipulation. Relatively little has yet been done from the latter aspect, though we are rapidly accumulating a mass of numerical data. The acute, antigen–driven phases of the fluA and γHV–specific response look rather similar, but CD8+T–cell numbers are maintained in the long term at a higher ‘set point’ in the persistent infection. Similarly, these ‘memory’ T cells continue to divide at a much greater rate in the γHV–infected mice. New insights have also been generated on the nature of the recall response following secondary challenge in both experimental systems, and the extent of protection conferred by large numbers of virus–specific CD8+T cells has been determined. However, there are still many parameters that have received little attention, partly because they are difficult to measure. These include the rate of antigen–specific CD8+T–cell loss, the extent of the lymphocyte ‘diaspora’ to other tissues, and the diversity of functional characteristics, turnover rates, clonal life spans and recirculation profiles. The basic question for immunologists remains how we reconcile the extraordinary plasticity of the immune system with the mechanisms that maintain a stable milieu interieur. This new capacity to quantify CD8+T–cell responses in readily manipulated mouse models has obvious potential for illuminating homeostatic control, particularly if the experimental approaches to the problem are designed in the context of appropriate predictive models.
Allele age and a test for selection on rare alleles
Authors: Slatkin Montgomery
Published: July 2002

An approximate expression for the probability distribution of the age of a neutral allele as a function of its frequency is derived for a population undergoing arbitrary changes in population size. A simple maximum–likelihood estimator of allele age based on frequency is also obtained. The distribution of allele age, combined with a model predicting the extent of intra–allelic variability generated by mutation and recombination, leads to a statistical test of whether a rare allele has experienced natural selection. The test is based on finding whether there is too little or too much intra–allelic variability to be consistent with the observed frequency. The test is applied to the locus, BRCA1, associated with early–onset breast cancer in humans and shows that two common disease–associated alleles (5382insC and 185delAG) appear to have been subject to natural selection.
Neuroscience databases: tools for exploring brain structure–function relationships
Authors: Kötter R.
Published: July 2002

Faster than ever, neuroscience is generating vast amounts of data that await cross–referencing, comparison, integration and interpretation in the endeavour to unravel the mechanisms of the brain. The complex, diverse and distributed nature of these data requires the development of advanced neuroinformatics methodologies for databases and associated tools that are now beginning to emerge. This paper presents an overview of current issues in the representation, integration and analysis of neuroscience data from molecular to brain systems levels, including issues of implementation, standardization, management, quality control, copyright, confidentiality and acceptance. Particular emphasis is given to integrative neuroinformatics approaches for exploring structure–function relationships in the brain.
Genomic Analysis of the Olfactory Receptor Region of the Mouse and Human T-Cell Receptor α/δ Loci
Authors: Lane Robert P. , Roach Jared C. , Lee Inyoul Y. , Boysen Cecilie , Smit Arian , Trask Barbara J. , Hood Leroy
Published: July 2002

We have conducted a comparative genomic analysis of several olfactory receptor (OR) genes that lie immediately 5′ to the V-α gene segments at the mouse and human T-cell receptor (TCR) α/δ loci. Five OR genes are identified in the human cluster. The murine cluster has at least six OR genes; the first five are orthologous to the human genes. The sixth mouse gene has arisen since mouse-human divergence by a duplication of a ∼10-kb block. One pair of OR paralogs found at the mouse and human loci are more similar to each other than to their corresponding orthologs. This paralogous “twinning” appears to be under selection, perhaps to increase sensitivity to particular odorants or to resolve structurally-similar odorants. The promoter regions of the mouse OR genes were identified by RACE-PCR. Orthologs share extensive 5′ UTR homology, but we find no significant similarity among paralogs. These findings extend previous observations that suggest that OR genes do not share local significant regulatory homology despite having a common regulatory agenda. We also identified a diverged TCR-α gene segment that uses a divergent recombination signal sequence (RSS) to initiate recombination in T-cells from within the OR region. We explored the hypothesis that OR genes may use DNA recombination in expressing neurons, e.g., to recombine ORs into a transcriptionally active locus. We searched the mouse sequence for OR-flanking RSS motifs, but did not find evidence to suggest that these OR genes use TCR-like recombination target sequences.
Neonatal Exposure to Novel Environment Enhances Hippocampal-Dependent Memory Function During Infancy and Adulthood
Authors: Tang Akaysha C.
Published: July 2002

