bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Authors: Andrade M A , Valencia A
Published: July 2002

MOTIVATION: Annotation of the biological function of different protein sequences is a time-consuming process currently performed by human experts. Genome analysis tools encounter great difficulty in performing this task. Database curators, developers of genome analysis tools and biologists in general could benefit from access to tools able to suggest functional annotations and facilitate access to functional information. APPROACH: We present here the first prototype of a system for the automatic annotation of protein function. The system is triggered by collections of s related to a given protein, and it is able to extract biological information directly from scientific literature, i.e. MEDLINE abstracts. Relevant keywords are selected by their relative accumulation in comparison with a domain-specific background distribution. Simultaneously, the most representative sentences and MEDLINE abstracts are selected and presented to the end-user. Evolutionary information is considered as a predominant characteristic in the domain of protein function. Our system consequently extracts domain-specific information from the analysis of a set of protein families. RESULTS: The system has been tested with different protein families, of which three examples are discussed in detail here: 'ataxia-telangiectasia associated protein', 'ran GTPase' and 'carbonic anhydrase'. We found generally good correlation between the amount of information provided to the system and the quality of the annotations. Finally, the current limitations and future developments of the system are discussed. AVAILABILITY: The current system can be considered as a prototype system. As such, it can be accessed as a server at http://columba.ebi.ac. uk:8765/andrade/abx. The system accepts text related to the protein or proteins to be evaluated (optimally, the result of a MEDLINE search by keyword) and the results are returned in the form of Web pages for keywords, sentences and s. SUPPLEMENTARY INFORMATION: Web pages containing full information on the examples mentioned in the text are available at: http://www.cnb.uam.es/ approximately cnbprot/keywords/ CONTACT: valencia@cnb.uam.es
Domain identification by clustering sequence alignments.
Authors: Guan X , Du L
Published: July 2002

MOTIVATION: As sequence databases grow rapidly, results from sequence comparison searches using fast search methods such as BLAST and FASTA tend to be long and difficult to digest. RESULTS: In this paper, we present a new method to extract domain information from sequence comparison searches by clustering the resulting alignments according to their similarity to the query sequence. Efficient tree structures and algorithms are used to organize the alignment data such that structurally conserved elements can be easily identified. The hierarchical nature of the data structures used and the flexible X-Window-based interface provide an efficient and intuitive means to explore the alignment data at different levels so that the common domains, as well as distantly related features, can be explored. AVAILABILITY: The clustering program is available by anonymous ftp at: ftp.embl-ebi.ac.uk under directory /pub/software/unix, file: clustering.tar.Z.
Engineering support vector machine kernels that recognize

translation initiation sites
Authors: Zien A. , Rätsch G. , Mika S. , Schölkopf B. , Lengauer T. , Müller K.-R.
Published: July 2002

Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS).

Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

Contact: {Alexander.Zien,Gunnar.Raetsch,Sebastian. Mika}@gmd.de; bsc@microsoft.com

To whom correspondence should be addressed.
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
Authors: Schacherer Frank , Choi Claudia , Götze Ulrike , Krull Mathias , Pistor Susanne , Wingender Edgar
Published: July 2002

TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al. , Nucleic Acids Res. , 28, 316–319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like complexes, signaling molecules, and their states are stored together with information about their interaction in an object-oriented database. The database interface provides clickable maps and automatically generated pathway cascades as additional ways to explore the data. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others).

Availability: The database is available over (http://transpath.gbf.de) for interactive perusal. As an exchange format for the data, eXtensible Markup Language (XML) flatfiles and a Document Type Definition (DTD) are provided.

Contact: frs@biobase.de; cch@biobase.de; ulg@biobase.de; mkl@biobase.de; ewi@biobase.de; spi@biobase.de
The Drosophila homolog of the human AF10 is an HP1‐interacting suppressor of position effect variegation
Authors: Linder Britta , Gerlach Nina , Jäckle Herbert
Published: July 2002

In chromosomal rearrangements of acute myeloid leukaemia patients the mixed lineage leukaemia (MLL) gene, a human homolog of the Drosophila gene trithorax, is frequently fused to AF10. Here we describe the identification and a functional characterization of the Drosophila homolog dAF10. We show that dAF10 functions in heterochromatin‐dependent genomic silencing of position effect variegation, a phenomenon associated with chromosomal rearrangements that cause mosaic expression of euchromatic genes when relocated next to heterochromatin. We also demonstrate that dAF10 can associate with the heterochromatin protein 1 (HP1) in vitro and in vivo. The results indicate that dAF10 is an HP1‐interacting component of the heterochromatin‐dependent gene silencing pathway, which either contributes to the stability of the heterochromatin complex or to its function.
The Cdk5‐p35 kinase associates with the Golgi apparatus and regulates membrane traffic
Authors: Paglini Gabriela , Peris Leticia , Diez‐Guerra Javier , Quiroga Santiago , Cáceres Alfredo
Published: July 2002

