bluuebunny/crossref_metadata_2025 huggingface dataset:
Convergence of a multiscale finite element method for elliptic problems with rapidly oscillating coefficients
Authors: Hou Thomas , Wu Xiao-Hui , Cai Zhiqiang
Published: July 2002

We propose a multiscale finite element method for solving second order elliptic equations with rapidly oscillating coefficients. The main purpose is to design a numerical method which is capable of correctly capturing the large scale components of the solution on a coarse grid without accurately resolving all the small scale features in the solution. This is accomplished by incorporating the local microstructures of the differential operator into the finite element base functions. As a consequence, the base functions are adapted to the local properties of the differential operator. In this paper, we provide a detailed convergence analysis of our method under the assumption that the oscillating coefficient is of two scales and is periodic in the fast scale. While such a simplifying assumption is not required by our method, it allows us to use homogenization theory to obtain a useful asymptotic solution structure. The issue of boundary conditions for the base functions will be discussed. Our numerical experiments demonstrate convincingly that our multiscale method indeed converges to the correct solution, independently of the small scale in the homogenization limit. Application of our method to problems with continuous scales is also considered.
On Noether’s bound for polynomial invariants of a finite group
Authors: Fogarty John
Published: July 2002

E. Noether’s a priori bound, viz., the group order

g
g

, for the degrees of generating polynomial invariants of a finite group, is extended from characteristic 0 to characteristic prime to

g
g

.
Combining evidence using p-values: application to sequence homology searches.
Authors: Bailey T L , Gribskov M
Published: July 2002

MOTIVATION: To illustrate an intuitive and statistically valid method for combining independent sources of evidence that yields a p-value for the complete evidence, and to apply it to the problem of detecting simultaneous matches to multiple patterns in sequence homology searches. RESULTS: In sequence analysis, two or more (approximately) independent measures of the membership of a sequence (or sequence region) in some class are often available. We would like to estimate the likelihood of the sequence being a member of the class in view of all the available evidence. An example is estimating the significance of the observed match of a macromolecular sequence (DNA or protein) to a set of patterns (motifs) that characterize a biological sequence family. An intuitive way to do this is to express each piece of evidence as a p-value, and then use the product of these p-values as the measure of membership in the family. We derive a formula and algorithm (QFAST) for calculating the statistical distribution of the product of n independent p-values. We demonstrate that sorting sequences by this p-value effectively combines the information present in multiple motifs, leading to highly accurate and sensitive sequence homology searches.
Structural basis for triplet repeat disorders: a computational
analysis
Authors: Baldi Pierre , Brunak Søren , Chauvin Yves , Gorm Pedersen Anders
Published: July 2002

Motivation: Over a dozen major degenerative disorders, including myotonic distrophy, Huntington’s disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases?

Results: Using several different computational models of DNA structure, we show that the triplets involved in the pathological repeats generally fall into extreme classes. Thus, CAG/CTG repeats are particularly flexible, whereas GCC, CGG and GAA repeats appear to display both flexible and rigid (but curved) characteristics depending on the method of analysis. The fact that (1) trinucleotide repeats often become increasingly unstable when they exceed a length of approximately 50 repeats, and (2) repeated 12-mers display a similar increase in instability above 13 repeats, together suggest that approximately 150 bp is a general threshold length for repeat instability. Since this is about the length of DNA wrapped up in a single nucleosome core particle, we speculate that chromatin structure may play an important role in the expansion mechanism. We furthermore suggest that expansion of a dodecamer repeat, which we predict to have very high flexibility, may play a role in the pathogenesis of the neurodegenerative disorder multiple system atrophy (MSA).

Contact: pfbaldi@ics.uci.edu, yves@netid.com, brunak@cbs.dtu.dk, gorm@cbs.dtu.dk
A comparison of sequence and structure protein domain families as a basis for structural genomics.
Authors: Elofsson A , Sonnhammer E L
Published: July 2002

MOTIVATION: Protein families can be defined based on structure or sequence similarity. We wanted to compare two protein family databases, one based on structural and one on sequence similarity, to investigate to what extent they overlap, the similarity in definition of corresponding families, and to create a list of large protein families with unknown structure as a resource for structural genomics. We also wanted to increase the sensitivity of fold assignment by exploiting protein family HMMs. RESULTS: We compared Pfam, a protein family database based on sequence similarity, to Scop, which is based on structural similarity. We found that 70% of the Scop families exist in Pfam while 57% of the Pfam families exist in Scop. Most families that occur in both databases correspond well to each other, but in some cases they are different. Such cases highlight situations in which structure and sequence approaches differ significantly. The comparison enabled us to compile a list of the largest families that do not occur in Scop; these are suitable targets for structure prediction and determination, and may be useful to guide projects in structural genomics. It can be noted that 13 out of the 20 largest protein families without a known structure are likely transmembrane proteins. We also exploited Pfam to increase the sensitivity of detecting homologs of proteins with known structure, by comparing query sequences to Pfam HMMs that correspond to Scop families. For SWISSPROT+TREMBL, this yielded an increase in fold assignment from 31% to 42% compared to using FASTA only. This method assigned a structure to 22% of the proteins in Saccharomyces cerevisiae, 24% in Escherichia coli, and 16% in Methanococcus jannaschii.
Assessing the accuracy of prediction algorithms for
classification: an overview
Authors: Baldi Pierre , Brunak Søren , Chauvin Yves , Andersen Claus A. F. , Nielsen Henrik
Published: July 2002

