bluuebunny/crossref_metadata_2025_split huggingface dataset:
ISMB/ECCB 2009 Stockholm
Authors: Sagot Marie-France , McKay B.J. Morrison , Myers Gene 
Published: May 2009

Abstract
The International Society for Computational Biology (ISCB; http://www.iscb.org) presents the Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), organized jointly with the Eighth Annual European Conference on Computational Biology (ECCB; http://bioinf.mpi-inf.mpg.de/conferences/eccb/eccb.htm), in Stockholm, Sweden, 27 June to 2 July 2009. The organizers are putting the finishing touches on the year's premier computational biology conference, with an expected attendance of 1400 computer scientists, mathematicians, statisticians, biologists and scientists from other disciplines related to and reliant on this multi-disciplinary science. ISMB/ECCB 2009 (http://www.iscb.org/ismbeccb2009/) follows the framework introduced at the ISMB/ECCB 2007 (http://www.iscb.org/ismbeccb2007/) in Vienna, and further refined at the ISMB 2008 (http://www.iscb.org/ismb2008/) in Toronto; a framework developed to specifically encourage increased participation from often under-represented disciplines at conferences on computational biology. During the main ISMB conference dates of 29 June to 2 July, keynote talks from highly regarded scientists, including ISCB Award winners, are the featured presentations that bring all attendees together twice a day. The remainder of each day offers a carefully balanced selection of parallel sessions to choose from: proceedings papers, special sessions on emerging topics, highlights of the past year's published research, special interest group meetings, technology demonstrations, workshops and several unique sessions of value to the broad audience of students, faculty and industry researchers. Several hundred posters displayed for the duration of the conference has become a standard of the ISMB and ECCB conference series, and an extensive commercial exhibition showcases the latest bioinformatics publications, software, hardware and services available on the market today. The main conference is preceded by 2 days of Special Interest Group (SIG) and Satellite meetings running in parallel to the fifth Student Council Symposium on 27 June, and in parallel to Tutorials on 28 June. All scientific sessions take place at the Stockholmsmässan/Stockholm International Fairs conference and exposition facility.
Contact: bj@iscb.org
Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome
Authors: Becher Verónica , Deymonnaz Alejandro , Heiber Pablo 
Published: May 2009

Abstract
Motivation: There is a significant ongoing research to identify the number and types of repetitive DNA sequences. As more genomes are sequenced, efficiency and scalability in computational tools become mandatory. Existing tools fail to find distant repeats because they cannot accommodate whole chromosomes, but segments. Also, a quantitative framework for repetitive elements inside a genome or across genomes is still missing.
Results: We present a new efficient algorithm and its implementation as a software tool to compute all perfect repeats in inputs of up to 500 million nucleotide bases, possibly containing many genomes. Our algorithm is based on a suffix array construction and a novel procedure to extract all perfect repeats in the entire input, that can be arbitrarily distant, and with no bound on the repeat length. We tested the software on the Homo sapiens DNA genome NCBI 36.49. We computed all perfect repeats of at least 40 bases occurring in any two chromosomes with exact matching. We found that each H.sapiens chromosome shares ∼10% of its full sequence with every other human chromosome, distributed more or less evenly among the chromosome surfaces. We give statistics including a quantification of repeats by diversity, length and number of occurrences. We compared the computed repeats against all biological repeats currently obtainable from Ensembl enlarged with the output of the dust program and all elements identified by TRF and RepeatMasker (ftp://ftp.ebi.ac.uk/pub/databases/ensembl/jherrero/.repeats/all_repeats.txt.bz2). We report novel repeats as well as new occurrences of repeats matching with known biological elements.
Availability: The source code, results and visualization of some statistics are accessible from http://kapow.dc.uba.ar/patterns/
Contact: vbecher@dc.uba.ar
cis-Element- and Transcriptome-Based Screening of Root Hair-Specific Genes and Their Functional Characterization in Arabidopsis
Authors: Won Su-Kyung , Lee Yong-Ju , Lee Ha-Yeon , Heo Yoon-Kyung , Cho Misuk , Cho Hyung-Taeg 
Published: May 2009

