bluuebunny/crossref_metadata_2025 huggingface dataset:
A Structural Rearrangement in the Sodium Channel Pore Linked to Slow Inactivation and Use Dependence
Authors: Ong Boon-Hooi , Tomaselli Gordon F. , Balser Jeffrey R.
Published: July 2002

Voltage-gated sodium (Na+) channels are a fundamental target for modulating excitability in neuronal and muscle cells. When depolarized, Na+ channels may gradually enter long-lived, slow-inactivated conformational states, causing a cumulative loss of function. Although the structural motifs that underlie transient, depolarization-induced Na+ channel conformational states are increasingly recognized, the conformational changes responsible for more sustained forms of inactivation are unresolved. Recent studies have shown that slow inactivation components exhibiting a range of kinetic behavior (from tens of milliseconds to seconds) are modified by mutations in the outer pore P-segments. We examined the state-dependent accessibility of an engineered cysteine in the domain III, P-segment (F1236C; rat skeletal muscle) to methanethiosulfonate-ethylammonium (MTSEA) using whole-cell current recordings in HEK 293 cells. F1236C was reactive with MTSEA applied from outside, but not inside the cell, and modification was markedly increased by depolarization. Depolarized F1236C channels exhibited both intermediate (IM; τ ∼ 30 ms) and slower (IS; τ ∼ 2 s) kinetic components of slow inactivation. Trains of brief, 5-ms depolarizations, which did not induce slow inactivation, produced more rapid modification than did longer (100 ms or 6 s) pulse widths, suggesting both the IM and IS kinetic components inhibit depolarization-induced MTSEA accessibility of the cysteine side chain. Lidocaine inhibited the depolarization-dependent sulfhydryl modification induced by sustained (100 ms) depolarizations, but not by brief (5 ms) depolarizations. We conclude that competing forces influence the depolarization-dependent modification of the cysteine side chain: conformational changes associated with brief periods of depolarization enhance accessibility, whereas slow inactivation tends to inhibit the side chain accessibility. The findings suggest that slow Na+ channel inactivation and use-dependent lidocaine action are linked to a structural rearrangement in the outer pore.
A Conducting State with Properties of a Slow Inactivated State in a Shaker K+ Channel Mutant
Authors: Olcese Riccardo , Sigg Daniel , Latorre Ramon , Bezanilla Francisco , Stefani Enrico
Published: July 2002

In Shaker K+ channel, the amino terminus deletion Δ6-46 removes fast inactivation (N-type) unmasking a slow inactivation process. In Shaker Δ6-46 (Sh-IR) background, two additional mutations (T449V-I470C) remove slow inactivation, producing a noninactivating channel. However, despite the fact that Sh-IR-T449V-I470C mutant channels remain conductive, prolonged depolarizations (1 min, 0 mV) produce a shift of the QV curve by about −30 mV, suggesting that the channels still undergo the conformational changes typical of slow inactivation. For depolarizations longer than 50 ms, the tail currents measured during repolarization to −90 mV display a slow component that increases in amplitude as the duration of the depolarizing pulse increases. We found that the slow development of the QV shift had a counterpart in the amplitude of the slow component of the ionic tail current that is not present in Sh-IR. During long depolarizations, the time course of both the increase in the slow component of the tail current and the change in voltage dependence of the charge movement could be well fitted by exponential functions with identical time constant of 459 ms. Single channel recordings revealed that after prolonged depolarizations, the channels remain conductive for long periods after membrane repolarization. Nonstationary autocovariance analysis performed on macroscopic current in the T449V-I470C mutant confirmed that a novel open state appears with increasing prepulse depolarization time. These observations suggest that in the mutant studied, a new open state becomes progressively populated during long depolarizations (>50 ms). An appealing interpretation of these results is that the new open state of the mutant channel corresponds to a slow inactivated state of Sh-IR that became conductive.
Extracellular Blockade of K+ Channels by Tea
Authors: Crouzy Serge , Bernèche Simon , Roux Benoît
Published: July 2002

TEA is a classical blocker of K+ channels. From mutagenesis studies, it has been shown that external blockade by TEA is strongly dependent upon the presence of aromatic residue at Shaker position 449 which is located near the extracellular entrance to the pore (Heginbotham, L., and R. MacKinnon. 1992. Neuron. 8:483–491). The data suggest that TEA interacts simultaneously with the aromatic residues of the four monomers. The determination of the 3-D structure of the KcsA channel using X-ray crystallography (Doyle, D.A., J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998. Science. 280:69–77) has raised some issues that remain currently unresolved concerning the interpretation of these observations. In particular, the center of the Tyr82 side chains in KcsA (corresponding to position 449 in Shaker) forms a square of 11.8-Å side, a distance which is too large to allow simultaneous interactions of a TEA molecule with the four aromatic side chains. In this paper, the external blockade by TEA is explored by molecular dynamics simulations of an atomic model of KcsA in an explicit phospholipid bilayer with aqueous salt solution. It is observed, in qualitative accord with the experimental results, that TEA is stable when bound to the external side of the wild-type KcsA channel (with Tyr82), but is unstable when bound to a mutant channel in which the tyrosine residue has been substituted by a threonine. The free energy profile of TEA relative to the pore is calculated using umbrella sampling simulations to characterize quantitatively the extracellular blockade. It is found, in remarkable agreement with the experiment, that the TEA is more stably bound by 2.3 kcal/mol to the channel with four tyrosine residues. In the case of the wild-type KcsA channel, TEA (which has the shape of a flattened oblate spheroid) acts as an ideal plug blocking the pore. In contrast, it is considerably more off-centered and tilted in the case of the mutant channel. The enhanced stability conferred by the tyrosine residues does not arise from Π–cation interactions, but appears to be due to differences in the hydration structure of the TEA. Finally, it is shown that the experimentally observed voltage dependence of TEA block, which is traditionally interpreted in terms of the physical position of the TEA along the axis of the pore, must arise indirectly via coupling with the ions in the pore.
Logarithmic convexity of extended mean values
Authors: Qi Feng
Published: July 2002

