bluuebunny/crossref_metadata_2025_split huggingface dataset:
A System for Information Management in BioMedical Studies—SIMBioMS
Authors: Krestyaninova Maria , Zarins Andris , Viksna Juris , Kurbatova Natalja , Rucevskis Peteris , Neogi Sudeshna Guha , Gostev Mike , Perheentupa Teemu , Knuuttila Juha , Barrett Amy , Lappalainen Ilkka , Rung Johan , Podnieks Karlis , Sarkans Ugis , McCarthy Mark I , Brazma Alvis 
Published: July 2009

Abstract
Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented.
Availability: The source code, documentation and initialization scripts are available at http://simbioms.org.
Contact: support@simbioms.org; mariak@ebi.ac.uk
Accessible methods for the dynamic time-scale decomposition of biochemical systems
Authors: Surovtsova Irina , Simus Natalia , Lorenz Thomas , König Artjom , Sahle Sven , Kummer Ursula 
Published: July 2009

Abstract
Motivation: The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the system without any heuristics employed. Important for the success of such an approach is its accessibility and the clarity of the presentation of the results.
Results: In order to achieve this goal, we developed a method which is a modification of the classical approach of time-scale separation. This modified method as well as the more classical approach have been implemented for time-dependent application within the widely used software COPASI. The implementation includes different possibilities for the representation of the results including 3D-visualization.
Availability: The methods are included in COPASI which is free for academic use and available at www.copasi.org.
Contact: irina.surovtsova@bioquant.uni-heidelberg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees
Authors: Lee Bongshin , Nachmanson Lev , Robertson George , Carlson Jonathan M. , Heckerman David 
Published: July 2009

Abstract
Summary: Evolutionary biologists are often interested in finding correlations among biological traits across a number of species, as such correlations may lead to testable hypotheses about the underlying function. Because some species are more closely related than others, computing and visualizing these correlations must be done in the context of the evolutionary tree that relates species. In this note, we introduce PhyloDet (short for PhyloDetective), an evolutionary tree visualization tool that enables biologists to visualize multiple traits mapped to the tree.
Availability: http://research.microsoft.com/cue/phylodet/
Contact: bongshin@microsoft.com.
Mining gene functional networks to improve mass-spectrometry-based protein identification
Authors: Ramakrishnan Smriti R. , Vogel Christine , Kwon Taejoon , Penalva Luiz O. , Marcotte Edward M. , Miranker Daniel P. 
Published: July 2009

Abstract
Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly.
Results: We develop a method that analyzes MS/MS experiments in the larger context of the biological processes active in a cell. Our method, MSNet, improves protein identification in shotgun proteomics experiments by considering information on functional associations from a gene functional network. MSNet substantially increases the number of proteins identified in the sample at a given error rate. We identify 8–29% more proteins than the original MS experiment when applied to yeast grown in different experimental conditions analyzed on different MS/MS instruments, and 37% more proteins in a human sample. We validate up to 94% of our identifications in yeast by presence in ground-truth reference sets.
Availability and Implementation: Software and datasets are available at http://aug.csres.utexas.edu/msnet
Contact: miranker@cs.utexas.edu, marcotte@icmb.utexas.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
Authors: Marco Antonio , Konikoff Charlotte , Karr Timothy L. , Kumar Sudhir 
Published: July 2009

Abstract
Motivation: In functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common sequence motifs. The underlying assumption is that co-expressed genes are more likely to contain shared TFBS and, thus, TFBS can be identified computationally. Indeed, gene pairs with a very high expression correlation show a significant excess of shared binding sites in yeast. We have tested this assumption in a more complex organism, Drosophila melanogaster, by using experimentally determined TFBS and microarray expression data. We have also examined the reverse relationship between the expression correlation and the extent of TFBS sharing.
Results: Pairs of genes with shared TFBS show, on average, a higher degree of co-expression than those with no common TFBS in Drosophila. However, the reverse does not hold true: gene pairs with high expression correlations do not share significantly larger numbers of TFBS. Exception to this observation exists when comparing expression of genes from the earliest stages of embryonic development. Interestingly, semantic similarity between gene annotations (Biological Process) is much better associated with TFBS sharing, as compared to the expression correlation. We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics.
Contact: amarcoca@asu.edu
Auxin Stimulates Its Own Transport by Shaping Actin Filaments
Authors: Nick Peter , Han Min-Jung , An Gyeunhung 
Published: July 2009

