bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative
Authors: Bickel David R. , Montazeri Zahra , Hsieh Pei-Chun , Beatty Mary , Lawit Shai J. , Bate Nicholas J. 
Published: February 2009

Abstract
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential equations that describe transcriptional kinetics. Practical approximations of kinetic models would enable inferring causal relationships between genes from expression data of microarray, tag-based and conventional platforms, but conclusions are sensitive to the assumptions made.
Results: The representation of a sufficiently large portion of genome enables computation of an upper bound on how much confidence one may place in influences between genes on the basis of expression data. Information about which genes encode transcription factors is not necessary but may be incorporated if available. The methodology is generalized to cover cases in which expression measurements are missing for many of the genes that might control the transcription of the genes of interest. The assumption that the gene expression level is roughly proportional to the rate of translation led to better empirical performance than did either the assumption that the gene expression level is roughly proportional to the protein level or the Bayesian model average of both assumptions.
Availability: http://www.oisb.ca points to R code implementing the methods (R Development Core Team 2004).
Contact: dbickel@uottawa.ca
Supplementary information: http://www.davidbickel.com
CGAS: comparative genomic analysis server
Authors: Itoh Masumi , Watanabe Hidemi 
Published: February 2009

Abstract
Summary: Comparative approach is one of the most essential methods for extracting functional and evolutionary information from genomic sequences. So far, a number of sequence comparison tools have been developed, and most are either for on-site use, requiring program installation but providing a wide variety of analyses, or for the online search of user's sequences against given databases on a server. We newly devised an Asynchronous JavaScript and XML (Ajax)-based system for comparative genomic analyses, CGAS, with highly interactive interface within a browser, requiring no software installation. The current version, CGAS version 1, provides functionality for viewing similarity relationships between user's sequences, including a multiple dot plot between sequences with their annotation information. The scrollbar-less ‘draggable’ interface of CGAS is implemented with Google Maps API version 2. The annotation information associated with the genomic sequences compared is synchronously displayed with the comparison view. The multiple-comparison viewer is one of the unique functionalities of this system to allow the users to compare the differences between different pairs of sequences. In this viewer, the system tells orthologous correspondences between the sequences compared interactively. This web-based tool is platform-independent and will provide biologists having no computational skills with opportunities to analyze their own data without software installation and customization of the computer system.
Availability and Implementation: CGAS is available at http://cgas.ist.hokudai.ac.jp/.
Contact: watanabe@ist.hokudai.ac.jp
Impact of exercise training on myostatin expression in the myocardium and skeletal muscle in a chronic heart failure model
Authors: Lenk Karsten , Schur Robert , Linke Axel , Erbs Sandra , Matsumoto Yasuharu , Adams Volker , Schuler Gerhard 
Published: February 2009

AimsIn late‐stage chronic heart failure (CHF), elevated cytokines and cachexia are often observed. Several studies have shown that exercise training exerts beneficial effects on skeletal muscle in this setting. Furthermore, it has been shown that the expression of myostatin, a key regulator of skeletal muscle mass, is increased in a variety of cachectic states. This study aimed to investigate the expression of myostatin in CHF, the influence of exercise training on myostatin levels, and regulation of myostatin by tumour necrosis factor‐α (TNF‐α).Methods and resultsIn an animal model of CHF (LAD‐ligation model), protein expression of myostatin was elevated 2.4‐fold in the skeletal muscle and more than four‐times in the myocardium, compared with control (Co). Exercise training on a treadmill over 4 weeks led to a significant reduction in myostatin protein expression in the skeletal muscle and the myocardium of CHF animals, with values returning to baseline levels. In differentiated C2C12 cells, TNF‐α induced the expression of myostatin through a p38MAPK‐dependent pathway involving nuclear factor kappa‐B (NF‐κB). The increased TNF‐α mRNA levels in the skeletal muscle of CHF animals correlated significantly with myostatin expression.ConclusionThese alterations in myostatin expression in the skeletal and heart muscle following exercise training could help to explain the beneficial anti‐catabolic effects of exercise training in CHF.
Delay effects in brain dynamics
Authors: Stepan Gabor 
Published: February 2009

There are in our existence spots of time,
That with distinct pre-eminence retain
A renovating virtue, whence … our minds

Are nourished and invisibly repaired;…(Wordsworth 1888, ||. 208–211,
The prelude—book twelfth, imagination and taste, how impaired and restored
, written in 1805)

