bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of variance components in gene expression data
Authors: Chen James J. , Delongchamp Robert R. , Tsai Chen-An , Hsueh Huey-miin , Sistare Frank , Thompson Karol L. , Desai Varsha G. , Fuscoe James C.
Published: March 2004

Motivation: A microarray experiment is a multi-step process, and each step is a potential source of variation. There are two major sources of variation: biological variation and technical variation. This study presents a variance-components approach to investigating animal-to-animal, between-array, within-array and day-to-day variations for two data sets. The first data set involved estimation of technical variances for pooled control and pooled treated RNA samples. The variance components included between-array, and two nested within-array variances: between-section (the upper- and lower-sections of the array are replicates) and within-section (two adjacent spots of the same gene are printed within each section). The second experiment was conducted on four different weeks. Each week there were reference and test samples with a dye-flip replicate in two hybridization days. The variance components included week-to-week, animal-to-animal and between-array and within-array variances.

Results: We applied the linear mixed-effects model to quantify different sources of variation. In the first data set, we found that the between-array variance is greater than the between-section variance, which, in turn, is greater than the within-section variance. In the second data set, for the reference samples, the week-to-week variance is larger than the between-array variance, which, in turn, is slightly larger than the within-array variance. For the test samples, the week-to-week variance has the largest variation. The animal-to-animal variance is slightly larger than the between-array and within-array variances. However, in a gene-by-gene analysis, the animal-to-animal variance is smaller than the between-array variance in four out of five housekeeping genes. In summary, the largest variation observed is the week-to-week effect. Another important source of variability is the animal-to-animal variation. Finally, we describe the use of variance-component estimates to determine optimal numbers of animals, arrays per animal and sections per array in planning microarray experiments.
galaxie—CGI scripts for sequence identification through automated phylogenetic analysis
Authors: Nilsson R. Henrik , Larsson Karl-Henrik , Ursing Björn M.
Published: March 2004

Motivation: The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis.

Results: Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable.

Availability: A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se
Gap statistics for whole genome shotgun DNA sequencing projects
Authors: Wendl Michael C. , Yang Shiaw-Pyng
Published: March 2004

Motivation: Investigators utilize gap estimates for DNA sequencing projects. Standard theories assume sequences are independently and identically distributed, leading to appreciable under-prediction of gaps.

Results: Using a statistical scaling factor and data from 20 representative whole genome shotgun projects, we construct regression equations that relate coverage to a normalized gap measure. Prokaryotic genomes do not correlate to sequence coverage, while eukaryotes show strong correlation if the chaff is ignored. Gaps decrease at an exponential rate of only about one-third of that predicted via theory alone. Case studies suggest that departure from theory can largely be attributed to assembly difficulties for repeat-rich genomes, but bias and coverage anomalies are also important when repeats are sparse. Such factors cannot be readily characterized a priori, suggesting upper limits on the accuracy of gap prediction. We also find that diminishing coverage probability discussed in other studies is a theoretical artifact that does not arise for the typical project.
Amplicon: software for designing PCR primers on aligned DNA sequences
Authors: Jarman Simon N.
Published: March 2004

Summary: Amplicon is a program for designing PCR primers on aligned groups of DNA sequences. The most important application for Amplicon is the design of ‘group-specific’ PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups.

Availability: Amplicon is freely available as a script that will run on any platform with Python 2.3 installed (http://www.python.org). It is also available as a Windows executable. Free downloads that do not require registration can be found at http://www.aad.gov.au/amplicon
OBIYagns: a grid-based biochemical simulator with a parameter estimator
Authors: Kimura Shuhei , Kawasaki Takuji , Hatakeyama Mariko , Naka Takashi , Konishi Fumikazu , Konagaya Akihiko
Published: March 2004

Summary: OBIYagns (yet another gene network simulator) is a biochemical system simulator that comprises a multiple-user Web-based graphical interface, an ordinary differential equation solver and a parameter estimators distributed over an open bioinformatics grid (OBIGrid). This grid-based biochemical simulation system can achieve high performance and provide a secure simulation environment for estimating kinetic parameters in an acceptable time period. OBIYagns can be applied to larger system biology-oriented simulation projects.

Availability: OBIYagns example models, methods and user guide are available at https://access.obigrid.org/yagns/

Supplementary information: Please refer to Bioinformatics online.
SeqExpress: desktop analysis and visualization tool for gene expression experiments
Authors: Boyle John
Published: March 2004

Summary: SeqExpress is a stand-alone desktop application for the identification of relevant genes within collections of microarray or SAGE experiments. A number of analysis, filtering and visualization tools are provided to aid in the selection of groups of genes. If R is installed then the application can use this to provide further analysis.

