bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating antibody-catalyzed ozone generation by human neutrophils
Authors: Babior Bernard M. , Takeuchi Cindy , Ruedi Julie , Gutierrez Abel , Wentworth Paul
Published: March 2003

Recent studies have suggested that antibodies can catalyze the generation of previously unknown oxidants including dihydrogen trioxide (H
2
O
3
) and ozone (O
3
) from singlet oxygen (
1
O

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) and water. Given that neutrophils have the potential both to produce
1
O

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and to bind antibodies, we considered that these cells could be a biological source of O
3
. We report here further analytical evidence that antibody-coated neutrophils, after activation, produce an oxidant with the chemical signature of O
3
. This process is independent of surface antibody concentration down to 50% of the resting concentration, suggesting that surface IgG is highly efficient at intercepting the neutrophil-generated
1
O

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. Vinylbenzoic acid, an orthogonal probe for ozone detection, is oxidized by activated neutrophils to 4-carboxybenzaldehyde in a manner analogous to that obtained for its oxidation by ozone in solution. This discovery of the production of such a powerful oxidant in a biological context raises questions about not only the capacity of O
3
to kill invading microorganisms but also its role in amplification of the inflammatory response by signaling and gene activation.
Type III secretion systems and bacterial flagella: Insights into their function from structural similarities
Authors: Blocker Ariel , Komoriya Kaoru , Aizawa Shin-Ichi
Published: March 2003

Type III secretion systems and bacterial flagella are broadly compared at the level of their genetic structure, morphology, regulation, and function, integrating structural information, to provide an overview of how they might function at a molecular level.
A
Saccharomyces cerevisiae
mutant strain defective in acetyl-CoA carboxylase arrests at the G
2
/M phase of the cell cycle
Authors: Al-Feel Walid , DeMar James C. , Wakil Salih J.
Published: March 2003

To elucidate the essential functions of acetyl-CoA carboxylase (ACC1/FAS3) in
Saccharomyces cerevisiae
, a temperature-sensitive mutant (
acc1
ts
) was constructed. When the acc1
ts
cells were synchronized in G
1
phase with α-factor at the permissive temperature of 24°C and then released from the blockade and incubated at the restrictive temperature of 37°C, 95% of the cell population became arrested at the G
2
/M phase of the cell cycle despite the presence of fatty acids (C
14
-C
26
) in the medium. These cells developed large undivided nuclei, and the spindles of the arrested mutant cells were short. Shifting the G
2
arrested cells back to the permissive temperature resulted in a reversal of the cell-cycle arrest, with cells initiating mitosis. However, after 3 h of incubation at 37°C, G
2
arrested mutant cells lost viability and displayed a uniquely altered nuclear envelope. Using [1-
14
C]acetate as a precursor for fatty acids synthesis, we identified the phospholipids and sphingolipids derived from acc1
ts
cells and wild-type cells at 24°C and 37°C, respectively. The levels of inositol-ceramides [IPC, MIPC, and M(IP)
2
C] and very long-chain fatty acids C
24
and C
26
declined sharply in the G
2
/M arrested cells because of ACC inactivation. Shifting the acc1
ts
cells to 24°C after 2 h of incubation at 37°C resulted in reactivation of the ACC and elevation of the ceramides and very long-chain fatty acid syntheses with normal cell-cycle progression. In contrast, synthesis of wild-type inositol-ceramides, C
24
and C
26
, fatty acids were elevated on incubation at 37°C and declined when the cells shifted to the permissive temperature of 24°C.
Transcription termination control of the S box system: Direct measurement of
S
-adenosylmethionine by the leader RNA
Authors: McDaniel Brooke A. Murphy , Grundy Frank J. , Artsimovitch Irina , Henkin Tina M.
Published: March 2003

Modulation of the structure of a leader RNA to control formation of an intrinsic termination signal is a common mechanism for regulation of gene expression in bacteria. Expression of the S box genes in Gram-positive organisms is induced in response to limitation for methionine. We previously postulated that methionine availability is monitored by binding of a regulatory factor to the leader RNA and suggested that methionine or
S
-adenosylmethionine (SAM) could serve as the metabolic signal. In this study, we show that efficient termination of the S box leader region by bacterial RNA polymerase depends on SAM but not on methionine or other related compounds. We also show that SAM directly binds to and induces a conformational change in the leader RNA. Both binding of SAM and SAM-directed transcription termination were blocked by leader mutations that cause constitutive expression
in vivo
. Overproduction of SAM synthetase in
Bacillus subtilis
resulted in delay in induction of S box gene expression in response to methionine starvation, consistent with the hypothesis that SAM is the molecular effector
in vivo
. These results indicate that SAM concentration is sensed directly by the nascent transcript in the absence of a trans-acting factor.
Engene: the processing and exploratory analysis of gene expression data
Authors: García de la Nava Jorge , Santaella Daniel Franco , Alba Jesús Cuenca , Carazo José María , Trelles Oswaldo , Pascual-Montano Alberto
Published: March 2003

Summary: Engene is a versatile, and platform-independent web tool for exploratory analysis of gene expression data that aims at storing, visualizing and processing large sets of gene expression patterns.