4 Also at the Department of Biological Sciences, University of California, Irvine, USA, to whom all correspondence should be addressed.

We provide a unified overview of methods that currently are widely used to assess the accuracy of prediction algorithms, from raw percentages, quadratic error measures and other distances, and correlation coefficients, and to information theoretic measures such as relative entropy and mutual information. We briefly discuss the advantages and disadvantages of each approach. For classification tasks, we derive new learning algorithms for the design of prediction systems by directly optimising the correlation coefficient. We observe and prove several results relating sensitivity and specificity of optimal systems. While the principles are general, we illustrate the applicability on specific problems such as protein secondary structure and signal peptide prediction.

Contact: pfbaldi@ics.uci.edu
Tolerating some redundancy significantly speeds up clustering
of large protein databases
Authors: Li Weizhong , Jaroszewski Lukasz , Godzik Adam
Published: July 2002

Motivation: Sequence clustering replaces groups of similar sequences in a database with single representatives. Clustering large protein databases like the NCBI Non-Redundant database (NR) using even the best currently available clustering algorithms is very time-consuming and only practical at relatively high sequence identity thresholds. Our previous program, CD-HI, clustered NR at 90% identity in ∼1 h and at 75% identity in ∼1 day on a 1 GHz Linux PC (Li et al. , Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases are rapidly growing and many applications desire a lower attainable thresholds.

Results: For our previous algorithm (CD-HI), we have employed short-word filters to speed up the clustering. In this paper, we show that tolerating some redundancy makes for more efficient use of these short-word filters and increases the program’s speed 100 times. Our new program implements this technique and clusters NR at 70% identity within 2 h, and at 50% identity in ∼5 days. Although some redundancy is present after clustering, our new program’s results only differ from our previous program’s by less than 0.4%.

Availability: The program and its previous version are available at http://bioinformatics.burnham-inst.org/cd-hi

Contact: liwz@burnham-inst.org; adam@burnham-inst.org

* To whom correspondence should be addressed.
The G·U wobble base pair
Authors: Varani Gabriele , McClain William H
Published: July 2002

The G·U wobble base pair is a fundamental unit of RNA secondary structure that is present in nearly every class of RNA from organisms of all three phylogenetic domains. It has comparable thermodynamic stability to Watson–Crick base pairs and is nearly isomorphic to them. Therefore, it often substitutes for G·C or A·U base pairs. The G·U wobble base pair also has unique chemical, structural, dynamic and ligand‐binding properties, which can only be partially mimicked by Watson–Crick base pairs or other mispairs. These features mark sites containing G·U pairs for recognition by proteins and other RNAs and allow the wobble pair to play essential functional roles in a remarkably wide range of biological processes.
A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome
Authors: Davy Anne , Bello Paul , Thierry‐Mieg Nicolas , Vaglio Philippe , Hitti Joseph , Doucette‐Stamm Lynn , Thierry‐Mieg Danielle , Reboul Jérôme , Boulton Simon , Walhout Albertha J M , Coux Olivier , Vidal Marc
Published: July 2002

The ubiquitin‐proteasome proteolytic pathway is pivotal in most biological processes. Despite a great level of information available for the eukaryotic 26S proteasome—the protease responsible for the degradation of ubiquitylated proteins—several structural and functional questions remain unanswered. To gain more insight into the assembly and function of the metazoan 26S proteasome, a two‐hybrid‐based protein interaction map was generated using 30 Caenorhabditis elegans proteasome subunits. The results recapitulate interactions reported for other organisms and reveal new potential interactions both within the 19S regulatory complex and between the 19S and 20S subcomplexes. Moreover, novel potential proteasome interactors were identified, including an E3 ubiquitin ligase, transcription factors, chaperone proteins and other proteins not yet functionally annotated. By providing a wealth of novel biological hypotheses, this interaction map constitutes a framework for further analysis of the ubiquitin‐proteasome pathway in a multicellular organism amenable to both classical genetics and functional genomics.
ROS, stress‐activated kinases and stress signaling in cancer
Authors: Benhar Moran , Engelberg David , Levitzki Alexander
Published: July 2002