We show here that an active Cdk5‐p35 kinase is present in Golgi membranes, where it associates with a detergent‐insoluble fraction containing actin. In addition, Cdk5‐p35‐dependent phosphorylation of α‐PAK immunoreactive protein species was detected in Golgi membranes, as well as an interaction with the small GTPase, Cdc42. Moreover, antisense oligonucleotide suppression of Cdk5 or p35 in young cultured neurons, as well as inhibition of Cdk5 activity with olomoucine, blocks the formation of membrane vesicles from the Golgi apparatus. Taken together, these results show a novel subcellular localization of this kinase and suggest a role for Cdk5‐p35 in membrane traffic during neuronal process outgrowth.
Slaves of the environment: the movement of herbivorous insects in relation to their ecology and genotype
Authors: Loxdale Hugh D. , Lushai Gugs
Published: July 2002

The majority of insect species do not show an innate behavioural migration, but rather populations expand into favourable new habitats or contract away from unfavourable ones by random changes of spatial scale. Over the past 50 years, the scientific fascination with dramatic long–distance and directed mass migratory events has overshadowed the more universal mode of population movement, involving much smaller stochastic displacement during the lifetime of the insects concerned. This may be limiting our understanding of insect population dynamics. In the following synthesis, we provide an overview of how herbivorous insect movement is governed by both abiotic and biotic factors, making these animals essentially ‘slaves of their environment’. No displaced insect or insect population can leave a resource patch, migrate and flourish, leaving descendants, unless suitable habitat and/or resources are reached during movement. This must have constrained insects over geological time, bringing about species–specific adaptation in behaviour and movements in relation to their environment at a micro– and macrogeographical scale. With insects that undergo long–range spatial displacements, e.g. aphids and locusts, there is presumably a selection against movement unless overruled by factors, such as density–dependent triggering, which cause certain genotypes within the population to migrate. However, for most insect species, spatial changes of scale and range expansion are much slower and may occur over a much longer time–scale, and are not innate (nor directed). Ecologists may say that all animals and plants are figuratively speaking ‘slaves of their environments’, in the sense that their distribution is defined by their ecology and genotype. But in the case of insects, a vast number must perish daily, either out at sea or over other hostile habitats, having failed to find suitable resources and/or a habitat on which to feed and reproduce. Since many are blown by the vagaries of the wind, their chances of success are serendipitous in the extreme, especially over large distances. Hence, the strategies adopted by mass migratory species (innate pre–programmed flight behaviour, large population sizes and/or fast reproduction), which improve the chances that some of these individuals will succeed. We also emphasize the dearth of knowledge in the various interactions of insect movement and their environment, and describe how molecular markers (protein and DNA) may be used to examine the details of spatial scale over which movement occurs in relation to insect ecology and genotype.
Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways inStreptomyces coelicolorusing DNA microarrays
Authors: Huang Jianqiang , Lih Chih-Jian , Pan Kuang-Hung , Cohen Stanley N.
Published: July 2002

The eubacterial speciesStreptomyces coelicolorproceeds through a complex growth cycle in which morphological differentiation/development is associated with a transition from primary to secondary metabolism and the production of antibiotics. We used DNA microarrays and mutational analysis to investigate the expression of individual genes and multigene antibiotic biosynthetic pathways during these events. We identified expression patterns in biosynthetic, regulatory, and ribosomal protein genes that were associated highly specifically with particular stages of development. A knowledge-based algorithm that correlates temporal changes in expression with chromosomal position identified groups of contiguous genes expressed at discrete stages of morphological development, inferred the boundaries of known antibiotic synthesis gene loci, and revealed novel physical clusters of coordinately regulated genes. Microarray analysis of RNA from cells mutated in genes regulating synthesis of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red) identified proximate and distant sites that contain putative ABC transporter and two-component system genes expressed coordinately with genes of specific biosynthetic pathways and indicated the existence of two functionally and physically discrete regulons in the Red pathway.
Role of the single disulphide bond of β2‐microglobulin in amyloidosis in vitro
Authors: Smith David P. , Radford Sheena E.
Published: July 2002

The aggregation of β2‐microglobulin (β2m) into amyloid fibrils occurs in the condition known as dialysis‐related amyloidosis (DRA). The protein has a β‐sandwich fold typical of the immunoglobulin family, which is stabilized by a highly conserved disulphide bond linking Cys25 and Cys80. Oxidized β2m forms amyloid fibrils rapidly in vitro at acidic pH and high ionic strength. Here we investigate the role of the single disulphide bond of β2m in amyloidosis in vitro. We show that reduction of the disulphide bond destabilizes the native protein such that non‐native molecules are populated at neutral pH. These species are prone to oligomerization but do not form amyloid fibrils when incubated for up to 8 mo at pH 7.0 in 0.4 M NaCl. Over the pH range 4.0–1.5 in the presence of 0.4 M NaCl, however, amyloid fibrils of reduced β2m are formed. These fibrils are ∼10 nm wide, but are shorter and assemble more rapidly than those produced from the oxidized protein. These data show that population of non‐native conformers of β2m at neutral pH by reduction of its single disulphide bond is not sufficient for amyloid formation. Instead, association of one or more specific partially unfolded molecules formed at acid pH are necessary for the formation of β2m amyloid in vitro. Further experiments will now be needed to determine the role of different oligomeric species of β2m in the toxicity of the protein in vivo.
Identification of a region in G protein γ subunits conserved across species but hypervariable among subunit isoforms
Authors: Cook Lana A. , Schey Kevin L. , Cleator John H. , Wilcox Michael D. , Dingus Jane , Hildebrandt John D.
Published: July 2002