Early life experience affects behavior and brain mechanisms. Handling rats during the first three weeks in life can slow age-related cognitive decline (as measured by a hippocampal-dependent spatial learning task) and reduce age-related hippocampal neuron loss. It is not clear, however, whether this early environmental influence on learning is selective for old age or is more general, affecting cognitive development during infancy and young adulthood as well. We briefly exposed neonatal rats to a novel non-home environment for 3 min daily during the first three weeks of life (as a component of the handling method). We found that this brief early environmental manipulation resulted in enhanced hippocampal-dependent learning immediately after weaning and that this learning enhancement persisted into adulthood. These results suggest that subtle early life events can affect cognitive development in all developmental stages and that changes in neural mechanisms other than neuron number are likely to mediate the learning enhancement at multiple developmental stages.
Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics study
Authors: Amara Patricia , Andreoletti Pierre , Jouve HéLène Marie , Field Martin J.
Published: July 2002

The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H2O2 →1/2 O2 + H2O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, ideied in the X‐ray model, which allows access to the active site. This channel is the only pathway to the active site observed during the dynamics, and both the products and reactant use it. H2O and O2 are also detected in a cavity defined by the heme and Ser196, which could play an important role during the reaction. Free energy profiles of the ligands diffusing through the major channel indicate that the barriers to ligand diffusion are less than 20 kJ mol−1 for each of the species. It is not clear from our study that minor channels play a role for access to the protein active site or to the protein surface.
Alignment of a volumetric tomography system
Authors: Stevens Grant M. , Saunders Rowland , Pelc Norbert J.
Published: July 2002

A test‐bed system has been developed for imaging phantoms with tomosynthesis and volumetric computed tomography. This system incorporates an amorphous silicon flat panel detector on a movable gantry and a computer‐controlled rotational positioning stage. In this paper, an analysis of the sensitivity of reconstructed images to geometrical misalignment is presented. Application of this method to circular digital tomosynthesis is examined, with spatial resolution in the focal plane as the criterion for evaluating the effect of misalignment. A software‐based method is presented for correcting data for imperfect system alignment prior to image reconstruction. Experimental results yield reconstructed images with spatial resolution approaching the theoretical limit based on detector pixel size and accounting for data interpolation.
Comparison of an amorphous silicon/cesium iodide flat‐panel digital chest radiography system with screen/film and computed radiography systems — A contrast‐detail phantom study
Authors: Rong Xiujiang J. , Shaw Chris C. , Liu Xinming , Lemacks Michael R. , Thompson Stephen K.
Published: July 2002

Flat‐panel (FP) based digital radiography systems have recently been introduced as a new and improved digital radiography technology; it is important to evaluate and compare this new technology with currently widely used conventional screen/film (SF) and computed radiography (CR) techniques. In this study, the low‐contrast performance of an amorphous silicon/cesium iodide ‐based flat‐panel digital chest radiography system is compared to those of a screen/film and a computed radiography system by measuring their contrast‐detail curves. Also studied were the effects of image enhancement in printing the digital images and dependence on kVp and incident exposure. It was found that the FP system demonstrated significantly better low‐contrast performance than the SF or CR systems. It was estimated that a dose savings of 70%–90% could be achieved to match the low‐contrast performance of the FP images to that of the SF images. This dose saving was also found to increase with the object size. No significant difference was observed in low‐contrast performances between the SF and CR systems. The use of clinical enhancement protocols for printing digital images was found to be essential and result in better low‐contrast performance. No significant effects were observed for different kVps. From the results of this contrast‐detail phantom study, the aSi/CsI‐based flat‐panel digital chest system should perform better under clinical situations for detection of low‐contrast objects such as lung nodules. However, proper processing prior to printing would be essential to realizing this better performance.
Multileaf collimator leaf sequencing algorithm for intensity modulated beams with multiple static segments
Authors: Xia Ping , Verhey Lynn J.
Published: July 2002

