bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.
Authors: Mendoza L , Thieffry D , Alvarez-Buylla E R
Published: July 2002

MOTIVATION: A large number of molecular mechanisms at the basis of gene regulation have been described during the last few decades. It is now becoming possible to address questions dealing with both the structure and the dynamics of genetic regulatory networks, at least in the case of some of the best-characterized organisms. Most recent attempts to address these questions deal with microbial or animal model systems. In contrast, we analyze here a gene network involved in the control of the morphogenesis of flowers in a model plant, Arabidopsis thaliana. RESULTS: The genetic control of flower morphogenesis in Arabidopsis involves a large number of genes, of which 10 are considered here. The network topology has been derived from published genetic and molecular data, mainly relying on mRNA expression patterns under wild-type and mutant backgrounds. Using a 'generalized logical formalism', we provide a qualitative model and derive the parameter constraints accounting for the different patterns of gene expression found in the four floral organs of Arabidopsis (sepals, petals, stamens and carpels), plus a 'non-floral' state. This model also allows the simulation or the prediction of various mutant phenotypes. On the basis of our model analysis, we predict the existence of a sixth stable pattern of gene expression, yet to be characterized experimentally. Moreover, our dynamical analysis leads to the prediction of at least one more regulator of the gene LFY, likely to be involved in the transition from the non-flowering state to the flowering pathways. Finally, this work, together with other theoretical and experimental considerations, leads us to propose some general conclusions about the structure of gene networks controlling development.
TEXtopo: shaded membrane protein topology plots in LaTEX2ε
Authors: Beitz Eric
Published: July 2002

Summary: TEXtopo is a LaTEX2ε macro package for plotting topology data directly from PHD predictions or SwissProt database files in publication-ready quality. The plot can be shaded automatically to emphasize conserved residues or functional properties of the residue sidechains. The addition of rich decorations, such as labels, annotations and legends, is easily accomplished.

Availability: The TEXtopo macro package and a full on-line documentation are freely available at http://homepages.uni-tuebingen.de/beitz/

Contact: eric.beitz@uni-tuebingen.de
SPLASH: structural pattern localization analysis by sequential
histograms
Authors: Califano Andrea
Published: July 2002

Motivation: The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered.

Results: This paper introduces a deterministic pattern discovery algorithm, called Splash, which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence, can be discovered without significant loss in performances.

Splash is extremely efficient and embarrassingly parallel by nature. Large databases, such as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a typical workstation. Alternatively, a protein family or superfamily, with low overall homology, can be analyzed to discover common functional or structural signatures. Some examples of biologically interesting motifs discovered by Splash are reported for the histone I and for the G-Protein Coupled Receptor families. Due to its efficiency, Splash can be used to systematically and exhaustively identify conserved regions in protein family sets. These can then be used to build accurate and sensitive PSSM or HMM models for sequence analysis.

Availability: Splash is available to non-commercial research centers upon request, conditional on the signing of a test field agreement.

Contact: acal@us.ibm.com, Splash main page http://www.research.ibm.com/splash
Human MRE11 is inactivated in mismatch repair‐deficient cancers
Authors: Giannini Giuseppe , Ristori Elisabetta , Cerignoli Fabio , Rinaldi Christian , Zani Massimo , Viel Alessandra , Ottini Laura , Crescenzi Marco , Martinotti Stefano , Bignami Margherita , Frati Luigi , Screpanti Isabella , Gulino Alberto
Published: July 2002

Mutations of the ATM and NBS1 genes are responsible for the inherited Ataxia‐Telangiectasia and Nijmegen Breakage Syndrome, both of which are associated with a predisposition to cancer. A related syndrome, the Ataxia‐Telangiectasia‐like disorder, is due to mutations of the MRE11 gene. However, the role of this gene in cancer development has not been established. Here we describe an often homozygous mutation of the poly(T)11 repeat within human MRE11 intron 4 that leads to aberrant splicing, impairment of wild‐type MRE11 expression and generation of a truncated protein. This mutation is present in mismatch repair‐deficient, but not proficient, colorectal cancer cell lines and primary tumours and is associated with reduced expression of the MRE11–NBS1–RAD50 complex, an impaired S‐phase checkpoint and abrogation of MRE11 and NBS1 ionizing radiation‐induced nuclear foci. Our findings identify MRE11 as a novel and major target for inactivation in mismatch repair‐defective cells and suggest its impairment may contribute to the development of colorectal cancer.
A role for endogenous glucocorticoids in wound repair
Authors: Grose Richard , Werner Silke , Kessler Daniela , Tuckermann Jan , Huggel Katharina , Durka Silke , Reichardt Holger M , Werner Sabine
Published: July 2002

