bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing Near-Perfect Phylogenies with multiple homoplasy events
Authors: Satya Ravi Vijaya , Mukherjee Amar , Alexe Gabriela , Parida Laxmi , Bhanot Gyan 
Published: July 2006

Abstract
Motivation: We explore the problem of constructing near-perfect phylogenies on bi-allelic haplotypes, where the deviation from perfect phylogeny is entirely due to homoplasy events. We present polynomial-time algorithms for restricted versions of the problem. We show that these algorithms can be extended to genotype data, in which case the problem is called the near-perfect phylogeny haplotyping (NPPH) problem. We present a near-optimal algorithm for the H1-NPPH problem, which is to determine if a given set of genotypes admit a phylogeny with a single homoplasy event. The time-complexity of our algorithm for the H1-NPPH problem is O(m2(n + m)), where n is the number of genotypes and m is the number of SNP sites. This is a significant improvement over the earlier O(n4) algorithm.
We also introduce generalized versions of the problem. The H(1, q)-NPPH problem is to determine if a given set of genotypes admit a phylogeny with q homoplasy events, so that all the homoplasy events occur in a single site. We present an O(mq+1(n + m)) algorithm for the H(1,q)-NPPH problem.
Results: We present results on simulated data, which demonstrate that the accuracy of our algorithm for the H1-NPPH problem is comparable to that of the existing methods, while being orders of magnitude faster.
Availability: The implementation of our algorithm for the H1-NPPH problem is available upon request.
Contact: rvijaya@cs.ucf.edu
Indel seeds for homology search
Authors: Mak Denise , Gelfand Yevgeniy , Benson Gary 
Published: July 2006

Abstract
We are interested in detecting homologous genomic DNA sequences with the goal of locating approximate inverted, interspersed, and tandem repeats. Standard search techniques start by detecting small matching parts, called seeds, between a query sequence and database sequences. Contiguous seed models have existed for many years. Recently, spaced seeds were shown to be more sensitive than contiguous seeds without increasing the random hit rate. To determine the superiority of one seed model over another, a model of homologous sequence alignment must be chosen. Previous studies evaluating spaced and contiguous seeds have assumed that matches and mismatches occur within these alignments, but not insertions and deletions (indels). This is perhaps appropriate when searching for protein coding sequences (&lt;5% of the human genome), but is inappropriate when looking for repeats in the majority of genomic sequence where indels are common. In this paper, we assume a model of homologous sequence alignment which includes indels and we describe a new seed model, called indel seeds, which explicitly allows indels. We present a waiting time formula for computing the sensitivity of an indel seed and show that indel seeds significantly outperform contiguous and spaced seeds when homologies include indels. We discuss the practical aspect of using indel seeds and finally we present results from a search for inverted repeats in the dog genome using both indel and spaced seeds.
Contact: dyfmak@bu.edu
Comparative genomics reveals unusually long motifs in mammalian genomes
Authors: Jones Neil C. , Pevzner Pavel A. 
Published: July 2006

Abstract
Between short regulatory motifs and long ‘ultraconserved’ regions lies a whole spectrum of functional elements that remains uncharted.
– Manolis Kellis, RECOMB Regulatory Genomics satellite workshop, December 2005
Motivation: The recent discovery of the first small modulatory RNA (smRNA) presents the challenge of finding other molecules of similar length and conservation level. Unlike short interfering RNA (siRNA) and micro-RNA (miRNA), effective computational and experimental screening methods are not currently known for this species of RNA molecule, and the discovery of the one known example was partly fortuitous because it happened to be complementary to a well-studied DNA binding motif (the Neuron Restrictive Silencer Element).
Results: The existing comparative genomics approaches (e.g., phylogenetic footprinting) rely on alignments of orthologous regions across multiple genomes. This approach, while extremely valuable, is not suitable for finding motifs with highly diverged “non-alignable” flanking regions. Here we show that several unusually long and well conserved motifs can be discovered de novo through a comparative genomics approach that does not require an alignment of orthologous upstream regions. These motifs, including Neuron Restrictive Silencer Element, were missed in recent comparative genomics studies that rely on phylogenetic footprinting. While the functions of these motifs remain unknown, we argue that some may represent biologically important sites.
Availability: Our comparative genomics software, a web-accessible database of our results and a compilation of experimentally validated binding sites for NRSE can be found at .
Contact: ppevzner@cs.ucsd.edu
Finding motifs from all sequences with and without binding sites
Authors: Leung Henry C. M. , Chin Francis Y. L. 
Published: July 2006