The “stop and shoot” method of producing intensity modulation using combinations of static multileaf collimator (MLC) segments has a number of advantages including precise dose delivery, easy verification, and general availability. However, due to the potential limitation of prolonged treatment time, it is essential to keep the number of required segments to a reasonable number. We propose an algorithm to minimize the number of segments for an intensity modulated field. In this algorithm, the sequence of delivery intensity is proposed to be a series of powers of 2, depending on the maximum intensity level in the matrix. The MLC leaf position sequence is designed directly on the two‐dimensional intensity matrix to irradiate the largest possible area in each segment. The algorithm can be applied directly to MLC systems with different motion constraints. This algorithm has been evaluated by generating 1000 random intensity matrices, each having from 3 to 16 intensity levels. Five clinical intensity modulated fields generated from the NOMOS CORVUS planning system for a complex clinical head and neck case were also tested with this and two other algorithms. The results of both the statistical and clinical studies showed that for all the intensity matrices tested, the proposed algorithm results in the smallest number of segments with a moderately increased monitor units. Thus it is well‐suited for use in static MLC intensity modulation beam delivery. For MLC systems with interleaf motion constraint, we prove mathematically that this constraint reduces the tongue and groove effect at the expense of an increase of 25% in the number of segments.
Beam orientation optimization in intensity‐modulated radiation treatment planning
Authors: Pugachev A. B. , Boyer A. L. , Xing L.
Published: July 2002

Beam direction optimization is an important problem in radiation therapy. In intensity modulated radiation therapy (IMRT), the difficulty for computer optimization of the beam directions arises from the fact that they are coupled with the intensity profiles of the incident beams. In order to obtain the optimal incident beam directions using iterative or stochastic methods, the beam profiles ought to be optimized after every change of beam configuration. In this paper we report an effective algorithm to optimize gantry angles for IMRT. In our calculation the gantry angles and the beam profiles (beamlet weights) were treated as two separate groups of variables. The gantry angles were sampled according to a simulated annealing algorithm. For each sampled beam configuration, beam profile calculation was done using a fast filtered backprojection (FBP) method. Simulated annealing was also used for beam profile optimization to examine the performance of the FBP for beam orientation optimization. Relative importance factors were incorporated into the objective function to control the relative importance of the target and the sensitive structures. Minimization of the objective function resulted in the best possible beam orientations and beam profiles judged by the given objective function. The algorithm was applied to several model problems and the results showed that the approach has potential for IMRT applications.
Photon dose calculation of a three‐dimensional treatment planning system compared to the Monte Carlo code BEAM
Authors: Francescon Paolo , Cavedon Carlo , Reccanello Sonia , Cora Stefania
Published: July 2002

The purpose of this work is to compare the photon dose calculation of a commercially available three‐dimensional (3D) treatment planning system based on the collapsed cone convolution technique against BEAM, a Monte Carlo code that allows detailed simulation of a radiotherapy accelerator. The first part of the work is devoted to the commissioning of BEAM for a 6 MV photon beam and to the optimization of the linac description to fit the experimental data. This step also involves a comparison with radiochromic film data on an inhomogeneous phantom built to simulate electronic nonequilibrium conditions. Commissioning the selected photon beams required a careful description of the treatment head and the fine tuning of physical parameters such as electron beam energy and radius. The second part shows the dose comparison for real patient's CT data sets: A mediastinal treatment and a breast treatment were simulated. Doses in terms of absolute values per monitor unit were calculated based on the BEAM simulation of the CT data sets. For comparisons of real‐patient cases, differences between the treatment planning system and BEAM ranged from 0 to 2.6% and were within ±2 standard deviations for the dose calculated at the prescription point. Dose‐volume histogram analysis indicated that there is no consistent difference between the Monte Carlo and the convolution calculations. On the basis of the results presented in this study, we can conclude that the CCC algorithm is capable of giving results absolutely comparable to those of a Monte Carlo calculation, as far as common 3D radiotherapy planning is concerned.
A calculation of the time-of-flight distribution of trapped atoms
Authors: Yavin I. , Weel M. , Andreyuk A. , Kumarakrishnan A.
Published: July 2002

We consider the ballistic expansion of a cloud of trapped atoms falling under the influence of gravity. Using a simple coordinate transformation, we derive an analytical expression for the time-of-flight signal. The properties of the signal can be used to infer the initial temperature of the cloud. We first assume a point size cloud with an isotropic velocity distribution to explain the physical basis of the calculation. The treatment is then generalized to include a finite-size cloud with an anisotropic velocity distribution, and an exact result for the signal is derived. The properties of the signal are discussed, and an intuitive picture is presented to explain how initial conditions determine the features of the signal.
The radiation efficiency grouping of free-space acoustic radiation modes
Authors: Cunefare Kenneth A. , Currey M. Noelle , Johnson M. E. , Elliott S. J.
Published: July 2002