Anticancer therapy is frequently efficient in early stages of the disease, whereas advanced tumors are usually resistant to the same treatments. The molecular basis for this change is not entirely understood. Many anticancer agents are DNA‐ or cytoskeleton‐damaging drugs that show some specificity towards dividing cells. However, recent studies show that these agents also activate stress‐signaling cascades that may play a role in eliciting the observed therapeutic effects. We discuss recent findings that suggest that induction of stress signaling in oncogenically transformed cells is integrated into apoptotic pathways. Reactive oxygen species (ROS) and stress‐activated protein kinases (SAPKs), which are potentiated in recently transformed cells, emerge as key effectors of cell death. In advanced tumors, however, these agents are downregulated and, consequently, death signaling is suppressed. Such changes in ROS and SAPK activity levels during the course of tumor development may underlie the changes in responsiveness to anticancer therapy.
Resistance exercise decreases skeletal muscle tumor necrosis factor α in frail elderly humans
Authors: GREIWE JEFFREY S. , CHENG BO , RUBIN DEBORAH C. , YARASHESKI KEVIN E. , SEMENKOVICH CLAY F.
Published: July 2002

Skeletal muscle protein and function decline with advancing age but the underlying pathophysiology is poorly understood. To test the hypothesis that the catabolic cytokine tumor necrosis factor alpha (TNF‐α) contributes to this process, we studied the effects of aging and resistance exercise on TNF‐α expression in human muscle. Using in situ hybridization, TNF‐α message was localized to myocytes in sections of skeletal muscle from elderly humans. Both TNF‐α mRNA and protein levels were elevated in skeletal muscle from frail elderly (81±1 year) as compared to healthy young (23±1 year) men and women. To determine whether resistance exercise affects TNF‐α expression, frail elderly men and women were randomly assigned to a training group or to a nonexercising control group. Muscle biopsies were performed before and after 3 months. Muscle TNF‐α mRNA and protein levels decreased in the exercise group but did not change in the control group. Muscle protein synthesis rate in the exercise group was inversely related to levels of TNF‐α protein. These data suggest that TNF‐α contributes to age‐associated muscle wasting and that resistance exercise may attenuate this process by suppressing skeletal muscle TNF‐α expression.—Greiwe, J. S., Cheng, B., Rubin, D. C., Yarasheski, K. E., Semenkovich, C. F. Resistance exercise decreases skeletal muscle tumor necrosis factor α in frail elderly humans. FASEB J. 15, 475‐482 (2001)
The effects of selective logging on the distribution of moths in a Bornean rainforest
Authors: Willottf S. J.
Published: July 2002

The effects of selective logging on the diversity and species composition of moths were investigated by sampling from multiple sites in primary forest, both understorey and canopy, and logged forest at Danum Valley, Sabah, Malaysia. The diversity of individual sites was similar, although rarefied species richness of logged forest was 17% lower than for primary forest (understorey and canopy combined). There was significant heterogeneity in faunal composition and measures of similarity (NESS index) among primary forest understorey sites which may be as great as those between primary understorey and logged forest. The lowest similarity values were between primary forest understorey and canopy, indicating a distinct canopy fauna. A number of species encountered in the logged forest were confined to, or more abundant in, the canopy of primary forest. Approximately 10% of species were confined to primary forest across a range of species’ abundances, suggesting this is a minimum estimate for the number of species lost following logging. The importance of accounting for heterogeneity within primary forest and sampling in the canopy when measuring the effects of disturbance on tropical forest communities are emphasized.
Life: past, present and future
Authors: Nealson Kenneth H. , Conrad Pamela G.
Published: July 2002

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote–centric (five–kingdoms) view of the planet to one that is peculiarly prokarote–centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen–using, carbon–eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such ‘metabolic extremophily’ forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.
The neuron as a dynamic electrogenic machine: modulation of sodium–channel expression as a basis for functional plasticity in neurons
Authors: Waxman Stephen G.
Published: July 2002

Neurons signal each other via regenerative electrical impulses (action potentials) and thus can be thought of as electrogenic machines. V oltage–gated sodium channels produce the depolarizations necessary for action potential activity in most neurons and, in this respect, lie close to the heart of the electrogenic machinery. Although classical neurophysiological doctrine accorded ‘the’ sodium channel a crucial role in electrogenesis, it is now clear that nearly a dozen genes encode distinct sodium channels with different molecular structures and functional properties, and the majority of these channels are expressed within the mammalian nervous system. The transcription of these sodium–channel genes, and the deployment of the channels that they encode, can change significantly within neurons following various injuries. Moreover, the transcription of these genes and the deployment of various types of sodium channels within neurons of the normal nervous system can change markedly as neurons respond to changing milieus or physiological inputs. As a result of these changes in sodium–channel expression, the membranes of neurons may be retuned so as to alter their transductive and/or encoding properties. Neurons within the normal and injured nervous system can thus function as dynamic electrogenic machines with electroresponsive properties that change not only in response to pathological insults, but also in response to shifting functional needs.
The degeneration of Y chromosomes
Authors: Charlesworth Brian , Charlesworth Deborah
Published: July 2002

