bluuebunny/crossref_metadata_2025 huggingface dataset:
Algorithms and software for support of gene identification experiments.
Authors: Sze S H , Roytberg M A , Gelfand M S , Mironov A A , Astakhova T V , Pevzner P A
Published: July 2002

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.
SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments.
Authors: Rognes T , Seeberg E
Published: July 2002

MOTIVATION: Optimal sequence alignment based on the Smith-Waterman algorithm is usually too computationally demanding to be practical for searching large sequence databases. Heuristic programs like FASTA and BLAST have been developed which run much faster, but at the expense of sensitivity. RESULTS: In an effort to approximate the sensitivity of an optimal alignment algorithm, a new algorithm has been devised for the computation of a gapped alignment of two sequences. After scanning for high-scoring words and extensions of these to form fragments of similarity, the algorithm uses dynamic programming to build an accurate alignment based on the fragments initially identified. The algorithm has been implemented in a program called SALSA and the performance has been evaluated on a set of test sequences. The sensitivity was found to be close to the Smith-Waterman algorithm, while the speed was similar to FASTA (ktup = 2). AVAILABILITY: Searches can be performed from the SALSA homepage at http://dna.uio.no/salsa/ using a wide range of databases. Source code and precompiled executables are also available. CONTACT: torbjorn.rognes@labmed.uio.no
JavaShade: multiple sequence alignment box-and-shading on the World Wide Web.
Authors: Southern M R , Lewis A P
Published: July 2002

RESULTS: JavaShade is a multiple sequence alignment box-and-shade tool for generating high quality printed output that uses a variety of methods for boxing and shading, allowing the most appropriate functions to be chosen for displaying the most meaningful positions in an alignment. AVAILABILITY: JavaShade is available from the WWW at http://industry.ebi.ac.uk/JavaShade
SECOST: sequence-conformation-structure database for amino acid residues in proteins.
Authors: Shats O , Vaisman I I , Shats A , Sherman S
Published: July 2002

The sequence-conformation-structure database for amino acid residues contains information on 114 828 individual residues derived from the spatial structures of 473 high-quality non-homologous proteins. The information in the database is obtained using a variety of different methods and can be used in various protein modeling applications.
A brief history of genome research and bioinformatics in France
Authors: Danchin Antoine
Published: July 2002

The development of in silico genomics has progressed slowly in France for a number of political reasons. Two administrative organizations, the Groupement de Recherche sur les Génomes (GREG) and the Groupement de Recherche 1029 (GDR 1029) of the Centre National de la Recherche Scientifique (CNRS) have been established. These organizations have created the dynamics that hopefully will place France (which coordinated consortia that completed several of the first large microbial genomes) among the developed nations that support Large-Scale Biology.

Contact: adanchin@pasteur.fr
GABAagent: a system for integrating data on GABA receptors
Authors: Rachedi Abdelkrim , Rebhan Michael , Xue Hong
Published: July 2002

Motivation: Scientific data pertaining to GABA receptors, which are of medical importance, are widely scattered throughout numerous heterogeneous Internet resources. This situation has made the integrated acquisition of such data difficult and substantially time consuming even for researchers who are Internet aficionados. Thus, there exists a genuine need for the development of Internet applications, such as GABAagent, which provide efficient and timely access to concise and integrated information.

Results: We report here the establishment of a novel server (GABAagent) which has been written in Perl script, and which is freely accessible through the Internet. GABAagent is designed to assist researchers in retrieving focused and integrated information related to GABA receptors from various public domain databases.

GABAagent relies on server-side flat-file databases that have been created through data mining from Internet sources such as the PubMed, DDBJ, SWISS-PROT and TrEMBL, in addition to the many World Wide Web (Web) sites which are accessible through Excite (E-Web). These warehouse databases are regularly updated and contain among other things, information concerning: (i) GABA receptor publications, (ii) DNA and protein sequences and (iii) the contents of related E-Web sites along with their addresses. Our system also provides hard links to the above-mentioned Web sites and E-Web sites; the feature which adds to it the character of virtual federation type of database.

The current version of GABAagent provides two user-friendly services. The first is a search engine possessing intelligent query reformulation support (GABAengine), the second an elaborate email alert service was designed into the system (GABAalert). The GABAengine allows the user to search server-side databases exclusively for GABA receptor-related queries. Whereas, GABAalert allows the user, by means of subscription, to receive immediate and/or monthly updates automatically.

Availability: GABAagent is freely accessible at the following Web address http://www.ust.hk/gaba.