Exogenous glucocorticoids are known to inhibit wound repair, but the roles and mechanisms of action of endogenous glucocorticoids during the healing process are as yet unknown. Therefore, we wounded mice expressing a DNA‐binding‐defective mutant version of the glucocorticoid receptor (GRdim mice) and also analysed fibroblasts from these animals in vitro. We found a remarkably enlarged granulation tissue with a high fibroblast density in GRdim mice. This difference is likely to result from an increased migratory and proliferative capacity of GRdim fibroblasts and from elevated expression levels of soluble factors involved in granulation tissue formation in wounds of GRdim mice. In spite of the larger granulation tissue seen in early wounds, late wounds appeared normal, most likely due to an enhanced ability of GRdim fibroblasts to contract collagen. These results demonstrate an as yet unidentified role of endogenous glucocorticoids in the regulation of wound repair.
Stress‐mediated inhibition of the classical nuclear protein import pathway and nuclear accumulation of the small GTPase Gsp1p
Authors: Stochaj Ursula , Rassadi Roozbeh , Chiu James
Published: July 2002

Stress modifies all aspects of cellular physiology, including the targeting of macromolecules to the nucleus. To determine how distinct types of stress affect classical nuclear protein import, we followed the distribution of NLS‐GFP, a reporter protein containing a classical nuclear localization sequence (NLS) fused to green fluorescent protein GFP. Nuclear accumulation of NLS‐GFP requires import to be constitutively active; inhibition of import redistributes NLS‐GFP throughout the nucleus and cytoplasm. In the yeast Saccharomyces cerevisiae, starvation, heat shock, ethanol and hydrogen peroxide rapidly inhibited classical nuclear import, whereas osmotic stress had no effect. To define the mechanisms underlying the inhibition of classical nuclear import, we located soluble components of the nuclear transport apparatus. Failure to accumulate NLS‐GFP in the nucleus always correlated with a redistribution of the small GTPase Gsp1p. Whereas predominantly nuclear under normal conditions, Gsp1p equilibrated between nucleus and cytoplasm in cells exposed to starvation, heat, ethanol or hydrogen peroxide. Furthermore, analysis of yeast strains carrying mutations in different nuclear transport factors demonstrated a role for NTF2, PRP20 and MOG1 in establishing a Gsp1p gradient, as conditional lethal alleles of NTF2 and PRP20 or a deletion of MOG1 prevented Gsp1p nuclear accumulation. On the basis of these results, we now propose that certain types of stress release Gsp1p from its nuclear anchors, thereby promoting a collapse of the nucleocytoplasmic Gsp1p gradient and inhibiting classical nuclear protein import.
Following the invisible trail: kinematic analysis of mate-tracking in the copepod Temora longicornis
Authors: Weissburg Marc J. , Doall M. H. , Yen Jeannette
Published: July 2002

We have analysed the fine-scale kinematics of movement of male and female copepods,Temora longicornis, to resolve how these small animals find their mates. Location of the trail initially involves rapid random turning and high rates of directional change. Males subsequently increase their rate of movement as they follow the trail, and execute a regular pattern of counter turns in bothx,zandy,zplanes to stay near or within the central axis of the odour field. Pursuit behaviour of males is strongly associated with female swimming behaviour, suggesting that quantifiable variations in the structure of the odour signal released by females affects male tracking. The behavioural components of mate tracking inTemoraare very similar to those of other animals that employ chemically mediated orientation in their search for mates and food, and we conclude that maleTemorafind their mates using chemoperception. The kinematic analysis indicates both sequential and simultaneous taxis mechanisms are used byTemorato follow the odour signal. This, in turn, indicates that rather than responding to a diffuse plume, males are following a signal more accurately characterized as a chemical trail, and copepods appear to use mechanisms that are similar to those employed by trail-following terrestrial insects such as ants. WhileTemoraexpresses similar behaviours to those of a variety of chemosensory organisms, the ability to track a three-dimensional odour trail appears unique, and possibly depends on the persistence of fluid-borne odour signals created in low Reynolds number hydrodynamic regimes.
A computational theory of visual attention
Authors: Bundesen Claus
Published: July 2002

A computational theory of visual attention is presented. The basic theory (TVA) combines the biased–choice model for single–stimulus recognition with the fixed–capacity independent race model (FIRM) for selection from multi–element displays. TVA organizes a large body of experimental findings on performance in visual recognition and attention tasks. A recent development (CTVA) combines TVA with a theory of perceptual grouping by proximity. CTVA explains effects of perceptual grouping and spatial distance between items in multi–element displays. A new account of spatial focusing is proposed in this paper. The account provides a framework for understanding visual search as an interplay between serial and parallel processes.
The corneal surface of aquatic vertebrates: microstructures with optical and nutritional function?
Authors: Collin H. Barry , Collin Shaun P.
Published: July 2002