Availability: SeqExpress is available at: http://www.seqexpress.com
A general computational model of mitochondrial metabolism in a whole organelle scale
Authors: Yugi Katsuyuki , Tomita Masaru
Published: March 2004

Summary: A computational tool for mitochondrial systems biology has been developed as a simulation model of E-Cell2, a publicly available simulation system. The general model consists of 58 enzymatic reactions and 117 metabolites, representing the respiratory chain, the TCA cycle, the fatty acid β-oxidation and the inner-membrane transport system. It is based on previously published enzyme kinetics studies in the literature; we have successfully integrated and packaged them into a single large model. The model can be easily extended and modified so that mitochondrial biologists/physiologists can integrate their own models and evaluate them in the context of the whole organelle metabolism.

Availability: The mitochondrial model is bundled up with E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences.

Supplementary information: All the kinetic data are available via http://www.e-cell.org
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
Authors: Grasso Catherine , Lee Christopher
Published: March 2004

Motivation: Partial order alignment (POA) has been proposed as a new approach to multiple sequence alignment (MSA), which can be combined with existing methods such as progressive alignment. This is important for addressing problems both in the original version of POA (such as order sensitivity) and in standard progressive alignment programs (such as information loss in complex alignments, especially surrounding gap regions).

Results: We have developed a new Partial Order–Partial Order alignment algorithm that optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. Using this algorithm, we show the combined Progressive POA alignment method yields results comparable with the best available MSA programs (CLUSTALW, DIALIGN2, T-COFFEE) but is far faster. For example, depending on the level of sequence similarity, aligning 1000 sequences, each 500 amino acids long, took 15 min (at 90% average identity) to 44 min (at 30% identity) on a standard PC. For large alignments, Progressive POA was 10–30 times faster than the fastest of the three previous methods (CLUSTALW). These data suggest that POA-based methods can scale to much larger alignment problems than possible for previous methods.

Availability: The POA source code is available at http://www.bioinformatics.ucla.edu/poa
BioOptimizer: a Bayesian scoring function approach to motif discovery
Authors: Jensen Shane T. , Liu Jun S.
Published: March 2004

Motivation: Transcription factors (TFs) bind directly to short segments on the genome, often within hundreds to thousands of base pairs upstream of gene transcription start sites, to regulate gene expression. The experimental determination of TFs binding sites is expensive and time-consuming. Many motif-finding programs have been developed, but no program is clearly superior in all situations. Practitioners often find it difficult to judge which of the motifs predicted by these algorithms are more likely to be biologically relevant.

Results: We derive a comprehensive scoring function based on a full Bayesian model that can handle unknown site abundance, unknown motif width and two-block motifs with variable-length gaps. An algorithm called BioOptimizer is proposed to optimize this scoring function so as to reduce noise in the motif signal found by any motif-finding program. The accuracy of BioOptimizer, which can be used in conjunction with several existing programs, is shown to be superior to using any of these motif-finding programs alone when evaluated by both simulation studies and application to sets of co-regulated genes in bacteria. In addition, this scoring function formulation enables us to compare objectively different predicted motifs and select the optimal ones, effectively combining the strengths of existing programs.

Availability: BioOptimizer is available for download at www.fas.harvard.edu/~junliu/BioOptimizer/
Evaluating the predictability of conformational switching in RNA
Authors: Voss Björn , Meyer Carsten , Giegerich Robert
Published: March 2004

Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule that can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structural switching must be verified experimentally.

Results: After reviewing the strategy used in paRNAss, we present recent improvements on the algorithmic level of the approach, and the results of an evaluation procedure, comprising 1500 RNA sequences. It could be shown that the paRNAss approach performs well on known examples for conformational switching in RNA. The overall number of positive predictions was small, whereas for human 3′ UTRs, representing regulatory important regions, it was substantially higher than for arbitrary natural and random sequences.

Availability:  paRNAss is available as a Web service at http://bibiserv.techfak.uni-bielefeld.de/parnass

Supplementary information: Detailed information on the analyses summarized in Table 1 can be found at http://bibiserv.techfak.uni-bielefeld.de/parnass/examples.html
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements
Authors: Huber Wolfgang , Gentleman Robert
Published: March 2004

Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation of data packages for curating, distributing and working with probe sequence data in a uniform, across-types-of-microarrays manner. While the implementation is specific to the Bioconductor project, the ideas and general strategies are more general and could be easily adopted by other projects.