Contact: gaba@ust.hk
Quick selection of representative protein chain sets based on
customizable requirements
Authors: Noguchi Tamotsu , Onizuka Kentaro , Ando Makoto , Matsuda Hideo , Akiyama Yutaka
Published: July 2002

Motivation: Protein structure classification has been recognized as one of the most important research issues in protein structure analysis. A substantial number of methods for the classification have been proposed, and several databases have been constructed using these methods. Since some proteins with very similar sequences may exhibit structural diversities, we have proposed PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), which strategy of selection is based not only on sequence similarity but also on structural similarity. Forty-eight representative sets whose similarity criteria were predetermined were made available over the World Wide Web (WWW). However, the sets were insufficient in number to satisfy users researching protein structures by various methods.

Result: We have improved the system for PDB-REPRDB so that the user may obtain a quick selection of representative chains from PDB. The selection of representative chains can be dynamically configured according to the user’s requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. This paper describes the method we use to classify chains and select the representatives in the system. We also describe the interface used to set the parameters.

Availability: The system for PDB-REPRDB is available at the PAPIA WWW server (http://www.rwcp.or.jp/papia/).

Contact: noguchi@trc.rwcp.or.jp

* To whom correspondence should be addressed.

3 Present address: Information Processing Systems Department, NKK Corporation, 1-1-2 Marunouchi, Chiyoda-ku, Tokyo 100-8202, Japan
In silico identification of transcripts and SNPs from

a region of 4p linked with bipolar affective disorder
Authors: Semple C. A. M. , Morris S. W. , Porteous D. J. , Evans K. L.
Published: July 2002

Contact: c.semple@hgu.mrc.ac.uk

Availability: Files containing the accession numbers of all EST clusters and SNPs from this study are available at ftp://ftp.hgu.mrc.ac.uk/pub/colins.

To whom correspondence should be addressed.
Visualizing plant metabolomic correlation networks using
clique–metabolite matrices
Authors: Kose Frank , Weckwerth Wolfram , Linke Thomas , Fiehn Oliver
Published: July 2002

Motivation: Today, metabolite levels in biological samples can be determined using multiparallel, fast, and precise metabolomic approaches. Correlations between the levels of various metabolites can be searched to gain information about metabolic links. Such correlations are the net result of direct enzymatic conversions and of indirect cellular regulation over transcriptional or biochemical processes. In order to visualize metabolic networks derived from correlation lists graphically, each metabolite pair may be represented as vertices connected by an edge. However, graph complexity rapidly increases with the number of edges and vertices. To gain structural information from metabolite correlation networks, improvements in clarity are needed.

Results: To achieve this clarity, three algorithms are combined. First, a list of linear metabolite correlations is generated that can be regarded as a set of pairs of edges (or as 2-cliques). Next, a branch-and-bound algorithm was developed to find all maximal cliques by combining submaximal cliques. Due to a clique assignment procedure, the generation of unnecessary submaximal cliques is avoided in order to maintain high efficiency. Differences and similarities to the Bron–Kerbosch algorithm are pointed out. Lastly, metabolite correlation networks are visualized by clique–metabolite matrices that are sorted to minimize the length of lines that connect different cliques and metabolites. Examples of biochemical hypotheses are given that can be built from interpretation of such clique matrices.

Availability: The algorithms are implemented in Visual Basic and can be downloaded from our web site along with a test data set (http://www.mpimp-golm.mpg.de/fiehn/projekte/data-mining-e.html).

Contact: kose@mpimp-golm.mpg.de

* To whom correspondence should be addressed.
Clustering of highly homologous sequences to reduce the size of

large protein databases
Authors: Li Weizhong , Jaroszewski Lukasz , Godzik Adam
Published: July 2002

Summary: We present a fast and flexible program for clustering large protein databases at different sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and clustering of the non-redundant protein database of over 560000 sequences on a high-end PC. The output database, including only the representative sequences, can be used for more efficient and sensitive database searches.

Availability: The program is available from http://bioinformatics.burnham-inst.org/cd-hi

Contact: liwz@sdsc.edu or adam@burnham-inst.org

* To whom correspondence should be addressed.
Cladogramer: incorporating haplotype frequency into cladogram
analysis
Authors: Zhang Louxin , Heng Chew-Kiat , Tan Tin Wee
Published: July 2002

Summary: We implement a program that incorporates polymorphic sites data, haplotype frequency arrays, and other factors, into cladogram estimation.

Availability: It is available at http://sdmc.krdl.org.sg:8080/~lxzhang/cladogramer

Contact: lxzhang@krdl.org.sg
Missing value estimation methods for DNA microarrays
Authors: Troyanskaya Olga , Cantor Michael , Sherlock Gavin , Brown Pat , Hastie Trevor , Tibshirani Robert , Botstein David , Altman Russ B.
Published: July 2002

Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical clustering and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods for imputing missing data are needed, therefore, to minimize the effect of incomplete data sets on analyses, and to increase the range of data sets to which these algorithms can be applied. In this report, we investigate automated methods for estimating missing data.