The anterior surface of the mammalian cornea plays an important role in maintaining a smooth optical interface and consequently a sharp retinal image. The smooth surface is produced by a tear film, which adheres to a variety of microprojections, which increase the cell surface area, improve the absorbance of oxygen and nutrients and aid in the movement of metabolic products across the outer cell membrane. However, little is known of the structural adaptations and tear film support provided in other vertebrates from different environments. Using field emission scanning electron microscopy, this study examines the density and surface structure of corneal epithelial cells in representative species of the classes Cephalaspidomorphi, Chondrichthyes, Osteichthyes, Amphibia, Reptilia, Aves and Mammalia, including some Marsupialia. Variations in cell density and the structure and occurrence of microholes, microridges, microplicae and microvilli are described with respect to the demands placed upon the cornea in different aquatic environments such as marine and freshwater. A progressive decrease in epithelial cell density occurs from marine (e.g. 29348 cells mm
−2
in the Dover sole
Microstomius pacificus
) to estuarine or freshwater (e.g. 5999 cells mm
−2
in the black bream
Acanthopagrus butcheri
) to terrestrial (e.g. 2126 cells mm
−2
in the Australian koala
Phascolarctos cinereus
) vertebrates, indicating the reduction in osmotic stress across the corneal surface. The microholes found in the Southern Hemisphere lampreys, namely the pouched lamprey (
Geotria australis
) and the shorthead lamprey (
Mordacia mordax
) represent openings for the release of mucus, which may protect the cornea from abrasion during their burrowing phase. Characteristic of marine teleosts, fingerprint–like patterns of corneal microridges are a ubiquitous feature, covering many types of sensory epithelia (including the olfactory epithelium and the oral mucosa). Like microplicae and microvilli, microridges stabilize the tear film to maintain a smooth optical surface and increase the surface area of the epithelium, assisting in diffusion and active transport. The clear interspecific differences in corneal surface structure suggest an adaptive plasticity in the composition and stabilization of the corneal tear film in various aquatic environments.
The thymus and central tolerance
Authors: Sprent Jonathan , Kishimoto Hidehiro
Published: July 2002

T–cell differentiation in the thymus generates a peripheral repertoire of mature T cells that mounts strong responses to foreign antigens but is largely unresponsive to self–antigens. This state of specific immunological tolerance to self–components involves both central and peripheral mechanisms. Here we review the process whereby many T cells with potential reactivity for self–antigens are eliminated in the thymus during early T–cell differentiation. This process of central tolerance (negative selection) reflects apoptosis and is a consequence of immature T cells receiving strong intracellular signalling through T–cell receptor (TCR) recognition of peptides bound to major histocompatibility complex (MHC) molecules. Central tolerance occurs mainly in the medullary region of the thymus and depends upon contact with peptide–MHC complexes expressed on bone–marrow–derived antigen–presenting cells (APCs); whether tolerance also occurs in the cortex is still controversial. Tolerance induction requires a combination of TCR ligation and co–stimulatory signals. Co–stimulation reflects interaction between complementary molecules on T cells and APCs and probably involves multiple molecules acting in consort, which may account for why deletion of individual molecules with known or potential co–stimulatory function has little or no effect on central tolerance. The range of self–antigens that induce central tolerance is considerable and, via low–level expression in the thymus, may also include tissue–specific antigens; central tolerance to these latter antigens, however, is likely to be limited to high–affinity T cells, leaving low–affinity cells to escape. Tolerance to alloantigens and the possibility of using central tolerance to promote acceptance of allografts are discussed.
Parental care and adaptive brood sex ratio manipulation in birds
Authors: Hasselquist D. , Kempenaers B.
Published: July 2002

Under many circumstances, it might be adaptive for parents to bias the investment in offspring in relation to sex. Recently developed molecular techniques that allow sex determination of newly hatched offspring have caused a surge in studies of avian sex allocation. Whether females bias the primary brood sex ratio in relation to factors such as environmental and parental quality is debated. Progress is hampered because the mechanisms for primary sex ratio manipulation are unknown. Moreover, publication bias against non–significant results may distort our view of adaptive sex ratio manipulation. Despite this, there is recent experimental evidence for adaptive brood sex ratio manipulation in birds. Parental care is a particularly likely candidate to affect the brood sex ratio because it can have strong direct effects on the fitness of both parents and their offspring. We investigate and make predictions of factors that can be important for adaptive brood sex ratio manipulation under different patterns of parental care. We encourage correlational studies based on sufficiently large datasets to ensure high statistical power, studies identifying and experimentally altering factors with sex–differential fitness effects that may cause brood sex ratio skew, and studies that experimentally manipulate brood sex ratio and investigate fitness effects.
Parentally biased favouritism: why should parents specialize in caring for different offspring?
Authors: Lessells C. M.
Published: July 2002

