bluuebunny/crossref_metadata_2025 huggingface dataset:
A relational schema for both array-based and SAGE gene

expression experiments
Authors: Stoeckert C. , Pizarro A. , Manduchi E. , Gibson M. , Brunk B. , Crabtree J. , Schug J. , Shen-Orr S. , Overton G. C.
Published: July 2002

Motivation and Results: A relational schema is described for capturing highly parallel gene expression experiments using different technologies. This schema grew out of efforts to build a database for collaborators working on different biological systems and using different types of platforms in their gene expression experiments as well as different types of image quantification software. The tables are conceptually organized into three categories of information: Platform, Experiment (which includes image scanning and quantification), and Data. The strengths of the schema are: (i) integrating information on array elements using a gene index; (ii) describing samples using ontologies; (iii) reducing an experiment to a single RNA source for precise descriptions yet not losing the relationships between experiments done at the same time or for the same project; and (iv) maintaining both raw and processed (e.g. cleansed and normalized) data and recording how the data is processed. The result is a novel schema, which can hold both array and non-array data, is extensible for detailed experimental descriptions that are precise and consistent, and allows for meaningful comparisons of genes between experiments.

Availability: The schema is available at http://www.cbil.upenn.edu/cgi-bin/RAD2/schemaBrowserRAD.pl.

Contact: stoeckrt@pcbi.upenn.edu

* To whom correspondence should be addressed.

2 Present address: Department of Molecular Cell Biology, Weizmann Institute of Science, Israel.
TreeGeneBrowser: phylogenetic data mining of gene sequences
from public databases
Authors: Jakobsen Ingrid B. , Saleeba Jennifer A. , Poidinger Michael , Littlejohn Timothy G.
Published: July 2002

Motivation: Sequence databases represent an enormous resource of phylogenetic information, but there is a lack of tools for accessing that information in order to assess the amount of evolutionary information in these databases that may be suitable for phylogenetic reconstruction and for identifying areas of the taxonomy that are under-represented for specific gene sequences.

Results: We have developed TreeGeneBrowser which allows inspection and evaluation of gene sequence data for phylogenetic reconstruction. This program improves the efficiency of identification of genes that may be useful for particular phylogenetic studies and identifies taxa and taxonomic branches that are under-represented in sequence databases.

Availability: The software described here is available for download from ftp://ftp.angis.org.au/pub/TreeGeneBrowser.

Contact: tim@entigen.com

* To whom correspondence should be addressed.
Visualization of expression clusters using Sammon’s
non-linear mapping
Authors: Ewing Rob M. , Cherry J. Michael
Published: July 2002

Summary: A method of exploratory analysis and visualization of multi-dimensional gene expression data using Sammon’s Non-Linear Mapping (NLM) is presented.

Availability: Scripts are available from the authors.

Contact: ewing@genome.stanford.edu

* To whom correspondence should be addressed.
Physics-based gene identification: proof of concept for
Plasmodium falciparum
Authors: Yeramian Edouard , Bonnefoy Serge , Langsley Gordon
Published: July 2002

The ab initio prediction of new genes in eukaryotic genomes represents a difficult task, notably for the identification of complex split genes. A Physics-Based Gene Identification (PBGI) method was formulated recently (Yeramian, Gene, 255, 139–150, 151–168, 2000a,b) to address this problem, taking as a model the Plasmodium falciparum genome. Here, the predictive power of this method is put under experimental test for this genome. The presented results demonstrate the usefulness of the PBGI as a gene-identification tool for P. falciparum, notably for the discovery of new genes with no homology to known genes. Perspectives opened by this new method for other eukaryotic genomes are also mentioned.
ZTR: a new format for DNA sequence trace data
Authors: Bonfield James K. , Staden Rodger
Published: July 2002

Motivation: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth.

Results: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive.

Availability: Source code is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/io_lib.tar.gz. A complete format description can be found at http://www.mrc-lmb.cam.ac.uk/pubseq/ztr.html. Test data is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/test_data.

Contact: jkb@mrc-lmb.cam.ac.uk

* To whom correspondence should be addressed.
Improved database searches for orthologous sequences by
conditioning on outgroup sequences
Authors: Cotter Philip J. , Caffrey Daniel R. , Shields Denis C.
Published: July 2002

Motivation: Searches of biological sequence databases are usually focussed on distinguishing significant from random matches. However, the increasing abundance of related sequences on databases present a second challenge: to distinguish the evolutionarily most closely related sequences (often orthologues) from more distantly related homologues. This is particularly important when searching a database of partial sequences, where short orthologous sequences from a non-conserved region will score much more poorly than non-orthologous (outgroup) sequences from a conserved region.

