bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-specific independence mixture modeling for positional weight matrices
Authors: Georgi Benjamin , Schliep Alexander 
Published: July 2006

Abstract
Motivation: A positional weight matrix (PWM) is a statistical representation of the binding pattern of a transcription factor estimated from known binding site sequences. Previous studies showed that for factors which bind to divergent binding sites, mixtures of multiple PWMs increase performance. However, estimating a conventional mixture distribution for each position will in many cases cause overfitting.
Results: We propose a context-specific independence (CSI) mixture model and a learning algorithm based on a Bayesian approach. The CSI model adjusts complexity to fit the amount of variation observed on the sequence level in each position of a site. This not only yields a more parsimonious description of binding patterns, which improves parameter estimates, it also increases robustness as the model automatically adapts the number of components to fit the data.
Evaluation of the CSI model on simulated data showed favorable results compared to conventional mixtures. We demonstrate its adaptive properties in a classical model selection setup. The increased parsimony of the CSI model was shown for the transcription factor Leu3 where two binding-energy subgroups were distinguished equally well as with a conventional mixture but requiring 30% less parameters. Analysis of the human-mouse conservation of predicted binding sites of 64 JASPAR TFs showed that CSI was as good or better than a conventional mixture for 89% of the TFs and for 70% for a single PWM model.
Availability:
Contact: georgi@molgen.mpg.de, schliep@molgen.mpg.de
Informative priors based on transcription factor structural class improve de novo motif discovery
Authors: Narlikar Leelavati , Gordân Raluca , Ohler Uwe , Hartemink Alexander J. 
Published: July 2006

Abstract
Motivation: An important problem in molecular biology is to identify the locations at which a transcription factor (TF) binds to DNA, given a set of DNA sequences believed to be bound by that TF. In previous work, we showed that information in the DNA sequence of a binding site is sufficient to predict the structural class of the TF that binds it. In particular, this suggests that we can predict which locations in any DNA sequence are more likely to be bound by certain classes of TFs than others. Here, we argue that traditional methods for de novo motif finding can be significantly improved by adopting an informative prior probability that a TF binding site occurs at each sequence location. To demonstrate the utility of such an approach, we present priority, a powerful new de novo motif finding algorithm.
Results: Using data from TRANSFAC, we train three classifiers to recognize binding sites of basic leucine zipper, forkhead, and basic helix loop helix TFs. These classifiers are used to equip priority with three class-specific priors, in addition to a default prior to handle TFs of other classes. We apply priority and a number of popular motif finding programs to sets of yeast intergenic regions that are reported by ChIP-chip to be bound by particular TFs. priority identifies motifs the other methods fail to identify, and correctly predicts the structural class of the TF recognizing the identified binding sites.
Availability: Supplementary material and code can be found at .
Contact: lee@cs.duke.edu, raluca@cs.duke.edu, uwe.ohler@duke.edu, amink@cs.duke.edu.
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree
Authors: Schliep Alexander , Rahmann Sven 
Published: July 2006

Abstract
Motivation: The reliable identification of presence or absence of biological agents (“targets”), such as viruses or bacteria, is crucial for many applications from health care to biodiversity. If genomic sequences of targets are known, hybridization reactions between oligonucleotide probes and targets performed on suitable DNA microarrays will allow to infer presence or absence from the observed pattern of hybridization. Targets, for example all known strains of HIV, are often closely related and finding unique probes becomes impossible. The use of non-unique oligonucleotides with more advanced decoding techniques from statistical group testing allows to detect known targets with great success. Of great relevance, however, is the problem of identifying the presence of previously unknown targets or of targets that evolve rapidly.
Results: We present the first approach to decode hybridization experiments using non-unique probes when targets are related by a phylogenetic tree. Using a Bayesian framework and a Markov chain Monte Carlo approach we are able to identify over 94% of known targets and assign up to 70% of unknown targets to their correct clade in hybridization simulations on biological and simulated data.
Availability: Software implementing the method described in this paper and datasets are available from .
Contact: alexander.schliep@molgen.mpg.de, Sven.Rahmann@cebitec.uni-bielefeld.de
A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk
Authors: Koh Geoffrey , Teong Huey Fern Carol , Clément Marie-Véronique , Hsu David , Thiagarajan P.S. 
Published: July 2006