In this article, the logarithmic convexity of the extended mean values are proved and an inequality of mean values is presented. As by-products, two analytic inequalities are derived. Two open problems are proposed.
Weak-type endpoint bounds for Riesz means
Authors: Tao Terence
Published: July 2002

We use

L
2

L^2

restriction theory to prove optimal weak-type bounds of Bochner-Riesz multipliers and Riesz means of elliptic pseudo-differential operators on compact manifolds, for

p
≤
2
(
n
+
1
)

/

(
n
+
3
)

p \leq 2(n+1)/(n+3)

.
The dynamical properties of Penrose tilings
Authors: Robinson E.
Published: July 2002

The set of Penrose tilings, when provided with a natural compact metric topology, becomes a strictly ergodic dynamical system under the action of

R

2

\mathbf {R}^2

by translation. We show that this action is an almost 1:1 extension of a minimal

R

2

\mathbf {R}^2

action by rotations on

T

4

\mathbf {T}^4

, i.e., it is an

R

2

\mathbf {R}^2

generalization of a Sturmian dynamical system. We also show that the inflation mapping is an almost 1:1 extension of a hyperbolic automorphism on

T

4

\mathbf {T}^4

. The local topological structure of the set of Penrose tilings is described, and some generalizations are discussed.
Palmitoylation of Tetraspanin Proteins: Modulation of CD151 Lateral Interactions, Subcellular Distribution, and Integrin-dependent Cell Morphology
Authors: Yang Xiuwei , Claas Christoph , Kraeft Stine-Kathrein , Chen Lan Bo , Wang Zemin , Kreidberg Jordan A. , Hemler Martin E.
Published: July 2002

Here we demonstrate that multiple tetraspanin (transmembrane 4 superfamily) proteins are palmitoylated, in either the Golgi or a post-Golgi compartment. Using CD151 as a model tetraspanin, we identified and mutated intracellular N-terminal and C-terminal cysteine palmitoylation sites. Simultaneous mutations of C11, C15, C242, and C243 (each to serine) eliminated >90% of CD151 palmitoylation. Notably, palmitoylation had minimal influence on the density of tetraspanin protein complexes, did not promote tetraspanin localization into detergent-resistant microdomains, and was not required for CD151-α3β1 integrin association. However, the CD151 tetra mutant showed markedly diminished associations with other cell surface proteins, including other transmembrane 4 superfamily proteins (CD9, CD63). Thus, palmitoylation may be critical for assembly of the large network of cell surface tetraspanin-protein interactions, sometimes called the “tetraspanin web.” Also, compared with wild-type CD151, the tetra mutant was much more diffusely distributed and showed markedly diminished stability during biosynthesis. Finally, expression of the tetra-CD151 mutant profoundly altered α3 integrin-deficient kidney epithelial cells, such that they converted from a dispersed, elongated morphology to an epithelium-like cobblestone clustering. These results point to novel biochemical and biological functions for tetraspanin palmitoylation.
Peroxisomes Are Formed from Complex Membrane Structures inPEX6-deficient CHO Cells upon Genetic Complementation
Authors: Hashiguchi Noriyo , Kojidani Tomoko , Imanaka Tsuneo , Haraguchi Tokuko , Hiraoka Yasushi , Baumgart Eveline , Yokota Sadaki , Tsukamoto Toshiro , Osumi Takashi
Published: July 2002

Pex6p belongs to the AAA family of ATPases. Its CHO mutant, ZP92, lacks normal peroxisomes but contains peroxisomal membrane remnants, so called peroxisomal ghosts, which are detected with anti–70-kDa peroxisomal membrane protein (PMP70) antibody. No peroxisomal matrix proteins were detected inside the ghosts, but exogenously expressed green fluorescent protein (GFP) fused to peroxisome targeting signal-1 (PTS-1) accumulated in the areas adjacent to the ghosts. Electron microscopic examination revealed that PMP70-positive ghosts in ZP92 were complex membrane structures, rather than peroxisomes with reduced matrix protein import ability. In a typical case, a set of one central spherical body and two layers of double-membraned loops were observed, with endoplasmic reticulum present alongside the outer loop. In the early stage of complementation by PEX6 cDNA, catalase and acyl-CoA oxidase accumulated in the lumen of the double-membraned loops. Biochemical analysis revealed that almost all the peroxisomal ghosts were converted into peroxisomes upon complementation. Our results indicate that 1) Peroxisomal ghosts are complex membrane structures; and 2) The complex membrane structures become import competent and are converted into peroxisomes upon complementation with PEX6.
SpSld3 Is Required for Loading and Maintenance of SpCdc45 on Chromatin in DNA Replication in Fission Yeast
Authors: Nakajima Reiko , Masukata Hisao
Published: July 2002