Results: Such inferences are shown to be improved by conditioning the search results on the scores of an outgroup sequence. The log-odds score for each target sequence identified on the database has the log-odds score of the outgroup sequence subtracted from it. A test group of Caenorhabditis elegans kinase sequences and their identified C.elegans outgroups were searched against a test database of human Expressed Sequence Tag (EST) sequences, where the sets of true target sequences were known in advance. The outgroup conditioned method was shown to identify 58% more true positives ahead of the first false positive, compared to the straightforward search without an outgroup. A test dataset of 151 proteins drawn from the C.elegans genome, where the putative ‘outgroup’ was assigned automatically, similarly found 50% more true positives using outgroup conditioning. Thus, outgroup conditioning provides a means to improve the results of database searching with little increase in the search computation time.

Availability: Perl scripts for the Outgroup Conditioned Score (OCS) method are available without charge for non-profit academic use from http://www.bioinf.org/vibe/software/OCS/. Scripts have been optimized for Linux or OSF with a Perl v5 interpreter.

Contact: dshields@rcsi.ie.

* Non-standard abbreviations: OCS: Outgroup Conditioned Score, HOCS Heuristic Outgroup Conditioned Score, HOCP: Heuristic Outgroup Conditioned P-value ratio, EST: Expressed Sequence Tag.

1 To whom correspondence should be addressed.
Assembly of fingerprint contigs: parallelized FPC
Authors: Ness S. R. , Terpstra W. , Krzywinski M. , Marra M. A. , Jones S. J. M.
Published: July 2002

Summary: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest ‘fingerprints’ of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of ‘parallelized FPC’ has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints.

Availability: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.

Contact: fpc@bcgsc.bc.ca

* To whom correspondence should be addressed.
Genome‐wide analysis of mRNAs targeted to yeast mitochondria
Authors: Marc Philippe , Margeot Antoine , Devaux Frédéric , Blugeon Corinne , Corral‐Debrinski Marisol , Jacq Claude
Published: July 2002

It is agreed that nuclear‐encoded mitochondrial proteins are post‐translationally targeted to mitochondria, even if, in some cases, a co‐translational phase can assist the import of precursor proteins. We used yeast DNA microarrays to analyse the mRNA populations associated with free and mitochondrion‐bound polysomes. As expected, many mRNAs, known to encode mitochondrial proteins, are localized to free cytoplasmic polysomes, but many are localized to mitochondrion‐bound polysomes. Furthermore, the 3′‐UTR of six randomly chosen mitochondrion‐bound mRNAs contains sufficient information to target, in vivo, non‐translatable RNA to the vicinity of mitochondria. Interestingly, genes producing mRNAs that are targeted to mitochondria are mainly of ancient bacterial origin, whereas those producing mRNAs that are translated in the cytoplasm are mainly of eukaryotic origin. These observations, which support the recent hypotheses concerning the dual origin of the mitochondrial proteome, provide new insights into the biogenesis of mitochondria.
Brief communication. High levels of conservation at microsatellite loci among ictalurid catfishes
Authors: Liu Z , Tan G , Kucuktas H , Li P , Karsi A , Yant DR , Dunham RA
Published: July 2002

The potential of microsatellite sequences as genetic markers in channel catfish (Ictalurus punctatus) was investigated with respect to their variability, inheritance, and usefulness in related species. Six small insert genomic DNA libraries enriched for six families of microsatellites of channel catfish were constructed. We describe here the isolation, characterization, and PCR amplification of 32 microsatellites from channel catfish. The flanking primer regions of microsatellite loci were highly conserved between channel catfish and blue catfish (I. furcatus). Of the 32 loci, 29 were amplified from blue catfish using primers designed from channel catfish, indicating conservation of primer binding sequences. Most of the amplified alleles from channel catfish and blue catfish were polymorphic. White catfish (Ameiurus catus) and flathead catfish (Pylodictus olivaris) loci were also amplified. The microsatellite markers are highly polymorphic for all catfish species tested and are inherited as codominant markers. They should be highly useful for construction of genetic linkage maps of catfish and for marker-assisted selection.
Allergen mimotopes for 3‐dimensional epitope search and induction of antibodies inhibiting human IgE
Authors: Ganglberger Erika , Grunberger Kurt , Guntaka Ramareddy V. , Sponer Barbara , Breiteneder Heimo , Boltz‐Nitulescu George , Scheiner Otto , Jensenjarolim Erika
Published: July 2002