The use of a modal representation for the exterior acoustic field of a structure has received increasing attention in recent years. This modal approach generally seeks a set of orthogonal functions, representing independent surface velocity distributions, termed acoustic radiation modes, which diagonalize a radiation operator in the exterior domain of the structure. These orthogonal acoustic radiation modes may be found, among other methods, through an eigenvalue analysis of a radiation operator and possess a corresponding set of eigenvalues that are proportional to the radiation efficiencies of the acoustic radiation modes. In free space, the acoustic radiation modes of a sphere display a grouping characteristic in their radiation efficiencies, where each acoustic radiation mode’s radiation efficiency within a group has the same frequency dependency. This is a consequence of the fact that the acoustic radiation modes of a sphere are the spherical harmonics. Further, the acoustic radiation modes of an arbitrary three-dimensional structure exhibit the same frequency grouping as those for the sphere. The basis for the arbitrary structure’s grouping follows from the sphere’s grouping. The observation that the acoustic radiation modes of an arbitrary body are dominated by spherical harmonics provides insight on the behavior of such modes. These results have significance for various applications of acoustic radiation modes, including active noise control design, radiation modeling, etc.
Backscattering from buried sediment layers: The equivalent input backscattering strength model
Authors: Guillon Laurent , Lurton Xavier
Published: July 2002

Signals received by low-frequency multibeam echosounders are strongly affected by sound penetration inside the upper sediment layers and by backscattering from buried layers down to depths of a few meters; this may lead to serious ambiguities and misinterpretations of experimental data. These phenomena are modeled here using a concept of equivalent input backscattering strength (EIBS), based on a combination of classical models of local backscattering strength and propagation inside fluid layered media. The local backscattering strength at a buried interface is expressed first to account for the impedance adaptation due to the overlying layers, for the angular refraction effects due to the velocity profile, and for the layered structure of the underlying medium. It is then transferred to the upper water–sediment interface, accounting for propagation inside the layered stack; the transfer coefficient is obtained from the classical theory of plane wave propagation in layered media. The volume backscattering effects are processed in the same way and account for the finite thickness of the layers. The various contributions are finally summed to give the backscattering strength, at the upper interface, that features the various effects of propagation and attenuation inside the layered structure.
Energy: Converting from acoustic to biological resource units
Authors: Benoit-Bird Kelly J. , Au Whitlow W. L.
Published: July 2002

Acoustic backscattering strength is often used as an index of biomass; however, the relationship between these variables has not been directly validated. Relationships were investigated between acoustic cross section at 200 kHz, measured as part of a previous study, and measured values of length, biovolume, dry weight, ash-free dry weight, and caloric content of the same individual specimens. Animals were part of the Hawaiian mesopelagic boundary community and included shrimps, squids, and myctophid fishes. The strong relationships found between all the variables measured make it possible to approximate any one variable from the measured values of others within a class of animals. The data show that for these midwater animals, acoustic scattering can be used as an index of biomass. Dorsal-aspect acoustic cross section at 200 kHz predicted dry weight and ash-free dry weight at least as well as did body length, a standard predictor. Dorsal-aspect acoustic cross section at 200 kHz was also a strong predictor of total caloric content. The relationship between dorsal-aspect acoustic cross section and caloric content of Hawaiian mesopelagic animals was linear and additive. Consequently, it is possible to directly convert acoustic energy from these animals to organic resource units without having knowledge of the size distribution of the populations being studied.
Matched-field localization for multiple sources in an uncertain environment, with application to Arctic ambient noise
Authors: Greening Michael V. , Zakarauskas Pierre , Dosso Stan E.
Published: July 2002