Availability: The R package matchprobes is available under LGPL at http://www.bioconductor.org

Supplementary information: The package contains documentation in the form of a vignette and manual pages.
Protein backbone angle prediction with machine learning approaches
Authors: Kuang Rui , Leslie Christina S. , Yang An-Suei
Published: March 2004

Motivation: Protein backbone torsion angle prediction provides useful local structural information that goes beyond conventional three-state (α, β and coil) secondary structure predictions. Accurate prediction of protein backbone torsion angles will substantially improve modeling procedures for local structures of protein sequence segments, especially in modeling loop conformations that do not form regular structures as in α-helices or β-strands.

Results: We have devised two novel automated methods in protein backbone conformational state prediction: one method is based on support vector machines (SVMs); the other method combines a standard feed-forward back-propagation artificial neural network (NN) with a local structure-based sequence profile database (LSBSP1). Extensive benchmark experiments demonstrate that both methods have improved the prediction accuracy rate over the previously published methods for conformation state prediction when using an alphabet of three or four states.

Availability: LSBSP1 and the NN algorithm have been implemented in PrISM.1, which is available from www.columbia.edu/~ay1/.

Supplementary information: Supplementary data for the SVM method can be downloaded from the Website www.cs.columbia.edu/compbio/backbone.
Mixture models for assessing differential expression in complex tissues using microarray data
Authors: Ghosh Debashis
Published: March 2004

Motivation: The use of DNA microarrays has become quite popular in many scientific and medical disciplines, such as in cancer research. One common goal of these studies is to determine which genes are differentially expressed between cancer and healthy tissue, or more generally, between two experimental conditions. A major complication in the molecular profiling of tumors using gene expression data is that the data represent a combination of tumor and normal cells. Much of the methodology developed for assessing differential expression with microarray data has assumed that tissue samples are homogeneous.

Results: In this paper, we outline a general framework for determining differential expression in the presence of mixed cell populations. We consider study designs in which paired tissues and unpaired tissues are available. A hierarchical mixture model is used for modeling the data; a combination of methods of moments procedures and the expectation–maximization algorithm are used to estimate the model parameters. The finite-sample properties of the methods are assessed in simulation studies; they are applied to two microarray datasets from cancer studies. Commands in the R language can be downloaded from the URL http://www.sph.umich.edu/~ghoshd/COMPBIO/COMPMIX/.
Protein homology detection using string alignment kernels
Authors: Saigo Hiroto , Vert Jean-Philippe , Ueda Nobuhisa , Akutsu Tatsuya
Published: March 2004

Motivation: Remote homology detection between protein sequences is a central problem in computational biology. Discriminative methods involving support vector machines (SVMs) are currently the most effective methods for the problem of superfamily recognition in the Structural Classification Of Proteins (SCOP) database. The performance of SVMs depends critically on the kernel function used to quantify the similarity between sequences.

Results: We propose new kernels for strings adapted to biological sequences, which we call local alignment kernels. These kernels measure the similarity between two sequences by summing up scores obtained from local alignments with gaps of the sequences. When tested in combination with SVM on their ability to recognize SCOP superfamilies on a benchmark dataset, the new kernels outperform state-of-the-art methods for remote homology detection.

Availability: Software and data available upon request.
Fuzzy J-Means and VNS methods for clustering genes from microarray data
Authors: Belacel Nabil , Čuperlović-Culf Miroslava , Laflamme Mark , Ouellette Rodney
Published: March 2004

Motivation: In the interpretation of gene expression data from a group of microarray experiments that include samples from either different patients or conditions, special consideration must be given to the pleiotropic and epistatic roles of genes, as observed in the variation of gene coexpression patterns. Crisp clustering methods assign each gene to one cluster, thereby omitting information about the multiple roles of genes.

Results: Here, we present the application of a local search heuristic, Fuzzy J-Means, embedded into the variable neighborhood search metaheuristic for the clustering of microarray gene expression data. We show that for all the datasets studied this algorithm outperforms the standard Fuzzy C-Means heuristic. Different methods for the utilization of cluster membership information in determining gene coregulation are presented. The clustering and data analyses were performed on simulated datasets as well as experimental cDNA microarray data for breast cancer and human blood from the Stanford Microarray Database.