The heterotrimeric GTP binding proteins, G proteins, consist of three distinct subunits: α, β, and γ. There are 12 known mammalian γ subunit genes whose products are the smallest and most variable of the G protein subunits. Sequencing of the bovine brain γ10 protein by electrospray mass spectrometry revealed that it differs from the human protein by an Ala to Val substitution near the N‐terminus. Comparison of γ isoform subunit sequences indicated that they vary substantially more at the N‐terminus than at other parts of the protein. Thus, species variation of this region might reflect the lack of conservation of a functionally unimportant part of the protein. Analysis of 38 γ subunit sequences from four different species shows that the N‐terminus of a given γ subunit isoform is as conserved between different species as any other part of the protein, including highly conserved regions. These data suggest that the N‐terminus of γ is a functionally important part of the protein exhibiting substantial isoform‐specific variation.
Monte Carlo study of correction factors for Spencer–Attix cavity theory at photon energies at or above 100 keV
Authors: Borg Jette , Kawrakow Iwan , Rogers D. W. O. , Seuntjens Jan P.
Published: July 2002

To develop a primary standard for sources, the basic science on which this standard is based, i.e., Spencer–Attix cavity theory, must be established. In the present study Monte Carlo techniques are used to investigate the accuracy of this cavity theory for photons in the energy range from 20 to 1300 keV, since it is usually not applied at energies below that of Ma and Nahum [Phys. Med. Biol. 36, 413–428 (1991)] found that in low‐energy photon beams the contribution from electrons caused by photons interacting in the cavity is substantial. For the average energy of the spectrum they found a departure from Bragg–Gray conditions of up to 3% caused by photon interactions in the cavity. When Monte Carlo is used to calculate the response of a graphite ion chamber to an encapsulated source it is found that it differs by less than 0.3% from the value predicted by Spencer–Attix cavity theory. Based on these Monte Carlo calculations, for cavities in graphite it is concluded that the Spencer–Attix cavity theory with is applicable within 0.5% for photon energies at 300 keV or above despite the breakdown of the assumption that there is no interaction of photons within the cavity. This means that it is possible to use a graphite ion chamber and Spencer–Attix cavity theory to calibrate an source. It is also found that the use of Δ related to the mean chord length instead of improves the agreement with Spencer–Attix cavity theory at from 0.2% to within 0.1% of unity. This is at the level of accuracy of which the Monte Carlo code EGSnrc calculates ion chamber responses. In addition, it is shown that the effects of other materials, e.g., insulators and holders, have a substantial effect on the ion chamber response and should be included in the correction factors for a primary standard of air kerma.
Beta‐particle dosimetry of the trabecular skeleton using Monte Carlo transport within 3D digital images
Authors: Jokisch D. W. , Bouchet L. G. , Patton P. W. , Rajon D. A. , Bolch W. E.
Published: July 2002

Presently, skeletal dosimetry models utilized in clinical medicine simulate electron path lengths through skeletal regions based upon distributions of linear chords measured across bone trabeculae and marrow cavities. In this work, a human thoracic vertebra has been imaged via nuclear magnetic resonance (NMR) spectroscopy yielding a three‐dimensional voxelized representation of this skeletal site. The image was then coupled to the radiation transport codeEGS4 allowing for 3D tracing of electron paths within its true 3D structure. The macroscopic boundaries of the trabecular regions, as well as the cortex of cortical bone surrounding the bone site, were explicitly considered in the voxelized transport model. For the case of a thoracic vertebra, energy escape to the cortical bone became significant at source energies exceeding ∼2 MeV. Chord‐length distributions were acquired from the same NMR image, and subsequently used as input for a chord‐based dosimetry model. Differences were observed in the absorbed fractions given by the chord‐based model and the voxel transport model, suggesting that some of the input chord distributions for the chord‐based models may not be accurate. Finally, this work shows that skeletal mass estimates can be made from the same NMR image in which particle transport is performed. This feature allows one to determine a skeletalS‐value using absorbed fraction and mass data taken from the same anatomical tissue sample. The techniques developed in this work may be applied to a variety of skeletal sites, thus allowing for the development of skeletal dosimetry models at all skeletal sites for both males and females and as a function of subject age.
Electron dose calculations using the Method of Moments
Authors: Larsen Edward W. , Miften Moyed M. , Fraass Benedick A. , Bruinvis Iaı̈n A. D.
Published: July 2002