Abstract
Parameter estimation is a critical problem in modeling biological pathways. It is difficult because of the large number of parameters to be estimated and the limited experimental data available. In this paper, we propose a decompositional approach to parameter estimation. It exploits the structure of a large pathway model to break it into smaller components, whose parameters can then be estimated independently. This leads to significant improvements in computational efficiency. We present our approach in the context of Hybrid Functional Petri Net modeling and evolutionary search for parameter value estimation. However, the approach can be easily extended to other modeling frameworks and is independent of the search method used. We have tested our approach on a detailed model of the Akt and MAPK pathways with two known and one hypothesized crosstalk mechanisms. The entire model contains 84 unknown parameters. Our simulation results exhibit good correlation with experimental data, and they yield positive evidence in support of the hypothesized crosstalk between the two pathways.
Contact: thiagu@comp.nus.edu.sg
A top-level ontology of functions and its application in the Open Biomedical Ontologies
Authors: Burek Patryk , Hoehndorf Robert , Loebe Frank , Visagie Johann , Herre Heinrich , Kelso Janet 
Published: July 2006

Abstract
Motivation: A clear understanding of functions in biology is a key component in accurate modelling of molecular, cellular and organismal biology. Using the existing biomedical ontologies it has been impossible to capture the complexity of the community's knowledge about biological functions.
Results: We present here a top-level ontological framework for representing knowledge about biological functions. This framework lends greater accuracy, power and expressiveness to biomedical ontologies by providing a means to capture existing functional knowledge in a more formal manner. An initial major application of the ontology of functions is the provision of a principled way in which to curate functional knowledge and annotations in biomedical ontologies. Further potential applications include the facilitation of ontology interoperability and automated reasoning. A major advantage of the proposed implementation is that it is an extension to existing biomedical ontologies, and can be applied without substantial changes to these domain ontologies.
Availability: The Ontology of Functions (OF) can be downloaded in OWL format from . Additionally, a UML profile and supplementary information and guides for using the OF can be accessed from the same website.
Contact: bioonto@lists.informatik.uni-leipzig.de
To permute or not to permute
Authors: Huang Yifan , Xu Haiyan , Calian Violeta , Hsu Jason C. 
Published: July 2006

Abstract
Permutation test is a popular technique for testing a hypothesis of no effect, when the distribution of the test statistic is unknown. To test the equality of two means, a permutation test might use a test statistic which is the difference of the two sample means in the univariate case. In the multivariate case, it might use a test statistic which is the maximum of the univariate test statistics. A permutation test then estimates the null distribution of the test statistic by permuting the observations between the two samples.
We will show that, for such tests, if the two distributions are not identical (as for example when they have unequal variances, correlations or skewness), then a permutation test for equality of means based on difference of sample means can have an inflated Type I error rate even when the means are equal. Our results illustrate permutation testing should be confined to testing for non-identical distributions.
Contact: calian@raunvis.hi.is
ARCS: an aggregated related column scoring scheme for aligned sequences
Authors: Song Bin , Choi Jeong-Hyeon , Chen Guangyu , Szymanski Jacek , Zhang Guo-Qiang , Tung Anthony K. H. , Kang Jaewoo , Kim Sun , Yang Jiong 
Published: July 2006

Abstract
Motivation: Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.
Results: This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.
Availability: The source code is available on and
Contacts: jiong.yang@case.edu, sunkim2@indiana.edu
Supplementary Material: and
Corporate strategy development and related management development: the case for the incremental approach, part 1 – the development of strategy
Authors: Rees W. David , Porter Christine 
Published: July 2006