Availability: Access to engene is available on request at http://www.engene.cnb.uam.es

Contact: pascual@cnb.uam.es

* To whom correspondence should be addressed.
The Z curve database: a graphic representation of genome sequences
Authors: Zhang Chun-Ting , Zhang Ren , Ou Hong-Yu
Published: March 2003

Motivation: Genome projects for many prokaryotic and eukaryotic species have been completed and more new genome projects are being underway currently. The availability of a large number of genomic sequences for researchers creates a need to find graphic tools to study genomes in a perceivable form. The Z curve is one of such tools available for visualizing genomes. The Z curve is a unique three-dimensional curve representation for a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z curve database for more than 1000 genomes have been established here.

Results: The database contains the Z curves for archaea, bacteria, eukaryota, organelles, phages, plasmids, viroids and viruses, whose genomic sequences are currently available. All the 3-dimensional Z curves and their three component curves are stored in the database. The applications of the Z curve database on comparative genomics, gene prediction, computation of G+C content with a windowless technique, prediction of replication origins and terminations of bacterial and archaeal genomes and study of local deviations from the Chargaff Parity Rule 2 etc. are presented in detail. The Z curve database reported here is a treasure trove in which biologists could find useful biological knowledge.

Availability: The Z curve database is freely available at the website: http://tubic.tju.edu.cn/zcurve/

Contact: ctzhang@tju.edu.cn

* To whom correspondence should be addressed.
DigiNorthern, digital expression analysis of query genes based on ESTs
Authors: Wang Jianxin , Liang Ping
Published: March 2003

Summary: DigiNorthern (DN) is a web-based tool for virtually displaying expression profiles of query genes based on EST sequences. Two utilities are available: DN1 takes one query gene and quantitatively display its expression levels in tissues/organs that express the gene with comparison between normal and neoplastic status of each tissue; DN2 takes two sequences as query genes and compares their expression profiles side by side.

Availability: DN is currently available for analyses of human and mouse genes and is accessible at http://falcon.roswellpark.org/DN. Options for other species may become available in future depending on user’s request and EST data availability.

Contact: ping.liang@roswellpark.org

* To whom correspondence should be addressed.
Mapping multiple co-sequenced T-DNA integration sites
within the Arabidopsis genome
Authors: Presting Gernot G.
Published: March 2003

Motivation: Insertion mutagenesis, using transgenes or endogenous transposons, is a popular method for generating null mutations (knockouts) in model organisms. Insertions are mapped to specific genes by amplifying (via TAIL-PCR) and sequencing genomic regions flanking the inserted DNA. The presence of multiple TAIL-PCR templates in one sequencing reaction results in chimeric sequence of intermittently low quality. Standard processing of this sequence by applying Phred quality requirements results in loss of informative sequence, whereas not trimming low-quality sequence causes inclusion of low-complexity homopolymers from the ends of sequence runs. Accurate mapping of the flanking sequences is complicated by the presence of gene families.

Results: Methods for extracting informative regions from sequence traces obtained by sequencing multiple TAIL-PCR fragments in a single reaction are described. The completely sequenced Arabidopsis genome was used to identify informative TAIL-PCR sequence regions. Methods were devised to define and select high quality matches and precisely map each insert to the correct genome location. These methods were used to analyze sequence of TAIL-PCR-amplified flanking regions of the inserts from individual plants in a T-DNA-mutagenized population of Arabidopsis thaliana, and are applicable to similar situations where a reference genome can be used to extract information from poor-quality sequence.

Contact: gernot@genome.clemson.edu

Supplementary information: Tables of the calculated T-DNA insertion sites and supplementary data are available at http://www.tmri.org/pages/collaborations/garlic_files/Bioinfo.html

* To whom correspondence should be addressed.
PedNavigator: a pedigree drawing servlet for large and
inbred populations
Authors: Mancosu Gianmaria , Ledda Giuseppe , Melis Paola M.
Published: March 2003

Summary: PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to ‘walk’ through family ties by point-and-clicking on person’s symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.

Availability: Available upon request to author.

Contact: mancosu@shardna.it

* To whom correspondence should be addressed.
PCA disjoint models for multiclass cancer analysis using gene
expression data
Authors: Bicciato S. , Luchini A. , Di Bello C.
Published: March 2003

Motivation: Microarray expression profiling appears particularly promising for a deeper understanding of cancer biology and to identify molecular signatures supporting the histological classification schemes of neoplastic specimens. However, molecular diagnostics based on microarray data presents major challenges due to the overwhelming number of variables and the complex, multiclass nature of tumor samples. Thus, the development of marker selection methods, that allow the identification of those genes that are most likely to confer high classification accuracy of multiple tumor types, and of multiclass classification schemes is of paramount importance.