Availability: The source code of the clustering software (C programming language) is freely available from Nabil.Belacel@nrc-cnrc.gc.ca
Why neural networks should not be used for HIV-1 protease cleavage site prediction
Authors: Rögnvaldsson Thorsteinn , You Liwen
Published: March 2004

Summary: Several papers have been published where nonlinear machine learning algorithms, e.g. artificial neural networks, support vector machines and decision trees, have been used to model the specificity of the HIV-1 protease and extract specificity rules. We show that the dataset used in these studies is linearly separable and that it is a misuse of nonlinear classifiers to apply them to this problem. The best solution on this dataset is achieved using a linear classifier like the simple perceptron or the linear support vector machine, and it is straightforward to extract rules from these linear models. We identify key residues in peptides that are efficiently cleaved by the HIV-1 protease and list the most prominent rules, relating them to experimental results for the HIV-1 protease.

Motivation: Understanding HIV-1 protease specificity is important when designing HIV inhibitors and several different machine learning algorithms have been applied to the problem. However, little progress has been made in understanding the specificity because nonlinear and overly complex models have been used.

Results: We show that the problem is much easier than what has previously been reported and that linear classifiers like the simple perceptron or linear support vector machines are at least as good predictors as nonlinear algorithms. We also show how sets of specificity rules can be generated from the resulting linear classifiers.

Availability: The datasets used are available at http://www.hh.se/staff/bioinf/
‘Harvester’: a fast meta search engine of human protein resources
Authors: Liebel Urban , Kindler Bjoern , Pepperkok Rainer
Published: March 2004

Summary: We have developed a Web-based tool named ‘Harvester’ that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. The information on every single protein is assembled on a single HTML page as a combination of database screen-shots and plain text. A full text meta search engine, similar to Google™, allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. A feedback forum allows users to comment on Harvester and to report database inconsistencies.

Availability: The service is freely available to the academic community at http://harvester.embl.de.
Primer design using genetic algorithm
Authors: Wu Jain-Shing , Lee Chungnan , Wu Chien-Chang , Shiue Yow-Ling
Published: March 2004

Motivation: Before performing a polymerase chain reaction experiment, a pair of primers to clip the target DNA subsequence is required. However, this is a tedious task as too many constraints need to be satisfied. Various kinds of approaches for designing a primer have been proposed in the last few decades, but most of them do not have restriction sites on the designed primers and do not satisfy the specificity constraint.

Results: The proposed algorithm imitates nature's process of evolution and genetic operations on chromosomes in order to achieve optimal solutions, and is a best fit for DNA behavior. Experimental results indicate that the proposed algorithm can find a pair of primers that not only obeys the design properties but also has a specific restriction site and specificity. Gel electrophoresis verifies that the proposed method really can clip out the target sequence.

Availability: A public version of the software is available on request from the authors.
Haplotypes histories as pathways of recombinations
Authors: El-Mabrouk Nadia , Labuda Damian
Published: March 2004

Motivation: The diversity of a haplotype, represented as a string of polymorphic sites along a DNA sequence, increases exponentially with the number of sites if recombinations are taking place. Reconstructing the history of recombinations compared with that of the polymorphic sites is thus extremely difficult. However, in the human genome, because of the relatively simple pattern of haplotype diversity dominated by a few ancestral haplotypes, the complexity of the recombinational network can be reduced, thus making its reconstruction feasible. We focus on the problem of inferring the recombination pathways starting with putative ancestral haplotypes and leading to new rare recombinant haplotypes.

Results: We describe classes of recombinations that represent the whole set of minimal recombination pathways leading to a new haplotype. We present an O(n2) algorithm that outputs such representative recombination pathways. We apply it to haplotypes of the 8 kb dystrophin gene segment dys44.

Availability: A software implementing the algorithm and some other extentions has been developed on a Java platform (JDK 1.3.1). It is freely available at http://www.iro.umontreal.ca/~mabrouk/
Haplotype reconstruction from genotype data using Imperfect Phylogeny
Authors: Halperin Eran , Eskin Eleazar
Published: March 2004

Critical to the understanding of the genetic basis for complex diseases is the modeling of human variation. Most of this variation can be characterized by single nucleotide polymorphisms (SNPs) which are mutations at a single nucleotide position. To characterize the genetic variation between different people, we must determine an individual's haplotype or which nucleotide base occurs at each position of these common SNPs for each chromosome. In this paper, we present results for a highly accurate method for haplotype resolution from genotype data. Our method leverages a new insight into the underlying structure of haplotypes that shows that SNPs are organized in highly correlated ‘blocks’. In a few recent studies, considerable parts of the human genome were partitioned into blocks, such that the majority of the sequenced genotypes have one of about four common haplotypes in each block. Our method partitions the SNPs into blocks, and for each block, we predict the common haplotypes and each individual's haplotype. We evaluate our method over biological data. Our method predicts the common haplotypes perfectly and has a very low error rate (<2% over the data) when taking into account the predictions for the uncommon haplotypes. Our method is extremely efficient compared with previous methods such as PHASE and HAPLOTYPER. Its efficiency allows us to find the block partition of the haplotypes, to cope with missing data and to work with large datasets.