AbstractUnderstanding the cellular differentiation of multicellular organisms requires the characterization of genes whose expression is modulated in a cell type-specific manner. The Arabidopsis (Arabidopsis thaliana) root hair cell is one model for studying cellular differentiation. In this study, root hair cell-specific genes were screened by a series of in silico and experimental filtration procedures. This process included genome-wide screening for genes with a root hair-specific cis-element in their promoters, filtering root-specific genes from the root hair-specific cis-element-containing genes, further filtering of genes that were suppressed in root hair-defective plant lines, and experimental confirmation by promoter assay. These procedures revealed 19 root hair-specific genes, including many protein kinases and cell wall-related genes, most of which have not been characterized thus far. Functional analyses of these root hair-specific genes with loss-of-function mutants and overexpressing transformants revealed that they play roles in hair growth and morphogenesis. This study demonstrates that a defined cis-element can serve as a filter to screen certain cell type-specific genes and implicates many new root hair-specific genes in root hair development.
Managing university libraries
Authors: Walton Graham , Burke Liz , Oldroyd Margaret 
Published: May 2009

PurposeThe purpose of this paper is to investigate the management function of second tier posts in both Australia and the UK university libraries, including the identification of trends about their demography and responsibility range. The study aims to examine the major managerial challenges they face as individuals as well as the challenges for the wider university library. Various aspects of the skills needed by second tier university library manager are to be explored.Design/methodology/approachData were gathered using an online questionnaire completed by second tier university library managers in both Australia and the UKFindingsVarious trends are shown about the age, length of time in post and intended retirement age of second tier mangers as well as the range of their responsibilities. Key challenges are determined for them as individuals as well as those for the wider university library.Research limitation/implicationsThe study demonstrates how effective research can be done across countries relying solely on information and communication technologies (ICT) for data collection and project communication/management.Practical implicationsClear direction and guidance is provided by the outcomes of the study into the development of future second tier university library managersOriginality/valueNo other study has been published in this area for over ten years and very little has taken place before then. It is also the first cross‐national investigation on second tier roles.
Auditing the library's quality system
Authors: Balagué Núria 
Published: May 2009

PurposeThe purpose of the paper is to describe the main features of a university library quality management system, focusing specially on internal auditing.Design/methodology/approachAdopting a case study approach, the paper attempts to show how auditing is a useful information management tool to improve library services.FindingsInternal auditing helps to consolidate the culture of quality and promote appropriate ethics and values.Research limitations/implicationsThe paper is based on a study case and the professional experience of the author.Practical implicationsA view on a consolidated library's quality management system is presented in the paper.Originality/valueThe paper provides ideas on how a library approaches an internal audit.
The information commons at Sichuan University Jiang'an Library
Authors: Yao Leye , Liu Liu , Cai Na 
Published: May 2009

PurposeThis paper aims to give a snapshot of planning, building and developing the information commons at a comprehensive research university library in China. It seeks to frame and confirm a new and effective strategy for the future development of university libraries illustrated by its actually positive outcomes.Design/methodology/approachThe paper begins with an overview of information commons as a major international concern that represents a strategic direction of library development, followed by the changing academic landscape in China. It then explains the background and process of building the information commons at Sichuan University Jiang'an Library with its emphasis on its positive outcomes, illustrated by the latest factual data compared with other university libraries in Sichuan. It also discusses the future prospects of developing the information commons.FindingsThe paper reveals that information commons is undergoing its international journey from theory to practice and has proved its positive impact on improving the usage of physical and virtual space, resources and services of university libraries in the changing information environment.Practical implicationsDetailed recommendations regarding the construction and development of information commons in Chinese university libraries are provided.Originality/valueThis case study offers insight into practical and effective approaches to enhancing the usage of university libraries in China and emphasizes the importance of integrating the actual situation and background of the university, the region and the nation.
Job characteristics, work attitudes and behaviors in a non‐western context
Authors: Abu Elanain Hossam M. 
Published: May 2009

PurposePrevious studies on job characteristics have been performed mainly in Western contexts. More empirical evidence is needed to understand the important job characteristics of positive job outcomes in a non‐Western context. Therefore, this research has two objectives: to assess the impact of five job characteristics on work attitudes and behaviors in the UAE, and to test the mediating impact of distributive justice on the job characteristics‐work outcomes relationship.Design/methodology/approachThe study reports responses of 350 employees from five large organizations operating in Dubai. Data were collected on a structured questionnaire containing standards scales of job characteristics, job satisfaction, organizational commitment, turnover intentions, distributive justice, and some demographic variables. After testing scales reliability and validity, the proposed linear relationships were tested using a series of separate hierarchical regression analyses. Proposed mediation hypotheses were tested using Baron and Kenny's recommendations.FindingsConsistent with studies conducted in a Western context, the study showed that skill variety and feedback have functional impacts on job satisfaction, organizational commitment and turnover intentions. Contrary to Western studies, the study reported that task identity and task significance have functional effects on work attitudes and behaviors. Autonomy also showed unexpected positive relationship with turnover intentions. Additionally, distributive justice mediates some of the relationships between job characteristics and work outcomes.Research limitations/implicationsThe limitations of common method bias and cross‐sectional data are discussed in the light of implications for future research. Nevertheless, the results provide new insights on the influence of job characteristics on work outcomes in a non‐Western context of the UAE. Also, the study reported evidence for the mediating impact of distributive justice on the job characteristics‐work outcomes relationship.Practical implicationsThe study has implications for enhancing work behaviors and attitudes. In general, enhancing certain job characteristics can result in higher‐level employee outcomes. Also, managers should improve some of the contextual factor (i.e. distributive justice) in order to enhance the impact of job characteristics on work outcomes.Originality/valueThe study is considered to be one of the first to examine the job characteristics‐work outcomes relationship in a non‐western context of the UAE. Also, it is among the first studies to test the role of distributive justice as a mediator for the job characteristics‐work outcome relationship.
Library communication outside a library context: instant messaging as library service
Authors: Jørn Nielsen Hans 
Published: May 2009