This paper describes a general method to localize multiple broadband sources in a range- and azimuth-dependent environment when properties of the environment are not well known. Both the source locations and the unknown environmental parameters are included as variables in a simulated annealing inversion that searches for the best match between the measured and modeled fields. The example used to illustrate the method involves localizing an unknown number of ice-ridge building events in an Arctic environment where the bathymetry is poorly known. A number of aspects of this problem are examined in a synthetic study, including the effect of errors in the bathymetry on localization, the importance of simultaneous localization, and determining the number of sources present. The inversion accurately localizes multiple synthetic sources, particularly in cases where the sources are spatially separated and the spectral shape is known. The inversion is also applied to a set of ambient noise measurements recorded in the Lincoln Sea. The results indicate that a small number of ice-ridging sources is sufficient to accurately model the measured fields. Estimates of the number of sources and the source bearings are unambiguous and are reasonably consistent between samples; however, source ranges could not be estimated unambiguously.
Application of piezoelectric composites and net-shape PZT ceramics as acoustic sensors and actuators
Authors: Near C. , Gentilman R. , Pazol B. , Fiore D. , Serwatka W. , Pham-Nguyen H. , Markowski K. , McGuire P. , Bowen L.
Published: July 2002

A ceramic injection molding process is used to custom manufacture piezoelectric composites for both sensors and actuators with operational frequencies from 100 Hz and 10 MHz. These piezoelectric composites can be specifically tailored to couple acoustic energy into and from a wide variety of mediums including air, water, biological tissue, polymers, composites, and metals. Both 1-3 and 2-2 piezoelectric composites have been made with different lead zirconate-titanate (PZT) formulations, element dimensions, PZT volume fractions, and polymeric matrices. Piezoelectric composite transducers are easily conformed to various substructures, shaded to adjust beam patterns, and sectioned into arrays for imaging. Examples include face-plated SonoPanels (and stiff matrix 1-3 piezoelectric composites for underwater actuation, sensing, and imaging. SmartPanels, capable of both sensing and actuating, have been recently introduced for active surface control. These devices integrate 1-3 piezoelectric composite actuators and pressure sensors and net-shape molded PZT velocity sensors in a large-area, low-profile panel. Multiple net-shape molded accelerometer elements have been designed, fabricated, and tested. Both single and double layer 100×100-mm SmartPanels have been characterized for sensor sensitivities, actuator authority, surface displacement uniformity, and sensor-actuator coupling. Also, recent developments of injection molded PZT bender arrays for low-frequency air acoustic transducers will be presented. [Work supported by ONR and DARPA.]
Fractal dimension of sustained vowel productions in neurological dysphonias: An acoustic and electroglottographic analysis
Authors: Hertrich Ingo , Lutzenberger Werner , Spieker Sybille , Ackermann Hermann
Published: July 2002

In order to investigate whether nonlinear methods of signal analysis provide a measure of phonatory irregularities in neurogenic voice disorders, the present study computed the fractal dimension (D) both of the electroglottographic (EGG) and the acoustic signal of sustained vowel productions obtained from patients with Parkinson’s disease (PD) and cerebellar atrophy (CA). Compared with normal speakers, the female PD group as well as the male and female CA patients showed an increased dimension (D) of the EGG. The dimensional complexity of the acoustic signal largely depended on vowel type. Furthermore, the dimension of the acoustic signal was reduced in male PD patients as compared to the respective controls.
The acoustic radiation force in lossless fluids in Eulerian and Lagrangian coordinates
Authors: Beissner K.
Published: July 2002

A general theory of the (Langevin) acoustic radiation force in three-dimensional fields in lossless fluids in Eulerian and Lagrangian coordinates is given. It is based on Brillouin’s approach of an acoustic radiation stress identified in Eulerian coordinates with the negative time average of the momentum flux density and in Lagrangian coordinates with the time average of the Piola–Kirchhoff–Boussinesq stress. It is shown in comparison to other statements from the literature that these stresses are not in general identical but that in the linear-acoustics approximation, the difference between the results in the two representations vanishes if the radiation force acting on an object entirely surrounded by the sound-propagating fluid is considered. It is just this situation which is of experimental relevance.
Capped ceramic underwater sound projector: The “cymbal” transducer
Authors: Tressler James F. , Newnham Robert E. , Hughes W. Jack
Published: July 2002