There is no definite information available on the structural characteristics of IgE binding epitopes on allergenic molecules, although it is widely accepted that most of them are conformational. In the current study we aimed to characterize the IgE epitope of Bet v 1, the major birch pollen allergen, by the application of phage display peptide libraries. We purified IgE specific for Bet v 1 from allergic patients’ sera to select mimotopes representing artificial IgE epitopes by biopanning of phage libraries. By linear alignment, it was not possible to attribute mimotope sequences to the primary structure of Bet v 1. We developed a computeraided, 3‐dimensional coarse‐grained epitope search. The 3‐dimensional search, followed by statistical analysis, revealed an exposed area on the Bet v 1 molecule (located between residues 9–22 and 104–123) as the IgE binding structure. The IgE epitope was located at a 30 Å distance from a previously described IgG epitope and the respective mimotope, designated Bet mim E. Such mimotopes could potentially be used for the induction of IgG capable of interfering with the IgE/allergen interaction. To test this hypothesis, we immunized BALB/c mice with the phage‐displayed Bet mim E. Immunizations resulted in the induction of Bet v 1‐specific IgG, which was able to block the IgE binding to Bet v 1 in vitro. Based on these observations, we propose that immunotherapy with IgE mimotopes generated by biopannings result in formation of blocking IgG. We conclude that mimotope immunotherapy may represent a new and promising concept for treatment of type I allergic disease.—Ganglberger, E., Grimberger, K., Sponer, B., Radauer, C., Breiteneder, H., Boltz‐Nitulescu, G., Scheiner, O., Jensen‐Jarolim, E. Allergen mimotopes for 3‐dimensional epitope search and induction of antibodies inhibiting human IgE. FASEB J. 14, 2177–2184 (2000)
The eyes of deep–sea fishes and the changing nature of visual scenes with depth
Authors: Warrant Eric
Published: July 2002

The visual scenes viewed by ocean animals change dramatically with depth. In the brighter epipelagic depths, daylight provides an extended field of illumination. In mesopelagic depths down to 1000 m the visual scene is semi–extended, with the downwelling daylight providing increasingly dim extended illumination with depth. In contrast, greater depths increase the prominence of point–source bioluminescent flashes. In bathypelagic depths (below 1000 m) daylight no longer penetrates, and the visual scene consists exclusively of point–source bioluminescent flashes. In this paper, I show that the eyes of fishes match this change from extended to point–source illumination, becoming increasingly foveate and spatially acute with increasing depth. A sharp fovea is optimal for localizing point sources. Quite contrary to their reputation as ‘degenerate’ and ‘regressed’, I show here that the remarkably prominent foveae and relatively large pupils of bathypelagic fishes give them excellent perception and localization of bioluminescent flashes up to a few tens of metres distant. In a world with almost no food, where fishes are weak and must swim very slowly, this range of detection (and interception) is energetically realistic, with distances greater than this physically beyond range. Larger and more sensitive eyes would give bathypelagic fishes little more than the useless ability to see flashes beyond reach.
In goldfish the discriminative ability for odours persists after reduction of the olfactory epithelium, and rapidly returns after olfactory nerve axotomy and crossing bulbs
Authors: Zippel Hans Peter
Published: July 2002

Goldfish are ideal vertebrates for the study of regeneration within the peripheral and the central olfactory system. The present behavioural investigations studied the effects of bilateral lesions on the animals' ability to qualitatively discriminate two amino acids (107
-6
M) and their performance in two more difficult tasks: (i) rewarded amino acid applied in a lower concentration, and (ii) rewarded stimulus contaminated. A 50 and 85% reduction of the olfactory epithelium resulted in no recordable behavioural deficit. After axotomy of olfactory nerves and lateral olfactory tractotomy, fishes were anosmic for seven to ten days. Following replacement of sensory cells in the epithelium, and after regeneration of olfactory tract fibres a full functional recovery, i.e. a highly specific regeneration, was recorded. After three surgical modifications of the olfactory bulbs' position, (i) crossing olfactory tracts and bulbs, (ii) crossing tracts and turning bulbs, and (iii) turning bulbs upside down, a full functional recovery was recorded for amino-acid discrimination in a similar concentration. A permanent, and similar slight deficit was, however, found during application of different concentrations, and of contaminated stimuli when medial lateral halves of the bulb were in ‘incorrect’ position (i) and (iii), or olfactory bulbs were positioned in the vicinity of the contralateral epithelium (i) and (ii).
Dynamic publication model for neurophysiology databases
Authors: Gardner Daniel , Abato Michael , Knuth Kevin H. , DeBellis Robert , Erde Steven M.
Published: July 2002

We have implemented a pair of database projects, one serving cortical electrophysiology and the other invertebrate neurones and recordings. The design for each combines aspects of two proven schemes for information interchange. The journal article metaphor determined the type, scope, organization and quantity of data to comprise each submission. Sequence databases encouraged intuitive tools for data viewing, capture, and direct submission by authors. Neurophysiology required transcending these models with new datatypes. Time–series, histogram and bivariate datatypes, including illustration–like wrappers, were selected by their utility to the community of investigators. As interpretation of neurophysiological recordings depends on context supplied by metadata attributes, searches are via visual interfaces to sets of controlled–vocabulary metadata trees. Neurones, for example, can be specified by metadata describing functional and anatomical characteristics. Permanence is advanced by data model and data formats largely independent of contemporary technology or implementation, including Java and the XML standard. All user tools, including dynamic data viewers that serve as a virtual oscilloscope, are Java–based, free, multiplatform, and distributed by our application servers to any contemporary networked computer. Copyright is retained by submitters; viewer displays are dynamic and do not violate copyright of related journal figures. Panels of neurophysiologists view and test schemas and tools, enhancing community support.
Flowering in time: genes controlling photoperiodic flowering inArabidopsis
Authors: Putterill Jo
Published: July 2002