PurposeThe purpose of this paper is to put librarian use of instant messaging (IM) into a context of new media development. The paper aims to evaluate use of IM from findings in a research project of a Danish IM test.Design/methodology/approachThe paper is grounded on findings related to the author's research of a specific Danish instant messaging test called Need2Know. With help of theories of communication patterns on the internet and of media theory of Web 2.0 IM is assessed as a tool for public libraries.FindingsInstant messaging is an instance of expanding conversational and decentralized ways of communication on the internet. It is a useful communication tool to get in touch with young users, but it may be a waste of resources if the purpose primarily is to answer short questions of encyclopaedic facts. If the service is not anchored in an explicit library context or in library resources, the ask service easily will decay to a type of “living search machine” and not be part of a participatory culture promised by Web 2.0.Originality/valueThe paper assesses an instant messaging tool, Need2Know. The Need2Know service mirrors a traditional attitude to the relationship between users and library. Today users are able to find simple information themselves, and they are even able to disseminate and share this information through numerous social technologies.
Customized mapping and metadata transfer from DSpace to OCLC to improve ETD work flow
Authors: Deng Sai , Reese Terry 
Published: May 2009

PurposeThe purpose of this paper is to present methods for customized mapping and metadata transfer from DSpace to Online Computer Library Center (OCLC), which aims to improve Electronic Theses and Dissertations (ETD) work flow at libraries using DSpace to store theses and dissertations by automating the process of generating MARC records from Dublin Core (DC) metadata in DSpace and exporting them to OCLC.Design/methodology/approachThis paper discusses how the Shocker Open Access Repository (SOAR) at Wichita State University (WSU) Libraries and ScholarsArchive at Oregon State University (OSU) Libraries harvest theses data from the DSpace platform using the Metadata Harvester in MarcEdit developed by Terry Reese at OSU Libraries. It analyzes certain challenges in transformation of harvested data including handling of authorized data, dealing with data ambiguity and string processing. It addresses how these two institutions customize Library of Congress's XSLT (eXtensible Stylesheet Language Transformations) mapping to transfer DC metadata to MarcXML metadata and how they export MARC data to OCLC and Voyager.FindingsThe customized mapping and data transformation for ETD data can be standardized while also requiring a case‐by‐case analysis. By offering two institutions' experiences, it provides information on the benefits and limitations for those institutions that are interested in using MarcEdit and customized XSLT to transform their ETDs from DSpace to OCLC and Voyager.Originality/valueThe new method described in the paper can eliminate the need for double entry in DSpace and OCLC, meet local needs and significantly improve ETD work flow. It offers perspectives on repurposing and managing metadata in a standard and customizable way.
Modeling non‐linear passive direct methanol fuel cells
Authors: Alotto Piergiorgio , Guarnieri Massimo , Moro Federico 
Published: May 2009