Abstract
Motivation: Finding common patterns, motifs, from a set of promoter regions of coregulated genes is an important problem in molecular biology. Most existing motif-finding algorithms consider a set of sequences bound by the transcription factor as the only input. However, we can get better results by considering sequences that are not bound by the transcription factor as an additional input.
Results: First, instead of using the simple hyper-geometric analysis, we propose to calculate the likelihood based on a more precise probabilistic analysis which considers motif length, sequence length and number of binding sites as input parameters for testing whether motif is found. Second, we adopt an heuristic algorithm bases on our analysis to find motifs. For the simulated and real datasets, our algorithm ALSE compares favorably against common motif-finding programs such as SeedSearch and MEME in all cases and performs very well, especially when each input sequence contains more than one binding site.
Availability: ALSE is available for download at the homepage
Contact: cmleung2@cs.hku.hk
What should be expected from feature selection in small-sample settings
Authors: Sima Chao , Dougherty Edward R. 
Published: July 2006

Abstract
Motivation: High-throughput technologies for rapid measurement of vast numbers of biological variables offer the potential for highly discriminatory diagnosis and prognosis; however, high dimensionality together with small samples creates the need for feature selection, while at the same time making feature-selection algorithms less reliable. Feature selection must typically be carried out from among thousands of gene-expression features and in the context of a small sample (small number of microarrays). Two basic questions arise: (1) Can one expect feature selection to yield a feature set whose error is close to that of an optimal feature set? (2) If a good feature set is not found, should it be expected that good feature sets do not exist?
Results: The two questions translate quantitatively into questions concerning conditional expectation. (1) Given the error of an optimal feature set, what is the conditionally expected error of the selected feature set? (2) Given the error of the selected feature set, what is the conditionally expected error of the optimal feature set? We address these questions using three classification rules (linear discriminant analysis, linear support vector machine and k-nearest-neighbor classification) and feature selection via sequential floating forward search and the t-test. We consider three feature-label models and patient data from a study concerning survival prognosis for breast cancer. With regard to the two focus questions, there is similarity across all experiments: (1) One cannot expect to find a feature set whose error is close to optimal, and (2) the inability to find a good feature set should not lead to the conclusion that good feature sets do not exist. In practice, the latter conclusion may be more immediately relevant, since when faced with the common occurrence that a feature set discovered from the data does not give satisfactory results, the experimenter can draw no conclusions regarding the existence or nonexistence of suitable feature sets.
Availability:
Contact: edward@ece.tamu.edu
JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins
Authors: Hiller Karsten , Grote Andreas , Maneck Matthias , Münch Richard , Jahn Dieter 
Published: July 2006

Abstract
Motivation: After the publication of JVirGel 1.0 in 2003 we got many requests and suggestions from the proteomics community to further improve the performance of the software and to add additional useful new features.
Results: The integration of the PrediSi algorithm for the prediction of signal peptides for the Sec-dependent protein export into JVirGel 2.0 allows the exclusion of most exported preproteins from calculated proteomic maps and provides the basis for the calculation of Sec-based secretomes. A tool for the identification of transmembrane helices carrying proteins (JCaMelix) and the prediction of the corresponding membrane proteome was added. Finally, in order to directly compare experimental and calculated proteome data, a function to overlay and evaluate predicted and experimental two-dimensional gels was included.
Availability: JVirGel 2.0 is freely available as precompiled package for the installation on Windows or Linux operating systems. Furthermore, there is a completely platform-independent Java version available for download. Additionally, we provide a Java Server Pages based version of JVirGel 2.0 which can be operated in nearly all web browsers. All versions are accessible at .
Contact: d.jahn@tu-bs.de
Bayesian search of functionally divergent protein subgroups and their function specific residues
Authors: Marttinen Pekka , Corander Jukka , Törönen Petri , Holm Liisa 
Published: July 2006

Abstract
Motivation: The rapid increase in the amount of protein sequence data has created a need for an automated identification of evolutionarily related subgroups from large datasets. The existing methods typically require a priori specification of the number of putative groups, which defines the resolution of the classification solution.
Results: We introduce a Bayesian model-based approach to simultaneous identification of evolutionary groups and conserved parts of the protein sequences. The model-based approach provides an intuitive and efficient way of determining the number of groups from the sequence data, in contrast to the ad hoc methods often exploited for similar purposes. Our model recognizes the areas in the sequences that are relevant for the clustering and regards other areas as noise. We have implemented the method using a fast stochastic optimization algorithm which yields a clustering associated with the estimated maximum posterior probability. The method has been shown to have high specificity and sensitivity in simulated and real clustering tasks. With real datasets the method also highlights the residues close to the active site.
Availability: Software ‘kPax’ is available at
Contact: pekka.marttinen@helsinki.fi
Supplementary information:
Defining the digital divide: the role of e‐readiness indicators
Authors: Luyt Brendan 
Published: July 2006

