bluuebunny/crossref_metadata_2025 huggingface dataset:
Consistent blind protein structure generation from NMR chemical shift data
Authors: Shen Yang , Lange Oliver , Delaglio Frank , Rossi Paolo , Aramini James M. , Liu Gaohua , Eletsky Alexander , Wu Yibing , Singarapu Kiran K. , Lemak Alexander , Ignatchenko Alexandr , Arrowsmith Cheryl H. , Szyperski Thomas , Montelione Gaetano T. , Baker David , Bax Ad
Published: March 2008

Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for
de novo
protein structure generation, using as input experimental parameters the
13
C
α
,
13
C
β
,
13
C′,
15
N,
1
H
α
and
1
H
N
NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7–1.8 Å root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination.
The distribution of category and location information across object-selective regions in human visual cortex
Authors: Schwarzlose Rebecca F. , Swisher Jascha D. , Dang Sabin , Kanwisher Nancy
Published: March 2008

Since Ungerleider and Mishkin [Underleider LG, Mishkin M (1982) Two cortical visual systems.
Analysis of Visual Behavior
, eds Ingle MA, Goodale MI, Masfield RJW (MIT Press, Cambridge, MA), pp 549–586] proposed separate visual pathways for processing object shape and location, steady progress has been made in characterizing the organization of the two kinds of information in extrastriate visual cortex in humans. However, to date, there has been no broad-based survey of category and location information across all major functionally defined object-selective regions. In this study, we used an fMRI region-of-interest (ROI) approach to identify eight regions characterized by their strong selectivity for particular object categories (faces, scenes, bodies, and objects). Participants viewed four types of stimuli (faces, scenes, bodies, and cars) appearing in each of three different spatial locations (above, below, or at fixation). Analyses based on the mean response and voxelwise patterns of response in each ROI reveal location information in almost all of the known object-selective regions. Furthermore, category and location information can be read out independently of one another such that most regions contain both position-invariant category information and category-invariant position information. Finally, we find substantially more location information in ROIs on the lateral than those on the ventral surface of the brain, even though these regions have equal amounts of category information. Although the presence of both location and category information in most object-selective regions argues against a strict physical separation of processing streams for object shape and location, the ability to extract position-invariant category information and category-invariant position information from the same neural population indicates that form and location information nonetheless remain functionally independent.
Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
Authors: Gold Bert , Kirchhoff Tomas , Stefanov Stefan , Lautenberger James , Viale Agnes , Garber Judy , Friedman Eitan , Narod Steven , Olshen Adam B. , Gregersen Peter , Kosarin Kristi , Olsh Adam , Bergeron Julie , Ellis Nathan A. , Klein Robert J. , Clark Andrew G. , Norton Larry , Dean Michael , Boyd Jeff , Offit Kenneth
Published: March 2008

We performed a three-phase genome-wide association study (GWAS) using cases and controls from a genetically isolated population, Ashkenazi Jews (AJ), to identify loci associated with breast cancer risk. In the first phase, we compared allele frequencies of 150,080 SNPs in 249 high-risk,
BRCA1/2
mutation-negative AJ familial cases and 299 cancer-free AJ controls using χ
2
and the Cochran–Armitage trend tests. In the second phase, we genotyped 343 SNPs from 123 regions most significantly associated from stage 1, including 4 SNPs from the
FGFR2
region, in 950 consecutive AJ breast cancer cases and 979 age-matched AJ controls. We replicated major associations in a third independent set of 243 AJ cases and 187 controls. We obtained a significant allele
P
value of association with AJ breast cancer in the
FGFR2
region (
P
= 1.5 × 10
−5
, odds ratio (OR) 1.26, 95% confidence interval (CI) 1.13–1.40 at rs1078806 for all phases combined). In addition, we found a risk locus in a region of chromosome 6q22.33 (
P
= 2.9 × 10
−8
, OR 1.41, 95% CI 1.25–1.59 at rs2180341). Using several SNPs at each implicated locus, we were able to verify associations and impute haplotypes. The major haplotype at the 6q22.33 locus conferred protection from disease, whereas the minor haplotype conferred risk. Candidate genes in the 6q22.33 region include
ECHDC1
, which encodes a protein involved in mitochondrial fatty acid oxidation, and also
RNF146
, which encodes a ubiquitin protein ligase, both known pathways in breast cancer pathogenesis.
Organization of the core structure of the postsynaptic density
Authors: Chen Xiaobing , Winters Christine , Azzam Rita , Li Xiang , Galbraith James A. , Leapman Richard D. , Reese Thomas S.
Published: March 2008