This brief introductory paper reviews the methods and the results presented in the special issue. The general destabilizing effects of time delays in nonlinear dynamical systems are summarized and some similarities in the philosophical approaches of neural systems research in distinct disciplines are pointed out. All the invited papers focus on the central role of time delays in the dynamics of neural systems. The research contributions are set in order according to the increasing number of neurons involved in the corresponding study from a couple of neurons through neural fields to populations and clusters of neurons.
CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL Function Synergistically in the Circadian Clock of Arabidopsis
Authors: Lu Sheen X. , Knowles Stephen M. , Andronis Christos , Ong May S. , Tobin Elaine M. 
Published: February 2009

Abstract
The circadian clock is an endogenous mechanism that coordinates biological processes with daily and seasonal changes in the environment. Heterodimerization of central clock components is an important way of controlling clock function in several different circadian systems. CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) are Myb-related proteins that function in or close to the central oscillator in Arabidopsis (Arabidopsis thaliana). Single mutants of cca1 and lhy have a phenotype of short-period rhythms. cca1 lhy double mutants show an even shorter period phenotype than the cca1 single mutant, suggesting that CCA1 and LHY are only partially functionally redundant. To determine whether CCA1 and LHY act in parallel or synergistically in the circadian clock, we examined their expression in both light-grown and etiolated seedlings. We have shown that LHY and CCA1 bind to the same region of the promoter of a Light-harvesting chlorophyll a/b protein (Lhcb, also known as CAB). CCA1 and LHY can form homodimers, and they also colocalize in the nucleus and heterodimerize in vitro and in vivo. In Arabidopsis, CCA1 and LHY physically interact in a manner independent of photoperiod. Moreover, results from gel filtration chromatography indicate that CCA1 and LHY are present in the same large complex in plants. Taken together, these results imply that CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.
Engineered Polyamine Catabolism Preinduces Tolerance of Tobacco to Bacteria and Oomycetes
Authors: Moschou Panagiotis N. , Sarris Panagiotis F. , Skandalis Nicholas , Andriopoulou Athina H. , Paschalidis Konstantinos A. , Panopoulos Nickolas J. , Roubelakis-Angelakis Kalliopi A. 
Published: February 2009

Abstract
Polyamine oxidase (PAO) catalyzes the oxidative catabolism of spermidine and spermine, generating hydrogen peroxide. In wild-type tobacco (Nicotiana tabacum ‘Xanthi’) plants, infection by the compatible pathogen Pseudomonas syringae pv tabaci resulted in increased PAO gene and corresponding PAO enzyme activities; polyamine homeostasis was maintained by induction of the arginine decarboxylase pathway and spermine was excreted into the apoplast, where it was oxidized by the enhanced apoplastic PAO, resulting in higher hydrogen peroxide accumulation. Moreover, plants overexpressing PAO showed preinduced disease tolerance against the biotrophic bacterium P. syringae pv tabaci and the hemibiotrophic oomycete Phytophthora parasitica var nicotianae but not against the Cucumber mosaic virus. Furthermore, in transgenic PAO-overexpressing plants, systemic acquired resistance marker genes as well as a pronounced increase in the cell wall-based defense were found before inoculation. These results reveal that PAO is a nodal point in a specific apoplast-localized plant-pathogen interaction, which also signals parallel defense responses, thus preventing pathogen colonization. This strategy presents a novel approach for producing transgenic plants resistant to a broad spectrum of plant pathogens.
Roles for Auxin, Cytokinin, and Strigolactone in Regulating Shoot Branching
Authors: Ferguson Brett J. , Beveridge Christine A. 
Published: February 2009

AbstractMany processes have been described in the control of shoot branching. Apical dominance is defined as the control exerted by the shoot tip on the outgrowth of axillary buds, whereas correlative inhibition includes the suppression of growth by other growing buds or shoots. The level, signaling, and/or flow of the plant hormone auxin in stems and buds is thought to be involved in these processes. In addition, RAMOSUS (RMS) branching genes in pea (Pisum sativum) control the synthesis and perception of a long-distance inhibitory branching signal produced in the stem and roots, a strigolactone or product. Auxin treatment affects the expression of RMS genes, but it is unclear whether the RMS network can regulate branching independently of auxin. Here, we explore whether apical dominance and correlative inhibition show independent or additive effects in rms mutant plants. Bud outgrowth and branch lengths are enhanced in decapitated and stem-girdled rms mutants compared with intact control plants. This may relate to an RMS-independent induction of axillary bud outgrowth by these treatments. Correlative inhibition was also apparent in rms mutant plants, again indicating an RMS-independent component. Treatments giving reductions in RMS1 and RMS5 gene expression, auxin transport, and auxin level in the main stem were not always sufficient to promote bud outgrowth. We suggest that this may relate to a failure to induce the expression of cytokinin biosynthesis genes, which always correlated with bud outgrowth in our treatments. We present a new model that accounts for apical dominance, correlative inhibition, RMS gene action, and auxin and cytokinin and their interactions in controlling the progression of buds through different control points from dormancy to sustained growth.
The E3 Ubiquitin Ligase SCFTIR1/AFB and Membrane Sterols Play Key Roles in Auxin Regulation of Endocytosis, Recycling, and Plasma Membrane Accumulation of the Auxin Efflux Transporter PIN2 inArabidopsis thaliana
Authors: Pan Jianwei , Fujioka Shozo , Peng Jianling , Chen Jianghua , Li Guangming , Chen Rujin 
Published: February 2009