‘Parentally biased favouritism’ occurs when the two parents differentially care for individual offspring or kinds of offspring. Examples in birds include brood division and differential investment by the two parents in relation to the size or sex of the offspring. This paper uses mathematical models to investigate which ideas can, in theory, explain parentally biased favouritism. One previous explanation is that the parents differ in their cost of reproduction and that the parent who consequently invests least concentrates its care on the more valuable offspring. However, a mathematical model predicts the total care given by each parent and received by each offspring, not how much each parent cares for each offspring, and hence does not explain parentally biased favouritism. Parentally biased favouritism towards particular types of offspring can be explained by a difference between the parents in the benefits of caring for a given type of offspring or in the effort incurred in providing care to a given type of offspring, but then it is extreme, with at least one of the parents providing care to only one type of offspring. Parentally biased favouritism towards particular individual offspring (brood division) can be explained by parent–offspring conflict or sexual conflict.
Introduction
Authors: Balshine S. , Kempenaers B. , Székely T.
Published: July 2002

In the last decade, studies of parental care have rapidly proliferated. This increased interest in parental care has been stimulated by advances in three fields. First, the revolution in molecular biology has generated techniques that are increasingly used by behavioural scientists. Such techniques include DNA fingerprinting, which allows researchers to identify the genetic relatedness between putative parents and offspring, and molecular sex markers that allow researchers to determine the sex of offspring at an early stage before external differences have developed. In addition, gene sequencing, which is now fast and relatively inexpensive, has generated vast quantities of data, which are increasingly used to reveal evolutionary relationships that complement older morphology–based phylogenies. This has led to the second advance: several novel statistical techniques, which include parsimony and maximum–likelihood methods for phylogenetic reconstructions, have been developed to investigate past evolutionary events. These techniques provide new opportunities to examine the origins of parental care behaviour, the direction of parental care evolution and life history traits that may have influenced parental care evolution. Third, mathematical modelling of parental care has matured and now encompasses a range of game–theoretical models, some of which take account of state dependence and stochasticity. There has also been an effort to consider the feedback loops between parenting decisions and mating decisions. Some of these models were motivated by the growing consensus that parental care is one of the main battlefields for conflict between the sexes. New mathematical models have been essential in understanding aspects of these conflicts.
Emergence of influenza A viruses
Authors: Webby R. J. , Webster R. G.
Published: July 2002

Pandemic influenza in humans is a zoonotic disease caused by the transfer of influenza A viruses or virus gene segments from animal reservoirs. Influenza A viruses have been isolated from avian and mammalian hosts, although the primary reservoirs are the aquatic bird populations of the world. In the aquatic birds, influenza is asymptomatic, and the viruses are in evolutionary stasis. The aquatic bird viruses do not replicate well in humans, and these viruses need to reassort or adapt in an intermediate host before they emerge in human populations. Pigs can serve as a host for avian and human viruses and are logical candidates for the role of intermediate host. The transmission of avian H5N1 and H9N2 viruses directly to humans during the late 1990s showed that land-based poultry also can serve between aquatic birds and humans as intermediate hosts of influenza viruses. That these transmission events took place in Hong Kong and China adds further support to the hypothesis that Asia is an epicentre for influenza and stresses the importance of surveillance of pigs and live-bird markets in this area.
Genomic Microsatellites as Evolutionary Chronometers: A Test in Wild Cats
Authors: Driscoll Carlos A. , Menotti-Raymond Marilyn , Nelson George , Goldstein David , O'Brien Stephen J.
Published: July 2002

Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of historic population bottlenecks and founder effects. The observed rate of reconstruction of new alleles plus the growth in the breadth of microsatellite allele size (variance) was used here to develop genomic estimates of time intervals following historic founder events in cheetahs (12,000 yr ago), in North American pumas (10,000–17,000 yr ago), and in Asiatic lions of the Gir Forest (1000–4000 yr ago).

[Supplemental material available online at http://rex.nci.nih.gov/lgd/front_page.htm and athttp://www.genome.org.]
Hydrogen‐bonding classes in proteins and their contribution to the unfolding reaction
Authors: Ragone Raffaele
Published: July 2002

This paper proposes to assess hydrogen‐bonding contributions to the protein stability, using a set of model proteins for which both X‐ray structures and calorimetric unfolding data are known. Pertinent thermodynamic quantities are first estimated according to a recent model of protein energetics based on the dissolution of alkyl amides. Then it is shown that the overall free energy of hydrogen‐bond formation accounts for a hydrogen‐bonding propensity close to helix‐forming tendencies previously found for individual amino acids. This allows us to simulate the melting curve of an alanine‐rich helical 50‐mer with good precision. Thereafter, hydrogen‐bonding enthalpies and entropies are expressed as linear combinations of backbone‐backbone, backbone–side‐chain, side‐chain–backbone, and side‐chain–side‐chain donor‐acceptor contributions. On this basis, each of the four components shows a different free energy versus temperature trend. It appears that structural preference for side‐chain–side‐chain hydrogen bonding plays a major role in stabilizing proteins at elevated temperatures.
Examination of the folding of E. coli CspA through tryptophan substitutions
Authors: Vu Dung M. , Reid Katherine L. , Rodriguez Hector M. , Gregoret Lydia M.
Published: July 2002