PurposeTo show how e‐readiness indicators, specifically the Networked Readiness Index (NRI), participate in the work of defining policy problems.Design/methodology/approachThe article critically examines the Networked Readiness Index in terms of its presentation and its underlying model. It relies on an approach to policy analysis that views policy problems as socially constructed.FindingsE‐readiness assessment tools purport to show how ready the nations of the world are to exploit the potential of new information and communication technologies. Yet they do more than that; being actively engaged in constructing policy problems. In the case of the NRI, the problem of the international digital divide is defined in a particular way that privileges certain interests while at the same time legitimatizing its inclusion on the agenda of international organizations as a problem worthy of sustained attention.Practical implicationsThe findings of the article suggest a need for alternative indicators that register the voices of a wider range of groups and could therefore create a more inclusive digital divide policy problem.Originality/valueLittle critical (as opposed to technical) analysis of e‐readiness indicators exits in the literature. By focusing on these tools, the article contributes to the debate surrounding the issue of the digital divide.
Using ICT with people with special education needs: what the literature tells us
Authors: Williams Peter , Jamali Hamid R. , Nicholas David 
Published: July 2006

PurposeTo provide a review of the past studies on use of information and communications technology (ICT) for people with special education needs (SEN) to inform a major research project on using ICT to facilitate self‐advocacy and learning for SEN learners.Design/methodology/approachLiterature review, encompassing academic journals indexed in education, information science and social sciences databases, books, grey literature (including much internet‐based material), and government reports. Information was gathered on the perceived benefits of ICT in SEN, and the use of some specific applications with people having various conditions. A number of usability studies, mainly Internet and web technologies, are also outlined.FindingsAlthough the literature shows a great number of ICT initiatives for people with all kinds of disabilities, there has been a surprising lack of research into the usability of the various applications developed, and even less concerning those with learning difficulties. The review of existing literature indicates a lack of attention to the application of ICT for people with SEN, compared to the other groups of disabled people such as visually impaired.Originality/valueFindings highlight the need for more research on usability aspects of current and potential applications of ICT for people with SEN.
Time to take negotiation seriously
Authors: Gates Steve 
Published: July 2006

PurposeThe aim of this paper is to provide an overview of the skills needed for successful negotiations. It seeks to identify the benefits of training key staff in negotiations skills, including the difference it can make to a company's bottom line. It also aims to look at the risks to business of not developing these skills.Design/methodology/approachThe paper uses a mixture of case studies, examples, quotes and opinion.FindingsThe paper finds that only 5 per cent of the UK's training budget is spent on negotiations skills development. However, developing negotiation skills makes a significant difference to the performance of all staff, both in internal and external negotiations. Many big companies now appreciate the value of negotiation skills development and are leading the way in developing all staff in this way.Practical implicationsAll businesses should think about investing in negotiation skills development. Otherwise they are at risk of costing their company a significant margin.Originality/valueThis paper looks for the first time at the skills gap in UK businesses in terms of negotiation skills development. It will be of value to anyone involved in internal and external negotiations, including sales and buying teams, Human Resources staff and senior managers and directors. It will be of value in helping them decide how to make the best use of training.
Implementing successful mentoring programs: career definition vs mentoring approach
Authors: Poulsen Kirsten M. 
Published: July 2006

PurposeThe purpose of this paper is to present the challenges posed by designing and implementing mentoring programs when program coordinators, managers and participants may hold different assumptions about what mentoring is and what career development is. It aims to create an awareness of the inherent conflicts between the old and the new definitions of careers when implementing mentoring programs.Design/methodology/approachThe paper is a presentation of the different definitions of careers as well as the different approaches to mentoring and a discussion of the implications of these in corporate mentoring programs.FindingsThis paper presents viewpoints on where to focus the attention in designing and implementing mentoring programs to achieve maximum results for the organization as well as for the participants.Originality/valueHuman resource professionals, managers and potential mentors and mentees might find value in reading this paper to become aware of obstacles for learning and growth.
Redefining information science: from “information science” to “knowledge science”
Authors: Zins Chaim 
Published: July 2006

PurposeThis philosophical essay aims to explore the concept of information science.Design/methodology/approachThe philosophical argumentation is composed of five phases. It is based on clarifying the meanings of its basic concept “data”, “information” and “knowledge”.FindingsThe study suggests that the name of the field “information science” should be changed to “knowledge science”.Originality/valueThe paper offers reflections on the explored phenomena of information science.
Repositories for research: Southampton's evolving role in the knowledge cycle
Authors: Simpson Pauline , Hey Jessie 
Published: July 2006