Much is known about the composition and function of the postsynaptic density (PSD), but less is known about its molecular organization. We use EM tomography to delineate the organization of PSDs at glutamatergic synapses in rat hippocampal cultures. The core of the PSD is dominated by vertically oriented filaments, and ImmunoGold labeling shows that PSD-95 is a component of these filaments. Vertical filaments contact two types of transmembrane structures whose sizes and positions match those of glutamate receptors and intermesh with two types of horizontally oriented filaments lying 10–20 nm from the postsynaptic membrane. The longer horizontal filaments link adjacent NMDAR-type structures, whereas the smaller filaments link both NMDA- and AMPAR-type structures. The orthogonal, interlinked scaffold of filaments at the core of the PSD provides a structural basis for understanding dynamic aspects of postsynaptic function.
Soft Substrate Up-regulates the Interaction of STIM1 with Store-operated Ca2+Channels That Lead to Normal Epithelial Cell Apoptosis
Authors: Chiu Wen-Tai , Tang Ming-Jer , Jao Hsiao-Chun , Shen Meng-Ru
Published: March 2008

We have demonstrated that soft substrate induced apoptosis in polarized cells, but not in transformed cells by disturbance of Ca2+homeostasis. This study aims to further investigate the regulatory mechanisms underlying the disruption of Ca2+-signaling integrity in soft substrate–induced epithelial apoptosis. Soft substrate up-regulated the store-operated Ca2+(SOC) entry across the plasma membrane of normal cervical epithelial cells, which resulted in increased cytosolic Ca2+levels. Concomitantly, soft substrate induced the aggregation and translocation of stromal interacting molecule 1 (STIM1) toward the cell periphery to colocalize with Orai1, an essential pore subunit of SOC channel, detected by fluorescence resonance energy transfer approach and confocal image analyses. The disturbed Ca2+homeostasis resulted in the activation of μ-calpain, which cleaved α-spectrin, induced actin disorganization, and caused apoptosis. In contrast, soft substrate did not disturb Ca2+homeostasis or induce apoptosis in cervical cancer cells. Chelating extracellular Ca2+by EGTA and down-regulated SOC entry by small interfering RNA targeting STIM1 or inhibitors targeting Ca2+-binding site of calpain significantly inhibited soft substrate–induced activation of μ-calpain and epithelial cell apoptosis. Thus, soft substrate up-regulates the interaction of STIM1 with SOC channels, which results in the activation of μ-calpain and subsequently induces normal epithelial cell apoptosis.
Respiratory Performance Offered by N95 Respirators and Surgical Masks: Human Subject Evaluation with NaCl Aerosol Representing Bacterial and Viral Particle Size Range
Authors: Lee Shu-An , Grinshpun Sergey A. , Reponen Tiina
Published: March 2008

Objectives: This study aimed at determining the protection factors (PFs) provided by N95 filtering facepiece respirators and surgical masks against particles representing bacterial and viral size ranges (aerodynamic size: 0.04–1.3 μm).

Methods: The protection levels of N95 filtering facepiece respirators (four models) and surgical masks (three models) were investigated while they were donned by 12 subjects performing the OSHA (US Occupational Safety and Health Administration) fit-testing exercises in a test chamber.

Results: About 29% of N95 respirators and ∼100% of surgical masks had PFs <10, which is the assigned PF designated for this type of respirator by the OSHA. On average, the PFs of N95 respirators were 8–12 times greater than those of surgical masks. The minimum PFs were observed in the size range of 0.04–0.2 μm. No significant difference in PF results was found between N95 respirators with and without an exhalation valve.

Conclusions: The study indicates that N95 filtering facepiece respirators may not achieve the expected protection level against bacteria and viruses. An exhalation valve on the N95 respirator does not affect the respiratory protection; it appears to be an appropriate alternative to reduce the breathing resistance.
MiSearch adaptive pubMed search tool
Authors: States David J. , Ade Alex S. , Wright Zachary C. , Bookvich Aaron V. , Athey Brian D.
Published: March 2008

Summary: MiSearch is an adaptive biomedical literature search tool that ranks citations based on a statistical model for the likelihood that a user will choose to view them. Citation selections are automatically acquired during browsing and used to dynamically update a likelihood model that includes authorship, journal and PubMed indexing information. The user can optionally elect to include or exclude specific features and vary the importance of timeliness in the ranking.