Successful sexual reproduction in plants relies upon the strict coordination of flowering time with favourable seasons of the year. One of the most important seasonal cues for the model plantArabidopsis thaliana(Arabidopsis) is day length. Genes influencing flowering time inArabidopsishave been isolated, some of which are involved in the perception and signalling of day length. This review discusses recent progress that has been made in understanding howArabidopsisintegrates environmental and internal signals to ensure a sharp transition to flowering and new insights on the role of the circadian clock in controlling the expression of genes that promote flowering in response to day length.
Functional genomics of pathogenic bacteria
Authors: Moxon E. R. , Hood D. W. , Saunders N. J. , Schweda E. K. H. , Richards J. C.
Published: July 2002

Microbial diseases remain the commonest cause of global mortality and morbidity. Automated–DNA sequencing has revolutionized the investigation of pathogenic microbes by making the immense fund of information contained in their genomes available at reasonable cost. The challenge is how this information can be used to increase current understanding of the biology of commensal and virulence behaviour of pathogens with particular emphasis on
in vivo
function and novel approaches to prevention. One example of the application of whole–genome–sequence information is afforded by investigations of the pathogenic role of
Haemophilus influenzae
lipopolysaccharide and its candidacy as a vaccine.
Circularly permuted proteins in the protein structure database
Authors: Jung Jongsun , Lee Byungkook
Published: July 2002

Some proteins are homologous to others after their sequence is circularly permuted. A few such proteins have been recognized, mainly by sequence comparison, but also by comparing their three‐dimensional structures. Here we report the result of a systematic search for all protein pairs in the SCOP 90% id domain database that become structurally superimposable when the sequence of one of the pairs is circularly permuted. Using a reasonable set of criteria, we find that 47% of all protein domains are superimposable to at least one other protein domain in the database after their sequence is circularly permuted. Many of these are symmetric proteins, which superimpose to another protein both with and without a circular permutation of the sequence. However, 412 of the total 3035 domains are nonsymmetric, and these become structurally superimposable to another protein only after a circular permutation of the sequence. These include most known and many previously undetected circularly permuted proteins with remote homology.
The CATH extended protein‐family database: Providing structural annotations for genome sequences
Authors: Pearl Frances M.G. , Lee David , Bray James E. , Buchan Daniel W.A. , Shepherd Adrian J. , Orengo Christine A.
Published: July 2002

An automatic sequence search and analysis protocol (DomainFinder) based on PSI‐BLAST and IMPALA, and using conservative thresholds, has been developed for reliably integrating gene sequences from GenBank into their respective structural families within the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath_new). DomainFinder assigns a new gene sequence to a CATH homologous superfamily provided that PSI‐BLAST identifies a clear relationship to at least one other Protein Data Bank sequence within that superfamily. This has resulted in an expansion of the CATH protein family database (CATH‐PFDB v1.6) from 19,563 domain structures to 176,597 domain sequences. A further 50,000 putative homologous relationships can be identified using less stringent cut‐offs and these relationships are maintained within neighbour tables in the CATH Oracle database, pending further evidence of their suggested evolutionary relationship. Analysis of the CATH‐PFDB has shown that only 15% of the sequence families are close enough to a known structure for reliable homology modeling. IMPALA/PSI‐BLAST profiles have been generated for each of the sequence families in the expanded CATH‐PFDB and a web server has been provided so that new sequences may be scanned against the profile library and be assigned to a structure and homologous superfamily.
Mass spectrometric analysis of the kinetics of in vivo rhodopsin phosphorylation
Authors: Lee Kimberly A. , Craven Kimberley B. , Niemi Gregory A. , Hurley James B.
Published: July 2002

On stimulation, rhodopsin, the light‐sensing protein in the rod cells of the retina, is phosphorylated at several sites on its C terminus as the first step in deactivation. We have developed a mass spectrometry–based method to quantify the kinetics of phosphorylation at each site in vivo. After exposing either a freshly dissected mouse retina or the eye of an anesthetized mouse to a flash of light, phosphorylation and dephosphorylation reactions are terminated by rapidly homogenizing the retina or enucleated eye in 8 M urea. The C‐terminal peptide containing all known phosphorylation sites is cleaved from rhodopsin, partially purified by ultracentrifugation, and analyzed by liquid chromatography coupled with mass spectrometry (LCMS). The mass spectrometer responds linearly to the peptide from 10 fmole to 100 pmole. The relative sensitivity to peptides with zero to five phosphates was determined using purified phosphopeptide standards. High pressure liquid chromatography (HPLC) coupled with tandem mass spectrometry (LCMS/MS) was used to distinguish the three primary sites of phosphorylation, Ser 334, Ser 338, and Ser 343. Peptides monophosphorylated on Ser 334 were separable from those monophosphorylated on Ser 338 and Ser 343 by reversed‐phase HPLC. Although peptides monophosphorylated at Ser 338 and Ser 343 normally coelute, the relative amounts of each species in the single peak could be determined by monitoring the ratio of specific daughter ions characteristic of each peptide. Doubly phosphorylated rhodopsin peptides with different sites of phosphorylation also were distinguished by LCMS/MS. The sensitivity of these methods was evaluated by using them to measure rhodopsin phosphorylation stimulated either by light flashes or by continuous illumination over a range of intensities.
Digital radiology using active matrix readout of amorphous selenium: Geometrical and effective fill factors
Authors: Pang G. , Zhao W. , Rowlands J. A.
Published: July 2002