Y chromosomes are genetically degenerate, having lost most of the active genes that were present in their ancestors. The causes of this degeneration have attracted much attention from evolutionary theorists. Four major theories are reviewed here: Muller's ratchet, background selection, the Hill–Robertson effect with weak selection, and the ‘hitchhiking’ of deleterious alleles by favourable mutations. All of these involve a reduction in effective population size as a result of selective events occurring in a non–recombining genome, and the consequent weakening of the efficacy of selection. We review the consequences of these processes for patterns of molecular evolution and variation at loci on Y chromosomes, and discuss the results of empirical studies of these patterns for some evolving Y–chromosome and neo–Y–chromosome systems. These results suggest that the effective population sizes of evolving Y or neo–Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes leading to degeneration are operative. It is, however, currently unclear which of the various processes is most important; some directions for future work to help to resolve this question are discussed.
Folding defects in fibrillar collagens
Authors: Byers Peter H.
Published: July 2002

Fibrillar collagens have a long triple helix in which glycine is in every third position for more than 1000 amino acids. The three chains of these molecules are assembled with specificity into several different molecules that have tissue–specific distribution. Mutations that alter folding of either the carboxy–terminal globular peptides that direct chain association, or of the regions of the triple helix that are important for nucleation, or of the bulk of the triple helix, all result in identifiable genetic disorders in which the phenotype reflects the region of expression of the genes and their tissue–specific distribution. Mutations that result in changed amino–acid sequences in any of these regions have different effects on folding and may have different phenotypic outcomes. Substitution for glycine residues in the triple helical domains are among the most common effects of mutations, and the nature of the substituting residue and its location in the chain contribute to the effect on folding and also on the phenotype. More complex mutations, such as deletions or insertions of triple helix, also affect folding, probably because of alterations in helical pitch along the triple helix. These mutations all interfere with the ability of these molecules to form the characteristic fibrillar array in the extracellular matrix and many result in intracellular retention of abnormal molecules.
Complex bird clocks
Authors: Gwinner Eberhard , Brandstatter Roland
Published: July 2002

The circadian pacemaking system of birds comprises three major components: (i) the pineal gland, which rhythmically synthesizes and secretes melatonin; (ii) a hypothalamic region, possibly equivalent to the mammalian suprachiasmatic nuclei; and (iii) the retinae of the eyes. These components jointly interact, stabilize and amplify each other to produce a highly self–sustained circadian output. Their relative contribution to overt rhythmicity appears to differ between species and the system may change its properties even within an individual depending, for example, on its state in the annual cycle or its photic environment. Changes in pacemaker properties are partly mediated by changes in certain features of the pineal melatonin rhythm. It is proposed that this variability is functionally important, for instance, for enabling high–Arctic birds to retain synchronized circadian rhythms during the low–amplitudezeitgeberconditions in midsummer or for allowing birds to adjust quickly their circadian system to changing environmental conditions during migratory seasons. The pineal melatonin rhythm, apart from being involved in generating the avian pacemaking oscillation, is also capable of retaining day length information after isolation from the animal. Hence, it appears to participate in photoperiodic after–effects. Our results suggest that complex circadian clocks have evolved to help birds cope with complex environments.
Biological liquid crystal elastomers
Authors: Knight D. P. , Vollrath F.
Published: July 2002

Liquid crystal elastomers (LCEs) have recently been described as a new class of matter. Here we review the evidence for the novel conclusion that the fibrillar collagens and the dragline silks of orb web spiders belong to this remarkable class of materials. Unlike conventional rubbers, LCEs are ordered, rather than disordered, at rest. The identification of these biopolymers as LCEs may have a predictive value. It may explain how collagens and spider dragline silks are assembled. It may provide a detailed explanation for their mechanical properties, accounting for the variation between different members of the collagen family and between the draglines in different spider species. It may provide a basis for the design of biomimetic collagen and dragline silk analogues by genetic engineering, peptide- or classical polymer synthesis. Biological LCEs may exhibit a range of exotic properties already identified in other members of this remarkable class of materials. In this paper, the possibility that other transversely banded fibrillar proteins are also LCEs is discussed.
Synaptic Plasticity in the Lateral Amygdala: A Cellular Hypothesis of Fear Conditioning
Authors: Blair Hugh T. , Schafe Glenn E. , Bauer Elizabeth P. , Rodrigues Sarina M. , LeDoux Joseph E.
Published: July 2002