Availability: The algorithm is available via a Web server at http://www.calit2.net/compbio/hap/
Sight: automating genomic data-mining without programming skills
Authors: Meskauskas Audrius , Lehmann-Horn Frank , Jurkat-Rott Karin
Published: March 2004

Summary: We created and tested Sight, a Java-based package that provides a user-friendly interface to generate and connect agents for automatic genomic data-mining for individual requirements without requiring programming skills from the user.

Availability:  http://physiologie.uni-ulm.de//Seiten/Arbeitsgruppe/Jurkat-Rott/Jurkat-Rott.htm. The system does not require additional components and runs on IBM PCs under Windows (NT 4.0, 2000 and XP) or Linux (Phat 4.0 and Mandrake 9.0).
An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments
Authors: Anderssen R. S. , Wu Y. , Dolferus R. , Saunders I.
Published: March 2004

Motivation: Because of the high cost of sequencing, the bulk of gene discovery is performed using anonymous cDNA microarrays. Though the clones on such arrays are easier and cheaper to construct and utilize than unigene and oligonucleotide arrays, they are there in proportion to their corresponding gene expression activity in the tissue being examined. The associated redundancy will be there in any pool of possibly interesting differentially expressed clones identified in a microarray experiment for subsequent sequencing and investigation. An a posteriori sampling strategy is proposed to enhance gene discovery by reducing the impact of the redundancy in the identified pool.

Results: The proposed strategy exploits the fact that individual genes that are highly expressed in a tissue are more likely to be present as a number of spots in an anonymous library and, as a direct consequence, are also likely to give higher fluorescence intensity responses when present in a probe in a cDNA microarray experiment. Consequently, spots that respond with low intensities will have a lower redundancy and so should be sequenced in preference to those with the highest intensities. The proposed method, which formalizes how the fluorescence intensity of a spot should be assessed, is validated using actual microarray data, where the sequences of all the clones in the identified pool had been previously determined. For such validations, the concept of a repeat plot is introduced. It is also utilized to visualize and examine different measures for the characterization of fluorescence intensity. In addition, as confirmatory evidence, sequencing from the lowest to the highest intensities in a pool, with all the sequences known, is compared graphically with their random sequencing. The results establish that, in general, the opportunity for gene discovery is enhanced by avoiding the pooling of different biological libraries (because their construction will have involved different hybridization episodes) and concentrating on the clones with lower fluorescence intensities.
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
Authors: McAuliffe Jon D. , Pachter Lior , Jordan Michael I.
Published: March 2004

Motivation: Phylogenetic shadowing is a comparative genomics principle that allows for the discovery of conserved regions in sequences from multiple closely related organisms. We develop a formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden Markov phylogeny (GHMP), applies to a variety of situations where functional regions are to be inferred from evolutionary constraints.

Results: We show how GHMPs can be used to predict complete shared gene structures in multiple primate sequences. We also describe shadower, our implementation of such a prediction system. We find that shadower outperforms previously reported ab initio gene finders, including comparative human–mouse approaches, on a small sample of diverse exonic regions. Finally, we report on an empirical analysis of shadower's performance which reveals that as few as five well-chosen species may suffice to attain maximal sensitivity and specificity in exon demarcation.

Availability: A Web server is available at http://bonaire.lbl.gov/shadower
Genomic data visualization on the Web
Authors: Wu Wei , Noble William S.
Published: March 2004

Many types of genomic data can be represented in matrix format, with rows corresponding to genes and columns corresponding to gene features. The heat map is a popular technique for visualizing such data, plotting the data on a two-dimensional grid and using a color scale to represent the magnitude of each matrix entry. Prism is a Web-based software tool for generating annotated heat map visualizations of genome-wide data quickly. The tool provides a selection of genome-specific annotation catalogs as well as a catalog upload capability. The heat maps generated are clickable, allowing the user to drill down to examine specific matrix entries, and gene annotations are linked to relevant genomic databases.