Initiation of DNA replication in eukaryotic cells is regulated through the ordered assembly of replication complexes at origins of replication. Association of Cdc45 with the origins is a crucial step in assembly of the replication machinery, hence can be considered a target for the regulation of origin activation. To examine the process required for SpCdc45 loading, we isolated fission yeast SpSld3, a counterpart of budding yeast Sld3 that interacts with Cdc45. SpSld3 associates with the replication origin during G1–S phases and this association depends on Dbf4-dependent (DDK) kinase activity. In the corresponding period, SpSld3 interacts with minichromosome maintenance (MCM) proteins and then with SpCdc45. A temperature-sensitive sld3-10 mutation suppressed by the multicopy of the sna41+encoding SpCdc45 impairs loading of SpCdc45 onto chromatin. In addition, this mutation leads to dissociation of preloaded Cdc45 from chromatin in the hydroxyurea-arrested S phase, and DNA replication upon removal of hydroxyurea is retarded. Thus, we conclude that SpSld3 is required for stable association of Cdc45 with chromatin both in initiation and elongation of DNA replication. The DDK-dependent origin association suggests that SpSld3 is involved in temporal regulation of origin firing.
A classification of tasks in bioinformatics
Authors: Stevens Robert , Goble Carole , Baker Patricia , Brass Andy
Published: July 2002

Motivation: This paper reports on a survey of bioinformatics tasks currently undertaken by working biologists. The aim was to find the range of tasks that need to be supported and the components needed to do this in a general query system. This enabled a set of evaluation criteria to be used to assess both the biology and mechanical nature of general query systems.

Results: A classification of the biological content of the tasks gathered offers a checklist for those tasks (and their specialisations) that should be offered in a general bioinformatics query system. This semantic analysis was contrasted with a syntactic analysis that revealed the small number of components required to describe all bioinformatics questions. Both the range of biological tasks and syntactic task components can be seen to provide a set of bioinformatics requirements for general query systems. These requirements were used to evaluate two bioinformatics query systems.

Contact: robert.stevens@cs.man.ac.uk

Supplementary information: The questionnaire, responses and their summaries may be found at http://img.cs.man.ac.uk/tambis/questionnaire/bio-queries.html

* To whom correspondence should be addressed.
Analysis of mRNA expression and protein abundance data: an
approach for the comparison of the enrichment of features in the
cellular population of proteins and transcripts
Authors: Greenbaum Dov , Jansen Ronald , Gerstein Mark
Published: July 2002

Motivation: Protein abundance is related to mRNA expression through many different cellular processes. Up to now, there have been conflicting results on how correlated the levels of these two quantities are. Given that expression and abundance data are significantly more complex and noisy than the underlying genomic sequence information, it is reasonable to simplify and average them in terms of broad proteomic categories and features (e.g. functions or secondary structures), for understanding their relationship. Furthermore, it will be essential to integrate, within a common framework, the results of many varied experiments by different investigators. This will allow one to survey the characteristics of highly expressed genes and proteins.

Results: To this end, we outline a formalism for merging and scaling many different gene expression and protein abundance data sets into a comprehensive reference set, and we develop an approach for analyzing this in terms of broad categories, such as composition, function, structure and localization. As the various experiments are not always done using the same set of genes, sampling bias becomes a central issue, and our formalism is designed to explicitly show this and correct for it. We apply our formalism to the currently available gene expression and protein abundance data for yeast. Overall, we found substantial agreement between gene expression and protein abundance, in terms of the enrichment of structural and functional categories. This agreement, which was considerably greater than the simple correlation between these quantities for individual genes, reflects the way broad categories collect many individual measurements into simple, robust averages. In particular, we found that in comparison to the population of genes in the yeast genome, the cellular populations of transcripts and proteins (weighted by their respective abundances, the transcriptome and what we dub the translatome) were both enriched in: (i) the small amino acids Val, Gly, and Ala; (ii) low molecular weight proteins; (iii) helices and sheets relative to coils; (iv) cytoplasmic proteins relative to nuclear ones; and (v) proteins involved in ‘protein synthesis,’ ‘cell structure,’ and ‘energy production.’

Supplementary information: http://genecensus.org/expression/translatome

Contact: mark.gerstein@yale.edu

* To whom correspondence should be addressed.