Results: We present a comparative study of several methods for the estimation of missing values in gene microarray data. We implemented and evaluated three methods: a Singular Value Decomposition (SVD) based method (SVDimpute), weighted K-nearest neighbors (KNNimpute), and row average. We evaluated the methods using a variety of parameter settings and over different real data sets, and assessed the robustness of the imputation methods to the amount of missing data over the range of 1–20% missing values. We show that KNNimpute appears to provide a more robust and sensitive method for missing value estimation than SVDimpute, and both SVDimpute and KNNimpute surpass the commonly used row average method (as well as filling missing values with zeros). We report results of the comparative experiments and provide recommendations and tools for accurate estimation of missing microarray data under a variety of conditions.

Availability: The software is available at http://smi-web.stanford.edu/projects/helix/pubs/impute/

Contact: russ.altman@stanford.edu

* To whom correspondence should be addressed.
An HMM model for coiled-coil domains and a comparison with
PSSM-based predictions
Authors: Delorenzi Mauro , Speed Terry
Published: July 2002

Motivation: Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile.

Results: We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation.

Availability: The prediction program and the databases are available at http://www.wehi.edu.au/bioweb/Mauro/Marcoil

Contact: delorenzi@wehi.edu.au

* To whom correspondence should be addressed.
Stem cells in gastrointestinal epithelium: numbers, characteristics and death
Authors: Potten Christopher S.
Published: July 2002

The mammalian intestinal mucosa, with its distinctive polarity, high rate of proliferation and rapid cell migration, is an excellent model system to study proliferative hierarchies and the regulation of cell division, differentiation and cell death. Each crypt contains a few lineage ancestral stem cells (the ‘ultimate stem cells’). However, there are other potential stem cells within the early lineage, and many rapidly proliferating transit cells with no stem cell capabilities. Apoptosis under two circumstances has a specificity for the ultimate stem cells in the small intestine and this represents, in one case, part of the stem cell homeostatic process and, in another case, a protective mechanism against DNA damage. Apoptosis occurs with a lower frequency in the large intestine owing to the expression of thebcl–2gene in this region, and this probably contributes to the causes for the low cancer risk in the small bowel and the high risk in the large bowel. Current studies are beginning to unravel the complex interaction of growth factors and regulatory genes that determine whether a cell divides, differentiates or dies.
How do we select perceptions and actions? Human brain imaging studies
Authors: Rees Geraint , Frith Christopher D.
Published: July 2002

The selective nature of human perception and action implies a modulatory interaction between sensorimotor processes and attentional processes. This paper explores the use of functional imaging in humans to explore the mechanisms of perceptual selection and the fate of irrelevant stimuli that are not selected. Experiments with positron emission tomography show that two qualitatively different patterns of modulation of cerebral blood flow can be observed in experiments where non–spatial visual attention and auditory attention are manipulated. These patterns of modulation of cerebral blood flow modulation can be described as gain control and bias signal mechanisms. In visual and auditory cortex, the dominant change in cerebral blood flow associated with attention to either modality is related to a bias signal. The relation of these patterns of modulation to attentional effects that have been observed in single neurons is discussed. The existence of mechanisms for selective perception raises the more general question of whether irrelevant ignored stimuli are nevertheless perceived. Lavie‘apos; theory of attention proposes that the degree to which ignored stimuli are processed varies depending on the perceptual load of the current task. Evidence from behavioural and functional magnetic resonance imaging studies of ignored visual motion processing is presented in support of this proposal.
Neural representation of objects in space: a dual coding account
Authors: Humphreys Glyn W.
Published: July 2002

I present evidence on the nature of object coding in the brain and discuss the implications of this coding for models of visual selective attention. Neuropsychological studies of task–based constraints on: (i) visual neglect; and (ii) reading and counting, reveal the existence of parallel forms of spatial representation for objects: within–object representations, where elements are coded as parts of objects, and between–object representations, where elements are coded as independent objects. Aside from these spatial codes for objects, however, the coding of visual space is limited. We are extremely poor at remembering small spatial displacements across eye movements, indicating (at best) impoverished coding of spatial positionper se. Also, effects of element separation on spatial extinction can be eliminated by filling the space with an occluding object, indicating that spatial effects on visual selection are moderated by object coding. Overall, there are separate limits on visual processing reflecting: (i) the competition to code parts within objects; (ii) the small number of independent objects that can be coded in parallel; and (iii) task–based selection of whether within– or between–object codes determine behaviour. Between–object coding may be linked to the dorsal visual system while parallel coding of parts within objects takes place in the ventral system, although there may additionally be some dorsal involvement either when attention must be shifted within objects or when explicit spatial coding of parts is necessary for object identification.
A model for the emergence of pillars, walls and royal chambers in termite nests
Authors: Bonabeau E. , Theraulaz G. , Deneubourg J. , Franks N. R. , Rafelsberger O. , Joly J. , Blanco S.
Published: July 2002