Results: A computational procedure for marker identification and for classification of multiclass gene expression data through the application of disjoint principal component models is described. The identified features represent a rational and dimensionally reduced base for understanding the basic biology of diseases, defining targets for therapeutic intervention, and developing diagnostic tools for the identification and classification of multiple pathological states. The method has been tested on different microarray data sets obtained from various human tumor samples. The results demonstrate that this procedure allows the identification of specific phenotype markers and can classify previously unseen instances in the presence of multiple classes.

Availability: Matlab source codes are available from the authors.

Contact: silvio.bicciato@unipd.it

Supplementary information: http://www.dpci.unipd.it/PersPages/SBicciato/SIMCArray.html

* To whom correspondence should be addressed.
ASAP: automated sequence annotation pipeline for
web-based updating of sequence information with a local dynamic
database
Authors: Kossenkov Andrew , Manion Frank J. , Korotkov Eugene , Moloshok Thomas D. , Ochs Michael F.
Published: March 2003

Summary: The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.

Availability: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/

Contact: av_kossenkov@fccc.edufj_manion@fccc.edukatrin22@mtu-net.rutd_moloshok@fccc.edum_ochs@fccc.edu

* To whom correspondence should be addressed.
Automatic analysis of DNA microarray images using mathematical morphology
Authors: Angulo Jesús , Serra Jean
Published: March 2003

Motivation: DNA microarrays are an experimental technology which consists in arrays of thousands of discrete DNA sequences that are printed on glass microscope slides. Image analysis is an important aspect of microarray experiments. The aim of this step is to reduce an image of spots into a table with a measure of the intensity for each spot. Efficient, accurate and automatic analysis of DNA spot images is essential in order to use this technology in laboratory routines.

Results: We present an automatic non-supervised set of algorithms for a fast and accurate spot data extraction from DNA microarrays using morphological operators which are robust to both intensity variation and artefacts. The approach can be summarised as follows. Initially, a gridding algorithm yields the automatic segmentation of the microarray image into spot quadrants which are later individually analysed. Then the analysis of the spot quadrant images is achieved in five steps. First, a pre-quantification, the spot size distribution law is calculated. Second, the background noise extraction is performed using a morphological filtering by area. Third, an orthogonal grid provides the first approach to the spot locus. Fourth, the spot segmentation or spot boundaries definition is carried out using the watershed transformation. And fifth, the outline of detected spots allows the signal quantification or spot intensities extraction; in this respect, a noise model has been investigated. The performance of the algorithm has been compared with two packages: ScanAlyze and Genepix, showing its robustness and precision.

Availability: A prototype system integrated in PDI32 (an image processing software for Windows) may be obtained from the authors on request.

Contact: angulo,serra@cmm.ensmp.fr

Supplementary Information: http://cmm.ensmp.fr/~angulo/

* To whom correspondence should be addressed.
GPCR-GRAPA-LIB—a refined library of hidden Markov Models
for annotating GPCRs
Authors: Shigeta Ron , Cline Melissa , Liu Guoying , Siani-Rose Michael A.
Published: March 2003

Summary: GPCR-GRAPA-LIB is a library of HMMs describing G protein coupled receptor families. These families are initially defined by class of receptor ligand, with divergent families divided into subfamilies using phylogenic analysis and knowledge of GPCR function. Protein sequences are applied to the models with the GRAPA curve-based selection criteria. RefSeq sequences for Homo sapiens, Drosophila melanogaster, and Caenorhabditis elegans have been annotated using this approach.

Availability: The HMMs and sequence alignments are available at http://www.affymetrix.com/community/publications/affymetrix/index.affx. Annotation results are available at http://www.affymetrix.com/analysis/index.affx

Contact: ron_shigeta@affymetrix.com

* To whom correspondence should be addressed.
Effective dimension reduction methods for tumor classification
using gene expression data
Authors: Antoniadis A. , Lambert-Lacroix S. , Leblanc F.
Published: March 2003

Motivation: One particular application of microarray data, is to uncover the molecular variation among cancers. One feature of microarray studies is the fact that the number n of samples collected is relatively small compared to the number p of genes per sample which are usually in the thousands. In statistical terms this very large number of predictors compared to a small number of samples or observations makes the classification problem difficult. An efficient way to solve this problem is by using dimension reduction statistical techniques in conjunction with nonparametric discriminant procedures.