† These authors contributed equally to this work.
Strategic Groups and Rent Dissipation
Authors: Baik Kyung Hwan , Lee Sanghack
Published: July 2002

We consider a rent‐seeking contest in which players can form strategic groups before expending their outlays. We examine the profitability of endogenous group formation and the effect of such group formation on rent dissipation. We show the following: When just one strategic group is formed in equilibrium, group formation is beneficial both to the group members and to the nonmembers, and rent dissipation is smaller than with usual individual rent seeking. However, when more than two strategic groups are formed in equilibrium, group formation is never profitable to any players, and rent dissipation is greater than with individual rent seeking.
Involvement of state transitions in the switch between linear and cyclic electron flow in Chlamydomonas reinhardtii
Authors: Finazzi Giovanni , Rappaport Fabrice , Furia Alberto , Fleischmann Mark , Rochaix Jean‐David , Zito Francesca , Forti Giorgio
Published: July 2002

The energetic metabolism of photosynthetic organisms is profoundly influenced by state transitions and cyclic electron flow around photosystem I. The former involve a reversible redistribution of the light‐harvesting antenna between photosystem I and photosystem II and optimize light energy utilization in photosynthesis whereas the latter process modulates the photosynthetic yield. We have used the wild‐type and three mutant strains of the green alga Chlamydomonas reinhardtii—locked in state I (stt7), lacking the photosystem II outer antennae (bf4) or accumulating low amounts of cytochrome b6f complex (A‐AUU)—and measured electron flow though the cytochrome b6f complex, oxygen evolution rates and fluorescence emission during state transitions. The results demonstrate that the transition from state 1 to state 2 induces a switch from linear to cyclic electron flow in this alga and reveal a strict cause–effect relationship between the redistribution of antenna complexes during state transitions and the onset of cyclic electron flow.
Petites Bourgeoises and Penny Capitalists: Women in Retail in the Lille Area during the Nineteenth Century
Authors: Craig Béatrice
Published: July 2002

With few exceptions, historians have argued that in the nineteenth century women were excluded from most retail activities. In Europe women became increasingly concentrated in small-scale, undercapitalized, and short-lived stores. The “separate sphere” ideology in its different guises underlay this evolution. In North America, on the other hand, women capitalized on this ideology to carve a niche for themselves in trade and retailing. Women were not marginalized or segregated everywhere in Europe, however. In northern France the expansion of retail trade and overall improvements in standards of living provided women, especially married ones, with opportunities they were not reluctant to grasp. Though the activities of married women remained subordinated to the needs of their families, female retailers were neither particularly impoverished nor segregated in sectors deemed appropriate for persons of their sex.
An NMR and Mutational Study of the Pseudoknot Within the Gene 32 mRNA of Bacteriophage T2: Insights into a Family of Structurally Related RNA Pseudoknots
Authors: Du Zhihua , Hoffman David W.
Published: July 2002

NMR methods were used to investigate a series of mutants of the pseudoknot within the gene 32messenger RNA of bacteriophage T2, for the purpose of investigating the range of sequences, stem and loop lengths that can form a similar pseudoknot structure. This information is of particular relevance since the T2 pseudoknot has been considered a representative of a large family of RNA pseudoknots related by a common structural motif, previously referred to as ‘common pseudoknot motif 1’ or CPK1. In the work presented here, a mutated sequence with the potential to form a pseudoknot with a 6 bp stem2 was shown to adopt a pseudoknot structure similar to that of the wild-type sequence. This result is significant in that it demonstrates that pseudoknots with 6 bp in stem2 and a single nucleotide in loopl are indeed feasible. Mutated sequences with the potential to form pseudoknots with either 5 or 8 bp in stem2 yielded NMR spectra that could not confirm the formation of a pseudoknot structure. Replacing the adenosine nucleotide in loopl of the wild-type pseudoknot with any one of G, C or U did not significantly alter the pseudoknot structure. Taken together, the results of this study provide support for the existence of a family of similarly structured pseudoknots with two coaxially stacked stems, either 6 or 7 bp in stem2, and a single nucleotide in loop1. This family includes many of the pseudo-knots predicted to occur downstream of the frameshift or readthrough sites in a significant number of viral RNAs.
Polyglutamine pathogenesis
Authors: Ross Christopher A. , Wood Jonathan D. , Schilling Gabriele , Peters Matthew F. , Nucifora Frederick C. , Cooper Jillian K. , Sharp Alan H. , Margolis Russell L. , Borchelt David R.
Published: July 2002

An increasing number of neurodegenerative disorders have been found to be caused by expanding CAG triplet repeats that code for polyglutamine. Huntington's disease (HD) is the most common of these disorders and dentato-rubral-pallidoluysian atrophy (DRPLA) is very similar to HD, but is caused by mutation in a different gene, making them good models to study. In this review, we will concentrate on the roles of protein aggregation, nuclear localization and proteolytic processing in disease pathogenesis. In cell model studies of HD, we have found that truncated N-terminal portions of huntingtin (the HD gene product) with expanded repeats form more aggregates than longer or full length huntingtin polypeptides. These shorter fragments are also more prone to aggregate in the nucleus and cause more cell toxicity. Further experiments with huntingtin constructs harbouring exogenous nuclear import and nuclear export signals have implicated the nucleus in direct cell toxicity. We have made mouse models of HD and DRPLA using an N-terminal truncation of huntingtin (N171) and full-length atrophin-1 (the DRPLA gene product), respectively. In both models, diffuse neuronal nuclear staining and nuclear inclusion bodies are observed in animals expressing the expanded glutamine repeat protein, further implicating the nucleus as a primary site of neuronal dysfunction. Neuritic pathology is also observed in the HD mice. In the DRPLA mouse model, we have found that truncated fragments of atrophin-1 containing the glutamine repeat accumulate in the nucleus, suggesting that proteolysis may be critical for disease progression. Taken together, these data lead towards a model whereby proteolytic processing, nuclear localization and protein aggregation all contribute to pathogenesis.
Molecular mechanism of autophagy in yeast, Saccharomyces cerevisiae
Authors: Ohsumi Y.
Published: July 2002