A simple model of the emergence of pillars in termite nests by Deneubourg is modified to include several additional features that break the homogeneity of the original model: (i) a convection air stream that drives molecules of pheromone along a given direction; (ii) a net flux of individuals in a specific direction; (iii) a well–defined self–maintained pheromone trail; and (iv) a pheromonal template representing the effect of the presence of a queen that continuously emits pheromone. It is shown that, under certain conditions, pillars are transformed into walls or galleries or chambers, and that this transformation may not be driven by any change in the termites' behaviour. Because the same type of response at the individual level can generate different patterns under different conditions, and because previous construction modifies current building conditions, we hypothesize that nest complexity can result from the unfolding of a morphogenetic process that progressively generates a diversity of history–dependent structures.
Molecular genetic evidence for the human settlement of the Pacific: analysis of mitochondrial DNA, Y chromosome and HLA markers
Authors: Hagelberg E. , Kayser M. , Nagy M. , Roewer L. , Zimdahl H. , Krawczak M. , Lió P. , Schiefenhöve W.
Published: July 2002

Present–day Pacific islanders are thought to be the descendants of Neolithic agriculturalists who expanded from island South–east Asia several thousand years ago. They speak languages belonging to the Austronesian language family, spoken today in an area spanning half the circumference of the world, from Madagascar to Easter Island, and from Taiwan to New Zealand. To investigate the genetic affinities of the Austronesian–speaking peoples, we analysed mitochondrial DNA, HLA and Y chromosome polymorphisms in individuals from eight geographical locations in Asia and the Pacific (China, Taiwan, Java, New Guinea highlands, New Guinea coast, Trobriand Islands, New Britain and Western Samoa). Our results show that the demographic expansion of the Austronesians has left a genetic footprint. However, there is no simple correlation between languages and genes in the Pacific.
Self–assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed
Authors: Butler P. J. G.
Published: July 2002

The tobacco mosaic virus (TMV) particle was the first macromolecular structure to be shown to self–assemble
in vitro
, allowing detailed studies of the mechanism.

Nucleation of TMV self–assembly is by the binding of a specific stem–loop of the single–stranded viral RNA into the central hole of a two–ring sub–assembly of the coat protein, known as the ‘disk’. Binding of the loop onto its specific binding site, between the two rings of the disk, leads to melting of the stem so more RNA is available to bind. The interaction of the RNA with the protein subunits in the disk cause this to dislocate into a proto–helix, rearranging the protein subunits in such a way that the axial gap between the rings at inner radii closes, entrapping the RNA.

Assembly starts at an internal site on TMV RNA, about 1 kb from its 3′–terminus, and the elongation in the two directions is different. Elongation of the nucleated rods towards the 5′–terminus occurs on a ‘travelling loop’ of the RNA and, predominantly, still uses the disk sub–assembly of protein subunits, consequently incorporating approximately 100 further nucleotides as each disk is added, while elongation towards the 3′–terminus uses smaller protein aggregates and does not show this ’quantized‘ incorporation.
Identification and study of tobacco mosaic virus movement function by complementation tests
Authors: Atabekov J. G. , Malyshenko S. I. , Morozov S. Yu. , Taliansky M. E. , Solovyev A. G. , Agranovsky A. A. , Shapka N. A.
Published: July 2002

The phenomenon of
trans
–complementation of cell–to–cell movement between plant positive–strand RNA viruses is discussed with an emphasis on tobamoviruses. Attention is focused on complementation between tobamoviruses (coding for a single movement protein, MP) and two groups of viruses that contain the triple block of MP genes and require four (potato virus X) or three (barley stripe mosaic virus) proteins for cell–to–cell movement. The highlights of complementation data obtained by different experimental approaches are given, including (i) double infections with movement–deficient (dependent) and helper viruses; (ii) infections with recombinant viral genomes bearing a heterologous MP gene; (iii) complementation of a movement–deficient virus in transgenic plants expressing the MP of a helper virus; and (iv) co–bombardment of plant tissues with the cDNAs of a movement–dependent virus genome and the MP gene of a helper virus.
Dynamics of the forest communities at Pasoh and Barro Colorado: comparing two 50–ha plots
Authors: Condit Richard , Ashton Peter S. , Manokaran N. , LaFrankie James V. , Hubbell Stephen P. , Foster Robin B.
Published: July 2002