Availability:  http://misearch.ncibi.org

Contact:  dstates@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
Authors: Lesk Victor I. , Sternberg Michael J. E.
Published: March 2008

Motivation: Reliable structural modelling of protein–protein complexes has widespread application, from drug design to advancing our knowledge of protein interactions and function. This work addresses three important issues in protein–protein docking: implementing backbone flexibility, incorporating prior indications from experiment and bioinformatics, and providing public access via a server. 3D-Garden (Global And Restrained Docking Exploration Nexus), our benchmarked and server-ready flexible docking system, allows sophisticated programming of surface patches by the user via a facet representation of the interactors’ molecular surfaces (generated with the marching cubes algorithm). Flexibility is implemented as a weighted exhaustive conformer search for each clashing pair of molecular branches in a set of 5000 models filtered from around ∼340 000 initially.

Results: In a non-global assessment, carried out strictly according to the protocols for number of models considered and model quality of the Critical Assessment of Protein Interactions (CAPRI) experiment, over the widely-used Benchmark 2.0 of 84 complexes, 3D-Garden identifies a set of ten models containing an acceptable or better model in 29/45 test cases, including one with large conformational change. In 19/45 cases an acceptable or better model is ranked first or second out of 340 000 candidates.

Availability:  http://www.sbg.bio.ic.ac.uk/3dgarden (server)

Contact:  v.lesk@ic.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Mapping translocation breakpoints by next-generation sequencing
Authors: Chen Wei , Kalscheuer Vera , Tzschach Andreas , Menzel Corinna , Ullmann Reinhard , Schulz Marcel Holger , Erdogan Fikret , Li Na , Kijas Zofia , Arkesteijn Ger , Pajares Isidora Lopez , Goetz-Sothmann Margret , Heinrich Uwe , Rost Imma , Dufke Andreas , Grasshoff Ute , Glaeser Birgitta , Vingron Martin , Ropers H. Hilger
Published: March 2008

Balanced chromosome rearrangements (BCRs) can cause genetic diseases by disrupting or inactivating specific genes, and the characterization of breakpoints in disease-associated BCRs has been instrumental in the molecular elucidation of a wide variety of genetic disorders. However, mapping chromosome breakpoints using traditional methods, such as in situ hybridization with fluorescent dye-labeled bacterial artificial chromosome clones (BAC-FISH), is rather laborious and time-consuming. In addition, the resolution of BAC-FISH is often insufficient to unequivocally identify the disrupted gene. To overcome these limitations, we have performed shotgun sequencing of flow-sorted derivative chromosomes using “next-generation” (Illumina/Solexa) multiplex sequencing-by-synthesis technology. As shown here for three different disease-associated BCRs, the coverage attained by this platform is sufficient to bridge the breakpoints by PCR amplification, and this procedure allows the determination of their exact nucleotide positions within a few weeks. Its implementation will greatly facilitate large-scale breakpoint mapping and gene finding in patients with disease-associated balanced translocations.
Decrease in Manganese Superoxide Dismutase Leads to Reduced Root Growth and Affects Tricarboxylic Acid Cycle Flux and Mitochondrial Redox Homeostasis
Authors: Morgan Megan J. , Lehmann Martin , Schwarzländer Markus , Baxter Charles J. , Sienkiewicz-Porzucek Agata , Williams Thomas C.R. , Schauer Nicolas , Fernie Alisdair R. , Fricker Mark D. , Ratcliffe R. George , Sweetlove Lee J. , Finkemeier Iris
Published: March 2008