Escherichia coli cold shock protein, CspA, folds very rapidly (time constant, τ = 4 msec) by an apparent two‐state mechanism. However, recent time‐resolved infrared (IR) temperature‐jump experiments indicate that the folding trajectory of CspA may be more complicated. The sole tryptophan of wild‐type CspA (Trp11), which is used to monitor the folding process by fluorescence spectroscopy, is located in an unusual aromatic cluster on the surface of CspA within the nucleic acid binding site. To gain a more global picture of the folding kinetics of CspA and to determine if there are any previously undetected intermediates, we have introduced a second tryptophan at three different surface locations in the protein. The three mutations did not significantly alter the tertiary structure of CspA, although two of the substitutions were found to be slightly stabilizing. Two‐state folding, as detected by stopped‐flow fluorescence spectroscopy, is preserved in all three mutants. These results indicate that the fast folding of CspA is driven by a concerted mechanism.
Monte Carlo‐aided dosimetry of a new high dose‐rate brachytherapy source
Authors: Daskalov Georgi M. , Löffler Edgar , Williamson Jeffrey F.
Published: July 2002

In this article we introduce a new high‐intensity source design for use in a recently reengineered microSelectron‐HDR remote afterloading device for high dose‐rate (HDR) brachytherapy. The maximum rigid length and outer diameter of the new source are reduced to 4.95 and 0.90 mm, respectively, compared to 5.50 and 1.10 mm for the previous source design introduced in 1991. In addition, a smaller diameter and more flexible steel cable are used, allowing the source cable to negotiate smaller diameter catheters or more tortuously curved catheters. Using Monte Carlo photon transport simulation, the complete two‐dimensional (2‐D) dose‐rate distribution is calculated over the 0.1–7 cm distance range and are presented both as conventional 2‐D Cartesian lookup tables and in the formalism recommended by the American Association of Physicists in Medicine Task Group 43 (TG‐43) Report. The dose distribution of this source is very similar to that of its predecessor, except near the source tip and in the shadow of the cable assembly, where differences of 5%–8% are apparent. The accuracy of various methods for extrapolating beyond the tabulated anisotropy functions to short distances is evaluated. It is demonstrated that linear extrapolation from the anisotropy functions defined by TG‐43 accurately (±2%) estimates dose rate at short and long distances lying outside the radial distance range of the original measured data from which the anisotropy and radial dose functions were derived. In contrast, the algorithm used on the vendor's planning system results in large calculation errors at distances less than 5 mm.
Modification of the University of Washington Neutron Radiotherapy Facility for optimization of neutron capture enhanced fast‐neutron therapy
Authors: Nigg David W. , Wemple Charles A. , Risler Ruedi , Hartwell John K. , Harker Yale D. , Laramore George E.
Published: July 2002

A modified neutron production target assembly has been developed to provide improved performance of the proton–cyclotron‐based neutron radiotherapy facility at the University of Washington for applications involving neutron capture enhanced fast‐neutron therapy. The new target produces a neutron beam that yields essentially the same fast‐neutron physical depth‐dose distribution as is produced by the current UW clinical system, but that also has an increased fraction of BNCT enhancement relative to the total therapeutic dose. The modified target is composed of a 5‐millimeter layer of beryllium, followed by a 2.5‐millimeter layer of tungsten, with a water‐cooled copper backing. Measurements of the free‐field neutron spectrum of the beam produced by the new target were performed using activation foils with a direct spectral unfolding technique. Water phantom measurements were performed using a tissue‐equivalent ion chamber to characterize the fast‐neutron depth‐dose curve and sodium activation in soda–lime glass beads to characterize the thermal‐neutron flux (and thus the expected neutron capture dose enhancement) as a function of depth. The results of the various measurements were quite consistent with expectations based on the design calculations for the modified target. The spectrum of the neutron beam produced by the new target features an enhanced low‐energy flux component relative to the spectrum of the beam produced by the standard UW target. However, it has essentially the same high‐energy neutron flux, with a reduced flux component in the mid‐range of the energy spectrum. As a result, the measured physical depth‐dose curve in a large water phantom has the same shape compared to the case of the standard UW clinical beam, but approximately twice the level of BNCT enhancement per unit background neutron dose at depths of clinical interest. In‐vivoclinical testing of BNCT‐enhanced fast‐neutron therapy for canine lung tumors using the new beam was recently initiated.
Particle size determination: An undergraduate lab in Mie scattering
Authors: Weiner I. , Rust M. , Donnelly T. D.
Published: July 2002