Dynamics of the Pasoh forest in Peninsular Malaysia were assessed by drawing a comparison with a forest in Panama, Central America, whose dynamics have been thoroughly described. Census plots of 50 ha were established at both sites using standard methods. Tree mortality at Pasoh over an eight–year interval was 1.46% yr−1for all stems greater than or equal to 10 mm diameter at breast height (dbh), and 1.48% yr−1for stems greater than or equal to 100 mm dbh. Comparable figures at the Barro Colorado Island site in Panama (BCI) were 2.55% and 2.03%. Growth and recruitment rates were likewise considerably higher at BCI than at Pasoh. For example, in all trees 500 to 700 mm in dbh, mean BCI growth over the period 1985 to 1995 was 6 mm yr−1, whereas mean Pasoh growth was about 3.5 mm yr−1. Examining growth and mortality rates for individual species showed that the difference between the forests can be attributed to a few light–demanding pioneer species at BCI, which have very high growth and mortality; Pasoh is essentially lacking this guild. The bulk of the species in the two forests are shade–tolerant and have very similar mortality, growth and recruitment. The Pasoh forest is more stable than BCI's in another way as well: few of its tree populations changed much over the eight–year census interval. In contrast, at BCI, over 10% of the species had populations increasing or decreasing at a rate of > 0.05 yr−1(compared to just 2% of the species at Pasoh). The faster species turnover at BCI can probably be attributed to severe droughts that have plagued the forest periodically over the past 30 years; Pasoh has not suffered such extreme events recently. The dearth of pioneer species at Pasoh is associated with low–nutrient soil and slow litter breakdown, but the exact mechanisms behind this association remain poorly understood.
Trichome morphogenesis inArabidopsis
Authors: Schwab Birgit , Folkers Ulrike , Ilgenfritz Hilmar , Hülskamp Martin
Published: July 2002

Trichomes (plant hairs) inArabidopsis thalianaare large non–secreting epidermal cells with a characteristic three–dimensional architecture. Because trichomes are easily accessible to a combination of genetic, cell biological and molecular methods they have become an ideal model system to study various aspects of plant cell morphogenesis. In this review we will summarize recent progress in the understanding of trichome morphogenesis.
The pit organs of elasmobranchs: a review
Authors: Peach Meredith B. , Marshall N. Justin
Published: July 2002

Elasmobranchs have hundreds of tiny sensory organs, called pit organs, scattered over the skin surface. The pit organs were noted in many early studies of the lateral line, but their exact nature has long remained a mystery. Although pit organs were known to be innervated by the lateral line nerves, and light micrographs suggested that they were free neuromasts, speculation that they may be external taste buds or chemoreceptors has persisted until recently. Electron micrographs have now revealed that the pit organs are indeed free neuromasts. Their functional and behavioural role(s), however, are yet to be investigated.
The KA/KS Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study
Authors: Nekrutenko Anton , Makova Kateryna D. , Li Wen-Hsiung
Published: July 2002

Comparative genomics is a simple, powerful way to increase the accuracy of gene prediction. In this study, we show the utility of a simple test for the identification of protein-coding exons using human/mouse sequence comparisons. The test takes advantage of the fact that in the vast majority of coding regions, synonymous substitutions (KS) occur much more frequently than nonsynonymous ones (KA) and uses theKA/KS ratio as the criterion. We show the following: (1) most of the human and mouse exons are sufficiently long and have a suitable degree of sequence divergence for the test to perform reliably; (2) the test is suited for the identification of long exons and single exon genes, which are difficult to predict by current methods; (3) the test has a false-negative rate, lower than most of current gene prediction methods and a false-positive rate lower than all current methods; (4) the test has been automated and can be used in combination with other existing gene-prediction methods.
Monte Carlo simulations of the differential beam hardening effect of a flattening filter on a therapeutic x‐ray beam
Authors: Lee Plato C.
Published: July 2002