Results: We view the classification problem as a regression problem with few observations and many predictor variables. We use an adaptive dimension reduction method for generalized semi-parametric regression models that allows us to solve the‘ curse of dimensionality problem’ arising in the context of expression data. The predictive performance of the resulting classification rule is illustrated on two well know data sets in the microarray literature: the leukemia data that is known to contain classes that are easy ‘separable’ and the colon data set.

Availability: Software that implements the procedures on which this paper focus are freely available at http://www-lmc.imag.fr/SMS/software/microarrays/

Contact: anestis.antoniadis@imag.fr

* To whom correspondence should be addressed.
The estimation of relative site variability among aligned homologous
protein sequences
Authors: Horner D. S. , Pesole G.
Published: March 2003

Motivation: Maximum likelihood-based methods to estimate site by site substitution rate variability in aligned homologous protein sequences rely on the formulation of a phylogenetic tree and generally assume that the patterns of relative variability follow a pre-determined distribution. We present a phylogenetic tree-independent method to estimate the relative variability of individual sites within large datasets of homologous protein sequences. It is based upon two simple assumptions. Firstly that substitutions observed between two closely related sequences are likely, in general, to occur at the most variable sites. Secondly that non-conservative amino acid substitutions tend to occur at more variable sites. Our methodology makes no assumptions regarding the underlying pattern of relative variability between sites.

Results: We have compared, using data simulated under a non-gamma distributed model, the performance of this approach to that of a maximum likelihood method that assumes gamma distributed rates. At low mean rates of evolution our method inferred site by site relative substitution rates more accurately than the maximum likelihood approach in the absence of prior assumptions about the relationships between sequences. Our method does not directly account for the effects of mutational saturation, However, we have incorporated an ‘ ad-hoc’ modification that allows the accurate estimation of relative site variability in fast evolving and saturated datasets.

Availability: A script which implements the methodology described in this paper (written in Biopython) is available from dsh on request.

Contact: graziano.pesole@unimi.it

* To whom correspondence should be addressed.
G1 cyclin-dependent kinases are insufficient to reverse dE2F2-mediated repression
Authors: Frolov Maxim V. , Stevaux Olivier , Moon Nam-Sung , Dimova Dessislava , Kwon Eun-Jeong , Morris Erick J. , Dyson Nicholas J.
Published: March 2003

Here we show that the cell cycle defects of dE2F1-depleted cells depend on the cooperative effects of dE2F2 and DACAPO (DAP), an inhibitor of Cyclin E/cyclin-dependent kinase 2 (CycE/cdk2). The different properties of cells lacking dE2F1/dE2F2 and dE2F1/DAP lead to the surprising observation that dE2F2-mediated repression differs from retinoblastoma family protein 1 (RBF1) inhibition of dE2F1, and is resistant to both CycE/cdk2 and Cyclin D/cyclin-dependent kinase 4 (CycD/cdk4). This resistance occurs even though dE2F2/RBF1 complexes are disrupted by CycE/cdk2, and may explain why dE2F2 is so potent in the absence ofde2f1. The implication of these results is that cells containing dE2F2 require dE2F1 to either prevent, or reverse, dE2F-mediated repression.
Coordinated temporal and spatial control of motor neuron and serotonergic neuron generation from a common pool of CNS progenitors
Authors: Pattyn Alexandre , Vallstedt Anna , Dias José M. , Samad Omar Abdel , Krumlauf Robb , Rijli Filippo M. , Brunet Jean-Francois , Ericson Johan
Published: March 2003

Neural progenitor cells often produce distinct types of neurons in a specific order, but the determinants that control the sequential generation of distinct neuronal subclasses in the vertebrate CNS remain poorly defined. We examined the sequential generation of visceral motor neurons and serotonergic neurons from a common pool of neural progenitors located in the ventral hindbrain. We found that the temporal specification of these neurons varies along the anterior-posterior axis of the hindbrain, and that the timing of their generation critically depends on the integrated activities of Nkx- and Hox-class homeodomain proteins. A primary function of these proteins is to coordinate the spatial and temporal activation of the homeodomain protein Phox2b, which in turn acts as a binary switch in the selection of motor neuron or serotonergic neuronal fate. These findings assign new roles for Nkx, Hox, and Phox2 proteins in the control of temporal neuronal fate determination, and link spatial and temporal patterning of CNS neuronal fates.
A novel lattice-spacing comparator with resolution of 10−8
Authors: Zhang Xiaowei , Sugiyama Hiroshi , Ando Masami , Imai Yoshihiko , Yoda Yoshitaka
Published: March 2003