A new type of transducer has been developed for use as a shallow-water sound projector at frequencies below 50 kHz. Dubbed the “cymbal,” it is similar to the more commonly known “moonie” and class V ring/shell flextensional designs. Prototype cymbal arrays 2 mm thick with a radiating area of 11.4 cm2 have been developed and calibrated. Two mounting schemes have been examined: unpotted (oil-filled) and potted in a 5-mm thick layer of stiff polyurethane. In both cases, a transmitting response comparable to the more widely used Tonpilz transducer (with an equivalent radiating area) is attainable. When tested under hydrostatic pressures, a standard cymbal configuration has been shown to withstand exposures of 2.5 MPa (which corresponds to 250 m of water depth) before failure.
The integration of nonsimultaneous frequency components into a single virtual pitch
Authors: Ciocca V. , Darwin C. J.
Published: July 2002

The integration of nonsimultaneous frequency components into a single virtual pitch was investigated by using a pitch matching task in which a mistuned 4th harmonic (mistuned component) produced pitch shifts in a harmonic series (12 equal-amplitude harmonics of a 155-Hz F0). In experiment 1, the mistuned component could either be simultaneous, stop as the target started (pre-target component), or start as the target stopped (post-target component). Pitch shifts produced by the pre-target components were significantly smaller than those obtained with simultaneous components; in the post-target condition, the size of pitch shifts did not decrease relative to the simultaneous condition. In experiment 2, a silent gap of 20, 40, 80, or 160 ms was introduced between the nonsimultaneous components and the target sound. In the pre-target condition, pitch shifts were reduced to zero for silent gaps of 80 ms or longer; by contrast, a gap of 160 ms was required to eliminate pitch shifts in the post-target condition. The third experiment tested the hypothesis that, when post-target components were presented, the processing of the pitch of the target tone started at the onset of the target, and ended at the gap duration at which pitch shifts decreased to zero. This hypothesis was confirmed by the finding that pitch shifts could not be observed when the target tone had a duration of 410 ms. Taken together, the results of these experiments show that nonsimultaneous components that occur after the onset of the target sound make a larger contribution to the virtual pitch of the target, and over a longer period, than components that precede the onset of the target sound.
Comparison of acoustic fields radiated from piezoceramic and piezocomposite focused radiators
Authors: Cathignol D. , Sapozhnikov O. A. , Theillère Y.
Published: July 2002

The acoustic field radiated from piezoelectric transducers is usually predicted supposing that the transducer vibrates in thickness mode. However, different reports have shown that not only thickness vibrations were excited, but also plate waves. These waves are responsible for discrepancy between the experimental acoustic fields and those predicted by the Rayleigh integral. It could be supposed that the plate waves are strongly attenuated in piezocomposite materials, as mechanical cross-talk between neighboring elements of the composite structure is fairly weak. A similar effect could be achieved in piezoceramic material by employing a heavy backing, which partially damps the plate waves. These opportunities of plate wave damping are investigated in the present paper. Three transducers are studied, which have identical geometrical characteristics, but are made from different materials. The plate waves in these transducers are indirectly compared by measuring corresponding ultrasound fields and comparing them with theoretically predicted field. It is shown that plate wave patterns are strongly material dependent and that it is only for piezocomposite sources (even when highly focused) that Rayleigh integral modeling can accurately predict the pressure field distribution.
Target detection by an echolocating harbor porpoise (Phocoena phocoena)
Authors: Kastelein R. A. , Au W. W. L. , Rippe H. T. , Schooneman N. M.
Published: July 2002

Two echolocation experiments are described. They were conducted on the same harbor porpoise housed in a sea pen, one year apart at Neeltje Jans, The Netherlands. The aims were to determine the target detection ability of an echolocating harbor porpoise, with the ultimate goal to predict the distance at which harbor porpoises can detect fishing nets. In experiment 1, the maximum distance at which the 3-year-old porpoise could detect a 7.62-cm diameter water-filled stainless-steel sphere by echolocation was determined psychophysically. The 50%-correct detection threshold was reached when the sphere was at a distance of 26 m from the porpoise’s rostrum. In experiment 2, conducted a year later, the maximum detection distance for a 5.08-cm water-filled stainless-steel sphere was 15.9 m. The target strengths of both targets were measured using simulated harbor porpoise echolocation signals and the results, coupled with transmission-loss calculations, indicated that the echo levels received by the porpoise with the targets at the threshold ranges in the two experiments were only 1.3 dB apart. Together with information on the target strengths of various fishing nets, the results of the present study can be used to predict the distance at which the nets can be detected by harbor porpoises.
Acoustic tomography of a coastal front in Haro Strait, British Columbia
Authors: Elisseeff P. , Schmidt H. , Johnson M. , Herold D. , Chapman N. R. , McDonald M. M.
Published: July 2002