A quantitative study of the differential beam hardening effect of the flattening filter on the 6‐MV beam of Clinac 2100C has been conducted with Monte Carlo simulations using EGS4 code. The fluence‐weighted photon energy of the unfiltered beam decreases from 1.35 MeV at central axis (CAX) to 1.22 MeV at an off‐axis distance (OAD) of 20.0 cm. Compared to the unfiltered beam, the fluence‐weighted photon energy of the filtered beam increases to 1.93 MeV at CAX and to 1.36 MeV at an OAD of 20.0 cm, respectively. The beam hardening effect was found to decrease with increasing OAD. The energy fluence of the unfiltered beam was found to be 2.1 times higher at CAX than at an OAD of 20.0 cm. With the differential filtration of the flattening filter, the photon energy fluence reduced to 44% and 78% at CAX and an OAD of 20.0 cm, respectively, resulting in the energy fluence of the filtered beam being flat from CAX to an OAD of 20.0 cm. The differential transmission ratios between the high energy and low energy photons decrease as the OAD increases. The percentage depth doses (PDDs) at field size offor both the filtered and unfiltered 6‐MV beams at CAX and at an OAD of 15.0 cm were calculated with a Monte Carlo technique based on the simulated spectra and fluence. The calculated PDDs were found to be consistent with the measured data for the filtered beam at CAX and an OAD of 15.0 cm. The beam quality (BQ) of the filtered beam was found to be higher than that of the unfiltered beam at the same OAD. The BQ of the filtered beam at CAX is also higher than that of the same beam at an OAD of 15.0 cm. All the above results quantitatively demonstrate the differential beam hardening effects of a flattening filter on a therapeutic x‐ray beam.
Automatic quality assessment protocol for MRI equipment
Authors: Bourel Philippe , Gibon David , Coste Eric , Daanen Vincent , Rousseau Jean
Published: July 2002

The authors have developed a protocol and software for the quality assessment of MRI equipment with a commercial test object. Automatic image analysis consists of detecting surfaces and objects, defining regions of interest, acquiring reference point coordinates and establishing gray level profiles. Signal‐to‐noise ratio, image uniformity, geometrical distortion, slice thickness, slice profile, and spatial resolution are checked. The results are periodically analyzed to evaluate possible drifts with time. The measurements are performed weekly on three MRI scanners made by the Siemens™ Company (VISION® 1.5T, EXPERT® 1.0T, and OPEN® 0.2T). The results obtained for the three scanners over approximately 3.5 years are presented, analyzed, and compared.
A virtual source model for Monte Carlo modeling of arbitrary intensity distributions
Authors: Chetty I. , DeMarco J. J. , Solberg T. D.
Published: July 2002

A photon virtual source model was developed for simulating arbitrary, external beam, intensity distributions using the Monte Carlo method. The source model consists of a photon fluence grid composed of a matrix of square elements, located 25‐cm downstream from the linear accelerator target. Each particle originating from the fluence map is characterized by the seven phase space parameters, positiondirectionand energy. The map was reconstructed from fluence and energy spectra acquired by modeling components of the linear accelerator treatment head using the Monte Carlo codeMCNP4B. The effect of contaminant electrons is accounted for by the use of a sub‐source derived from a phase‐space simulation of a 25‐MV linac treatment head using the codeBEAM. TheBEAMsub‐source was incorporated into theMCNP4Bphase‐space model and is sampled using a field‐size dependent sampling ratio. A Gaussian blurring kernel is convolved with the photon fluence map to account for the finite focal spot size and scattering effects from structures such as the flattening filter and MLC leaves. Depth dose and profile source calculations for 6‐MV and 25‐MV photon beams, forandfield sizes, are in good agreement with measurement and are well within acceptability criteria suggested by the AAPM Task Group Report No. 53. Irregular field calculations compared with film measurement and with a 3‐D pencil beam algorithm show that the source model is capable of accurately simulating arbitrary MLC fields.
Application of the lattice Green’s function for calculating the resistance of an infinite network of resistors
Authors: Cserti József
Published: July 2002

The resistance between two arbitrary grid points of several infinite lattice structures of resistors is calculated by using lattice Green’s functions. The resistance for d dimensional hypercubic, rectangular, triangular, and honeycomb lattices of resistors is discussed in detail. Recurrence formulas for the resistance between arbitrary lattice points of the square lattice are given. For large separation between nodes the asymptotic form of the resistance for a square lattice and the finite limiting value of the resistance for a simple cubic lattice are calculated. The relation between the resistance of the lattice and the van Hove singularity of the tight-binding Hamiltonian is given. The Green’s function method used in this paper can be applied in a straightforward manner to other types of lattice structures and can be useful didactically for introducing many concepts used in condensed matter physics.
Understanding the penetration of electromagnetic velocity fields into conductors
Authors: Boyer Timothy H.
Published: July 2002