Flat panel self‐scanned x‐ray detectors using amorphous selenium as the photoconductor are being developed to replace both film/screen cassette systems for radiography and image intensifier (XRII)/video systems for fluoroscopy. These use a two‐dimensional array of pixel electrodes to collect and readout the latent image charges formed on the photoconductor surface. The percentage of the area covered by the pixel electrodes (i.e., the geometrical fill factor ) is always less than unity. In this paper, a novel approach is introduced to make the charge collection by pixel electrodes almost complete (i.e., a close to unity effective fill factor). The idea is to bend the electric field lines in the layer in such a way that image charges cannot land in the gap region between electrodes. This is achieved by depositing holes in the gap region, which is possible because there are charge traps available at the /insulator interface. The distribution of holes required in the gap region is calculated. Various factors associated with the feasibility of this approach as well as a method to deposit these holes are discussed. Application of the approach to the case of mammography is also included.
Digital radiology using active matrix readout: Amplified pixel detector array for fluoroscopy
Authors: Matsuura Naomi , Zhao Wei , Huang Zhongshou , Rowlands J. A.
Published: July 2002

Active matrix array technology has made possible the concept of flat panel imaging systems for radiography. In the conventional approach a thin‐film circuit built on glass contains the necessary switching components (thin‐film transistors or TFTs) to readout an image formed in either a phosphor or photoconductor layer. Extension of this concept to real time imaging—fluoroscopy—has had problems due to the very low noise required. A new design strategy for fluoroscopic active matrix flat panel detectors has therefore been investigated theoretically. In this approach, the active matrix has integrated thin‐film amplifiers and readout electronics at each pixel and is called the amplified pixel detector array (APDA). Each amplified pixel consists of three thin‐film transistors: an amplifier, a readout, and a reset TFT. The performance of the APDA approach compared to the conventional active matrix was investigated for two semiconductors commonly used to construct active matrix arrays—hydrogenated amorphous silicon and polycrystalline silicon. The results showed that with amplification close to the pixel, the noise from the external charge preamplifiers becomes insignificant. The thermal and flicker noise of the readout and the amplifying TFTs at the pixel become the dominant sources of noise. The magnitude of these noise sources is strongly dependent on the TFT geometry and its fabrication process. Both of these could be optimized to make the APDA active matrix operate at lower noise levels than is possible with the conventional approach. However, the APDA cannot be made to operate ideally (i.e., have noise limited only by the amount of radiation used) at the lowest exposure rate required in medical fluoroscopy.
Multi‐layer energy filter for realizing conformal irradiation in charged particle therapy
Authors: Sakae Takeji , Nohtomi Akihiro , Maruhashi Akira , Sato Masaru , Terunuma Toshiyuki , Kohno Ryosuke , Akine Yasuyuki , Hayakawa Yoshinori , Koike Yasunori
Published: July 2002

A new type of filter for charged particle radiotherapy is developed to reduce unwanted dose transfer to the normal tissues around a tumor. The new filter can make a static irradiation field where the width of the spread‐out Bragg peak (SOBP) is two‐dimensionally adjusted. That makes the field conformal to the tumor three‐dimensionally. The filter is made of many layers produced by using stereolithography. The layer has a miniaturized structure that has geometrical similarity to the conventional ridge filter. Shapes of cone and pyramid are also usable for the unit‐cell constructing the layer. The spread of the field in the depth direction is decided by the thickness of the filter, or by the number of layers. The experimental result of the irradiation using the ridge‐type construction shows a good agreement with an estimate by the Monte Carlo calculation. By combining this technique with intensity modulation that has lateral position dependence, the conformal irradiation can be achieved by a simple procedure.
Is the light emitting diode (LED) an ultimate lamp?
Authors: Holonyak N.
Published: July 2002

Simple diagrams are used to show the transformation of a thin “slab” of intrinsic semiconductor (direct gap, kelec=khole) from an ideal “flat-band” photopumped recombination-radiation light source into an ultimate lamp, a p–n junction light emitting diode (LED). A photoexcited intrinsic slab of semiconductor can be regarded as an ideal (“flat-band”) light source, with, however, the photogenerated carriers and voltage available externally instead of as recombination radiation (light) if the slab is converted to half p type (one side) and half n type (the other side), i.e., to a p–n junction. If an equal, a “bucking,” external voltage is applied, resulting in an input current when the photoexcitation is removed, the slab becomes again (remains) an ideal “flat-band” light source, a p–n junction LED. In practice, the LED takes the form of a p–n heterostructure in order to improve electron–hole injection, reduce the absorption of recombination radiation, and to make possible—with proper geometries—improved photon escape.
The elusive chemical potential
Authors: Baierlein Ralph
Published: July 2002