Abstract
The directional transport of the plant hormone auxin has been identified as central element of axis formation and patterning in plants. This directionality of transport depends on gradients, across the cell, of auxin-efflux carriers that continuously cycle between plasma membrane and intracellular compartments. This cycling has been proposed to depend on actin filaments. However, the role of actin for the polarity of auxin transport has been disputed. The organization of actin, in turn, has been shown to be under control of auxin. By overexpression of the actin-binding protein talin, we have generated transgenic rice (Oryza sativa) lines, where actin filaments are bundled to variable extent and, in consequence, display a reduced dynamics. We show that this bundling of actin filaments correlates with impaired gravitropism and reduced longitudinal transport of auxin. We can restore a normal actin configuration by addition of exogenous auxins and restore gravitropism as well as polar auxin transport. This rescue is mediated by indole-3-acetic acid and 1-naphthyl acetic acid but not by 2,4-dichlorophenoxyacetic acid. We interpret these findings in the context of a self-referring regulatory circuit between polar auxin transport and actin organization. This circuit might contribute to the self-amplification of auxin transport that is a central element in current models of auxin-dependent patterning.
A Genetic Screen for Nitrate Regulatory Mutants Captures the Nitrate Transporter Gene NRT1.1
Authors: Wang Rongchen , Xing Xiujuan , Wang Yong , Tran Amy , Crawford Nigel M. 
Published: July 2009

Abstract
Nitrate regulatory mutants (nrg) of Arabidopsis (Arabidopsis thaliana) were sought using a genetic screen that employed a nitrate-inducible promoter fused to the yellow fluorescent protein marker gene YFP. A mutation was identified that impaired nitrate induction, and it was localized to the nitrate regulatory gene NLP7, demonstrating the validity of this screen. A second, independent mutation (nrg1) mapped to a region containing the NRT1.1 (CHL1) nitrate transporter gene on chromosome 1. Sequence analysis of NRT1.1 in the mutant revealed a nonsense mutation that truncated the NRT1.1 protein at amino acid 301. The nrg1 mutation disrupted nitrate regulation of several endogenous genes as induction of three nitrate-responsive genes (NIA1, NiR, and NRT2.1) was dramatically reduced in roots of the mutant after 2-h treatment using nitrate concentrations from 0.25 to 20 mm. Another nrt1.1 mutant (deletion mutant chl1-5) showed a similar phenotype. The loss of nitrate induction in the two nrt1.1 mutants (nrg1 and chl1-5) was not explained by reduced nitrate uptake and was reversed by nitrogen deprivation. Microarray analysis showed that nitrate induction of 111 genes was reduced and of three genes increased 2-fold or more in the nrg1 mutant. Genes involved in nitrate assimilation, energy metabolism, and pentose-phosphate pathway were most affected. These results strongly support the model that NRT1.1 acts as a nitrate regulator or sensor in Arabidopsis.
Molecular and Biochemical Characterization of AtPAP15, a Purple Acid Phosphatase with Phytase Activity, in Arabidopsis
Authors: Kuang Ruibin , Chan Kam-Ho , Yeung Edward , Lim Boon Leong 
Published: July 2009

Abstract
Purple acid phosphatase (PAP) catalyzes the hydrolysis of phosphate monoesters and anhydrides to release phosphate within an acidic pH range. Among the 29 PAP-like proteins in Arabidopsis (Arabidopsis thaliana), AtPAP15 (At3g07130) displays a greater degree of amino acid identity with soybean (Glycine max; GmPHY) and tobacco (Nicotiana tabacum) PAP (NtPAP) with phytase activity than the other AtPAPs. In this study, transgenic Arabidopsis that expressed an AtPAP15 promoter∷β-glucuronidase (GUS) fusion protein showed that AtPAP15 expression was developmentally and temporally regulated, with strong GUS staining at the early stages of seedling growth and pollen germination. The expression was also organ/tissue specific, with strongest GUS staining in the vasculature, pollen grains, and roots. The recombinant AtPAP purified from transgenic tobacco exhibited broad substrate specificity with moderate phytase activity. AtPAP15 T-DNA insertion lines exhibited a lower phytase and phosphatase activity in seedling and germinating pollen and lower pollen germination rate compared with the wild type and their complementation lines. Therefore, AtPAP15 likely mobilizes phosphorus reserves in plants, particularly during seed and pollen germination. Since AtPAP15 is not expressed in the root hair or in the epidermal cells, it is unlikely to play any role in external phosphorus assimilation.
The information literacy instruction assessment cycle
Authors: Oakleaf Megan 
Published: July 2009