The electromagnetic fields due to a point charge can be broken into velocity fields and acceleration fields. The acceleration fields give rise to electromagnetic waves whose penetration into ohmic conductors is described by exponential damping with a characteristic skin depth. The velocity fields allow a steady-current limit where the magnetic field penetrates even a good conductor. Here we note the contrasts between velocity fields and wave fields in their interactions with conductors. We derive a new time-integral invariant of the magnetic field in an ohmic conductor. Finally we note the disparate analyses in the literature and suggest the following summary regarding the penetration of the electromagnetic fields of a point charge moving parallel to a conducting surface. (1) The falloff of the electromagnetic fields is algebraic, not exponential, and cannot be characterized by a skin depth. (2) In the limit of low velocity, the magnetic field penetration is independent of the conductivity of the material. (3) In general the penetration of the electromagnetic fields depends upon the velocity of the particle and becomes vanishingly small for a perfect conductor. (4) The time integral of the magnetic field at a fixed spatial point inside (or outside) an ohmic conductor is independent of the conductivity of the material; thus as the conductivity of the material becomes larger and the magnetic field inside becomes smaller, the time of penetration becomes longer. The penetration of time-dependent velocity fields into conductors has become of interest largely in connection with the Aharonov–Bohm effect. It is curious that the classical explanation for the Aharonov–Bohm effect depends upon the time integral of the magnetic field, which is independent of the conductivity of any ohmic shielding material.
Optimization of asymmetric bimorphic disk transducers
Authors: Chang Shuo Hung , Du B. C.
Published: July 2002

The dynamic and static characteristics of asymmetric bimorphic disk transducers that consist of a piezoelectric layer laminated with an unequal radius elastic disks are optimized. An electroelastic laminated plate theory is developed to analyze the mechanical, electrical and electromechanical behaviors. Close form solutions are obtained for the mechanical displacement and electric potential in terms of Bessel functions. Special focus is on the electromechanical coupling coefficients (EMCC) that are shown sensitive to geometric variables, such as thickness and radius ratios of the piezoelectric and elastic materials. Optimum configurations to reach the maximum values of the EMCC or static displacement sensitivity and influence of material and geometric properties are presented. Experiments are conducted to verify the theoretical results with good agreement.
Acoustic absorption measurement of human hair and skin within the audible frequency range
Authors: Katz Brian F. G.
Published: July 2002

Utilizing the two-microphone impedance tube method, the acoustic absorption of human skin and hair is measured in the frequency range 1–6 kHz. Various locations on a number of human subjects are measured to determine if the presence of bone or an air pocket affects the acoustic absorption of human skin. The absorption coefficient of human hair is also measured. Additional techniques are utilized to minimize errors due to sample mounting methods. Techniques are employed to minimize potential errors in sensor and sample locations. The results of these measurements are compared to relevant historical papers on similar investigations. Results for skin measurements compare well with previous work. Measured hair absorption data do not agree with previous work in the area but do coincide with expected trends, which previous works do not.
Coherence in children’s speech perception
Authors: Nittrouer Susan , Crowther Court S.
Published: July 2002

Studies with adults have demonstrated that acoustic cues cohere in speech perception such that two stimuli cannot be discriminated if separate cues bias responses equally, but oppositely, in each. This study examined whether this kind of coherence exists for children’s perception of speech signals, a test that first required that a contrast be found for which adults and children show similar cue weightings. Accordingly, experiment 1 demonstrated that adults, 7-, and 5-year-olds weight F2-onset frequency and gap duration similarly in “spa” versus “sa” decisions. In experiment 2, listeners of these same ages made “same” or “not-the-same” judgments for pairs of stimuli in an AX paradigm when only one cue differed, when the two cues were set within a stimulus to bias the phonetic percept towards the same category (relative to the other stimulus in the pair), and when the two cues were set within a stimulus to bias the phonetic percept towards different categories. Unexpectedly, adults’ results contradicted earlier studies: They were able to discriminate stimuli when the two cues conflicted in how they biased phonetic percepts. Results for 7-year-olds replicated those of adults, but were not as strong. Only the results of 5-year-olds revealed the kind of perceptual coherence reported by earlier studies for adults. Thus, it is concluded that perceptual coherence for speech signals is present from an early age, and in fact listeners learn to overcome it under certain conditions.
Annihilation of shocks in forced oscillations of an air column in a closed tube
Authors: Sugimoto N. , Masuda M. , Hashiguchi T. , Doi T.
Published: July 2002

Effects of a periodic array of Helmholtz resonators on forced longitudinal oscillations of an air column in a closed tube are examined experimentally. The column is driven sinusoidally at a frequency near the lowest resonance frequency by oscillating bellows mounted on one end of the tube. Frequency responses are obtained for small and large amplitudes of the excitations. While the array lowers the resonance frequency and the peak value, its dispersive effect, i.e., the dependence of the sound speed on a frequency, can annihilate the shock effectively.
Multicomponent stimulus interactions observed in basilar-membrane vibration in the basal region of the chinchilla cochlea
Authors: Rhode William S. , Recio Alberto
Published: July 2002