This paper offers some qualitative understanding of the chemical potential, a topic that students invariably find difficult. Three “meanings” for the chemical potential are stated and then supported by analytical development. Two substantial applications—depression of the melting point and batteries—illustrate the chemical potential in action. The origin of the term “chemical potential” has its surprises, and a sketch of the history concludes the paper.
Student understanding of the wave nature of matter: Diffraction and interference of particles
Authors: Vokos Stamatis , Shaffer Peter S. , Ambrose Bradley S. , McDermott Lillian C.
Published: July 2002

This paper reports on a study of student understanding of the wave nature of matter in the context of the pattern produced by the diffraction and interference of particles. Students in first-year, second-year, and third-year physics courses were asked to predict and explain how a single change in an experimental setup would affect the pattern produced when electrons or other particles are incident on a single slit, double slit, or crystal lattice. The errors made by students after standard instruction indicated the presence of similar conceptual and reasoning difficulties at all levels. Among the most serious was an inability to interpret diffraction and interference in terms of a basic wave model. Other errors revealed a lack of a functional understanding of the de Broglie wavelength. Students often treated it as a fixed property of a particle, not as a function of the momentum. An important goal of this investigation was to provide a research base for the design of instruction to help students develop and apply a basic wave model for matter.
Japanese monkeys perceive sensory consonance of chords
Authors: Izumi Akihiro
Published: July 2002

Consonance/dissonance affects human perception of chords from early stages of development [e.g., Schellenberg and Trainor, J. Acoust. Soc. Am. 100, 3321–3328 (1996)]. To examine whether consonance has some role in audition of nonhumans, three Japanese monkeys (Macaca fuscata) were trained to discriminate simultaneous two-tone complexes (chords). The task was serial discrimination (AX procedure) with repetitive presentation of background stimuli. Each tone in a chord was comprised of six harmonics, and chords with complex ratios of fundamental frequency (e.g., frequency ratio of 8:15 in major seventh) resulted in dissonance. The chords were transposed for each presentation to make monkeys attend to cues other than the absolute frequency of a component tone. Monkeys were initially trained to detect changes from consonant (octave) to dissonant (major seventh). Following the successful acquisition of the task, transfer tests with novel chords were conducted. In these transfer tests, the performances with detecting changes from consonant to dissonant chords (perfect fifth to major seventh; perfect fourth to major seventh) were better than those with detecting reverse changes. These results suggested that the consonance of chords affected the performances of monkeys.
Determination of the complex Young and shear dynamic moduli of viscoelastic materials
Authors: Willis R. Lance , Wu Lei , Berthelot Yves H.
Published: July 2002

The Young and shear dynamic moduli of viscoelastic materials are determined from laser vibrometric measurements of the surface motion of a three-dimensional sample excited by a piezoelectric actuator inside a chamber with controllable temperature and static pressure. The moduli are estimated from an inversion code that minimizes the difference between the data and the predictions from a finite element model in which the elastic moduli are the adjustable parameters. The technique is first used to measure the dynamic properties of homogeneous samples and the results are compared with those obtained by the standard rod resonance technique. Results are then obtained with microvoided samples in the 0.5–3 kHz frequency range, at temperatures ranging from 7 to 40 °C, and static pressures ranging from ambient to 34 atm (3.45 MPa or 500 psi). The limitations of the technique are discussed.
Localization and visual verification of a complex minke whale vocalization
Authors: Gedamke Jason , Costa Daniel P. , Dunstan Andy
Published: July 2002

A recently described population of minke whales (Balaenoptera acutorostrata) offered a unique opportunity to study its acoustic behavior. The often-inquisitive dwarf minke whale is seen on the Great Barrier Reef nearly coincident with its suspected calving and breeding seasons. During drifting encounters with whales, a towed hydrophone array was used to record sounds for subsequent localization of sound sources. Shipboard and in-water observers linked these sounds to the closely circling minke whale. A complex and stereotyped sound sequence, the “star-wars” (SW) vocalization, was recorded during a series of visual and acoustic observations. The SW vocalization spanned a wide frequency range (50 Hz–9.4 kHz) and was composed of distinct and stereotypically repeated units with both amplitude and frequency-modulated components. Broadband source levels between 150 and 165 dB re 1 μPa at 1 m were calculated. Passive acoustic studies can utilize this distinct vocalization to help determine the behavior, distribution, and movements of this animal. While the SW vocalization’s function remains unknown, the regularly repeated and complex sound sequence was common in low latitude, winter month aggregations of minke whales. At this early stage, the SW vocalization appears similar to the songs of other whale species and has characteristics consistent with those of reproductive advertisement displays.
The acoustic emission of a distributed mode loudspeaker near a porous layer
Authors: Prokofieva E. Yu. , Horoshenkov Kirill V. , Harris N.
Published: July 2002