PurposeTo provide an overview of how open access (OA) repositories have grown to take a premier place in the e‐research knowledge cycle and offer Southampton's route from project to sustainable institutional repository.Design/methodology/approachThe evolution of institutional repositories and OA is outlined raising questions of multiplicity of repository choice for the researcher. A case study of the University of Southampton research repository (e‐Prints Soton) route to sustainability is explored with a description of a new project that will contribute to e‐research by linking text and data.FindingsA model for IR sustainability.Originality/valueThe TARDis project was one of the first IRs to achieve central university funding in the UK. Combined with increased visibility and citation, the research assessment exercise route has become the “hook” on which a number of IRs are basing their business models.
Personal name identification in the practice of digital repositories
Authors: Xia Jingfeng 
Published: July 2006

PurposeTo propose improvements to the identification of authors' names in digital repositories.Design/methodology/approachAnalysis of current name authorities in digital resources, particularly in digital repositories, and analysis of some features of existing repository applications.FindingsThis paper finds that the variations of authors' names have negatively affected the retrieval capability of digital repositories. Two possible solutions include using composite identifiers that combine author name, publication date, and author affiliation, and also asking authors to input the variants of their name, if any, at the time of depositing articles.Originality/valueThis is the first time that the approach of authors self‐depositing their name variations is proposed. This approach will be able to reduce confusions in name identification.
A dynamic approach to make CDS/ISIS databases interoperable over the internet using the OAI protocol
Authors: Jayakanth F. , Maly K. , Zubair M. , Aswath L. 
Published: July 2006

PurposeA dynamic approach to making legacy databases, like CDS/ISIS, interoperable with OAI‐compliant digital libraries (DLs).Design/methodology/approachThere are many bibliographic databases that are being maintained using legacy database systems. CDS/ISIS is one such legacy database system. It was designed and developed specifically for handling textual data. Over the years, many databases have been developed using this package. There is, however, no mechanism supported by the package for seamless interoperability of databases. The open archives initiative (OAI) addresses the issue of interoperability by using a framework to facilitate the discovery of content stored in distributed archives or bibliographic databases through the use of the OAI Protocol for Metadata Harvesting (OAI‐PMH). The protocol is becoming a de facto standard for interoperability of DLs. Many of the legacy database systems that are in use today, to the best of our knowledge, for various reasons, are not OAI‐compliant. This makes it difficult for the legacy databases to share their metadata automatically. There are two possible approaches to make legacy databases OAI‐compliant – static and dynamic. In this paper, we discuss the dynamic approach to make CDS/ISIS databases OAI‐compliant.FindingsThe dynamic approach is a simple way to make legacy databases OAI‐compliant so that they become interoperable with other OAI‐compliant DLs.Research limitations/implicationDeveloping a general‐purpose tool to make legacy databases OAI‐compliant may be difficult as the driver software needed for database connectivity may not be easily available. Also, the structure of the databases are likely be so varied that identifying the fields that make up the databases programmatically will be very challenging.Originality/valueProvides a dynamic approach to making legacy databases interoperable with OAI‐compliant libraries.
Options for putting CDS/ISIS databases on the internet
Authors: Buxton Andrew 
Published: July 2006

PurposeTo review the variety of software solutions available for putting CDS/ISIS databases on the internet. To help anyone considering which route to take.Design/methodology/approachBriefly describes the characteristics, history, origin and availability of each package. Identifies the type of skills required to implement the package and the kind of application it is suited to. Covers CDS/ISIS Unix version, JavaISIS, IsisWWW, WWWISIS Versions 3 and 5, Genisis, IAH, WWW‐ISIS, and OpenIsis.FindingsThere is no obvious single “best” solution. Several are free but may require more investment in acquiring the skills to install and configure them. The choice will depend on the user's experience with CDS/ISIS formatting language, HTML, programming languages, operating systems, open source software, and so on.Originality/valueThere is detailed documentation available for most of these packages, but little previous guidance to help potential users to distinguish and choose between them.
Prioritizing tactical quality improvement
Authors: Hales Douglas N. , Siha Samia M. , Sridharan V. , McKnew Judith I. 
Published: July 2006

PurposeThe purpose of this paper is to test a method for improving decision‐making at a tactical level – i.e. at the shop floor level. This is done by testing the use of the binary sorting algorithm (BSA) to improve decisions concerning quality improvement efforts among machine operators in a plastics manufacturer.Design/methodology/approachThe method used was the “action‐research” approach since the researchers were actively involved in the training, implementation, and use of the BSA.FindingsIt was found that using the BSA to prioritize quality improvement efforts by machine operators reduced the “scrap‐from‐line” rate in a plastics manufacturer.Research limitations/implicationsThe study should be replicated in different companies and industries using multiple methods because action‐research is limited in its generalizability. Also, since the researchers are actively involved in the process, our observations could not be considered objective.Originality/valueTo the authors' knowledge, this is the first application of the BSA to improve decision‐making at a tactical shop‐floor level in a manufacturing company.