Fear conditioning is a form of associative learning in which subjects come to express defense responses to a neutral conditioned stimulus (CS) that is paired with an aversive unconditioned stimulus (US). Considerable evidence suggests that critical neural changes mediating the CS–US association occur in the lateral nucleus of the amygdala (LA). Further, recent studies show that associative long-term potentiation (LTP) occurs in pathways that transmit the CS to LA, and that drugs that interfere with this LTP also disrupt behavioral fear conditioning when infused into the LA, suggesting that associative LTP in LA might be a mechanism for storing memories of the CS–US association. Here, we develop a detailed cellular hypothesis to explain how neural responses to the CS and US in LA could induce LTP-like changes that store memories during fear conditioning. Specifically, we propose that the CS evokes EPSPs at sensory input synapses onto LA pyramidal neurons, and that the US strongly depolarizes these same LA neurons. This depolarization, in turn, causes calcium influx through NMDA receptors (NMDARs) and also causes the LA neuron to fire action potentials. The action potentials then back-propagate into the dendrites, where they collide with CS-evoked EPSPs, resulting in calcium entry through voltage-gated calcium channels (VGCCs). Although calcium entry through NMDARs is sufficient to induce synaptic changes that support short-term fear memory, calcium entry through both NMDARs and VGCCs is required to initiate the molecular processes that consolidate synaptic changes into a long-term memory.
Crystal structure of oxidized flavodoxin, an essential protein in Helicobacter pylori
Authors: Freigang Jörg , Diederichs Kay , Schäfer Klaus P. , Welte Wolfram , Paul Ralf
Published: July 2002

The redox protein flavodoxin has been shown earlier to be reduced by the pyruvate‐oxidoreductase (POR) enzyme complex of Helicobacter pylori, and also was proposed to be involved in the pathogenesis of gastric mucosa‐associated lymphoid‐tissue lymphoma (MALToma). Here, we report its X‐ray structure, which is similar to flavodoxins of other bacteria and cyanobacteria. However, H. pylori flavodoxin has an alanine residue near the isoalloxazine ring of its cofactor flavin mononucleotide (FMN), while the other previously crystallized flavodoxins have a larger hydrophobic residue at this position. This creates a solute filled hole near the FMN cofactor of H. pylori flavodoxin. We also show that flavodoxin is essential for the survival of H. pylori, and conclude that its structure can be used as a starting point for the modeling of an inhibitor for the interaction between the POR‐enzyme complex and flavodoxin.
Knowledge‐based segmentation of thoracic computed tomography images for assessment of split lung function
Authors: Brown Matthew S. , Goldin Jonathan G. , McNitt‐Gray Michael F. , Greaser Lloyd E. , Sapra Amita , Li Kuo‐Tung , Sayre James W. , Martin Katherine , Aberle Denise R.
Published: July 2002

The assessment of differential left and right lung function is important for patients under consideration for lung resection procedures such as single lung transplantation. We developed an automated, knowledge‐based segmentation algorithm for purposes of deriving functional information from dynamic computed tomography (CT) image data. Median lung attenuation (HU) and area measurements were automatically calculated for each lung from thoracic CT images acquired during a forced expiratory maneuver as indicators of the amount and rate of airflow. The accuracy of these derived measures from fully automated segmentation was validated against those from segmentation using manual editing by an expert observer. A total of 1313 axial images were analyzed from 49 patients. The images were segmented using our knowledge‐based system that identifies the chest wall, mediastinum, trachea, large airways and lung parenchyma on CT images. The key components of the system are an anatomical model, an inference engine and image processing routines, and segmentation involves matching objects extracted from the image to anatomical objects described in the model. The segmentation results from all images were inspected by the expert observer. Manual editing was required to correct 183 (13.94%) of the images, and the sensitivity, specificity, and accuracy of the knowledge‐based segmentation were greater than 98.55% in classifying pixels as lung or nonlung. There was no significant difference between median lung attenuation or area values from automated and edited segmentations Using the knowledge‐based segmentation method we can automatically derive indirect quantitative measures of single lung function that cannot be obtained using conventional pulmonary function tests.
Thermodynamics and occupation numbers of a Fermi gas in the canonical ensemble
Authors: Schönhammer K.
Published: July 2002

Exact results for the thermodynamic properties and mean occupation numbers of a system of noninteracting fermions with equidistant level spacing are presented for an arbitrary number of particles. It is discussed quantitatively how the results converge to the corresponding ones in the grand canonical ensemble when the thermodynamic limit is reached. From the simple calculations it also follows that the thermodynamics of an infinite two-dimensional electron gas is identical to that of a one-dimensional harmonic chain with linearized dispersion. The results generalize and simplify previous approaches to this model published in this journal.
The two-capacitor problem with radiation
Authors: Boykin Timothy B. , Hite Dennis , Singh Nagendra
Published: July 2002