Bulk degradation of cytosol and organelles is important for cellular homeostasis under nutrient limitation, cell differentiation and development. This process occurs in a lytic compartment, and autophagy is the major route to the lysosome and/or vacuole. We found that yeast,
Saccharomyces cerevisiae
, induces autophagy under various starvation conditions. The whole process is essentially the same as macroautophagy in higher eukaryotic cells. However, little is known about the mechanism of autophagy at a molecular level. To elucidate the molecules involved, a genetic approach was carried out and a total of 16 autophagy–defective mutants (
apg
) were isolated. So far, 14
APG
genes have been cloned. Among them we recently found a unique protein conjugation system essential for autophagy. The C–terminal glycine residue of a novel modifier protein Apg12p, a 186–amino–acid protein, is conjugated to a lysine residue of Apg5p, a 294–amino–acid protein, via an isopeptide bond. We also found that
apg7
and
apg10
mutants were unable to form an Apg12p–Apg5p conjugate. The conjugation reaction is mediated via Apg7p, E1–like activating enzyme and Apg10p, indicating that it is a ubiquitination–like system. These
APG
genes have mammalian homologues, suggesting that the Apg12 system is conserved from yeast to human. Further molecular and cell biological analyses of
APG
gene products will give us crucial clues to uncover the mechanism and regulation of autophagy.
Structural model of F
1
–ATPase and the implications for rotary catalysis
Authors: Leslie A. G. W. , Walker J. E.
Published: July 2002

The crystal structure of bovine mitochondrial F
1
–ATPase is described. Several features of the structure are consistent with the binding change mechanism of catalysis, in which binding of substrates induces conformational changes that result in a high degree of cooperativity between the three catalytic sites. Furthermore, the structure also suggests that catalysis is accompanied by a physical rotation of the centrally placed γ–subunit relative to the approximately spherical α
3
β
3
sub–assembly.
Comparative structures and properties of elastic proteins
Authors: Tatham A. S. , Shewry P. R.
Published: July 2002

Elastic proteins are characterized by being able to undergo significant deformation, without rupture, before returning to their original state when the stress is removed. The sequences of elastic proteins contain elastomeric domains, which comprise repeated sequences, which in many cases appear to form β–turns. In addition, the majority also contain domains that form intermolecular cross-links, which may be covalent or non-covalent. The mechanism of elasticity varies between the different proteins and appears to be related to the biological role of the protein.
Human Paralogs of KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms
Authors: Crosier Moira , Viggiano Luigi , Guy Jane , Misceo Doriana , Stones Robert , Wei Wenbin , Hearn Tom , Ventura Mario , Archidiacono Nicoletta , Rocchi Mariano , Jackson Michael S.
Published: July 2002

KIAA0187 is a gene of unknown function that maps to 10q11 and has been subject to recent duplication events. Here we analyze 18 human paralogs of this gene and show that paralogs of exons 14–23 were formed through satellite-associated pericentromeric-directed duplication, whereas paralogs of exons 1–9 were created via chromosome-specific satellite-independent duplications. In silico, Northern, and RT-PCR analyses indicate that nine paralogs are transcribed, including four in which KIAA0187 exons are spliced onto novel sequences. Despite this, no new genes appear to have been created by these events. The chromosome 10 paralogs map to 10q11, 10q22, 10q23.1, and 10q23.3, forming part of a complex family of chromosome-specific repeats that includes GLUD1,Cathepsin L, and KIAA1099 pseudogenes. Phylogenetic analyses and comparative FISH indicates that the 10q23.1 and 10q23.3 repeats were created in 10q11 and relocated by a paracentric inversion 13 to 27 Myr ago. Furthermore, the most recent duplications, involving the KIAA1099 pseudogenes, have largely been confined to 10q11. These results indicate a simple model for the evolution of this repeat family, involving multiple rounds of centromere-proximal duplication and dispersal through intrachromosomal rearrangement. However, more complex events must be invoked to account for high sequence identity between some paralogs.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AJ298152 through AJ298168.]
The determination of dose characteristics of ruthenium ophthalmic applicators using radiochromic film
Authors: Taccini G. , Cavagnetto F. , Coscia G. , Garelli S. , Pilot A.
Published: July 2002

Ruthenium ophthalmic applicators are energetic beta ray sources, supplied in several shapes and dimensions, and used in intraocular tumor therapy. Because of their small dimensions, the determination of dosimetric characteristics represents a technical challenge. We developed a semi‐automatic method to define surface dose, dose distribution, and percentage depth dose of such applicators using radiochromic dosimetric media. These detectors consist of a thin (7 μm) radiation sensitive layer on polyester base (100 μm total thickness) changing color as a function of radiation exposure. Transmission images of exposed films were then grabbed with a TV‐digitizer system to obtain a gray‐level image from which dosimetric characteristics such as isodose distribution, dose values, and homogeneity of nuclide distribution were derived. Good agreement between experimental results and Monte Carlo simulation performed using the GEANT 3 code, appear to be a confirmation of the validity of the method. Moreover while manufacturer specifications of absolute and relative dose rates present a standard deviation error of on dose rate and on accuracy of relative dose values, the proposed method reduces the errors to and respectively.
A first order approximation of field‐size and depth dependence of wedge transmission
Authors: Tailor Ramesh C. , Followill David S. , Hanson William F.
Published: July 2002