PurposeThe purpose of this paper is to simulate micro direct methanol fuel cells (DMFCs) for portable electronic devices by means of a non‐linear equivalent circuit based on a fully coupled, dynamic, electrochemical model.Design/methodology/approachThe equivalent circuit accounts for electrochemical reactions and electric current generation inside the catalyst layers, electronic and protonic conduction, fuel crossover across the membrane, mass transport of reactants inside the diffusion layers. The V‐I characteristic of the device is obtained by combining mass transport and electric equations. The transient dynamics is accounted for by an equivalent capacitance, while the slow dynamics by the mass conservation equation. The equivalent circuit is embedded in the Matlab/Simulink® dynamic model of a hybrid system, consisting of a micro fuel cell and a Li‐ion rechargeable battery.FindingsAn original equivalent circuit of a passive DMFC suitable for static and dynamic simulations under variable loading conditions is proposed and validated.Research limitations/implicationsThe one‐dimensional model of the micro cell does not take into account transverse mass transfer and current density variations in the cell layers, which can be due to non‐homogeneous materials or to the complex dynamics of the convective mass flow in the reservoir and in the room air.Practical implicationsThe equivalent circuit can be used for simulating the dynamic performance in realistic operating conditions when the fuel cell is used to supply the electronic equipment through a power management unit.Originality/valueThe DMFC is described from an electrical point of view as a controlled non‐linear generator; such equivalent representation is particularly suited for designing power management units for electronic portable devices.
Scattering by a two‐dimensional doped photonic crystal presenting an optical Kerr effect
Authors: Godard Pierre , Zolla Frédéric , Nicolet André 
Published: May 2009

PurposeThe purpose of this paper is to discuss two‐dimensional electromagnetic diffraction by a finite set of parallel nonlinear rods (optical Kerr effect). To point out the versatility of this approach, a nonlinear (Kerr‐effect) finite crystal is considered.Design/methodology/approachIn this paper, a new route for obtaining the scattered field by nonlinear obstacles is proposed. The basic idea consists in simulating the real incident field (e.g. plane waves) by a virtual field emitted by an appropriate antenna, located in a meshed domain, and encompassing or lying above the obstacles. This latest problem is then solved by a finite element method that is well suited to take into account the material inhomogeneities due to the nonlinearity of the permittivity.FindingsThe transmission through a finite Kerr crystal doped by a microcavity is given and a resonant wavelength is obtained. At this resonant wavelength, it is shown that the nonlinearity has a large influence on the behaviour of the electromagnetic wave.Originality/valueIntroducing the concept of virtual antenna, the paper proposes a rigorous treatment of the scattering of an electromagnetic wave by a bounded nonlinear obstacle of arbitrary shape.
9th International Bielefeld Conference 2009: “Upgrading The eLibrary: Enhanced Information Services Driven by Technology and Economics”
Authors: Gastinger Almuth 
Published: May 2009

PurposeThe purpose of this paper is to share with readers the issues of the 9th International Bielefeld Conference.Design/methodology/approachThis is a descriptive report.FindingsThe conference discussed essential current and future developments towards enhanced libraries and information infrastructures meeting the emerging demands of eScience and eLearning.Originality/valueWill be of interest to library and information professionals.
The entrepreneurial library
Authors: Dhanjal Catherine 
Published: May 2009

PurposeThe purpose of this paper is to provide an overview of the recent Axiell conference on entrepreneurial activities in relation to libraries in the public sector.Design/methodology/approachProvide an overview of the conference.FindingsProvides an overview of the conference.Research limitations/implicationsProvides an overview of the conference subject to the author's interpretation.Practical implicationsProvides case studies and thoughts on entrepreneurship from the public library and other sectors which could be used to spark ideas for libraries in the public sector and beyond to help reinvent their services and offerings in the wake of Google, Amazon and other “competitor” services.Originality/valueOf interest to librarians in the public sector and beyond, in the UK and Nordic countries and further afield. A shorter version of this paper appears on the Axiell web site.
Boundary transfer operators in one‐way nesting schemes for heat flow problems
Authors: Shavelzon Evgeny , Givoli Dan 
Published: May 2009

PurposeThe interaction of a global model (GM) and a local (regional) model (LM) of heat flow is considered under the framework of so‐called “one‐way nesting”. In this framework, the GM is constructed in a large domain with coarse discretization in space and time, while the LM is set in a small subdomain with fine discretization.Design/methodology/approachThe GM is solved first, and its results are then used via some boundary transfer operator (BTO) on the GM–LM interface in order to solve the LM. Past experience in various fields of application has shown that one has to be careful in the choice of BTO to be used on the GM–LM interface, since this choice affects both the stability and accuracy of the computational scheme. Here the problem is first theoretically analyzed for the linear heat equation, and stable BTOs are identified. Then numerical experiments are performed with one‐way nesting in a two‐dimensional channel for heat flow with and without radiation emission and linear reaction, using four different BTOs.FindingsAmong other conclusions, it is shown that the “negative Robin” BTO is unstable, whereas the Dirichlet, Neumann and “positive Robin” BTO are all stable. It is also shown that in terms of accuracy, the Neumann and “positive Robin” BTOs should be preferred over the Dirichlet BTO.Originality/valueThis study may be the first step in analyzing BTO accuracy and stability for more general atmospheric systems.