TheMethod of Momentsis generalized to predict the dose deposited by a prescribed source of electrons in a homogeneous medium. The essence of this method is (i) to determine, directly from the linear Boltzmann equation, the exact mean fluence, mean spatial displacements, and mean‐squared spatial displacements, as functions of energy; and (ii) to represent the fluence and dose distributions accurately using this information. Unlike the Fermi–Eyges theory, the Method of Moments is not limited to small‐angle scattering and small angle of flight, nor does it require that all electrons at any specified depthzhave one specified energyE(z). The sole approximation in the present application is that for each electron energyE, the scalar fluence is represented as a spatial Gaussian, whose moments agree with those of the linear Boltzmann solution. Numerical comparisons with Monte Carlo calculations show that the Method of Moments yields expressions for the depth‐dose curve, radial dose profiles, and fluence that are significantly more accurate than those provided by the Fermi–Eyges theory.
Electron fluence correction factors for conversion of dose in plastic to dose in water
Authors: Ding G. X. , Rogers D. W. O. , Cygler J. E. , Mackie T. R.
Published: July 2002

In radiation dosimetry protocols, plastic is allowed as a phantom material for the determination of absorbed dose to water in electron beams. The electron fluence correction factor is needed in conversion of dose measured in plastic to dose in water. There are large discrepancies among recommended values as well as measured values of electron fluence correction factors when polystyrene is used as a phantom material. Using the Monte Carlo technique, we have calculated electron fluence correction factors for incident clinical beam energies between 5 and 50 MeV as a function of depth for clear polystyrene, white polystyrene and PMMA phantom materials and compared the results with those recommended in protocols as well as experimental values from published data. In the Monte Carlo calculations, clinical beams are simulated using the EGS4 user‐codeBEAMfor a variety of medical accelerators. The study shows that our calculated fluence correction factor,is a function of depth and incident beam energywith little dependence on other aspects of beam quality. However thevalues atare indirectly influenced by the beam quality since they vary with depth andalso varies with the beam quality. Calculatedvalues atare in a range of 1.005–1.045 for a clear polystyrene phantom, 1.005–1.038 for a white polystyrene phantom and 0.996–1.016 for a PMMA phantom. Our values ofare about 1–2% higher than those determined according to the AAPM TG‐25 protocol atfor clear or white polystyrene. Our calculated values ofalso explain some of the variations of measured data because of its depth dependence. A simple formula is derived which gives the electron fluence correction factoras a function ofator at the depth of 0.6for any clinical electron beam with energy between 5 and 25 MeV for three plastics: clear polystyrene, white polystyrene and PMMA. The study also makes a careful distinction betweenand the corresponding IAEA Code of Practice quantity,
GafChromic MD‐55: Investigated as a precision dosimeter
Authors: Klassen Norman V. , van der Zwan Len , Cygler Joanna
Published: July 2002

GafChromic MD‐55 is a fairly new, thin film dosimeter that develops a blue color when irradiated with ionizing radiation. The increase in absorbance is roughly proportional to the absorbed dose. In this study, GafChromic MD‐55 was irradiated with γ rays. A double irradiation method was used in which a dosimeter is given an unknown dose followed by a known, calibration dose. With this method, GafChromic MD‐55 was used to measure doses in the vicinity of 6 Gy with an uncertainty of less than 1%. It was found that the measured optical density of GafChromic MD‐55, as presently fabricated, is affected by the polarization of the analyzing light, an important consideration when using GafChromic MD‐55 as a precision dosimeter. GafChromic MD‐55 was found to consist of seven layers. The response to polarized light was measured for the whole dosimeter and for the three Mylar films which form part of the dosimeter.
Improved determination of biplane imaging geometry from two projection images and its application to three‐dimensional reconstruction of coronary arterial trees
Authors: Chen Shiuh‐Yung James , Metz Charles E.
Published: July 2002