The Radiological Physics Center, through its dosimetry review visits to participating institutions, is aware that many institutions ignore the field‐size and depth dependence of wedge transmission values. Reference wedge transmission values are normally measured by the Radiological Physics Center for a field at the calibration depth of 5 or 7 cm. Recently, additional measurements (1) for a field at 20‐cm depth and (2) for a field at the calibration depth were included. The transmission under these two conditions was compared with that under reference conditions. The relative transmission values for 138 photon beams from 88 separate linear accelerators (4–25 MV) and units were measured. Our data suggest that the dependence of the wedge transmission on field‐size and depth, in the first approximation, depends on the absolute value of the transmission under reference conditions. For wedges with a transmission value greater than 0.65%, field‐size dependence and change in depth dose are typically less than 2%. However, for wedges with transmission values less than 0.65%, field‐size dependence increases with decreasing reference wedge transmission. The change in wedge transmission with depth is significant only for photon energies less than or equal to 10 MV and can exceed 5% for thick wedges. Failure to include the depth and field‐size dependencies of wedge transmission in patient dosimetry calculations can result in significant tumor‐dose discrepancies.
Simple estimate of the human metabolic rate
Authors: Graham Daniel J. , Schacht David V.
Published: July 2002

A method for estimating the human metabolic rate is described. It entails measuring the rate at which carbon dioxide is produced by glucose oxidation during respiration. Such measurements can enhance classroom presentations of the concept of energy and its interconversion. Measurements of this type can also augment classroom discussions of related topics such as entropy production in nonequilibrium systems. The ideas are appropriate at both the high school and college levels and should appeal to student interest in metabolism, physiology, and medical physics.
The zeta function method and the harmonic oscillator propagator
Authors: Barone F. A. , Farina C.
Published: July 2002

We show how the pre-exponential factor of the Feynman propagator for the harmonic oscillator can be computed by the generalized ζ-function method. Also, we establish a direct equivalence between this method and Schwinger’s proper time method.
Resource Letter CF-1: Casimir Force
Authors: Lamoreaux S. K.
Published: July 2002

This resource letter provides an introductory guide to the literature on the Casimir force. Journal articles and books are cited for the following topics: introductory articles and books, calculations, dynamical Casimir effect, mechanical analogs, applications, and experiments.
Frequency doubled diode laser pumped Nd:YVO4 microchip laser
Authors: Zhdanov B. V. , Andersen G. P. , Knize R. J.
Published: July 2002

We describe the construction and operation of a compact diode laser pumped Nd:YVO4 microchip laser with intracavity frequency doubling. An output power of about 100 mW at 0.53 μm has been achieved. This device can be used in undergraduate teaching labs and for research applications as well. An experiment using this laser for holography is described.
A mathematical analysis of the peripheral auditory system mechanics in the goldfish (Carassius auratus)
Authors: Finneran James J. , Hastings Mardi C.
Published: July 2002

The dynamic response of the goldfish peripheral auditory system has been analyzed using lumped-parameter mechanical and fluid system models for the swimbladder, Weberian apparatus, and saccule. The swimbladder is treated as a two degree-of-freedom mechanical system consisting of two coupled mass-spring-damper arrangements. The swimbladder is coupled to the Weberian ossicles using a phenomenological analysis of the anterior swimbladder tunica externa which permits both stretching and sliding. Analysis of the saccule features only a single degree of freedom, corresponding to the direction of orientation of the ciliary bundles. Inputs to the saccule consist of the transverse canal fluid motion and the motion of the animal’s head (assumed to match the local acoustic particle motion). Mechanical properties required for the system equations were estimated from published literature, direct measurements, and curve fits to experimental data for the motions of the swimbladders. The results indicate that the Weberian apparatus has a significant impact on hearing ability over the entire auditory bandwidth, not just at higher frequencies, and that the saccule functions as a displacement sensor above approximately 300 Hz.
A method for individual identification of echolocation signals in free-ranging finless porpoises carrying data loggers
Authors: Akamatsu Tomonari , Wang Ding , Wang Kexiong , Naito Yasuhiko
Published: July 2002

Echolocation click events of a free-ranging juvenile and an adult finless porpoise (Neophocaena phocaenoides) were recorded with an acoustic data logger. Additionally, dive depth and swim speed of the juvenile were recorded with a behavior data logger. Echoes of echolocation signals from the water surface were clearly detected in shallow dives approximately less than 2 m. The delay time between a surface echo and a direct signal corresponded with the two-way transmission time for the animal’s depth, indicating that the signals originated from the animal wearing the data loggers. The finless porpoises produced echolocation signals frequently and were thought to be able to detect their depth by listening to echoes from the water surface.
Prediction models for sound leakage through noise barriers
Authors: Yiu Wong Hon , Ming Li Kai
Published: July 2002