Availability:  http://noble.gs.washington.edu/prism
GenAlyzer: interactive visualization of sequence similarities between entire genomes
Authors: Choudhuri Jomuna V. , Schleiermacher Chris , Kurtz Stefan , Giegerich Robert
Published: March 2004

Summary: Genalyzer is a software tool designed for the interactive visualization of sequence matches between DNA or protein sequences. It provides visualizations on different levels of granularity, from complete overviews via zoomed regions to alignments of particular matching substrings. Genalyzer can efficiently handle very large datasets, allowing to display tens of thousands of matches between sequences of tens of millions of bases.

Availability: Genalyzer is available free of charge for non-commercial research institutions. For more details, see http://www.genalyzer.de
Journal diffusion factors – a measure of diffusion?
Authors: Faber Frandsen Tove
Published: March 2004

This paper shows that the measure of diffusion introduced by Ian Rowlands called the journal diffusion factor (JDF) is highly negatively correlated with the number of citations, leading highly cited journals to get a low JDF, whereas less cited journals get a high JDF. This property reduces the utility of the JDF as a tool for evaluation of research influence. The paper presents a new definition of the JDF in order to attempt to improve it. This new JDF corrects the strong correlation with the number cited, but has a strongly statistically positive correlation with journal impact factors (JIF). However, the new JDF may still be used as an evaluation tool since, for journals with similar JIF values, the new JDF can be used to differentiate between them. Thereby, journal evaluation will be based on more than one aspect of journal influence when assessing journal influence with similar journal impact factor values.
New versions of PageRank employing alternative Web document models
Authors: Thelwall Mike , Vaughan Liwen
Published: March 2004

Introduces several new versions of PageRank (the link based Web page ranking algorithm), based on an information science perspective on the concept of the Web document. Although the Web page is the typical indivisible unit of information in search engine results and most Web information retrieval algorithms, other research has suggested that aggregating pages based on directories and domains gives promising alternatives, particularly when Web links are the object of study. The new algorithms introduced based on these alternatives were used to rank four sets of Web pages. The ranking results were compared with human subjects’ rankings. The results of the tests were somewhat inconclusive: the new approach worked well for the set that includes pages from different Web sites; however, it does not work well in ranking pages that are from the same site. It seems that the new algorithms may be effective for some tasks but not for others, especially when only low numbers of links are involved or the pages to be ranked are from the same site or directory.
The characteristics of users and non‐users of a kiosk information system
Authors: Nicholas David , Huntington Paul , Williams Peter
Published: March 2004

Touch‐screen kiosks are located in a variety of locations to provide the public with ready access to health information. This paper examines, via a questionnaire, the characteristics of adult users of a surgery‐based kiosk. The Esk Medical Centre is in Musselburgh, near Edinburgh. Just under 200 questionnaires were returned and analysed. The research establishes characteristics of users and non‐users, how the kiosk fits in with other consumer information sources, what health outcomes result from using the kiosk, and reasons for non‐use. The main finding is that the respondents’ attitude and previous experience with information technology has an impact on whether the touch‐screen kiosk is used.
Librarians and the claiming of new roles: how can we try to make a difference?
Authors: Fourie Ina
Published: March 2004

In a dynamic, information and technology‐driven society, librarians can create new roles by assessing changes in their environment, the potential effect and ways to reposition themselves. Scenario building, literature reviews, situation analysis, speculation and forecasting may be used. Librarians have a good idea of what they can offer, but are often unable to reposition themselves in time. Reasons for this generally slow reaction are speculated on and the future role of librarians (including expected knowledge and skills) is briefly reviewed. An argument is then pursued on how an educational perspective that supports a constructivist‐learning environment, portfolio assessment, and affective and metacognitive skills could support librarians in preparing for change. The value of task analysis, needs assessment, and market research are mentioned briefly. Apart from knowledge (cognitive level), teaching should focus on affective and metacognitive skills, decision‐making abilities, environmental scanning, change management and the typical personality characteristics required to survive in the cyber age (e.g. assertiveness, self‐confidence, creative thinking, and innovativeness).
The European consumers’ understanding and perceptions of the “organic” food regime
Authors: Aarset Bernt , Beckmann Suzanna , Bigne Enrique , Beveridge Malcolm , Bjorndal Trond , Bunting Jane , McDonagh Pierre , Mariojouls Catherine , Muir James , Prothero Andrea , Reisch Lucia , Smith Andrew , Tveteras Ragnar , Young James
Published: March 2004

This paper explores consumer understanding and perception of organic food, with specific reference to the relatively new concept of organic farmed salmon. Key themes associated with the term “organic” and its meaning, as determined by consumers, are explored and the role of labelling and regulatory authorities considered. Focus groups in five countries (UK, Germany, Spain, Norway and France) consisting of 196 participants showed that most consumers are confused about the meaning of the term organic and are largely unaware of the organic certification and labelling process. Many consumers were unsure, even sceptical about the concept of organic farmed salmon and display a large amount of distrust in the regulatory process. The implications for the concept of organic food and salmon production and directions for further research are discussed.
Strategic experimentation and innovation in rural Australia
Authors: Bhaskaran Suku
Published: March 2004