A technique has been developed for accurate estimation of three‐dimensional (3D) biplane imaging geometry and reconstruction of 3D objects based on two perspective projections acquired at arbitrary orientations, without the need of calibration. The required prior information (i.e., the intrinsic parameters of each single‐plane imaging system) for determination of biplane imaging geometry includes (a) the distance between each focal spot and its image plane, SID (the focal‐spot to imaging‐plane distance); (b) the pixel size,(e.g., 0.3 mm/pixel); (c) the distance between the two focal spotsor the known 3D distance between two points in the projection images; and (d) for each view, an approximation of the magnification factor, MF (e.g., 1.2), which is the ratio of the SID and the approximate distance of the object to the focal spot. Item (d) is optional but may provide a more accurate estimation if it is available. Given five or more corresponding object points in both views, a constrained nonlinear optimization algorithm is applied to obtain an optimal estimate of the biplane imaging geometry in the form of a rotation matrixRand a translation vectortthat characterize the position and orientation of one imaging system relative to the other. With the calculated biplane imaging geometry, 3D spatial information concerning the object can then be reconstructed. The accuracy of this method was evaluated by using a computer‐simulated coronary arterial tree and a cube phantom object. Our simulation study showed that a computer‐simulated coronary tree can be reconstructed from two views with less than 2 and 8.4 mm root‐mean‐square (rms) configuration (or relative‐position) error and absolute‐position error, respectively, even if the input errors in the corresponding 2D points are fairly large (more than two). In contrast, input image error of more than one pixel () can yield 3D position errors of 10 cm or more when other existing methods based on linear approaches are employed. For the cube phantom images acquired from a routine biplane system, rms errors in the 3D configuration of the cube and the 3D absolute position were 0.6–0.9 mm and 3.9–5.0 mm, respectively.
The use of deconvolution and total least squares in recovering a radiation detector line spread function
Authors: Charland Paule , El‐Khatib Ellen , Wolters John
Published: July 2002

We present a method for obtaining the line spread function (LSF) of any radiation detector from measured data. The problem of finding a LSF is essentially a discrete deconvolution from known values of the input (Monte Carlo generated data) and the output (measured data) which can be put into matrix form. We applied the total least squares (TLS) method which is particularly useful when there are errors in both the input and output data. Results from computer simulation as well as from actual data are shown. In a practical application, however, our technique is currently limited by the ability of the Monte Carlo data to simulate correctly the inherent data from the head of the linear accelerator (linac). To overcome this difficulty we have solved by deconvolution and TLS for a more realistic inherent beam profile of our linac using the information from both profile data as measured with film and the film densitometer response function. The LSF of the densitometer was estimated with a simple method of direct measurement of a slit image and a full width at half maximum (FWHM) of 0.997 mm was recorded. Additionally, using the knowledge of this realistic inherent profile of the linac, a blurring function representing the finite source size effect missing in our current Monte Carlo profile simulation was determined. Finally, with the realistic inherent beam profile we have applied the deconvolution and TLS method to find a LSF for the Markus chamber and found a resulting FWHM of 5.39 mm. The TLS approach for deconvolving can find a useful application for both finding the LSF and correcting for the detector size effect once its LSF is known. This type of correction is required when a high spatial resolution is needed (e.g., in small field off‐axis measurements). Convolved and measured profiles are also presented to illustrate the effect of the blurring due to different LSFs.
Frequency‐domain near‐infrared photo diffusion imaging: Initial evaluation in multitarget tissuelike phantoms
Authors: Jiang Huabei , Paulsen Keith D. , Österberg Ulf L. , Patterson Michael S.
Published: July 2002

In this paper, an initial evaluation of our finite element based frequency‐domain image reconstruction algorithm is performed for experiments where multiple millimeter‐sized heterogeneities are embedded within a tissue‐equivalent (optically) background medium having multicentimeter dimensions. The cases considered consist of several interesting geometry and optical property contrast combinations including (i) two different‐sized targets with the same contrast at three different separation distances; (ii) two different‐sized targets with different contrasts at two different separation distances; and (iii) three targets with the same and different sizes and contrasts, respectively. The reconstruction algorithm that has been used is an enhanced version of our originally developed regularized least squares approach that now includes total variation minimization, dual meshing, and spatial low‐pass filtering. Quantitative measures of image quality including the size, location, and shape of the embedded heterogeneities along with errors in their recovered optical property values are presented. The results show that multiple targets can be clearly detected for all combinations of locations, sizes, and contrast levels considered, but the quantitative nature of this detection is influenced by these parameters.
A practical target system for accelerator‐based BNCT which may effectively double the dose rate
Authors: Randers‐Pehrson G. , Brenner D. J.
Published: July 2002

A dose‐limiting component of a proton accelerator‐based source of epithermal neutrons is the neutron production target. Possible targets are lithium, producing high yield but having low melting point and thermal conductivity, and beryllium, presenting less engineering problems but a much smaller neutron yield. We propose that a hybrid Be‐Li target would provide the best of both worlds, with the upstream beryllium component producing neutrons and providing containment to the lithium, and the downstream liquid lithium in turn producing further neutrons as well as cooling the beryllium. The engineering considerations associated with such a target system are within the range of current technology. Calculations suggest a yield of such a practical target that is at least double that from pure beryllium.
Investigation of recoil collection method for production of high specific activity nuclear medicine isotopes
Authors: Cheng Kai‐Yuan , Kunze Jay F. , Ehrhardt Gary J.
Published: July 2002