A novel, fast and stable system for measuring the lattice spacing of a silicon crystal with a precision of 10−8is described. Self selection of monochromatic X-rays by a monolithic double channel-cut crystal monochromator (MDCM), producing silicon 264 and 624 diffraction, may lead to a stable, highly collimated and narrow-bandwidth beam. When utilizing the 264 and 624 Bragg reflections of a silicon sample, the angular distance between the two associated Bragg peaks must be extremely small, so that the diffraction angle can be determined with high precision and the traveling time from one peak to the other can be considerably reduced by the order of at least three compared with the established classical Bond method. This so-called self-reference comparator method can dramatically save measurement time and can provide an absolute measurement on the basis of the known X-ray wavelength available from the MDCM. Thus a lattice-spacing measurement with resolution of 10−8, within a few tens of seconds for an area of 1 mm2on a silicon sample, has been realised.
An intensity evaluation method:EVAL-14
Authors: Duisenberg Albert J. M. , Kroon-Batenburg Loes M. J. , Schreurs Antoine M. M.
Published: March 2003

A reflection intensity integration method is presented based uponab initiocalculation of three-dimensional (x, y, ω) reflection boundaries from a few physical crystal and instrument parameters. It is especially useful in challenging circumstances, such as the case of a crystal that is far from spherical, anisotropic mosaicity, α1α2peak splitting, interference from close neighbours, twin lattices or satellite reflections, and the case of streaks from modulated structures, all of which may frustrate the customary profile-learning and -fitting procedures. The method, calledEVAL-14, has been implemented and extensively tested on a Bruker Nonius KappaCCD diffractometer.
A Monte Carlo approach to crystal structure determination from powder diffraction data
Authors: Brodski V. , Peschar R. , Schenk H.
Published: March 2003

A new direct-space method forab initiosolution of crystal structures from powder diffraction data is presented. The approach consists of a combined global minimization ofRwpand the potential energy of the system. This method was tested on two organic compounds with known structure and also applied successfully in the structure determination of the previously unknown structure of melamine pyrophosphate.
X-Cell: a novel indexing algorithm for routine tasks and difficult cases
Authors: Neumann Marcus A.
Published: March 2003

X-Cellis a novel indexing algorithm that makes explicit use of systematic absences to search for possible indexing solutions from cells with low numbers of calculated reflections to cells with high numbers of reflections. Space groups with the same pattern of systematic absences are grouped together in powder extinction classes, and for a given peak number range an independent search is carried out in each powder extinction class. The method has the advantage that the correct cell is likely to be found before the rapid increase of possible solutions slows down the search significantly. A successive dichotomy approach is used to establish a complete list of all possible indexing solutions. The dichotomy procedure is combined with a search for the zero-point shift of the diffraction pattern, and impurity peaks can be dealt with by allowing for a user-defined portion of unindexed reflections. To rank indexing solutions with varying numbers of unindexed reflections, a new figure of merit is introduced that takes into account the highest level of agreement typically obtained for completely incorrect unit cells. The indexing of long and flat unit cells is facilitated by the possibility to search for rows or zones in reciprocal space first and then to use the lattice parameters of the dominant row or zone in the unit-cell search. The main advantages ofX-Cellare robustness and completeness, as demonstrated by a validation study on a variety of compounds. The dominant phase of phase mixtures can be indexed in the presence of up to 50% of impurity peaks if high-quality synchrotron data are available.
A Michelson interferometer for X-rays capable of high-order measurement
Authors: Nusshardt Michael , Bonse Ulrich
Published: March 2003

The first Michelson interferometer which was capable of working in the hard X-ray range featured geometric path-length differences of interfering beams of about 120 nm, corresponding to a scan range of more than 750 orders at a wavelength λ ≃ 0.15 nm. The new instrument uses the same principle,i.e.mixing of Laue- and Bragg-case beams diffracted by only one set of Bragg planes of two separate structures of perfect silicon crystals. Through modifying the geometry of beam paths, it has been possible to extend the scan range by a factor of 3.6 and to measure 2700 interference orders for the same wavelength. Six beat nodes of the CuKα1–Kα2doublet were recorded in Fourier spectrometric mode. Allowing for realistic reflection curves of Laue and Bragg components, the output spectrum was calculated and found to be in good agreement with the measured spectrum. The influence of thermal, acoustic and vibrational disturbances was studied in detail and special means were developed to cope with them. Applying the know-how obtained in this study in scaling up the present design, it should be feasible to extend the scanning range to ∼40000 orders, which would allow hard X-ray Fourier spectroscopy at spectroscopic resolutions λ/Δλ ≃ 20000.
Analysis of the small-angle intensity scattered by a porous and granular medium
Authors: Spalla O. , Lyonnard S. , Testard F.
Published: March 2003

Using X-ray scattering over a large range of scattering vectors, it is shown how to measure both the pore volume fraction and pore specific surface of an assembly of porous grains forming a powder. Depending on the presence or not of solvent in the inner pores and in the intergranular media, the scattered signal per unit volume of solid or per unit volume of grain are introduced, which allow a complete analysis even when the thickness of the layer and its compactness are unknown. The method is applied to three different systems presenting a well defined Porod regime at large scattering vector.
Structural refinements of the individual grains within polycrystals and powders
Authors: Schmidt S. , Poulsen H. F. , Vaughan G. B. M.
Published: March 2003