This article is a case study of a small‐scale family enterprise which successfully introduced a new crop, adopted new farming methods, formed a research, development and marketing alliance with a major international company, and fostered R&D alliance with several government organisations. The study was completed through reviewing government, consultant and industry reports, and in‐depth face‐to‐face interviews of key informants in industry and government. The findings showcase the importance of entrepreneurship (ingenuity to seize opportunities, effectively use personal contact networks, take risks, experiment through trial and error learning, adapt and, notwithstanding immense barriers, to continue with the venture) and a supportive national culture in fostering innovation and business development.
Problems of machine/component interference in very high‐speed assembly processes using continuous motion technology
Authors: Paillusseau François
Published: March 2004

Continuous motion technology allows very high machine outputs for assembly and test operations. This paper presents the main advantages of continuous motion process compared to slower ones, five case histories of very difficult component/machine interference at very high speed that we succeeded to overcome, and a recommendation on how this kind of situation should be managed between the customer and the machine builder.
Marching towards MEMS
Authors: Bak David
Published: March 2004

Standardized systems for feeding, gripping, and joining are needed to realize the potential of microsystem and nano‐system technology. This paper describes many several systems that are operating in this area and the applications for the new technology and the parts that can currently be manufactured. These include miniature pneumatic valves, matchstick sized motors and fluidic pumps.
A four‐degree‐of‐freedom microprehensile microrobot on chip
Authors: De Lit Pierre , Agnus Joël , Clévy Cédric , Chaillet Nicolas
Published: March 2004

This paper presents a cheap and easy‐to‐produce microprehensile microrobot on chip (MMOC). This four‐degree‐of‐freedom (DOFs) microprehensor is able to grip, hold and release submillimetric‐sized objects. The research conducted relied heavily on the design of a simple and efficient monolithic piezoelectric two‐DOF actuator, requiring no further motion transformation system and asking for no supplementary guiding system. The integration of all these functions in a single part eliminates nearly all assembly concerns. Each finger of the gripper is an actuator, called a duo‐bimorph, which provides higher deflections than piezoelectric tubes. The paper presents the developed MMOC prototype, comments its performances and details the functioning of the duo‐bimorph.
Aspects on design of high precision parallel robots
Authors: Hesselbach Jürgen , Wrege Jan , Raatz Annika , Becker Oliver
Published: March 2004

This paper presents a concept for a micro‐assembly station and shows different possibilities for increasing the positioning accuracy. The main part of the station consists of a spatial parallel structure with three translational degrees of freedom. An additional rotational axis is integrated into the working platform. This structure is constructed with low friction joints, which are nearly free of backlash. The construction of these high precision joints is presented and the characteristics of the robot such as workspace and resolution are discussed. After this an approach for increasing the accuracy of parallel robots by integrating flexure hinges into the structure is described.
Does training influence outcomes of organizations?
Authors: Savery Lawson K. , Luks J. Alan
Published: March 2004

From previous research it appears that training of employees is strongly related to profit. The Australian Government collected data on approximately 10,000 registered small and medium enterprises conducting business in four studies over a four‐year period. A panel of 3,867 firms were measured over the four years and the influence of strategic decisions made in year one (such as increase production) could be plotted on how they inclined decisions on other issues such as training. It seems that the amount of training is an important precursor for firms who wish to improve their productivity. Those firms who have desired to increase production in the following three years are also more likely to be involved in training whilst those who have decided to reduce their production levels tend to reduce their levels of training.
The importance level of ten teaching/learning techniques as rated by university business students and instructors
Authors: Rodrigues Carl A.
Published: March 2004

Four active‐like (A‐like) and six passive‐like (P‐like) business teaching/learning techniques are described. It is proposed that students enrolled and faculty teaching in the international business (INTB), marketing (MKT), and management (MAN) business concentrations would rate the A‐like techniques higher than students enrolled and faculty teaching in the management information systems (MIS), finance (FIN), and accounting (ACC) business concentrations. And that students enrolled and faculty teaching in the MIS, FIN, and ACC concentrations would rate the P‐like techniques higher than the students and faculty in the INTB, MKT, and MAN concentrations. Using a survey questionnaire, upper undergraduate and MBA university business students and faculty were asked to indicate the importance level for each technique. Students' ratings do not support the proposition in nine techniques and the faculty ratings do not support it in eight. The conclusion is that the study at least provides a framework that can aid instructors in understanding that different students prefer and different situations require different instructional techniques.
Philosophy in management
Authors: Small Michael W.
Published: March 2004