An experiment validating the concept of acoustically focused oceanographic sampling (AFOS) was recently implemented in Haro Strait, British Columbia (Canada). Four 16-element vertical receiver arrays were moored around the location of a coastal front driven by estuarine and tidal forcing. Various signals were transmitted from array to array and from a moving source to the arrays over a period of five weeks. Tomographic signals were transmitted over a wide frequency band (150 Hz to 15 kHz). The novelty of the Haro Strait data set resides in its unusual tomographic features: ranges are short (less than 3 km), sound speed perturbations are small (2 to 3 m/s), and currents are relatively strong (3.5 kts). Light-bulb-generated wideband acoustic signals are used in this paper in conjunction with local nonacoustic measurements in order to image the three-dimensional sound speed and current fields within the water mass enclosed by the moored arrays. The combined use of integral and local data leads to a significant decrease of the field estimate uncertainty while maintaining a coverage of the area not achievable by nonacoustic means.
On singular surfaces in isotropic linear thermoelasticity with initial stress
Authors: Montanaro A.
Published: July 2002

It will be shown that the theory of a fundamental paper of Chadwick and Powdrill on singular surfaces, propagating in a linear thermoelastic body which is stress-free, homogeneous, and isotropic, also holds when the medium is subjected to hydrostatic initial stress provided the two characteristic speeds are suitably changed. The result is obtained by using Biot’s linearization of the constitutive law for the stress.
Displacement of migrating bowhead whales by sounds from seismic surveys in shallow waters of the Beaufort Sea
Authors: Richardson W. John , Miller Gary W. , Greene Charles R.
Published: July 2002

Seismic surveys for subsea oil deposits were conducted each summer, 1996–98, mainly in water <20 m deep. Airgun arrays were used, with 6–16 airguns and total volumes 560–1500 cu.in. Low-frequency sound pulses were created at intervals of 8–20 s. Effective source levels for horizontal propagation were lower than nominal source levels, but pulses were often detectable to 50+ km offshore. Westward autumn migration of bowhead whales near and offshore of the exploration area was monitored by aerial surveys flown daily, weather permitting, during the three seasons. Aerial survey data from days with and without airgun operations were compared. Most bowheads avoided the area within 20 km of the operating airguns; bowheads were common there on days without airgun operations. In 1998, numbers sighted 20–30 km away were also significantly reduced during airgun operations. Conversely, sighting rates just beyond the avoidance zone were higher on days with airgun operations. Broadband received levels of airgun pulses at 20 km were typically 120–130 dB re: 1 μPa (rms over pulse duration), lower than those previously demonstrated to cause avoidance by bowheads. Many migrating bowheads 20 to 50+ km offshore were exposed to weaker but presumably detectable pulses. [Work supported by Western Geophysical and BP Exploration (Alaska), Inc.]
Head wave data inversion for geoacoustic parameters of the ocean bottom off Vancouver Island
Authors: Godin Oleg A. , Chapman N. Ross , Laidlaw Mark C. A. , Hannay David E.
Published: July 2002

Head wave signals from small explosive charges have been analyzed to determine a geoacoustic profile for a shallow water site off the West coast of Vancouver Island. The experimental design contained a vertical aperture, provided by a vertical line array, and a synthetic horizontal aperture from shots at different ranges from the vertical line array. The simultaneous use of travel time and amplitude data for both apertures provided improved accuracy and vertical resolution of the estimated geoacoustic profile. Travel time vs range data from head waves from three distinct sub-bottom interfaces were used to measure compressional speeds in the layers below the interfaces and estimate the layers’ thicknesses. Spatial filtering of the vertical line array data was necessary to resolve the head wave arrival from the shallowest layers. Analysis of the interference structure of the head wave power spectra at the vertical line array provided the means to measure the travel time of the head wave from the deepest layer. In addition, the head wave power spectra were used to estimate the compressional wave attenuation, using a method based on the variation with range of the logarithmic derivative with respect to frequency of the head wave spectrum.