A method is presented for simultaneous structural refinement of up to several hundred grains inside powders or polycrystals. The method is based on the use of hard X-rays and the indexing programGRAINDEX, where grain orientations are found by scanning in Euler space. Conventional experimental setups and refinement programs for single-crystal work can be applied. The method is validated by a study of a sintered plate of α-Al2O3, containing of the order of 1500 grains in the gauge volume. 57 of the largest grains were refined with respect to the Alzand Oxpositions as well as the isotropic atomic displacement parameters. TheR1 values were 3.4% and 3.8% for the grain average and the best grain, respectively. A discussion of the potential of the method is presented, as well as the main limitation: grain size and overlap of diffraction spots.
Intellectual capital and the capital market: the circulability of intellectual capital
Authors: Mouritsen Jan
Published: March 2003

This paper argues that intellectual capital and intangible assets are difficult resources for two different reasons. First, intellectual capital and intangibles assets are not (yet) disentangled by the institutions of the capital markets, and therefore they are not (yet) translatable with any degree of confidence into predictions about stock price behaviour. Second, intellectual capital and intangibles are not absent from capital market intelligence; they are just typically translated into financial form, when they are presented to actors in the capital markets, even if in forms that are themselves “invisible”. The capital market may have limited understanding of intellectual capital, but it is also always seeking to understand the complexity of business and (im)possible futures. Its appreciation of intellectual capital is therefore fragile.
The changing internal market for ethical discourses in the Canadian CA profession
Authors: Neu Dean , Friesen Constance , Everett Jeffery
Published: March 2003

Starting from the premise that formal ethical codes and other ethical discourses differ in their audiences, effects and characteristics, it is analyzed how practitioner‐directed ethical discourses have spoken and continue to speak about character‐based ethics. Borrowing from the literature on professions and Pierre Bourdieu’s theory of practice, starts from the assumption that editorials in practitioner‐oriented publications are a form of cultural good traded on an internal symbolic market. By providing access to symbolic capital, trade in this good acts to bind together members of the accounting profession, yet trade in this good also has the potential to obscure a number of important, underlying social issues. The study is based on a close (textual) reading of editorials in the Canadian Chartered Accountant (subsequently renamed CA Magazine) from 1911 to 1999, and this reading is framed in light of a number of macro‐level and meso‐level (contextual) changes. It is found that character‐based ethical discourses continue to pervade this professional field, though not without important changes which themselves need to be explained in light of the more widespread, non‐professional field.
The Scottish Postgraduate Archives Training Project – issues for the records management community
Authors: Rankin Frank
Published: March 2003

The Scottish Postgraduate Archives Training Project sought to gauge the feasibility of establishing postgraduate education for archivists and records managers in Scotland. The article summarises some of the key findings relating to records management.
Retail market orientation: a preliminary framework
Authors: Elg Ulf
Published: March 2003

Existing market orientation frameworks are based mostly on studies of manufacturers. Therefore, there is a need of a modified approach that acknowledges the special conditions for retailers. A framework is presented that includes both internal and relational aspects. Inter‐firm market orientation is presented as especially relevant for retailers. Antecedents to market orientation on a relationship level are also considered. Kohli and Jaworski’s three basic components are used, but the paper then discusses indicators that are especially useful in order to capture market orientation in a retail context. The suggested framework is further developed using a case study of a major British food retailer.
Quick response: perceptions of UK fashion retailers
Authors: Birtwistle Grete , Siddiqui Noreen , Fiorito Susan S.
Published: March 2003

Defines and discusses the level of quick response implementation by fashion retailers, their understanding of quality response (QR) is explored and the processes for replenishments examined. This exploratory study, based on a survey of fashion retailers trading in the UK, revealed that information technology is particularly important to the large, multiple “own brand” fashion retailers as it enables the various parties in the supply chain to communicate and to respond to demand. Results indicate that retailers have not fully understood the benefits of implementing a QR strategy and perceive it more often as a strategy for internal supply chain management rather than an external supply chain strategy.
Modeling individual differences in ferret external ear transfer functions
Authors: Schnupp Jan W. H. , Booth John , King Andrew J.
Published: March 2003