PurposeThe purpose of this paper is to examine the case for the incremental development of corporate strategy and related issues of management development.Design/methodology/approachA background in consultancy and management development in the UK and abroad is used to examine the potential dangers of radical and comprehensive innovations in corporate strategy and the potential benefits of an incremental approach. In addition, recent developments and examples are referred to as well as relevant literature.FindingsThe paper finds that there are two main potential dangers with the development of a comprehensive corporate strategy. The first is that the exercise may prove to be so daunting that it is effectively abandoned. The second is that comprehensive strategy innovations are based on too narrow a consideration of the issues and may be counter‐productive. A broad based consideration of corporate strategy may create a greater emphasis on the incremental approach.Research limitations/implicationsExamples partly from consultancy work have been relied on to make the case for a greater emphasis on the incremental development of corporate strategy and related academic coverage of the subject. The paper's main thesis is that if the process whereby strategy is developed is deficient, then the results may well be counter‐productive. This is especially likely if comprehensive change is planned.Originality/valueThe two‐part paper is a necessary examination of the dangers of corporate strategy development that is based on too narrow a range of functions and disciplines. The same limitations can be replicated in academic coverage of the area. The paper is meant to engender a necessary scepticism about the way corporate strategy can be realistically developed. Constructive advice is also given about broad‐based strategy development and related management learning and development issues.
What deep log analysis tells us about the impact of big deals: case study OhioLINK
Authors: Nicholas David , Huntington Paul , Jamali Hamid R. , Tenopir Carol 
Published: July 2006

PurposeThis article presents the early findings of an exploratory deep log analysis of journal usage on OhioLINK, conducted as part of the MaxData project funded by the US Institute of Museum and Library Services. OhioLINK, the original “big deal”, provides a single digital platform of nearly 6,000 full‐text journal for more than 600,000 people in the state of Ohio. The purpose of the paper is not only to present findings from the deep log analysis of journal usage on OhioLINK, but, arguably more importantly, to try test a new method of analysing online information user behaviour – deep log analysis.Design/methodology/approachThe raw server logs were obtained for the period June 2004 to December 2004. For this exploratory study one month (October) of the on‐campus usage logs and seven months of the off‐campus transaction logs were analysed.FindingsDuring this period approximately 1,215,000 items were viewed on campus in October 2004 and 1,894,000 items viewed off campus between June and December 2004. The paper presents a number of usage analyses including: number of journals used, titles of journals used, use over time, a returnee analysis and a special analysis of subject, date and method of access.Practical implicationsThe research findings help libraries evaluate the efficiency of big deal and one‐stop shopping for scholarly journals and also investigate their users' information seeking behaviours.Originality/valueThe research is a part of efforts to test the applications of a new methodology, deep log analysis, for use and user studies. It also represents the most substantial independent analysis of, possibly, the most important and significant of the journal big deals ever conducted.
An algorithm for suffix stripping
Authors: Porter M.F. 
Published: July 2006

PurposeThe automatic removal of suffixes from words in English is of particular interest in the field of information retrieval. This work was originally published in Program in 1980 and is republished as part of a series of articles commemorating the 40th anniversary of the journal.Design/methodology/approachAn algorithm for suffix stripping is described, which has been implemented as a short, fast program in BCPL.FindingsAlthough simple, it performs slightly better than a much more elaborate system with which it has been compared. It effectively works by treating complex suffixes as compounds made up of simple suffixes, and removing the simple suffixes in a number of steps. In each step the removal of the suffix is made to depend upon the form of the remaining stem, which usually involves a measure of its syllable length.Originality/valueThe piece provides a useful historical document on information retrieval.
Digital preservation in the context of institutional repositories
Authors: Hockx‐Yu Helen 
Published: July 2006

PurposeTo discuss the issues and challenges of digital preservation facing institutional repositories and to illustrate the Joint Information Systems Committee's (JISC) view on institutional repositories and its key initiatives in helping UK institutions address these issues.Design/methodology/approachA combination of published work and JISC documents (public facing or internal) were used as reference material.FindingsDigital preservation is a complex process and there are still many unsolved issues which make it a challenging task for institutional repositories. However, the wide deployment of institutional repositories also provides new opportunities for digital preservation. Much could be done to consider digital preservation from the outset, to involve the authors and to embed digital preservation into repository workflow, which will ease the later preservation tasks.Research limitations/implicationsA number of ongoing JISC‐funded projects are briefly reported which explore different models for the provision of digital preservation services for institutional repositories. These models may be a way forward to tackle collectively the issue of long‐term preservation within the setting of institutional repositories. Depending on the outcomes of the projects, further investigation and implementation could be undertaken to test the models.Practical implicationsThis paper will help the reader to gain a better understanding of the issues related to digital preservation in general and how JISC's work has helped to tackle these issues.Originality/valueThis paper clearly states JISC's view on, and future plan for, digital repositories. This is of value to the UK educational community as JISC works on its behalf and responds to its needs.
Measuring the operational performance of intensive care units using the analytic hierarchy process approach
Authors: Dey Prasanta Kumar , Hariharan Seetharaman , Clegg Benjamin Thomas 
Published: July 2006