The focus of this article is centred on two main ideas: persuading management students to study philosophy, and convincing them that a study of philosophy could be relevant for them in a business environment underscored by uncertainty. Three approaches were considered, an historical approach, an analytical approach and a literary approach. The first approach entailed a review of major philosophers, the second entailed an analysis of values such as trust, justice, honesty, integrity, fairness, prudence, respect, competition, professionalism, and the third entailed an appraisal of the work of persons better known for their contributions to literature which illustrated moral issues in their society. This article is a reflection of some of these thoughts on the idea of introducing a course in introductory philosophy into the management syllabus. The ideas are still in the formative stage, and are currently being put into practice.
Does country of origin matter for low‐involvement products?
Authors: Ahmed Zafar U. , Johnson James P. , Yang Xia , Kheng Fatt Chen , Sack Teng Han , Chee Boon Lim
Published: March 2004

This empirical study focusses on consumers’ attitude to low‐involvement products, bread and coffee, in a newly‐industrialized nation. Using data from 236 consumers in Singapore, the study examines the influence of country of origin (COO) relative to other product attributes in consumers’ evaluation of domestic and foreign food products. The results indicate that COO does matter when consumers evaluate low‐involvement products but, in the presence of other extrinsic cues (price and brand), the impact of COO is weak and brand becomes the determinant factor. In addition, the results suggest that a country's positive image in some product categories does not necessarily carry over to other product categories. The implications of these findings for marketing food products internationally are discussed.
The influence of behavioural and organisational characteristics on the success of international strategic alliances
Authors: Kauser Saleema , Shaw Vivienne
Published: March 2004

With the current trend toward globalisation and the increasing competitive and technological challenges of today's environment the formation of international strategic alliances has become an important part of many firm's international business strategies. Experience with international strategic alliances has shown that they face a number of problems, which can often result in the termination of the alliance. This study, therefore, aims to assess the impact of both behavioural and organisational characteristics on the success of international strategic alliances. The results show that behavioural characteristics play a more significant role in explaining overall alliance performance compared to organisational characteristics. High levels of commitment, trust, coordination, interdependence and communication are found to be good predictors of international strategic alliance success. Conflict, meanwhile, is found to hamper good performance. By contrast organisational characteristics such as structure and control mechanisms are found not to strongly influence the success of international strategic alliances.
International market entry mode strategies of manufacturing firms and service firms
Authors: Ekeledo Ikechi , Sivakumar K.
Published: March 2004

This research has two major purposes: developing and testing a resource‐based framework for entry mode choice and ascertaining the extent to which the determinants of foreign market entry mode choice in the manufacturing sector apply to foreign market entry mode choice in the non‐separable service sector. Using mail survey data collected from top‐level managers of US firms that had been engaged in international business, the article tests a number of research hypotheses concerning foreign market entry mode choice in the manufacturing and service sectors. The managerial and research implications of the findings are delineated and directions for future research are offered.
Total quality management (TQM): an overview
Authors: Talha Mohammad
Published: March 2004

In the manufacturing industry, product quality has become a key factor in determining a firm’s success or failure in the global marketplace. Advanced, highly reliable manufacturing methods have made it possible to achieve very high standards of product quality. As a result, more and more firms are making product quality a keystone of their competitive strategy. The success of many major Japanese companies is truly rooted in their long‐term commitment to the improvement of quality. The improvement of production quality is a long‐term commitment to continuous improvement in every aspect of the production process. Today’s competitive market, in almost every category of products and services, is characterized by accelerating changes, innovation, and massive amounts of new information. Changing customer needs fuels much of the rapid evolution in markets. Most organizations that have been successful with their quality improvement effort have adopted an integrated approach commonly referred to as total quality management (TQM).
Adopting e‐commerce Web site operation modes
Authors: Liu Jau‐Yang , Tarn J. Michael , Wen H. Joseph
Published: March 2004

This paper applies an analytical framework to assess e‐commerce (EC) Web sites of large US firms. It first examines the available EC operation modes and then discusses the EC factors – product, process, customer, and market – that influence the EC modes adoption. The Web sites of 50Fortune500 firms were randomly selected and analyzed. The findings show the current state of large US firms Web EC modes implementation and the characteristics of their EC factors.