A technique for determining the size of microscopic spherical particles using light scattering is presented as an undergraduate physics lab. Scatterer size is determined from angular scattering distribution measurements of laser light scattered from a dilute suspension of latex spheres with diameters of 4.99±0.05 and 6.038±0.045 μm. Previous experiments of this type used approximate theoretical corrections and required the construction of specialized sample cells to minimize complicating effects. As a significant improvement to these, we generate angular scattering distributions from Mie theory and, using an accurate numerical procedure, correct these distributions for Snell’s law and foreshortening effects. Scatterer size is then determined using a fast, robust fitting algorithm to compare these corrected angular scattering distributions to measured angular scattering distributions. We fit the scatter from a solution of 6.04-μm-diam spheres to spheres of 5.95±0.11 μm diameter, and that from a solution of 4.99-μm spheres to 4.85±0.15 μm. Additionally, scattering data for a 2:1 mixture of spheres of diameters 4.99 and 6.04 μm are taken, and after numerical adjustment for Snell’s law and foreshortening effects, good agreement with theory is obtained.
An experimental observation of Faraday’s law of induction
Authors: Kingman Robert , Rowland S. Clark , Popescu Sabin
Published: July 2002

A small neodymium magnet moves with constant velocity through a coil, and the voltage induced is recorded with a computer interface. The observed voltage is compared to that predicted by simple calculations of magnetic flux using spherical polar coordinates. The close agreement between predicted and observed values combined with the experience gained in modeling the magnetic dipole field make this a very good experiment for the undergraduate student.
Frequency selectivity as a function of level and frequency measured with uniformly exciting notched noise
Authors: Glasberg Brian R. , Moore Brian C. J.
Published: July 2002

Thresholds for detecting sinusoidal signals were measured as a function of the spectral width of a notch in a noise masker. The notch was positioned both symmetrically and asymmetrically around the signal frequency. The noise was designed to create equal excitation per ERB within its passbands (uniformly exciting noise), after allowing for the transfer function of the headphone and the middle ear. For a signal frequency of 250 Hz, the level per ERB ranged from 35 to 80 dB in 15-dB steps. For signal frequencies of 500, 1000, 2000, and 4000 Hz, the level per ERB ranged from 40 to 70 dB per ERB in 15-dB steps. Auditory filter shapes were derived from the data by modeling the auditory filter as the sum of a sharply tuned tip filter and a broader tail filter. The gain of the tip filter was assumed to be a function of level. The shape of the tip filter and the gain and shape of the tail filter were assumed to be level independent. The data for all levels were fitted simultaneously. The data were fitted best when the gain of the tip filter was assumed to be a function of the signal level (as opposed to the masker level per ERB). The filter shapes showed a level dependence that qualitatively resembled the level dependence of filtering on the basilar membrane. The maximum gain of the tip filter tended to increase with increasing center frequency up to 1 kHz, but to remain roughly constant for higher frequencies.
Investigation of the relationship among three common measures of precedence: Fusion, localization dominance, and discrimination suppression
Authors: Litovsky R. Y. , Shinn-Cunningham B. G.
Published: July 2002

Listeners have a remarkable ability to localize and identify sound sources in reverberant environments. The term “precedence effect” (PE; also known as the “Haas effect,” “law of the first wavefront,” and “echo suppression”) refers to a group of auditory phenomena that is thought to be related to this ability. Traditionally, three measures have been used to quantify the PE: (1) Fusion: at short delays (1–5 ms for clicks) the lead and lag perceptually fuse into one auditory event; (2) Localization dominance: the perceived location of the leading source dominates that of the lagging source; and (3) Discrimination suppression: at short delays, changes in the location or interaural parameters of the lag are difficult to discriminate compared with changes in characteristics of the lead. Little is known about the relation among these aspects of the PE, since they are rarely studied in the same listeners. In the present study, extensive measurements of these phenomena were made for six normal-hearing listeners using 1-ms noise bursts. The results suggest that, for clicks, fusion lasts 1–5 ms; by 5 ms most listeners hear two sounds on a majority of trials. However, localization dominance and discrimination suppression remain potent for delays of 10 ms or longer. Results are consistent with a simple model in which information from the lead and lag interacts perceptually and in which the strength of this interaction decreases with spatiotemporal separation of the lead and lag. At short delays, lead and lag both contribute to spatial perception, but the lead dominates (to the extent that only one position is ever heard). At the longest delays tested, two distinct sounds are perceived (as measured in a fusion task), but they are not always heard at independent spatial locations (as measured in a localization dominance task). These results suggest that directional cues from the lag are not necessarily salient for all conditions in which the lag is subjectively heard as a separate event.
Determination of Lamb mode eigenvalues
Authors: Pagneux V. , Maurel A.
Published: July 2002