PurposeThe aim of this paper is to present the Information Literacy Instruction Assessment Cycle (ILIAC), to describe the seven stages of the ILIAC, and to offer an extended example that demonstrates how the ILIAC increases librarian instructional abilities and improves student information literacy skills.Design/methodology/approachEmploying survey design methodology, the researcher and participants use a rubric to code artifacts of student learning into pre‐set rubric categories. These categories are assigned point values and statistically analyzed to evaluate students and examine interrater reliability and validity.FindingsBy engaging in the ILIAC, librarians gain important data about the information behavior of students and a greater understanding of student strengths and weaknesses. The ILIAC encourages librarians to articulate learning outcomes clearly, analyze them meaningfully, celebrate learning achievements, and diagnose problem areas. In short, the ILIAC results in improved student learning and increased librarian instructional skills. In this study, the ILIAC improves students' ability to evaluate web sites for authority.Research limitations/implicationsThe research focuses on librarians, instructors, and students at one institution. As a result, specific findings are not necessarily generalizable to those at other universities.Practical implicationsAcademic librarians throughout higher education struggle to demonstrate the impact of information literacy instruction on student learning and development. The ILIAC provides a much needed conceptual framework to guide information literacy assessment efforts.Originality/valueThe paper applies the assessment cycle and “assessment for learning” theory to information literacy instruction. The ILIAC provides a model for future information literacy assessment projects. It also enables librarians to demonstrate, document, and increase the impact of information literacy instruction on student learning and development.
The exploration of relationships between information fulfilment and organisational design
Authors: Burke Maria E. 
Published: July 2009

PurposeThe purpose of this paper is to explore the relationship between information fulfilment and organisational design.Design/methodology/approachThe exploration is undertaken in four ways. First, the early part of the paper places information fulfilment within the literature. Second, there is an attempt to further determine the meaning of information fulfilment. Third, the factors that impact on information fulfilment are identified within the context of organisational design. Fourth, empirical findings are reported in the form of a European project which investigated the “relationship” between organisational design and information fulfilment.FindingsInformation fulfilment is shown to be about the process of taking an intuitive “feel” and delineating a number of aspects which are concerned with what might be called emotion. Fulfilment is also connected with organisational roles and wider environmental issues.Originality/valueThe contribution of this paper to the discipline of information management is that information fulfilment is found to exist and to be an important issue influenced by the design of an organisation.
Information science: communication chain and domain analysis
Authors: Robinson Lyn 
Published: July 2009

PurposeThe purpose of this paper is to derive a conceptual model for information science, which is both academically sound and practically useful, particularly for curriculum design.Design/methodology/approachThe approach takes the form of a conceptual analysis, based on an extensive literature review, going back to the earliest days of information science.FindingsA conceptual model is derived, based on the study of components of the information chain through approaches of domain analysis, plus “fringe” topics and a meta‐level consideration of the discipline itself. Links to related subjects may be derived systematically from this model.Originality/valueThis is the first paper to suggest that a useful model for information science can be derived, based on the idea of studying the communication chain by means of domain analysis.
Examining information behavior through social networks
Authors: Schultz‐Jones Barbara 
Published: July 2009

PurposeThe purpose of this paper is to review the post‐1996 literature of information science and other disciplines for the application of social network theory and social network analysis to research that provides an understanding of information environments.Design/methodology/approachThe literature review involved a content analysis of 373 articles retrieved from five electronic journal databases offering broad disciplinary coverage, and a selection of nine peer‐reviewed electronic access journals in information science. Each database was limited to academic or peer reviewed journals and searched using two query phrases: social network theory (SNT) and social network analysis (SNA).FindingsThe paper demonstrates the growth of interest by information science and other disciplines in research that applies social network theory and utilizes social network analysis, indicating what research approaches and major focus trends differentiate the disciplines.Research limitations/implicationsThe search phrases overlook articles using social networks as the only key phrase for indexing. However, the intention was to examine the application of a theoretical concept and specific methodology, so the terms used were appropriate for this purpose.Practical implicationsThe paper identifies opportunities to apply social network theory and social network analysis to the study of the exchange of information resources.Originality/valueThe paper demonstrates that information science could advance valuable contributions to an understanding of information behavior using social network theory and social network analysis as a vehicle to connect with a significant body of existing research in other disciplines.
Web searching by the “general public”: an individual differences perspective
Authors: Ford Nigel , Eaglestone Barry , Madden Andrew , Whittle Martin 
Published: July 2009