AbstractThe PIN family of auxin efflux transporters exhibit polar plasma membrane (PM) localization and play a key role in auxin gradient-mediated developmental processes. Auxin inhibits PIN2 endocytosis and promotes its PM localization. However, the underlying mechanisms remain elusive. Here, we show that the inhibitory effect of auxin on PIN2 endocytosis was impaired in SCFTIR1/AFB auxin signaling mutants. Similarly, reducing membrane sterols impaired auxin inhibition of PIN2 endocytosis. Gas chromatography–mass spectrometry analyses indicate that membrane sterols were significantly reduced in SCFTIR1/AFB mutants, supporting a link between membrane sterols and auxin signaling in regulating PIN2 endocytosis. We show that auxin promoted PIN2 recycling from endosomes to the PM and increased PIN2 steady state levels in the PM fraction. Furthermore, we show that the positive effect of auxin on PIN2 levels in the PM was impaired by inhibiting membrane sterols or auxin signaling. Consistent with this, the sterol biosynthetic mutant fk-J79 exhibited pronounced defects in primary root elongation and gravitropic response. Our data collectively indicate that, although there are distinct processes involved in endocytic regulation of specific PM-resident proteins, the SCFTIR1/AFB-dependent processes are required for auxin regulation of endocytosis, recycling, and PM accumulation of the auxin efflux transporter PIN2 in Arabidopsis thaliana.
A Novel Fatty Acyl-CoA Synthetase Is Required for Pollen Development and Sporopollenin Biosynthesis inArabidopsis
Authors: de Azevedo Souza Clarice , Kim Sung Soo , Koch Stefanie , Kienow Lucie , Schneider Katja , McKim Sarah M. , Haughn George W. , Kombrink Erich , Douglas Carl J. 
Published: February 2009

AbstractAcyl-CoA Synthetase (ACOS) genes are related to 4-coumarate:CoA ligase (4CL) but have distinct functions. The Arabidopsis thaliana ACOS5 protein is in clade A of Arabidopsis ACOS proteins, the clade most closely related to 4CL proteins. This clade contains putative nonperoxisomal ACOS enzymes conserved in several angiosperm lineages and in the moss Physcomitrella patens. Although its function is unknown, ACOS5 is preferentially expressed in the flowers of all angiosperms examined. Here, we show that an acos5 mutant produced no pollen in mature anthers and no seeds by self-fertilization and was severely compromised in pollen wall formation apparently lacking sporopollenin or exine. The phenotype was first evident at stage 8 of anther development and correlated with maximum ACOS5 mRNA accumulation in tapetal cells at stages 7 to 8. Green fluorescent protein–ACOS5 fusions showed that ACOS5 is located in the cytoplasm. Recombinant ACOS5 enzyme was active against oleic acid, allowing kinetic constants for ACOS5 substrates to be established. Substrate competition assays indicated broad in vitro preference of the enzyme for medium-chain fatty acids. We propose that ACOS5 encodes an enzyme that participates in a conserved and ancient biochemical pathway required for sporopollenin monomer biosynthesis that may also include the Arabidopsis CYP703A2 and MS2 enzymes.
Map metadata: essential elements for search and storage
Authors: Beamer Ashley 
Published: February 2009

PurposeThe purpose of this paper is to develop an understanding of the issues surrounding the cataloguing of maps in archives and libraries. An investigation into appropriate metadata formats, such as MARC21, EAD and Dublin Core with RDF, shows how particular map data can be stored. Mathematical map elements, specifically co‐ordinates, are explored as a source of optimal retrieval.Design/methodology/approachThis paper is based on both the personal experiences of map cataloguers as well as previous literature on map retrieval elements, metadata formats and map retrieval systems.FindingsThe difficulties behind map cataloguing do not lie in metadata file formats but rather in maps themselves, staff and budget. They also lie in the lack of map‐appropriate retrieval systems and the lack of co‐ordinate search capabilities.Practical implicationsThe practical implications of this work reflect the necessity for strong map‐retrieval systems and strength of available metadata formats to store essential map data for retrieval. Future map cataloguers should secure appropriate systems for retrieval and include geographical location information, specifically numerical co‐ordinates.Originality/valueThis paper provides insight into current issues in map data and the file formats currently used for storing this data. It also investigates current map‐friendly systems in use by libraries and archives.
An integrated library platform
Authors: Bevan Paul , Tyler Alyson 
Published: February 2009