High specific activity radiopharmaceuticals cannot readily be produced by (n, gamma) reactions in nuclear reactors, because the great abundance of parent atoms remaining have the same chemical characteristics as the produced isotope. We have investigated the effectiveness of using recoil atom collection methods for separating the produced radioisotope. Gold‐198, produced from isotopically pure (natural) gold‐197, was chosen for these experiments, which were run in the high flux n/cm2 s thermal flux) of the reflector of the University of Missouri Research Reactor. Seven separate experiments were run, with a 2 mm separation between the emitter and the collector. Collection efficiencies were only a few percent of the radioisotope atoms produced in the top atomic layer of the emitter, instead of the 30% range anticipated. Furthermore, the collected radioisotope, instead of being nearly pure, contained a large quantity of the parent. Unless the reason for the “contamination” of product with the parent can be reduced by several orders of magnitude, this “surface hot atom recoil” method appears to offer no practical application for nuclear medicine isotope production.
IORT apparatus design improvement through the evaluation of electron spectral distributions using Monte Carlo methods
Authors: Price Robert A. , Ayyangar Komanduri M.
Published: July 2002

Clinically used IORT electron beam characteristics may vary with respect to typical external beams due to the decrease of lateral scatter equilibrium and the addition of the IORT apparatus itself. Additionally, chamber size effects may lead to inaccurate measurements of the changes in electron beam characteristics. The causal components of these beam characteristics are often difficult or impossible to measure using experimental techniques. For this reason, and for potential design improvement, the electron beams were modeled using theOMEGA/BEAMMonte Carlo software for radiation transport. The IORT electron beam characteristics of the Varian Clinac 1800 were studied for 6, 12, and 20 MeV electrons and 1–4 in. diameter flat‐end applicators. The characteristics studied include electron energy spectra, percentage depth dose, and cross‐plane profiles. It was found that by increasing the thickness of the aluminum base plate of the main attachment, the dose atoutside the primary field could be reduced from approximately 9% to 1% of maximum.
On the beam quality specification of high‐energy photons for radiotherapy dosimetry
Authors: Andreo Pedro
Published: July 2002

An overview of common photon beam quality specifiers used in radiotherapy dosimetry introduces a reasoned discussion on the advantages and disadvantages ofandIt is shown that some of the potential advantages ofare also present in other well known beam quality specifiers such asHowever, all PDD‐based beam quality indices, includingare subject to electron contamination and their determination is affected by practical limitations. The proposed filtration of contaminant electrons by Kosunen and Rogers [Med. Phys.20, 1181–1188 (1993)] and by Li and Rogers [Med. Phys.21, 791–798 (1994)] is questioned, not only with regard to the adequacy of using lead as an electron filter, but also in relation to its efficiency (ifthere were no contamination, restrictions for beam calibrations atwould be removed) and practical measurement. It is argued that (i) there is no unique beam quality specifier that works satisfactorily in all possible conditions, for the entire energy range of photon energies used in radiotherapy and all possible accelerators used in hospitals and in standards laboratories, and (ii)remains to be the most appropriate specifier for clinical photon beams as it has less practical drawbacks than PDD‐based quality indices. The final impact on clinical photon beam dosimetry resulting from the use of different photon beam quality specifiers, is that they are not expected to yield a significant change (i.e., more than 0.5% and in most cases well within 0.2%) in the absorbed dose to water in reference conditions for most clinical beams.
The effect of dose calculation uncertainty on the evaluation of radiotherapy plans
Authors: Keall P. J. , Siebers J. V. , Jeraj R. , Mohan R.
Published: July 2002

Monte Carlo dose calculations will potentially reduce systematic errors that may be present in currently used dose calculation algorithms. However, Monte Carlo calculations inherently contain random errors, or statistical uncertainty, the level of which decreases inversely with the square root of computation time. Our purpose in this study was to determine the level of uncertainty at which a lung treatment plan is clinically acceptable. The evaluation methods to decide acceptability were visual examination of both isodose lines on CT scans and dose volume histograms (DVHs), and reviewing calculated biological indices. To study the effect of systematic and/or random errors on treatment plan evaluation, a simulated “error‐free” reference plan was used as a benchmark. The relationship between Monte Carlo statistical uncertainty and dose was found to be approximately proportional toRandom and systematic errors were applied to a calculated lung plan, creating dose distributions with statistical uncertainties of between 0% and 16% (1 s.d.) at the maximum dose point and also distributions with systematic errors of −16% to 16% at the maximum dose point. Critical structure DVHs and biological indices are less sensitive to calculation uncertainty than those of the target. Systematic errors affect plan evaluation accuracy significantly more than random errors, suggesting that Monte Carlo dose calculation will improve outcomes in radiotherapy. A statistical uncertainty of 2% or less does not significantly affect isodose lines, DVHs, or biological indices.
Diffracted field by an arbitrary aperture
Authors: Dubra Alfredo , Ferrari José A.
Published: July 2002