Individual variations in head and outer ear size, as well as growth of these structures during development, can markedly alter the values of the binaural and monaural cues which form the basis for auditory localization. This study investigated individual differences in the directional component of the head-related transfer function of both adult and juvenile ferrets. In line with previous studies in humans and cats, intersubject spectral differences were found to be reduced by scaling one of the directional transfer functions on a log-frequency axis. The optimal scale factor correlated most highly with pinna cavity height. Optimal frequency scaling reduced interear spectral difference equally well for adult–juvenile comparisons as for comparisons between pairs of adult ears. This illustrates that the developmental changes in localization cue values should be at least partly predictable on the basis of the expected growth rate of the outer ear structures. Predictions of interaural time differences (ITDs) were also derived from the physical dimensions of the head. ITDs were found to be poorly fitted by the spherical head model, while much better predictions could be derived from a model based on von Mises spherical basis functions. Together, these findings show how more accurate estimates of spatial cue values can be made from knowledge of the dimensions of the head and outer ears, and may facilitate the generation of virtual acoustic space stimuli in the absence of acoustical measurements from individual subjects.
Investigation of the vibrational modes of edge-constrained fibrous samples placed in a standing wave tube
Authors: Song Bryan H. , Bolton J. Stuart
Published: March 2003

In earlier work it was suggested that the frictional constraint of a porous sample around its circumference in a standing wave tube resulted in shearing resonances of the sample. In the present work that effect has been confirmed by direct measurement of the spatial distribution of the velocity of the solid phase of a fibrous sample placed in a rigidly terminated standing wave tube and driven into motion by a plane, incident sound field. The measurements were performed using a standing wave tube to which a transparent downstream section was attached. A laser Doppler velocimeter was then used to measure the velocity of the solid phase of acoustically driven samples. The materials considered here were two types of aviation-grade glass fiber. A poroelastic finite element model was used to simulate the response of the constrained fibrous samples. Good agreement between measured and predicted mode shapes was found both when the samples were constrained only around their edges, and when an additional constraint plane was inserted axially through the samples. The present results confirm that glass fiber samples placed in a standing wave tube exhibit shearing modes and that those modes are associated with previously observed transmission loss minima.
Modal characteristics of in-plane vibration of circular plates clamped at the outer edge
Authors: Farag N. H. , Pan J.
Published: March 2003

The equations of in-plane vibration in thin flat plates are solved for free vibration in circular plates clamped at the outer edge. The mode shapes are represented by trigonometric functions in the circumferential direction and by series summation of Bessel functions in the radial direction. Accuracy of the predictions of natural frequencies and mode shapes is assessed by comparisons with finite-element predictions and with previously reported results. The present solution gives very accurate predictions. The work also highlights the nature of coupling between the different circumferential and radial modes and the response of different vibrational modes at the center of the plate. It is shown that the center point of the plate vibrates only for modes with unity circumferential wave number (number of nodal diameters). Nondimensional frequency parameters are listed and the radial mode shapes of natural vibration are depicted to illustrate the free-vibration behavior in the frequency range of practical interest.
Acoustic and mechanical response of reservoir rocks under variable saturation and effective pressure
Authors: Ravazzoli C. L. , Santos J. E. , Carcione J. M.
Published: March 2003

We investigate the acoustic and mechanical properties of a reservoir sandstone saturated by two immiscible hydrocarbon fluids, under different saturations and pressure conditions. The modeling of static and dynamic deformation processes in porous rocks saturated by immiscible fluids depends on many parameters such as, for instance, porosity, permeability, pore fluid, fluid saturation, fluid pressures, capillary pressure, and effective stress. We use a formulation based on an extension of Biot’s theory, which allows us to compute the coefficients of the stress–strain relations and the equations of motion in terms of the properties of the single phases at the in situ conditions. The dry-rock moduli are obtained from laboratory measurements for variable confining pressures. We obtain the bulk compressibilities, the effective pressure, and the ultrasonic phase velocities and quality factors for different saturations and pore-fluid pressures ranging from normal to abnormally high values. The objective is to relate the seismic and ultrasonic velocity and attenuation to the microstructural properties and pressure conditions of the reservoir. The problem has an application in the field of seismic exploration for predicting pore-fluid pressures and saturation regimes.
Investigation into the validity of two-dimensional models for sound radiation from waves in rails
Authors: Thompson D. J. , Jones C. J. C. , Turner N.
Published: March 2003

The sound radiation from a vibrating rail can be predicted using a two-dimensional model under certain conditions. This paper explores these conditions and shows that, if the decay rate of vibration along the rail becomes large or the wavelength in the rail becomes small, it becomes necessary to allow for three-dimensional radiation characteristics. In practice, however, noise from a rail can be predicted using a two-dimensional model for frequencies above about 250 Hz, and even where three-dimensional effects become important, these can be allowed for by simple correction terms. When the wavelength in the rail approaches that of acoustic waves in air, the angle between the direction of sound radiation from the rail and the normal to the rail increases, in some cases to more than 45°. This must be accounted for if the performance of noise barriers is to be calculated using a two-dimensional approach.
Experimental validation of two elastodynamic models for the wave field generated by ultrasonic transducers
Authors: Bakker Maarten C. M. , Verweij Martin D.
Published: March 2003