We discuss the two-capacitor problem found in many introductory physics texts in which there appears to be missing energy in an ideal, zero-resistance circuit, following the sudden charging of one capacitor from another. The paradox of this missing energy is traditionally ascribed to finite-resistance wires, the initial assumption of an ideal circuit and the rapid nature of the charging notwithstanding. By treating radiative effects in the simplest approximation, we show that the paradox is really nothing more than an inappropriately applied lumped-parameter model. In particular, we show that in the zero-resistance circuit, radiation fully accounts for all of the energy lost. To explore radiative effects in more realistic circuits, we also discuss numerical examples that include a small resistance and inductance.
Intraglottal pressure profiles for a symmetric and oblique glottis with a divergence angle of 10 degrees
Authors: Scherer Ronald C. , Shinwari Daoud , De Witt Kenneth J. , Zhang Chao , Kucinschi Bogdan R. , Afjeh Abdollah A.
Published: July 2002

Human phonation does not always involve symmetric motions of the two vocal folds. Asymmetric motions can create slanted or oblique glottal angles. This study reports intraglottal pressure profiles for a Plexiglas model of the larynx with a glottis having a 10-degree divergence angle and either a symmetric orientation or an oblique angle of 15 degrees. For the oblique glottis, one side was divergent and the other convergent. The vocal fold surfaces had 14 pressure taps. The minimal glottal diameter was held constant at 0.04 cm. Results indicated that for either the symmetric or oblique case, the pressure profiles were different on the two sides of the glottis except for the symmetric geometry for a transglottal pressure of 3 cm H2O. For the symmetric case, flow separation created lower pressures on the side where the flow stayed attached to the wall, and the largest pressure differences between the two sides of the channel were 5%–6% of the transglottal pressure. For the oblique case, pressures were lower on the divergent glottal side near the glottal entry and exit, and the cross-channel pressures at the glottis entrance differed by 27% of the transglottal pressure. The empirical pressure distributions were supported by computational results. The observed aerodynamic asymmetries could be a factor contributing to normal jitter values and differences in vocal fold phasing.
A bending wave simulator for investigating directional vibration sensing in insects
Authors: Miles Ronald N. , Cocroft Reginald B. , Gibbons Colum , Batt Daniel
Published: July 2002

Substrate vibrations are important in social and ecological interactions for many insects and other arthropods. Localization cues include time and amplitude differences among an array of vibration detectors. However, for small species these cues are greatly reduced, and localization mechanisms remain unclear. Here we describe a method of simulating the vibrational environment that facilitates investigation of localization mechanisms in small species. Our model species was the treehopper Umbonia crassicornis (Membracidae; length 1 cm), which communicates using bending waves that propagate along plant stems. We designed a simulator consisting of a length of dowel and two actuators. The actuators were driven with two time signals that created the relationship between slope and displacement characteristic of steady-state bending wave motion. Because the surface of the dowel does not bend, as would a natural stem, close approximation of bending wave motion was limited to a region in the center of the dowel. An example of measurements of the dynamic response of an insect on the simulator is provided to illustrate its utility in the study of directional vibration sensing in insects.
The acoustic bases for gender identification from children’s voices
Authors: Perry Theodore L. , Ohde Ralph N. , Ashmead Daniel H.
Published: July 2002

The purpose of this study was to examine the acoustic characteristics of children’s speech and voices that account for listeners’ ability to identify gender. In Experiment I, vocal recordings and gross physical measurements of 4-, 8-, 12-, and 16-year olds were taken (10 girls and 10 boys per age group). The speech sample consisted of seven nondiphthongal vowels of American English (/æ/ “had,” /ɛ/ “head,” /i/ “heed,” /I/ “hid,” /ɑ/ “hod,” /ʌ/ “hud,” and /u/ “who’d”) produced in the carrier phrase, “Say /hVd/ again.” Fundamental frequency (f0) and formant frequencies (F1, F2, F3) were measured from these syllables. In Experiment II, 20 adults rated the syllables produced by the children in Experiment I based on a six-point gender rating scale. The results from these experiments indicate (1) vowel formant frequencies differentiate gender for children as young as four years of age, while formant frequencies and f0 differentiate gender after 12 years of age, (2) the relationship between gross measures of physical size and vocal characteristics is apparent for at least 12- and 16-year olds, and (3) listeners can identify gender from the speech and voice of children as young as four years of age, and with respect to young children, listeners appear to base their gender ratings on vowel formant frequencies. The findings are discussed in relation to the development of gender identity and its perceptual representation in speech and voice.
Rate and timing cues associated with the cochlear amplifier: Level discrimination based on monaural cross-frequency coincidence detection
Authors: Heinz Michael G. , Colburn H. Steven , Carney Laurel H.
Published: July 2002