Two numerical models are presented for the prediction of sound leakage through openings in thin hard barriers. The first numerical method is based on a simple procedure of numerical integration that can be implemented straightforwardly. This model is a more general approach, suitable for barriers with arbitrary gaps. The second model is a new method that permits prediction of sound leakage due to the presence of horizontal gaps in a long barrier. In the new method, effective barriers of appropriate heights represent the edges of the horizontal gaps. The sound diffracted by each effective barrier is calculated by a closed-form analytic expression. The total sound-pressure level is determined from a sum of these diffracted fields. Hence, the new method is fast, simple, and intuitive, allowing the leakage to be assessed accurately. The validity of these two numerical models is confirmed by precise experimental measurements.
Spatial fluctuations in measures for spaciousness
Authors: de Vries Diemer , Hulsebos Edo M. , Baan Jan
Published: July 2002

In room acoustics, several measures have been defined that are supposed to quantify the apparent source width (ASW) in a hall, being one of the perceptual cues related to spaciousness. The most common ones are the lateral energy fraction (LF), i.e., the ratio between lateral and omnidirectional early energy, and the interaural cross correlation coefficient (IACC), all to be calculated from measured or simulated impulse responses. [Several versions of the LF are known in literature, having different names, generalized here as lateral energy fraction.] According to a method proposed by Berkhout et al. [J. Acoust. Soc. Am. 102, 2757–2770 (1997)], for a fixed source position impulse responses have been measured along an array of closely spaced microphone positions in several halls. The above measures, when calculated from these impulse responses, show large fluctuations with small variations in microphone position due to interference of the different components of the wave field to which the human ear is apparently insensitive. A revision of the measures is discussed, which contributes to the suppression of the interference effects. In order to assess their perceptual significance, the fluctuations have to be related to just-noticeable differences (jnd’s) in ASW. Since very different jnd values are given in the literature, the authors advise that new experiments should be conducted on this point.
Low-frequency sound generation by an individual open-ocean breaking wave
Authors: Means Steven L. , Heitmeyer Richard M.
Published: July 2002

Bubble cloud resonances have been proposed as an explanation of the low-frequency acoustic radiation produced by breaking waves. A previous model [H. N. Ogũz, J. Acoust. Soc. Am. 95, 1895–1912 (1994)] considered excitation of the bubble cloud by a rigid piston at the base of a hemispherical bubble cloud. The present model considers excitation of the cloud by individual point sources within the cloud. A Green’s function is obtained for a point source displaced from the origin of a hemispherical bubble cloud beneath a pressure release surface. The method of images and superposition allow one to obtain the field generated by a distribution of point sources within the bubble cloud. The frequency-dependent radiation pattern for two distributions of point sources within the cloud is obtained. Distributing the point sources within the forward sector of the bubble cloud generates spectral characteristics consistent with measured open-ocean breaking wave spectra.
Acoustic echo detection and arrival-time estimation using spectral tail energy
Authors: Ainsleigh Phillip L.
Published: July 2002

An algorithm is introduced for detecting signal and echo onsets and estimating their arrival times in multipath acoustic data. The algorithm accommodates superimposed narrow-band signals with continuous onsets, unknown envelopes, and arrival-time separations of less than one cycle at the dominant tonal frequency. It does not require the multipath components to be shifted and weighted replicas of each other or of a template signal. The separation of closely spaced signals is enabled by applying a prefilter that isolates spectral “tail” energy in which the onsets are discernible, and by operating on the filtered data using a matched-subspace detector that is conditioned on previously detected onsets. This algorithm has particular value for laboratory measurements, as it utilizes the high signal-to-noise ratios available in a laboratory to solve a previously intractable detection and estimation problem.
A correction to Maekawa’s curve for the insertion loss behind barriers
Authors: Menounou Penelope
Published: July 2002

Maekawa’s curve is one of the most established methods for predicting the insertion loss (IL) behind barriers. For the simple case of a barrier modeled as a half plane, the IL is given versus a single parameter, the Fresnel number (N1). Predictions obtained by Maekawa’s curve deviate largely from experimental data, and from predictions obtained by analytical solutions, when the receiver is either close to the barrier or at the boundary separating the illuminated from the shadow zone. It is shown that if a second Fresnel number (N2) is appropriately defined, the IL obtained by the existing analytical solutions can be expressed versus N1 and N2 for several types of incident radiation (plane, cylindrical, and spherical). Accordingly, the single curve in Maekawa’s chart can be replaced by a family of curves. Each curve corresponds to a different N2 and provides the IL versus N1. The Kurze–Anderson formula (a mathematical expression of Maekawa’s curve) is also modified to describe this set of curves. Besides providing increased accuracy in the areas where Maekawa’s curve does not, the graph proposed here addresses the more general problem of combining the simplicity of empirical models like Maekawa’s with the accuracy of sophisticated mathematical models.
Numerical simulations of xylophones. I. Time-domain modeling of the vibrating bars
Authors: Chaigne Antoine , Doutaut Vincent
Published: July 2002