Two different three-dimensional elastodynamic models are introduced to simulate the wave field generated in steel by two types of surface mounted ultrasonic transducers. By replacing the actual transducer by an equivalent surface source distribution, the models become amenable to an exact analytical analysis. The first model simulates the action of a contact transducer through a distribution of nonmoving line segment sources. The second model simulates the action of an angle beam transducer through a single moving line segment source. Almost any transducer aperture shape may be modeled, while the source may apply a nonuniform traction. To speed up the numerical space–time domain calculations, the Cagniard–De Hoop method is employed to analytically evaluate the wave field produced by a single nonmoving line segment source. This solution provides the integrand for both single-integral models. The models are experimentally validated for a contact transducer and three different angle beam transducers. The validation involves a comparison of the wave-field patterns, the directivity curves and some time-domain signals from the wave field. It is shown that the models reliably identify the wide variety of waves generated by ultrasonic transducers, such as focused waves, edge waves, Rayleigh waves and head waves.
A substructure approach for the midfrequency vibration of stochastic systems
Authors: Sarkar Abhijit , Ghanem Roger
Published: March 2003

A novel substructure coupling technique based on the proper orthogonal decomposition method is presented for the midfrequency range vibration of linear dynamical systems with parameter uncertainty. For a given frequency band, the methodology permits the derivation of an adaptive basis for each subsystem and the construction of a reduced-order model of the global structure. The formulation is directed toward the efficient probabilistic characterization of model-based predictions in the framework of a stochastic finite element method. The efficiency of the substructure method has been contrasted both from the viewpoint of adopting free–free and fixed–fixed substructure proper orthogonal modes in order to arrive at a reduced subsystem model. The distinction as well as similarity of the present methodology with the component mode synthesis is also pointed out. The proper orthogonal modes are obtained from both frequency- and time-domain approaches, and their suitability is discussed in relation to the behavior of a specific system. The substructure approach elegantly integrates with a version of stochastic finite elements based on orthogonal decompositions and projections of stochastic processes.
Experimental investigation of spatial correlation in broadband reverberant sound fields
Authors: Chun Ingyu , Rafaely Boaz , Joseph Phillip
Published: March 2003

The spatial correlation has previously been investigated for tonal and narrow-band sound fields. This letter presents an experimental investigation of the spatial correlation coefficients in a reverberation chamber driven by broadband signals. The main objective is to verify recent theoretical results for broadband spatial correlation in diffuse sound fields. Experimental results show good agreement with theoretical predictions when the frequency band of the sound field is entirely above the Schroeder frequency.
Investigations of the precedence effect in budgerigars: Effects of stimulus type, intensity, duration, and location
Authors: Dent Micheal L. , Dooling Robert J.
Published: March 2003

Auditory experiments on the localization of sounds in the presence of reflections, or echoes, that arrive later and from different directions are important to understanding hearing in natural environments. The perceived location of the auditory image can change with the time delay between the presentations of a leading and lagging sound. These changes in perceived location, encompassing the precedence effect, have been examined behaviorally or physiologically in humans and a number of animals. Here, these results are extended to include budgerigars. Behavioral methods were used to measure the discrimination performance between a stimulus presented at + and −90° azimuth with a delay (left-right), from the same two stimuli presented with the opposite delay (right-left). At short delays, where humans experience summing localization, budgerigars have difficulty discriminating between the two presentation types. With increasing delays, where humans experience localization dominance, budgerigars show improved discrimination performance. At even longer delays, where echo thresholds are found in humans, discrimination performance worsens again. The shapes of the discrimination functions are affected by the intensity, locations, and durations of the stimuli, and are subject to a buildup effect. These results show that budgerigars exhibit the phases of the precedence effect similar to humans and other animals.
Numerical simulation of self-sustained oscillation of a voice-producing element based on Navier–Stokes equations and the finite element method
Authors: de Vries Martinus P. , Hamburg Marc C. , Schutte Harm K. , Verkerke Gijsbertus J. , Veldman Arthur E. P.
Published: March 2003

Surgical removal of the larynx results in radically reduced production of voice and speech. To improve voice quality a voice-producing element (VPE) is developed, based on the lip principle, called after the lips of a musician while playing a brass instrument. To optimize the VPE, a numerical model is developed. In this model, the finite element method is used to describe the mechanical behavior of the VPE. The flow is described by two-dimensional incompressible Navier–Stokes equations. The interaction between VPE and airflow is modeled by placing the grid of the VPE model in the grid of the aerodynamical model, and requiring continuity of forces and velocities. By applying and increasing pressure to the numerical model, pulses comparable to glottal volume velocity waveforms are obtained. By variation of geometric parameters their influence can be determined. To validate this numerical model, an in vitro test with a prototype of the VPE is performed. Experimental and numerical results show an acceptable agreement.