The perceptual significance of the cochlear amplifier was evaluated by predicting level-discrimination performance based on stochastic auditory-nerve (AN) activity. Performance was calculated for three models of processing: the optimal all-information processor (based on discharge times), the optimal rate-place processor (based on discharge counts), and a monaural coincidence-based processor that uses a non-optimal combination of rate and temporal information. An analytical AN model included compressive magnitude and level-dependent-phase responses associated with the cochlear amplifier, and high-, medium-, and low-spontaneous-rate (SR) fibers with characteristic frequencies (CFs) spanning the AN population. The relative contributions of nonlinear magnitude and nonlinear phase responses to level encoding were compared by using four versions of the model, which included and excluded the nonlinear gain and phase responses in all possible combinations. Nonlinear basilar-membrane (BM) phase responses are robustly encoded in near-CF AN fibers at low frequencies. Strongly compressive BM responses at high frequencies near CF interact with the high thresholds of low-SR AN fibers to produce large dynamic ranges. Coincidence performance based on a narrow range of AN CFs was robust across a wide dynamic range at both low and high frequencies, and matched human performance levels. Coincidence performance based on all CFs demonstrated the “near-miss” to Weber’s law at low frequencies and the high-frequency “mid-level bump.” Monaural coincidence detection is a physiologically realistic mechanism that is extremely general in that it can utilize AN information (average-rate, synchrony, and nonlinear-phase cues) from all SR groups.
Binaural detection with narrowband and wideband reproducible noise maskers: I. Results for human
Authors: Evilsizer Mary E. , Gilkey Robert H. , Mason Christine R. , Colburn H. Steven , Carney Laurel H.
Published: July 2002

This study investigated binaural detection of tonal targets (500 Hz) using sets of individual masker waveforms with two different bandwidths. Previous studies of binaural detection with wideband noise maskers show that responses to individual noise waveforms are correlated between diotic (N0S0) and dichotic (N0Sπ) conditions [Gilkey et al., J. Acoust. Soc. Am. 78, 1207–1219 (1985)]; however, results for narrowband maskers are not correlated across interaural configurations [Isabelle and Colburn, J. Acoust. Soc. Am. 89, 352–359 (1991)]. This study was designed to allow direct comparison, in detail, of responses across bandwidths and interaural configurations. Subjects were tested on a binaural detection task using both narrowband (100-Hz bandwidth) and wideband (100 Hz to 3 kHz) noise maskers that had identical spectral components in the 100-Hz frequency band surrounding the tone frequency. The results of this study were consistent with the previous studies: N0S0 and N0Sπ responses were more strongly correlated for wideband maskers than for narrowband maskers. Differences in the results for these two bandwidths suggest that binaural detection is not determined solely by the masker spectrum within the critical band centered on the target frequency, but rather that remote frequencies must be included in the analysis and modeling of binaural detection with wideband maskers. Results across the set of individual noises obtained with the fixed-level testing were comparable to those obtained with a tracking procedure which was similar to the procedure used in a companion study of rabbit subjects [Zheng et al., J. Acoust. Soc. Am. 111, 346–356 (2002)].
Auditory stream segregation on the basis of amplitude-modulation rate
Authors: Grimault Nicolas , Bacon Sid P. , Micheyl Christophe
Published: July 2002

In this study, auditory stream segregation based on differences in the rate of envelope fluctuations—in the absence of spectral and temporal fine structure cues—was tested. The temporal sequences to segregate were composed of fully amplitude-modulated (AM) bursts of broadband noises A and B. All sequences were built by the reiteration of a ABA triplet where A modulation rate was fixed at 100 Hz and B modulation rate was variable. The first experiment was devoted to measuring the threshold difference in AM rate leading subjects to perceive the sequence as two streams as opposed to just one. The results of this first experiment revealed that subjects generally perceived the sequences as a single perceptual stream when the difference in AM rate between the A and B noises was smaller than 0.75 oct, and as two streams when the difference was larger than about 1.00 oct. These streaming thresholds were found to be substantially larger than, and not related to, the subjects’ modulation-rate discrimination thresholds. The results of a second experiment demonstrated that AM-rate-based streaming was adversely affected by decreases in AM depth, but that segregation remained possible as long as the AM of either the A or B noises was above the subject’s AM-detection threshold. The results of a third experiment indicated that AM-rate-based streaming effects were still observed when the modulations applied to the A and B noises were set individually, either at a constant level in dB above AM-detection threshold, or at levels at which they were of the same perceived strength. This finding suggests that AM-rate-based streaming is not necessarily mediated by perceived differences in AM depth. Altogether, the results of this study indicate that sequential sounds can be segregated on the sole basis of differences in the rate of their temporal fluctuations in the absence of other temporal or spectral cues.
Wheel/rail noise generation due to nonlinear effects and parametric excitation
Authors: Nordborg Anders
Published: July 2002