An original method is presented to determine the complex Lamb wave spectrum by using a numerical spectral method applied to the elasticity equations. This method presents the advantage to directly determine complex wave numbers for a given frequency via a classical matricial eigenvalue problem, and allows the wave numbers to be determined at relatively high frequencies (i.e., corresponding to many propagating modes). It does not need initial guess values for the wave numbers, contrary to the usual method of root finding of the Rayleigh–Lamb frequency equations (dispersion relation) in the complex plane. Results are presented and the method is discussed.
The intensity-difference limen for Gaussian-enveloped stimuli as a function of level: Tones and broadband noise
Authors: Nizami Lance , Reimer Jason F. , Jesteadt Walt
Published: July 2002

Van Schijndel et al. [J. Acoust. Soc. Am. 105, 3425–3435 (1999)] have proposed that the internal excitation evoked by an auditory stimulus is segmented into “windows” according to the stimulus spectrum and stimulus length. This “multiple looks” model accounts for the mid-duration hump they observed in plots of intensity-difference limens (DLs) versus pip duration for Gaussian-shaped 1- and 4-kHz tones, an effect replicated by Baer et al. [J. Acoust. Soc. Am. 106, 1907–1916 (1999)]. However, van Schijndel et al. and Baer et al. used few levels. A greater number of levels were used by Nizami (1999) for Gaussian-shaped 2-kHz tone-pips whose equivalent rectangular duration (D) was 1.25 ms. The DLs show the mid-level hump known for clicks [Raab and Taub, J. Acoust. Soc. Am. 46, 965–968 (1969)]. At some duration this pattern must become the “near-miss to Weber’s law.” To determine this duration, as well as the level-dependence of the mid-duration hump, DLs were established for Gaussian-shaped 2-kHz tone-pips of D=1.25, 2.51, and 10.03 ms at levels of 30–90 dB SPL. The across-subject average DLs for the tone-pips rise up at mid-levels for D=1.25 and D=2.51 ms. The DLs for D=2.51 ms are larger, creating the mid-duration hump. At all durations, the new DLs are smaller at high levels than at low levels, consistent with the near-miss to Weber’s law. DLs were also obtained here for Gaussian-shaped broadband-noise pips of D=0.63, 1.25, 2.51, 5.02, and 10.03 ms. The DLs for the noise-pip show a mid-level hump for all pip durations. The noise-pip DLs decrease as the pip lengthens, such that the plot of DL versus log duration shows a linear decline, with no mid-duration hump. Analysis of variance reveals that the mid-level hump coexists with the classical patterns of level-dependence, perhaps reflecting the existence of two level-encoding mechanisms, one that depends on firing-rates counted over single neurons and which is responsible for the classical patterns, and one that depends on the initial coordinated burst of neuronal spikes caused by rapid ramping, and which presumably causes the mid-level hump.
Active control of axial-flow fan noise
Authors: Lauchle Gerald C. , MacGillivray John R. , Swanson David C.
Published: July 2002

Discrete-frequency axial-flow fan noise reduction using active noise control is described. The unique aspect of the current research is the use of the fan itself as the antinoise source in the active noise control scheme. This is achieved by driving the entire fan unit axially with an electrodynamic shaker which mechanically couples the solid surfaces of the fan to the acoustic medium. The fan unit is thus transformed into a crude loudspeaker. A near-field microphone serves as an error sensor, where transfer function measurements between the electrical input to the shaker and the electrical output of the microphone are found to be reasonably free of phase distortions and linear. A feedforward algorithm utilizing the output of a tachometer as a reference signal is used. The experimental apparatus is composed of a baffled fan unit in a free field. A small cylindrical flow obstruction is placed on the inlet side of the fan to enhance noise emissions at the blade-pass frequency and harmonics. The experiment successfully demonstrates the concept of active control of tonal fan noise using a shaken fan as the cancellation source. For the fan operating in a planar baffle, the fundamental blade-passage frequency sound-pressure level at the location of the error sensor is reduced by 20 dB, while the second and third harmonic levels are reduced by 15 and 8 dB, respectively. Placing a cabinet enclosure over the baffled fan did not affect these results significantly, and free-field sound power measurements indicate similar level reductions with the active control in operation.
Rational square-root approximations for parabolic equation algorithms
Authors: Milinazzo Fausto A. , Zala Cedric A. , Brooke Gary H.
Published: July 2002

In this article, stable Padé approximations to the function 1+z are derived by choosing a branch cut in the negative half-plane. The Padé coefficients are complex and may be derived analytically to arbitrary order from the corresponding real coefficients associated with the principal branch defined by z<−1, I(z)=0 [I(z) denotes the imaginary part of z]. The characteristics of the corresponding square-root approximation are illustrated for various segments of the complex plane. In particular, for waveguide problems it is shown that an increasingly accurate representation may be obtained of both the evanescent part of the mode spectrum for the acoustic case and the complex mode spectrum for the elastic case. An elastic parabolic equation algorithm is used to illustrate the application of the new Padé approximations to a realistic ocean environment, including elasticity in the ocean bottom.
Estimating the compressional and shear wave speeds of a shallow water seabed from the vertical coherence of ambient noise in the water column
Authors: Carbone Nicholas M. , Deane Grant B. , Buckingham Michael J.
Published: July 2002