Experimental and theoretical modeling of the vibro-acoustic performance of a distributed mode loudspeaker (DML) suggest that their acoustic emission can be significantly affected by the presence of a porous layer. The amplitude of the surface velocity of the panel and the acoustic pressure on the porous surface are reduced largely in the vicinity of structural resonances due to the additional radiation damping and visco-thermal absorption phenomenon in the porous layer. The experimental results suggest that a porous layer between a rigid base and a DML panel can considerably alter its acoustic emission in the near field and in the far field. This is illustrated by a reduction in the level of fluctuations in the emitted acoustic pressure spectra. These fluctuations are normally associated with the interference between the sound emitted by the front surface of the speaker and that emitted from the back. Another contribution comes from the pronounced structural resonances in the surface velocity spectrum. The results of this work suggest that the acoustic boundary conditions near a DML can be modified by the porous layer so that a desired acoustic output can be attained.
Lamb waves in piezoelectric focused radiator as a reason for discrepancy between O’Neil’s formula and experiment
Authors: Cathignol D. , Sapozhnikov O. A. , Zhang J.
Published: July 2002

One of the well-known methods of ultrasound focusing is the use of a transducer having the form of a concave spherical cap. In the theoretical analysis, O’Neil’s formula is widely used, which describes acoustic pressure on the axis of the transducer under the assumption that normal velocity of its surface is uniform. Usually, it is believed that modern piezoelectric focused sources are very close to this theoretical model. The paper presented describes results of experimental investigation which showed that there exists a significant disagreement between the observed acoustic field and that predicted by the theory of O’Neil. Two types of measurements have been made to clarify this problem. The acoustic pressure field of a focused piezoceramic transducer (with aperture diameter of 100 mm, radius of curvature of 100 mm, resonance frequency of 1 MHz) has been measured in a water tank using a miniature hydrophone. In addition, the radiator surface vibration has been studied in air using an optical interferometric technique. Theoretical analysis and the measurements show that the disagreement between the theory and the experiment is due to Lamb waves, which originate at the radiator edge, propagate along the piezoceramic plate without significant attenuation, and thus radiate additional acoustic perturbations.
Implementation of an active headset by using the H∞ robust control theory
Authors: Bai Mingsian , Lee Dunjay
Published: July 2002

This paper presents a methodology for implementing an active headset by using H∞ robust control theory. The adopted structure is feedback tracking control. Performance, stability, and robustness of the closed-loop system have been taken into account in the design procedure by using a general framework of the H∞ theory. The resultant controller is realized on the basis of operational amplifier circuitry. Experiments are conducted to test the developed headset. The result shows that the headset achieves broadband attenuation up to approximately 15 dB in the band 200–800 Hz. The design considerations indicated in the experimental result are also addressed.
Source localization in shallow water with internal waves
Authors: Yoo Kwang , Yang T. C.
Published: July 2002

Source localization can be a difficult problem in temporally and spatially varying shallow-water environments. The SWARM 95 data indicate that the acoustic fields at 225 and 400 Hz change drastically in the time scale of several minutes. Since it is practically impossible to model the replica field at this time scale, one expects degraded performance for matched field processing (assuming a time-independent replica field). An alternate processing scheme is proposed here. First it is shown that internal waves cause mode conversions and that mode conversions degrade matched-field source localization. This is illustrated for the Garret–Munk internal waves, the solitary internal waves and the combination of both. It is then shown that source localization can be achieved by using only the uncoupled modes. This concept was implemented using matched-beam processing. The beam filter serves to suppress the contribution of the coupled modes. It is shown that this technique significantly improves the localization performance over conventional matched-field processing. [Work supported by the Office of Naval Research.]
Three-dimensional wave-envelope elements of variable order for acoustic radiation and scattering. Part II. Formulation in the time domain
Authors: Astley R. J. , Coyette J.-P. , Cremers L.
Published: July 2002

A variable-order, infinite “wave-envelope” element scheme is formulated for transient, unbounded acoustical problems. The transient formulation which is local in space and time is obtained by applying an inverse Fourier transformation to a time-harmonic wave-envelope model whose formulation is described in a companion article. This procedure yields a coupled system of second-order differential equations which can be integrated in time to yield transient pressure histories at discrete nodal points. Far-field transient pressures can also be obtained at adjusted times. The method can be applied quite generally to two-dimensional and three-dimensional problems and is compatible with a conventional finite element model in the near field. The utility of the method is confirmed by the presentation of transient solutions for axisymmetric and fully three-dimensional test problems. An implicit time integration scheme is used and computed results are compared to analytic solutions and to solutions obtained from alternative numerical schemes. Close correspondence is demonstrated and the scheme is shown to be stable for the problems which are presented. CPU times for a large three-dimensional problem are shown to compare favorably with those required for an equivalent transient boundary element computation.
Pitches of concurrent vowels
Authors: Assmann Peter F. , Paschall D. Dwayne
Published: July 2002