Diffraction patterns of apertures on screens uniformly illuminated are standard calculations in undergraduate optics and acoustics courses. These calculations imply two-dimensional (2-D) integrations which are often performed in the far zone, at moderate angles of diffraction, i.e., using Fresnel and Fraunhofer approximations. In this note, the 2-D integration is reduced to a 1-D parametric integration over the perimeter of the aperture—resembling the Rubinowicz’s representation of the Kirchhoff diffraction integral—which allows numerical evaluation with few computational resources. The proposed formula allows mathematically exact calculation of the near-field, in the context of scalar wave theory. Explicit calculations for circular and elliptical apertures are shown.
Penetration of acoustic waves into rippled sandy seafloors
Authors: Pouliquen E. , Lyons A. P. , Pace N. G.
Published: July 2002

The Helmholtz–Kirchhoff integral and the Kirchhoff approximation are applied to model the penetration of sound waves into rough sandy seafloors at grazing angles above and below the critical angle. As the seafloor of interest is anisotropic, emphasis is placed on simulating the response from a two-dimensional interface. The analytical development of the method is first presented, followed by numerical examples. Simulations and data acquired at sea are in very good agreement in the 2–15 kHz band [Maguer et al., J. Acoust. Soc. Am. 107, 1215–1225 (2000)]. The model predicts, in agreement with the 2–15 kHz acoustic data, the contributions due to roughness effects that dominate the evanescent wave component over most of this frequency band. Secondary effects such as coherent (Bragg) influence patterns and the loss of signal coherence with grazing angle or depth are correctly predicted. The model simulations strongly suggest that roughness of the sediment interface is most likely the cause of anomalous sound penetration into the seabed.
Neural representation of sound amplitude by functionally different auditory receptors in crickets
Authors: Imaizumi Kazuo , Pollack Gerald S.
Published: July 2002

The physiological characteristics of auditory receptor fibers (ARFs) of crickets, a model system for studying auditory behaviors and their neural mechanisms, are investigated. Unlike auditory receptor neurons of many animals, cricket ARFs fall into three distinct populations based on characteristic frequency (CF) [Imaizumi and Pollack, J. Neurosci. 19, 1508–1516 (1999)]. Two of these have CFs similar to the frequency component of communication signals or of ultrasound produced by predators, and a third population has intermediate CF. Here, sound-amplitude coding by ARFs is examined to gain insights to how behaviorally relevant sounds are encoded by populations of receptor neurons. ARFs involved in acoustic communication comprise two distinct anatomical types, which also differ in physiological parameters (threshold, response slope, dynamic range, minimum latency, and sharpness of tuning). Thus, based on CF and anatomy, ARFs comprise four populations. Physiological parameters are diverse, but within each population they are systematically related to threshold. The details of these relationships differ among the four populations. These findings open the possibility that different ARF populations differ in functional organization.
Approximate meridional leaky ray amplitudes for tilted cylinders: End-backscattering enhancements and comparisons with exact theory for infinite solid cylinders
Authors: Marston Philip L.
Published: July 2002

Leaky waves propagating on cylinders in (or close to) a meridional plane have been found to significantly enhance the high-frequency acoustic visibility of the ends of tilted cylinders [G. Kaduchak et al., J. Acoust. Soc. Am. 100, 64–71 (1996)]. The meridian of interest is in the plane containing the incident wave vector and the cylinder’s axis. A ray model for this enhancement is developed along with a ray model for a canonical test case: scattering by an infinite circular cylinder. To isolate a single high-frequency leaky wave contribution, numerical examples are shown for generalized Rayleigh waves on a solid circular cylinder. Partial wave series (PWS) calculations show that the meridional Rayleigh wave contribution is maximized when the tilt angle is close to the flat-surface coupling angle. The ray model approximates the superposition of leaky waves excited by the incident acoustic wave as a simple integral that accounts for the phase shift and attenuation for propagation from each illuminated surface point to a surface point of interest. While the model gives the spatial evolution of the leaky wave amplitude as would be measured by acoustic imaging, it also approximates the far-field amplitude. Important features of the canonical PWS calculation are reproduced by the model. The far-field magnitude of the end contribution can be larger than for reflection off a rigid sphere having the same radius as the cylinder. The end is assumed to be flat and perpendicular to the cylinder’s axis.
Consonant–vowel intensity ratios for maximizing consonant recognition by hearing-impaired listeners
Authors: Kennedy Elizabeth , Levitt Harry , Neuman Arlene C. , Weiss Mark
Published: July 2002