PurposeThis paper aims to outline the developments and strategies employed to supply online library services in Wales through a national platform: library.wales.org These services include: the “Cat Cymru” cross‐catalogue search, centrally procured subscription resources and local library microsites.Design/methodology/approachThe paper reviews the key areas of development against the backdrop of current library policy in Wales.FindingsBy reviewing the strategic and policy background, outlining the key elements of the projects, and reviewing the future directions for this work, the paper shows how a national approach is leading to an improved cohesive delivery of services to Welsh citizens.Originality/valueThe work outlined in this paper represents the significant and valuable progress made in Wales in regard to the provision of centrally funded online services to all libraries and library users.
Library consortia in developing countries: an overview
Authors: Galyani Moghaddam Golnessa , Talawar V.G. 
Published: February 2009

PurposeThe purpose of this paper is to review consortia efforts in developing countries.Design/methodology/approachThis paper reviews the literature on library consortia in developing countries in general and India in particular. The paper also outlines the advantages and disadvantages of consortia.Findings“Library consortia” refers to co‐operation, co‐ordination and collaboration between, and among, libraries for the purpose of sharing information resources. Libraries in developing countries have been working on consortia at national, regional and international level. However, some barriers such as poor technological and communication infrastructure, inadequate finances, culture and context, attitudes toward consortia and multiple efforts are reported to be limitations of consortia activities in developing countries.Originality and valueThe paper provides a useful overview of consortia in developing countries, particularly in India.
Does your library have a marketing culture? Implications for service providers
Authors: Singh Rajesh 
Published: February 2009

PurposeWhy are some libraries more market‐oriented than others? This paper seeks to answer this question by examining the pertinent issues underlying the marketing culture of Finnish research libraries and the library management's awareness of modern marketing theories and practices.Design/methodology/approachAn integrated methodological approach of qualitative as well as quantitative methods was used to gain knowledge on the pertinent issues lying behind the marketing culture of research libraries. The directors and consumers of 33 academic and special libraries participated as respondents in the study.FindingsThree kinds of marketing cultures were found: the strong (the high flyers); the medium (the brisk runners); and the weak (the slow walkers). These marketing cultures are explained by analyzing the libraries' marketing attitudes, knowledge, and behavior permeating their organizations.Research limitations/implicationsThe study shows the extent to which marketing attitudes, behavior, and knowledge are related. Moreover, the results indicate serious implications, not only in the Finnish context, but also for libraries in other cultural contexts as well.Practical implicationsThe practical implication for libraries is that it pays to be market‐oriented, the ultimate result being higher customer satisfaction.Originality/valueThe contribution of the paper lies in the framework showing linkages between the critical components of the marketing culture of a library: antecedents, market orientation, facilitators and consequences.
Methodology of analysis and interrelation of data about quality indexes of library services by using data‐ and knowledge‐ mining techniques
Authors: Meletiou Aristeidis , Katsirikou Anthi 
Published: February 2009

PurposeThis paper aims to describe a data analysis methodology using data‐ and knowledge‐mining techniques focused on libraries. It concerns data analysis techniques in general, as well as ways in which they could be applied to library management. The ultimate purpose of this data process is to make the exported information useful to decision makers, so as to help them with decision making and strategy planning. This will lead to a more efficient organisation of the internal processing, and to improvement of the services offered in a library.Design/methodology/approachMethodologies based on knowledge and data mining are used to analyse the real data in one specific case study library (Library of Technical University of Crete, Greece) in order to describe the concept better. The results obtained concern the extraction of information about the inter‐relations of data and the definition of factors that can be used in library management and strategic planning. The scope of the paper is to show how data coming from libraries can be analysed to give useful results for decision‐makers, in order to improve the services they offer.FindingsThe paper provides a detailed list of all existing data resources in a library and describes step‐by‐step an analysis methodology based on processes of knowledge discovery and mining from given data. It refers to general principles that should be used for choosing the data to be processed and for defining the way the data should be combined and connected.Research limitations/implicationsThe research reported in this paper can be extended to define other new indicators regarding the quality of services offered to libraries by using a greater amount of data for analysis.Practical implicationsChanges should be made in the way of choosing data for analysis. The way of choosing data here is based on a methodology according to knowledge and data‐mining principles. A definition of new indicators about the quality of services in libraries should be derived from this methodology.Originality/valueThe new thinking in the paper is in the way librarians and decision‐makers in libraries have to use data. The paper shows a way of choosing data that will be able to produce useful conclusions after a well‐described analysis. The paper will be useful for librarians and library managers who want to plan strategies for improving the services they offer.