A time-domain modeling of xylophone bars excited by the blow of a mallet is presented. The flexural vibrations of the bar, with nonuniform cross section, are modeled by a one-dimensional Euler–Bernoulli equation, modified by the addition of two damping terms for the modeling of losses and a restoring force for the modeling of the stiffness of the suspending cord. The action of the mallet against the bar is described by Hertz’s law of contact for linear elastic bodies. This action appears as a force density term on the right-hand side of the bending wave equation. The model is completed by the equation of motion for the mallet, and by free–free boundary conditions for the bar. The bending wave equation of the bar is put into a numerical form by means of an implicit finite-difference scheme, which ensures a sufficient spatial resolution for an accurate tuning of the bar. The geometrical, elastic, and damping parameters of the model are derived from experiments carried out on actual xylophones and mallets. The validity of the numerical model is confirmed by three different procedures: First, a comparison is made between numerical results and analytical solutions. The second series of tests consist of examining the effects of the number of spatial steps on the convergence of the solution. Finally, various comparisons are made between measured and simulated impact forces and bar accelerations. The present model reproduces adequately the main features of a real instrument. The most significant physical parameters of bars, mallets and players’ actions can be controlled independently for producing a remarkable variety of tones.
The variability of high-frequency acoustic backscatter from the region near the sea surface
Authors: Dahl Peter H. , Plant William J.
Published: July 2002

The temporal variability of acoustic backscattering from the region near the sea surface is examined for frequencies in the 30–70 kHz range. A variance spectrum of the scattering strength exhibits effects associated with three different processes. Below about 0.1 Hz, the spectrum contains a large contribution associated with temporal variations in the advection of bubble clouds through the measurement volume by large-scale processes. At high frequencies, the spectrum asymptotes to a level characteristic of a Gaussian backscattered pressure field from randomly moving bubbles within the scattering volume. The overall variability is treated as a slow modulation of this Gaussian process by larger-scale processes and a probability density function is derived for the scattering strength using Bayes’ theorem. Finally, in some cases, the spectrum exhibits a peak at the frequency of the dominant surface waves. Attempts to compute coherence functions between the backscattered acoustic power and surface wave orbital velocities, measured by a microwave system observing the same spot as the acoustic system, resulted in very low values. This leads to the belief that the wave-induced peak in the acoustic backscatter variance spectrum is caused by highly nonlinear processes. A time series of acoustic backscatter from a vertically pointing system confirms the existence of this modulation at the dominant wave frequency and also suggests its nonlinear character.
Fast and explicit Wentzel–Kramers–Brillouin mode sum for the bottom-interacting field, including leaky modes
Authors: Ainslie Michael A. , Packman Mark N. , Harrison Christopher H.
Published: July 2002

A fast and explicit method is presented for calculating the bottom-interacting field by means of a mode sum, using the Wentzel–Kramers–Brillouin approximation for the eigenfunctions and the Tindle–Weston formula for eigenvalue spacing. Both trapped and leaky modes are automatically included, requiring no numerical inversions for either eigenfunctions or eigenvalues. Examples are provided which demonstrate the speed and accuracy of the approach by comparison with reference solutions. The importance of leaky modes, especially in range-dependent environments with variable water depth, is demonstrated. A simple criterion for neglecting leaky modes is developed.
Directional acoustic startle response in the goldfish
Authors: Lewis Thomas N. , Rogers Peter H.
Published: July 2002

Fish exhibit a characteristic Mauthner-initiated startle response to sudden acoustic stimuli. This escape response is thought to be triggered by predatory attacks since an acoustic wave is launched ahead of a striking predator. The nature of acoustic stimuli which elicit the startle response was examined in free-swimming goldfish (Carassius auratus). The results showed that a threshold level of acoustic acceleration (−30 dB re: 1 m/s2), not pressure, was required to elicit a startle and that the threshold was invariant of bearing to the source. Near threshold, the fish turned in a random direction, but as the stimulus level increased, the fish was more likely to turn away from the source. The data indicated that the lateral component of the acoustic acceleration was the relevant parameter determining directionality. A proposed model uses the utricle to detect acoustic acceleration directly, the saccule to detect acoustic pressure indirectly, and logical wiring to perform the neural computation which explains the fish’s behavioral performance.
Results of underwater ambient noise measurements in three large tank exhibits at the Monterey Bay Aquarium
Authors: O’Neal Daniel M. , Baker Steven R.
Published: July 2002

Measurements have been made of the underwater ambient noise in three large tank exhibits at the Monterey Bay Aquarium: the Kelp Forest Exhibit (335 000 gal), the Monterey Bay Habitats Exhibit (350 000 gal), and the Outer Bay Waters Exhibit (1.4 million gal). A single, calibrated, Navy-type DT-276 was used. The hydrophone output voltage was preamplified and recorded using a 16-bit digital audio tape recorder with a sampling rate of 48 kHz. Measurements were made with various mechanical equipment (motors, fans, pumps, sprinklers, wave machine) turned on and off. On one occasion, the noise was measured in the largest tank, the Outer Bay Waters Exhibit, during a power shutdown. For comparison, measurements were also made at several locations and depths in the inner Monterey Bay. The results of one-third octave band and narrow-band analyses will be presented. Comparisons will be made between the aquarium and bay results and standard deep water ambient noise spectral density curves.