The effect of adjusting the consonant–vowel (C–V) intensity ratio on consonant recognition in 18 subjects with sensorineural hearing impairment was investigated. C–V intensity ratios in a set of 48 vowel–consonant nonsense syllables were adjusted in steps of 3–6 dB depending on the subject’s dynamic range of hearing. An increase in consonant intensity is referred to here as consonant enhancement (CE). The value of CE producing the highest consonant recognition score (CRmax) is defined as CEmax. Both CEmax and CRmax were determined for each subject for each of the 48 nonsense syllables. Consonant type was found to have a highly significant effect on CRmax, the gain in consonant recognition, and CEmax. The effect of vowel environment was also significant, but of much smaller magnitude. Audiogram configuration was found to have a small effect and was only significant for CRmax. The results of the study also showed that individualized adjustment of the C–V intensity ratio for each subject and consonant–vowel combination can produce substantial improvements in consonant recognition. These data can be used to estimate upper bounds of performance that, in principle, can be obtained by appropriate adjustment of the C–V intensity ratio.
Relations among interaural cross-correlation coefficient (IACCE), lateral fraction (LFE), and apparent source width (ASW) in concert halls
Authors: Okano Toshiyuki , Beranek Leo L. , Hidaka Takayuki
Published: July 2002

Relations are determined between one of the important subjective attributes of concert hall acoustics, the apparent source width, ASW, and three acoustical measures, interaural cross-correlation coefficient IACCE, LFE, and strength factor G. Although these measures previously have been found to correlate with ASW, their relations with it have not been examined sufficiently, especially in respect to their frequency characteristics. Herein, ASW’s are directly determined for electronically reproduced musical sound fields with extensive ranges of values for IACCE and LFE. Investigated as parameters are angles of incidence, the time delay difference between a pair of symmetric early lateral reflections, and the number of early lateral reflections. These studies indicate the relative efficacy of IACCE and LFE for determining ASW under conditions that are realistically encountered in concert halls. The results were compared with measured IACCE’s, LFE’s, and also the strength factor G’s in existing concert halls. It is concluded that the arithmetic average of [1−IACCE]’s at 500, 1 k and 2 k Hz combined with the strength factor Glow of the sound field at frequencies below 250 Hz are physical measures highly correlated with the subjective rank ordering of concert halls and that they cover the effects on ASW of the entire octave-band frequency range from 125 to 4 k Hz.
Efficiency of a noise barrier with an acoustically soft cylindrical edge for practical use
Authors: Okubo Tomonao , Fujiwara Kyoji
Published: July 2002

This paper examines the sound shielding efficiency of a noise barrier having an acoustically soft cylindrical edge, as it compares to that provided by the well-known absorptive cylindrical edge. It has been reported that the waterwheel-shaped cylinder (acoustic tubes in a radial arrangement) approximates a soft surface cylinder, and that the sound shielding efficiency of a noise barrier is improved by placing the cylinder on its edge. The efficiency of the waterwheel-shaped edge barrier is strongly frequency dependent, thus the improvement in overall sound pressure level is smaller than expected when the source is broadband noise. The present study investigates the use of varied tube depths to improve the efficiency of the waterwheel-shaped edge. It is shown that adding tubes of different depths can flatten the frequency dependence, and that such tubes are only needed in the upper half of the cylinder. These findings led to the design of a new edge device for controlling road traffic noise, whose numerical simulations suggest that it is twice as effective in overall sound pressure level as the original waterwheel with uniform-depth channels.
Development of a Universal Extensional Rheometer for the Uniaxial Extension of Polymer Melts
Authors: Meissner Joachim
Published: July 2002

A recent development in extensional rheometry of molten polymers is based on the use of a pair of gears as a ‘rotational clamp’. In a tensile tester for polymer melts, the rotational clamp provides the draw-down of the melt being extruded out of the die of a melt indexer. The result is a quick characterization of extensibility and tensile strength. In a new extensional rheometer, two rotational clamps are used which extend homogeneously a molten polymer rod floating on a silicone oil bath. For constant rotational speeds of the clamps, the (Hencky) strain rate is constant. The creep test with constant tensile stress can be performed in the same rheometer making use of a servo motor of quick response with an appropriate servo control. A further modification of the servo control is described by means of which any uniaxial stress or strain history can be imposed on the melt under test, with stress σ>0 the only constraint. In this rheometer, the extensional behavior of a LDPE melt was measured at 150°C under a variety of mechanical conditions. The data presented demonstrate the versatility of the apparatus.
Rheology and structural changes of polymer melts via nonequilibrium molecular dynamics
Authors: Kröger Martin , Loose Werner , Hess Siegfried
Published: July 2002

Results of nonequilibrium molecular dynamics computer simulations of a planar Couette flow are presented for the multibead anharmonic-spring model. The finitely extensible nonlinear elastic force law is used to connect the up to 100 beads of a chain molecule. Rheological data (shear viscosity, normal pressure differences) are discussed and compared with quantities describing the chain conformation (e.g., alignment tensor, static structure factor). This renders possible a test of the theoretical approaches which connect these quantities. In agreement with recent experiments, the static strucure factor exhibits characteristic elliptical distortions of the polymer coil whose magnitude depends on the distance from the gyration center. In our simulations the zero-shear-rate viscosity is found to scale linearly with the number of beads N up to chains with N=60. A weak upturn of the viscosity per bead for N=100 is found which may indicate the onset of the reptation regime.