When two vowels are presented simultaneously, listeners can report their phonemic identities more accurately if their fundamental frequencies (F0’s) are different rather than the same. If the F0 difference (ΔF0) is large, listeners hear two vowels on different pitches; if the ΔF0 is small the vowels are identified less accurately and they do not evoke different pitches. The present study used a matching task to obtain judgments of the pitches evoked by “double vowels” created from pairwise combinations of steady-state synthetic vowels /i/, /ɑ/, /u/, /æ/, and /ɚ/. One F0 was always 100 Hz; the other F0 was either 0, 0.25, 0.5, 1, 2, or 4 semitones higher. Experienced listeners adjusted the F0 of a tone complex to assign pitch matches to 50-ms or 200-ms double vowels. For ΔF0’s up to two semitones, listeners’ matches formed a single cluster in the frequency region spanned by the two F0’s. When the ΔF0 was 4 semitones, the matches generally formed two clusters close to the F0 of each vowel, suggesting that listeners perceive two distinct pitches when the ΔF0 is 4 semitones but only one clear pitch (possibly accompanied by one or more weaker pitches) with smaller ΔF0’s. When the duration was reduced from 200 ms to 50 ms, only a subset of the vowel pairs with a ΔF0 of 4 semitones produced a bimodal distribution of matches. In general, 50-ms stimuli were matched less consistently than their 200-ms counterparts, indicating that the pitches of concurrent vowels emerge less clearly when the stimuli are brief. Comparisons of pitch and vowel identification data revealed a moderate correlation between match intervals (defined as the absolute frequency difference between first and second pitch matches) and identification accuracy for the 200-ms stimuli with the largest ΔF0 of 4 semitones. The link between match intervals and vowel identification was weak or absent in conditions where the stimuli evoked only one pitch.
Experimental demonstration of the pseudo-Rayleigh (A0) wave
Authors: Ahyi A. C. , Pernod P. , Gatti O. , Latard V. , Merlen A. , Überall H.
Published: July 2002

It is well known that the circumferential waves supported by thin cylindrical, water-loaded shells correspond closely to those on a water-loaded plate, i.e., to the Scholte–Stoneley wave A and to the Lamb waves A0,A1,A2,…, and S0,S1,S2… . Until now, however, it had not been possible to definitely observe the acoustic excitation of the A0 wave on a shell using steady-state or long-pulse incident sound waves (while excitation of the A and S0 waves was clearly evident). The reason for this is the rapid decay of the propagating A0 waves, whose high attenuation also rendered their multicircuit resonances too broad to be individually observable. In the present experiment, carried out with ultrashort, spark-generated acoustic pulses whose diffraction by a steel shell is visualized by the shadowgraph method, the A0 (“pseudo-Rayleigh”) wave could be observed immediately after its excitation, before it had any time to decay. Spectral analysis of its observed re-radiation permitted the extraction of its phase-velocity dispersion curve, which by comparison with previously calculated dispersion curves uniquely characterized it as being the A0 wave.
Interface conditions for Biot’s equations of poroelasticity
Authors: Gurevich Boris , Schoenberg Michael
Published: July 2002

Interface conditions at a boundary between two porous media are derived directly from Biot’s equations of poroelasticity by replacing the discontinuity surface with a thin transition layer, in which the properties of the medium change rapidly yet continuously, and then taking the limit as the thickness of the transition layer approaches zero. The interface conditions obtained in this way, the well known “open-pore” conditions, are shown to be the only ones that are fully consistent with the validity of Biot’s equations throughout the poroelastic continuum, including surfaces across which the medium properties are discontinuous. But partially blocked or completely impermeable interfaces exist; these may be looked upon as the case of a thin layer with its permeability taken to be proportional to the layer thickness, again in the limit as layer thickness approaches zero. This approach can serve as a simple recipe for modeling such an interface in any heterogeneous numerical scheme for poroelastic media.
The underwater sounds produced by impacting snowflakes
Authors: Crum Lawrence A. , Pumphrey Hugh C. , Roy Ronald A. , Prosperetti Andrea
Published: July 2002

In 1985, Scrimger [Nature 318, 647 (1985)] reported measurements of noise levels significantly above the ambient level for snow falling on a quiet freshwater lake. He examined only the time-averaged sound levels and did not report measurements of individual snowflake impacts. Subsequently, the noise produced by individual and multiple snowflake impacts was examined for a number of different snowfalls. The radiated acoustic signals generated by the impact of individual snowflakes upon a body of water have a remarkable similarity to each other and differ principally in the frequency of the emitted sound wave. The acoustic signal of a snowflake impact thus generates a characteristic signature for snowfall that is clearly distinct from other forms of precipitation noise. Various aspects of this signature suggest that the radiated acoustic waveform from a snowflake impacting with water is due to the entrainment of a gas bubble into the liquid, and the subsequent oscillation of this bubble as it establishes its equilibrium state. Various scenarios are presented for bubble entrainment and approximations to the amplitude of the radiated signal and the acoustic waveform are obtained.