Due to the multiple bottom reflections encountered in shallow water environments, the spatial structure of the ambient noise field depends strongly on the geoacoustic properties of the seabed, which are invariant over time scales associated with most measurements. The vertical directionality and coherence are relatively stable features of the noise that are determined primarily by the seabed, rather than temporal variations in the surface source distribution. In this paper, estimates of the compressional and shear wave speeds are determined from ambient noise measurements over shear supporting seabeds. Using a model of wind-generated noise over an elastic seabed, it is shown that the noise is sensitive to the compressional and shear wave speeds in the upper few meters of seabed. An inversion procedure is developed based on a matched field of the complex, broadband coherence from a single hydrophone pair. Using ambient noise data from two shear supporting sites, compressional and shear wave estimates are obtained that are in good agreement with independent surveys. For one site where the bedrock is exposed, a half-space model of the seabed yields reasonable estimates of the seabed parameters. For the other site, the presence of a thin sedimentary layer results in a low estimate from the half-space model. However, when the layer is included in the model, the estimates of the underlying bedrock are in good agreement with a seismic survey.
Computed spectral and temporal emissions from a sonoluminescing bubble
Authors: Moss William C. , Young David A.
Published: July 2002

Although the mechanism of emission in single bubble sonoluminescence (SBSL) has still not been identified conclusively, the ‘‘plasma’’ model [Moss et al., Science 276, 1398–1401 (1997)] appears to explain more features of SBSL than other models. Recent measurements of the light pulses emitted by SBSL [Gompf et al., Phys. Rev. Lett. 79, 1405–1408 (1997)] show that the pulse widths may be longer than the original UCLA measurements and can vary between 60 and 250 ps. These new results provide information for improving the modeling of the energy loss and emission mechanisms in the plasma model. In particular, the plasma can be described more accurately as a ‘‘strongly coupled plasma’’ (a plasma with a small Debye screening length). The main difference between the strongly coupled plasma and our earlier plasma model is that there is less energy loss by electron thermal conduction in the strongly coupled plasma, which gives rise to longer calculated pulse widths that are consistent with the new experimental data. [This work was performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.]
Nonlinear, low-frequency sound generation in a bubble layer: Theory and laboratory experiment
Authors: Ostrovsky Lev A. , Sutin Alexander M. , Soustova Irina A. , Matveyev Alexander I. , Potapov Andrey I.
Published: July 2002

The difference-frequency sound generation as a result of interaction of two high-frequency harmonic waves in a bubble layer in water is investigated both theoretically and experimentally. Because the sound speed in the layer is less than that outside, the layer has resonance properties. As was shown before, this can considerably increase the efficiency of the nonlinear frequency transformation. However, unlike the cases considered before, the layer resonance is practically achievable only at the low (difference) frequency, whereas the high-frequency signal (pump) resonates at individual bubbles and then it strongly dissipates. Here the results of an experiment with a bubble layer with a thickness of about 10 cm in an anechoic tank are presented. One of the incident (primary) wave frequencies was 60 kHz, whereas the other could be varied, thus providing the low-frequency signal in the range of 0.8–14.8 kHz. Due to the first-mode layer resonance, this secondary signal had a pronounced maximum at a frequency of 2.4 kHz. The high attenuation of pump waves was due to resonant bubbles. A theory which agrees with the experimental results reasonably well, is developed for this type of interaction.
A novel microelectromechanical system (MEMS) design for an underwater acoustic field sensor
Authors: Bifano Thomas G. , Cleveland Robin O. , Compton Debora A. , Pierce Allan D.
Published: July 2002

A concept for underwater acoustic imaging exploits current technology for constructing MEMS devices from silicon wafers. Anisotropic etching creates frustum-shaped (pyramids with tops cut off) holes in a wafer chip; the bonding of two such chips creates double frustum-shaped holes, each analogous to an hour glass. The front side of each hole is a tapered duct with a baffled open end. The acoustic disturbance generated by an incident plane wave magnifies as the flow converges toward the waist. The back half of the double frustum is covered by a third silicon layer and acts as a Helmholtz resonator, the waist being the neck. The manufacturing process places a thin membrane across the waist which oscillates sychronously with the acoustically induced fluid motion. An appropriate design can achieve fluid velocities at the neck much larger than what would be associated with the incident acoustic wave in free space, and exploratory experiments confirm this. The oscillating membrane is sensed by an optical system, and theoretical extrapolation of the measured displacement amplitude yields a measurement of the amplitude of the incident acoustic wave. [Work supported by Indian Head Divison, Naval Surface Warfare Center, as part of the DARPA Sonoelectronics Program.]