PurposeThe purpose of this study is to develop a performance measurement model for service operations using the analytic hierarchy process approach.Design/methodology/approachThe study reviews current relevant literature on performance measurement and develops a model for performance measurement. The model is then applied to the intensive care units (ICUs) of three different hospitals in developing nations. Six focus group discussions were undertaken, involving experts from the specific area under investigation, in order to develop an understandable performance measurement model that was both quantitative and hierarchical.FindingsA combination of outcome, structure and process‐based factors were used as a foundation for the model. The analyses of the links between them were used to reveal the relative importance of each and their associated sub factors. It was considered to be an effective quantitative tool by the stakeholders.Research limitations/implicationsThis research only applies the model to ICUs in healthcare services.Practical implicationsPerformance measurement is an important area within the operations management field. Although numerous models are routinely being deployed both in practice and research, there is always room for improvement. The present study proposes a hierarchical quantitative approach, which considers both subjective and objective performance criteria.Originality/valueThis paper develops a hierarchical quantitative model for service performance measurement. It considers success factors with respect to outcomes, structure and processes with the involvement of the concerned stakeholders based upon the analytic hierarchy process approach. The unique model is applied to the ICUs of hospitals in order to demonstrate its effectiveness. The unique application provides a comparative international study of service performance measurement in ICUs of hospitals in three different countries.
Overcoming the barriers to e‐cluster development in a low product complexity business sector
Authors: Adebanjo Dotun , Kehoe Dennis , Galligan Peter , Mahoney Fred 
Published: July 2006

PurposeThe purpose of this paper is to investigate the issues that impact negatively on e‐cluster development in a low product complexity industry and identification of key factors to overcome the barriers.Design/methodology/approachStructured interviews were used to identify perceived value and user expectations from e‐clusters. Workshops involving assessment of a prototype e‐cluster validated user expectations. A mapping study and best practice review provided a basis for e‐cluster application development and assessing potential industry uptake.FindingsInterest and perceived value of e‐clusters varied according to size of organisation with smaller organisations primarily interested in e‐connectivity to retailers and e‐business development. Organisations of all sizes, however, indicated a willingness to learn from each other and partner although level of e‐connectivity was average and overall level of sophistication was low.Practical implicationsIndustrial review and acceptance of a prototype e‐cluster that would enable organisations manage several critical aspects of their operations from a single interface.Originality/valueThe paper provides new understanding of key issues that impact the operational benefits of e‐clusters and, in particular, factors that would underpin the success of e‐cluster success in a competitive, insular, low product complexity industry. This presents an informed basis for e‐cluster managers and members to successfully manage their initiative.
Robotunits takes a Lego‐brick approach to automation system building
Authors: Connolly Christine 
Published: July 2006

PurposeTo highlight an innovative approach to the construction of factory production equipment.Design/methodology/approachExplains the philosophy of the company and catalogues its range of components, which combine to build a wide assortment of industrial equipment.FindingsCareful design has produced components that are easy to assemble and yield rugged structures, whilst their interconnectivity has dramatically reduced the number of parts needed and increased the variety of constructions possible.Practical implicationsThis approach saves customers time and logistical effort.Originality/valueMakes assembly engineers aware of an alternative to welded steel construction.
A measurement system for brake connectors in automobiles
Authors: Wang Jin‐jiang , Zeng Jiang‐yun , Mo Xutao , Li Ren , Wang Peng , Liu Wen‐yao , Liu Ming 
Published: July 2006

PurposeThe brake connector of an automobile is one important part in the brake system. How to measure the matching surface quality is a problem, because the matching surface is a cone surface and has a deep aperture structure.Design/methodology/approachA new measurement system is presented which could assure illumination and image with a special beam splitter. The worker could observe the matching surface by better image.FindingsMore objective evaluation is given with image processing method.Research limitations/implicationsNow, this measurement system is used by Toyota (Tianjin) company and satisfied result is obtained.Originality/valueThis paper is an original work and focuses on an important issue in automobile production.