Multicomponent stimuli consisting of two to seven tones were used to study suppression of basilar-membrane vibration at the 3–4-mm region of the chinchilla cochlea with a characteristic frequency between 6.5 and 8.5 kHz. Three-component stimuli were amplitude-modulated sinusoids (AM) with modulation depth varied between 0.25 and 2 and modulation frequency varied between 100 and 2000 Hz. For five-component stimuli of equal amplitude, frequency separation between adjacent components was the same as that used for AM stimuli. An additional manipulation was to position either the first, third, or fifth component at the characteristic frequency (CF). This allowed the study of the basilar-membrane response to off-CF stimuli. CF suppression was as high as 35 dB for two-tone combinations, while for equal-amplitude stimulus components CF suppression never exceeded 20 dB. This latter case occurred for both two-tone stimuli where the suppressor was below CF and for multitone stimuli with the third component=CF. Suppression was least for the AM stimuli, including when the three AM components were equal. Maximum suppression was both level- and frequency dependent, and occurred for component frequency separations of 500 to 600 Hz. Suppression decreased for multicomponent stimuli with component frequency spacing greater than 600 Hz. Mutual suppression occurred whenever stimulus components were within the compressive region of the basilar membrane.
A note on nonlinear radiation from a gas bubble in liquids
Authors: Ye Zhen
Published: July 2002

This paper discusses nonlinear radiation from a gas bubble in liquids. The discrepant results from two previous approaches, the volume displacement approach and the radial displacement approach, were compared and discussed. By rederiving the governing equation used in the two approaches, it is shown that under the usual approximations the sound emission resulting from the volume displacement approach is correct, but the previous procedure which leads to the right answer is not rigorous; the lack of rigor has drawn considerable criticisms in the past.
Dynamic compressibility of air in porous structures at audible frequencies
Authors: Lafarge Denis , Lemarinier Pavel , Allard Jean F. , Tarnow Viggo
Published: July 2002

Measurements of dynamic compressibility of air-filled porous sound-absorbing materials are compared with predictions involving two parameters, the static thermal permeability k0′ and the thermal characteristic dimension Λ′. Emphasis on the notion of dynamic and static thermal permeability—the latter being a geometrical parameter equal to the inverse trapping constant of the solid frame—is apparently new. The static thermal permeability plays, in the description of the thermal exchanges between frame and saturating fluid, a role similar to the viscous permeability in the description of the viscous forces. Using both parameters, a simple model is constructed for the dynamic thermal permeability k′(ω), which is completely analogous to the Johnson et al. [J. Fluid Mech. 176, 379 (1987)] model of dynamic viscous permeability k(ω). The resultant modeling of dynamic compressibility provides predictions which are closer to the experimental results than the previously used simpler model where the compressibility is the same as in identical circular cross-sectional shaped pores, or distributions of slits, related to a given Λ′.
Flexural vibration of an infinite wedge
Authors: Gunda Rajendra , Vijayakar Sandeep M. , Singh Rajendra
Published: July 2002

A new solution to the problem of flexural vibration of an infinite wedge excited by a point harmonic load is obtained via a superposition of the geometric and diffraction fields, for simply supported and roller boundary conditions along the edges. The diffraction integrals are evaluated both in closed form in terms of the Faddeeva function and also as an asymptotic series using the steepest descent method. An eigensolution is also derived by expanding eigenfunctions in the angular direction and propagation terms in the radial direction. These two representations of the solution are compared numerically for accuracy and spatial distribution in different frequency regimes. The relative contribution of the geometric and diffraction fields to the overall solution is examined. This result is then compared to the second-order Helmholtz wave equation solution in order to demonstrate the near-field effects arising due to the fourth-order biharmonic formulation. The authors’ motivation for obtaining the solution for a wedge-shaped infinite plate is that it is an essential step toward devising numerical models for the vibration of arbitrary polygonal plates. By combining the contribution from diffraction at the vertices of a polygonal plate with the geometrical solution obtained by the method of images, the authors expect to obtain better predictions at mid and high frequencies than is possible by other available methods.
A novel approach to sound scattering by cylinders of finite length
Authors: Ye Zhen
Published: July 2002

This paper presents a new method for studying bistatic scattering of acoustic waves by finite cylinders. The method is based on the assumption that a differential element of the cylinder scatters sound as though it were part of an infinite cylinder of the same radius. Under this assumption, the scattering function of cylinder body is derived rigorously using the Kirchhoff integral theorem. The effect of scattering by the ends of finite cylinders is also considered. It is shown that the result from the previous cylinder method [T. K. Stanton, J. Acoust. Soc. Am. 83, 55–63 (1988)] is a special case of the present method. The new approach, particular-useful for calculating the bistatic scattering function, is compared to this previous method by various examples. The numerical computation shows that when the scattering direction is close to the incidence direction, the difference between the two methods is small, and the difference generally increases as the scattering direction moves increasingly away from the incidence direction. It is further shown that the difference between the two methods is more severe for weak scatterers.