Superoxide dismutases (SODs) are key components of the plant antioxidant defense system. While plastidic and cytosolic isoforms have been extensively studied, the importance of mitochondrial SOD at a cellular and whole-plant level has not been established. To address this, transgenic Arabidopsis (Arabidopsis thaliana) plants were generated in which expression of AtMSD1, encoding the mitochondrial manganese (Mn)SOD, was suppressed by antisense. The strongest antisense line showed retarded root growth even under control growth conditions. There was evidence for a specific disturbance of mitochondrial redox homeostasis in seedlings grown in liquid culture: a mitochondrially targeted redox-sensitive green fluorescent protein was significantly more oxidized in the MnSOD-antisense background. In contrast, there was no substantial change in oxidation of cytosolically targeted redox-sensitive green fluorescent protein, nor changes in antioxidant defense components. The consequences of altered mitochondrial redox status of seedlings were subtle with no widespread increase of mitochondrial protein carbonyls or inhibition of mitochondrial respiratory complexes. However, there were specific inhibitions of tricarboxylic acid (TCA) cycle enzymes (aconitase and isocitrate dehydrogenase) and an inhibition of TCA cycle flux in isolated mitochondria. Nevertheless, total respiratory CO2 output of seedlings was not decreased, suggesting that the inhibited TCA cycle enzymes can be bypassed. In older, soil-grown plants, redox perturbation was more pronounced with changes in the amount and/or redox poise of ascorbate and glutathione. Overall, the results demonstrate that reduced MnSOD affects mitochondrial redox balance and plant growth. The data also highlight the flexibility of plant metabolism with TCA cycle inhibition having little effect on overall respiratory rates.
Independence and Interaction of Regions of the INNER NO OUTER Protein in Growth Control during Ovule Development
Authors: Gallagher Thomas L. , Gasser Charles S.
Published: March 2008

The outer integument of the Arabidopsis (Arabidopsis thaliana) ovule develops asymmetrically, with growth and cell division occurring primarily along the region of the ovule facing the base of the gynoecium (gynobasal). This process is altered in the mutants inner no outer (ino) and superman (sup), which lead to absent or symmetrical growth of the outer integument, respectively. INO encodes a member of the YABBY family of putative transcription factors, and its expression is restricted to the gynobasal side of developing ovules via negative regulation by the transcription factor SUP. Other YABBY proteins (e.g. CRABS CLAW [CRC] and YABBY3 [YAB3]) can substitute for INO in promotion of integument growth, but do not respond to SUP regulation. In contrast, YAB5 fails to promote integument growth. To separately investigate the growth-promotive effects of INO and its inhibition by SUP, domain swaps between INO and YAB3, YAB5, or CRC were assembled. The ability of chimeric YABBY proteins to respond to SUP restriction showed a quantitative response proportional to the amount of INO protein and was more dependent on C-terminal regions of INO. A different response was seen when examining growth promotion where the number and identity of regions of INO in chimeric YABBY proteins were not the primary influence on promotion of outer integument growth. Instead, promotion of growth required a coordination of features along the entire length of the INO protein, suggesting that intramolecular interactions between regions of INO may coordinately facilitate the intermolecular interactions necessary to promote formation of the outer integument.
The Central Role of a SNRK2 Kinase in Sulfur Deprivation Responses
Authors: Gonzalez-Ballester David , Pollock Steve V. , Pootakham Wirulda , Grossman Arthur R.
Published: March 2008

In the absence of sulfur (S), Chlamydomonas reinhardtii increases the abundance of several transcripts encoding proteins associated with S acquisition and assimilation, conserves S amino acids, and acclimates to suboptimal growth conditions. A positive regulator, SAC1 (for sulfur acclimation protein 1), and a negative regulator, SAC3, were shown to participate in the control of these processes. In this study, we investigated two allelic mutants (ars11 and ars44) affected in a gene encoding a SNRK2 (for SNF1-related protein kinase 2) kinase designated SNRK2.1. Like the sac1 mutant, both snrk2.1 mutants were deficient in the expression of S-responsive genes. Furthermore, the mutant cells bleached more rapidly than wild-type cells during S deprivation, although the phenotypes of ars11 and ars44 were not identical: ars11 exhibited a more severe phenotype than either ars44 or sac1. The phenotypic differences between the ars11 and ars44 mutants reflected distinct alterations of SNRK2.1 mRNA splicing caused by insertion of the marker gene. The ars11 phenotype could be rescued by complementation with SNRK2.1 cDNA. In contrast to the nonepistatic relationship between SAC3 and SAC1, characterization of the sac3 ars11 double mutant showed that SNRK2.1 is epistatic to SAC3. These data reveal the crucial regulatory role of SNRK2.1 in the signaling cascade critical for eliciting S deprivation responses in Chlamydomonas. The phylogenetic relationships and structures of the eight members of the SNRK2 family in Chlamydomonas are discussed.
Isolation and Characterization of Mutants of Common Ice Plant Deficient in Crassulacean Acid Metabolism
Authors: Cushman John C. , Agarie Sakae , Albion Rebecca L. , Elliot Stewart M. , Taybi Tahar , Borland Anne M.
Published: March 2008

Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that improves water use efficiency by shifting part or all of net atmospheric CO2 uptake to the night. Genetic dissection of regulatory and metabolic attributes of CAM has been limited by the difficulty of identifying a reliable phenotype for mutant screening. We developed a novel and simple colorimetric assay to measure leaf pH to screen fast neutron-mutagenized populations of common ice plant (Mesembryanthemum crystallinum), a facultative CAM species, to detect CAM-deficient mutants with limited nocturnal acidification. The isolated CAM-deficient mutants showed negligible net dark CO2 uptake compared with wild-type plants following the imposition of salinity stress. The mutants and wild-type plants accumulated nearly comparable levels of sodium in leaves, but the mutants grew more slowly than the wild-type plants. The mutants also had substantially reduced seed set and seed weight relative to wild type under salinity stress. Carbon-isotope ratios of seed collected from 4-month-old plants indicated that C3 photosynthesis made a greater contribution to seed production in mutants compared to wild type. The CAM-deficient mutants were deficient in leaf starch and lacked plastidic phosphoglucomutase, an enzyme critical for gluconeogenesis and starch formation, resulting in substrate limitation of nocturnal C4 acid formation. The restoration of nocturnal acidification by feeding detached leaves of salt-stressed mutants with glucose or sucrose supported this defect and served to illustrate the flexibility of CAM. The CAM-deficient mutants described here constitute important models for exploring regulatory features and metabolic consequences of CAM.
A Third Phytoene Synthase Is Devoted to Abiotic Stress-Induced Abscisic Acid Formation in Rice and Defines Functional Diversification of Phytoene Synthase Genes
Authors: Welsch Ralf , Wüst Florian , Bär Cornelia , Al-Babili Salim , Beyer Peter
Published: March 2008

We here report on the characterization of a novel third phytoene synthase gene (PSY) in rice (Oryza sativa), OsPSY3, and on the differences among all three PSY genes with respect to the tissue-specific expression and regulation upon various environmental stimuli. The two already known PSYs are under phytochrome control and involved in carotenoid biosynthesis in photosynthetically active tissues and exhibit different expression patterns during chloroplast development. In contrast, OsPSY3 transcript levels are not affected by light and show almost no tissue-specific differences. Rather, OsPSY3 transcripts are up-regulated during increased abscisic acid (ABA) formation upon salt treatment and drought, especially in roots. The simultaneous induction of genes encoding 9-cis-epoxycarotenoid dioxygenases (NCEDs), involved in the initial steps of ABA biosynthesis, indicate that decreased xanthophyll levels are compensated by the induction of the third PSY gene. Furthermore, OsPSY3 and the OsNCEDs investigated were also induced by the application of ABA, indicating positive feedback regulation. The regulatory differences are mirrored by cis-acting elements in the corresponding promoter regions, with light-responsive elements for OsPSY1 and OsPSY2 and an ABA-response element as well as a coupling element for OsPSY3. The investigation of the gene structures and 5′ untranslated regions revealed that OsPSY1 represents a descendant of an ancient PSY gene present in the common ancestor of monocots and dicots. Since the genomic structures of OsPSY2 and OsPSY3 are comparable, we conclude that they originated from the most recent common ancestor, OsPSY1.
Modulation of Nitrosative Stress byS-Nitrosoglutathione Reductase Is Critical for Thermotolerance and Plant Growth inArabidopsis
Authors: Lee Ung , Wie Chris , Fernandez Bernadette O. , Feelisch Martin , Vierling Elizabeth
Published: March 2008