PurposeThe purpose of this paper is to explore the impact of a number of human individual differences on the web searching of a sample of the general public.Design/methodology/approachIn total, 91 members of the general public performed 195 controlled searches. Search activity and ratings of search difficulty and success were recorded and statistically analysed. The study was exploratory, and sought to establish whether there is a prima facie case for further systematic investigation of the selection and combination of variables studied here.FindingsResults revealed a number of interactions between individual differences, the use of different search strategies, and levels of perceived search difficulty and success. The findings also suggest that the open and closed nature of searches may affect these interactions. A conceptual model of these relationships is presented.Practical implicationsBetter understanding of factors affecting searching may help one to develop more effective search support, whether in the form of personalised search interfaces and mechanisms, adaptive systems, training or help systems. However, the findings reveal a complexity and variability suggesting that there is little immediate prospect of developing any simple model capable of driving such systems.Originality/valueThere are several areas of this research that make it unique: the study's focus on a sample of the general public; its use of search logs linked to personal data; its development of a novel search strategy classifier; its temporal modelling of how searches are transformed over time; and its illumination of four different types of experienced searcher, linked to different search behaviours and outcomes.
What is Library 2.0?
Authors: Holmberg Kim , Huvila Isto , Kronqvist‐Berg Maria , Widén‐Wulff Gunilla 
Published: July 2009

PurposeThe aim of this paper is to define both theoretically and empirically the concept of Library 2.0.Design/methodology/approachWritten answers to the question “What is Library 2.0?” given by practitioners and researchers (n=29) interested in Library 2.0 issues were analyzed by using co‐word analysis to map the underlying elements of the concept.FindingsThe study resulted in a model of Library 2.0, containing seven building‐blocks of the phenomenon: interactivity, users, participation, libraries and library services, web and web 2.0, social aspects, and technology and tools.Research limitations/implicationsThe model provides a basis for framing Library 2.0 as a research object and to map central themes of future research.Practical implicationsA comprehensive model enables both researchers and practitioners to frame the phenomenon more clearly, evaluate existing and planned services and their proximity to what is Library 2.0.Originality/valueUnlike earlier proposals for a definition of the notion Library 2.0, the present study presents an empirical and consensual crowd‐sourcing approach of defining the concept Library 2.0 and provides basis for discussing the future evolution of the notion and its implications for library and information science research and library practices.
An empirical study of the information‐seeking behavior of practicing visual artists
Authors: Hemmig William 
Published: July 2009

PurposeLittle is known about the information‐seeking behavior of practicing visual artists; what research exists has focused largely on art students, art faculty and librarians, although an untested model does emerge. The aim of this paper is to report the findings of an empirical study of a community of practicing visual artists, and to determine whether the model can be applied to such communities.Design/methodology/approachA quantitative study was administered to a sample of a community of practicing visual artists in order to determine the community's use of various information sources in the service of creative and sales activities.FindingsThe paper finds that the model may be applied to practicing visual artists. It provides a portrait of the information behavior of a specific community of practice, and suggests how information use may differ, while following the model, among different demographic groups within the community.Research limitations/implicationsThe research approach and findings do not conclusively define the uses that artists make of information. The sample size prohibits definitive analysis by demographic data. The quantitative approach facilitates effective identification of community behaviors, but qualitative research might enhance these findings by illuminating the information‐seeking and use processes of individuals.Practical implicationsInformation providers will have a means of gathering and analyzing data about the information behaviors of specific communities of visual artists to be used in the creation of enhanced information environments.Originality/valueThe paper presents the first published research into the information behavior of a community of practicing visual artists without regard to alternative sources of income, academic affiliation, or library use. It presents a means of focusing on these unstudied and underserved communities.