Two models are developed, one in the time domain and another in the frequency domain, to explain when a wheel/rail noise generation model requires the inclusion of discrete supports, parametric excitation, and the nonlinear contact spring. Numerical simulations indicate the inclusion of discrete supports to describe low frequency response, and also at higher frequencies, especially where the rail is very smooth or has a corrugation/wavelength corresponding to the pinned-pinned frequency. With a corrugation, it may become essential to include the nonlinear contact spring, as contact loss occurs at high corrugation amplitudes. As nonlinearity causes force generation over a broad frequency range, some contributions excite wheel resonances, resulting in high radiation levels, that require the inclusion of wheel/rail nonlinear effects and parametric excitation for accurate prediction.
Nonlinear seismo-acoustic land mine detection and discrimination
Authors: Donskoy Dimitri , Ekimov Alexander , Sedunov Nikolay , Tsionskiy Mikhail
Published: July 2002

A novel technique for detection and discrimination of artificial objects, such as land mines, pipes, containers, etc., buried in the ground, has been developed and tested. The developed approach utilizes vibration (using seismic or airborne acoustic waves) of buried objects, remote measurements of soil surface vibration (using laser or microwave vibrometers), and processing of the measured vibration to extract mine’s “vibration signatures.” The technique does not depend upon the material from which the mine is fabricated whether it be metal, plastic, wood, or any other material. It depends upon the fact that a mine is a “container” whose purpose is to contain explosive materials and associated detonation apparatus. The mine container is in contact with the soil in which it is buried. The container is an acoustically compliant article, whose compliance is notably different from the compliance of the surrounding soil. Dynamic interaction of the compliant container and soil on top of it leads to specific linear and nonlinear effects used for mine detection and discrimination. The mass of the soil on top of a compliant container creates a classical mass–spring system with a well-defined resonance response. Besides, the connection between mass (soil) and spring (mine) is not elastic (linear) but rather nonlinear, due to the separation of the soil/mine interface in the tensile phase of applied dynamic stress. These two effects, constituting the mine’s vibration signature have been measured in numerous laboratory and field tests, which proved that the resonance and nonlinear responses of a mine/soil system can be used for detection and discrimination of buried mines. Thus, the fact that the mine is buried is turned into a detection advantage. Because the seismo-acoustic technique intrinsically detects buried containers, it can discriminate mines from noncompliant false targets such as rocks, tree roots, chunks of metal, bricks, etc. This was also confirmed experimentally in laboratory and field tests.
Auditory-nerve fiber responses to clicks in guinea pigs with a damaged cochlea
Authors: Versnel Huib , Prijs Vera F. , Schoonhoven Ruurd
Published: July 2002

This paper describes auditory-nerve single-fiber responses to clicks in noise-damaged cochleas. Poststimulus time histograms (PSTHs) were recorded for various click intensities and for the two click polarities. The PSTHs found in fibers with elevated thresholds are discussed in relation to the frequency threshold curves (FTCs) measured in these fibers. Five types of abnormal FTCs are distinguished. Type I is elevated as a whole, type II has an elevated (and often broadened) tip and a tail at normal level, type III has low thresholds in the tail (often hypersensitive), type IV represents a flat tuning, and type V has no tip but shows a clear appearance of the tail (often hypersensitive). The click PSTHs of abnormal fibers were compared to normal PSTHs at equal sound-pressure levels, and various abnormal trends were found corresponding to the type of FTC. PSTHs for type I have longer dominant-peak latencies and smaller amplitudes; PSTHs for type II were normal well above the fiber’s threshold; PSTHs for type III revealed remarkable patterns with multiple peaks, part of them with a latency strongly varying with polarity; PSTHs for type IV showed narrow peaks and steep amplitude/intensity curves; PSTHs for type V showed a multiple peaked pattern and large amplitudes and steep amplitude/intensity curves to rarefaction polarity. The various features in the click responses were in most cases consistent with the type of FTC. The results can be used to explain deviations in whole-nerve recordings in abnormal cochleas.
Helmholtz equation–least-squares method for reconstructing the acoustic pressure field
Authors: Wang Zhaoxi , Wu Sean F.
Published: July 2002

A method using spherical wave expansion theory to reconstruct acoustic pressure field from a vibrating object is developed. The radiated acoustic pressures are obtained by means of an expansion of independent functions generated by the Gram–Schmidt orthonormalization with respect to the particular solutions to the Helmholtz equation on the vibrating surface under consideration. The coefficients associated with these independent functions are determined by requiring the assumed form of solution to satisfy the pressure boundary condition at the measurement points. The errors incurred in this process are minimized by the least-squares method. Once these coefficients are specified, the acoustic pressure at any point, including the source surface, is completely determined. In this paper, this method is used to reconstruct the surface acoustic pressures based on the measured acoustic pressure signals in the field. It is shown that this method can be applied to both separable and nonseparable geometries, and the solutions thus obtained are unique. However, the convergence may be worse for an elongated object subject to high-frequency excitations.