Nitric oxide (NO) is a key signaling molecule in plants. This analysis of Arabidopsis thaliana HOT5 (sensitive to hot temperatures), which is required for thermotolerance, uncovers a role of NO in thermotolerance and plant development. HOT5 encodes S-nitrosoglutathione reductase (GSNOR), which metabolizes the NO adduct S-nitrosoglutathione. Two hot5 missense alleles and two T-DNA insertion, protein null alleles were characterized. The missense alleles cannot acclimate to heat as dark-grown seedlings but grow normally and can heat-acclimate in the light. The null alleles cannot heat-acclimate as light-grown plants and have other phenotypes, including failure to grow on nutrient plates, increased reproductive shoots, and reduced fertility. The fertility defect of hot5 is due to both reduced stamen elongation and male and female fertilization defects. The hot5 null alleles show increased nitrate and nitroso species levels, and the heat sensitivity of both missense and null alleles is associated with increased NO species. Heat sensitivity is enhanced in wild-type and mutant plants by NO donors, and the heat sensitivity of hot5 mutants can be rescued by an NO scavenger. An NO-overproducing mutant is also defective in thermotolerance. Together, our results expand the importance of GSNOR-regulated NO homeostasis to abiotic stress and plant development.
A MYB Transcription Factor Regulates Very-Long-Chain Fatty Acid Biosynthesis for Activation of the Hypersensitive Cell Death Response inArabidopsis
Authors: Raffaele Sylvain , Vailleau Fabienne , Léger Amandine , Joubès Jérôme , Miersch Otto , Huard Carine , Blée Elisabeth , Mongrand Sébastien , Domergue Frédéric , Roby Dominique
Published: March 2008

Plant immune responses to pathogen attack include the hypersensitive response (HR), a form of programmed cell death occurring at invasion sites. We previously reported on Arabidopsis thaliana MYB30, a transcription factor that acts as a positive regulator of a cell death pathway conditioning the HR. Here, we show by microarray analyses of Arabidopsis plants misexpressing MYB30 that the genes encoding the four enzymes forming the acyl-coA elongase complex are putative MYB30 targets. The acyl-coA elongase complex synthesizes very-long-chain fatty acids (VLCFAs), and the accumulation of extracellular VLCFA-derived metabolites (leaf epidermal wax components) was affected in MYB30 knockout mutant and overexpressing lines. In the same lines, a lipid extraction procedure allowing high recovery of sphingolipids revealed changes in VLCFA contents that were amplified in response to inoculation. Finally, the exacerbated HR phenotype of MYB30-overexpressing lines was altered by the loss of function of the acyl-ACP thioesterase FATB, which causes severe defects in the supply of fatty acids for VLCFA biosynthesis. Based on these findings, we propose a model in which MYB30 modulates HR via VLCFAs by themselves, or VLCFA derivatives, as cell death messengers in plants.
The Leaf Epidermome ofCatharanthus roseusReveals Its Biochemical Specialization
Authors: Murata Jun , Roepke Jonathon , Gordon Heather , De Luca Vincenzo
Published: March 2008

Catharanthus roseus is the sole commercial source of the monoterpenoid indole alkaloids (MIAs), vindoline and catharanthine, components of the commercially important anticancer dimers, vinblastine and vincristine. Carborundum abrasion technique was used to extract leaf epidermis–enriched mRNA, thus sampling the epidermome, or complement, of proteins expressed in the leaf epidermis. Random sequencing of the derived cDNA library established 3655 unique ESTs, composed of 1142 clusters and 2513 singletons. Virtually all known MIA pathway genes were found in this remarkable set of ESTs, while only four known genes were found in the publicly available Catharanthus EST data set. Several novel MIA pathway candidate genes were identified, as demonstrated by the cloning and functional characterization of loganic acid O-methyltransferase involved in secologanin biosynthesis. The pathways for triterpene biosynthesis were also identified, and metabolite analysis showed that oleanane-type triterpenes were localized exclusively to the cuticular wax layer. The pathways for flavonoid and very-long-chain fatty acid biosynthesis were also located in this cell type. The results illuminate the biochemical specialization of Catharanthus leaf epidermis for the production of multiple classes of metabolites. The value and versatility of this EST data set for biochemical and biological analysis of leaf epidermal cells is also discussed.
Data sources for performing citation analysis: an overview
Authors: Neuhaus Christoph , Daniel Hans‐Dieter
Published: March 2008

Purpose

The purpose of this paper is to provide an overview of new citation‐enhanced databases and to identify issues to be considered when they are used as a data source for performing citation analysis.

Design/methodology/approach

The paper reports the limitations of Thomson Scientific's citation indexes and reviews the characteristics of the citation‐enhanced databases Chemical Abstracts, Google Scholar and Scopus.

Findings

The study suggests that citation‐enhanced databases need to be examined carefully, with regard to both their potentialities and their limitations for citation analysis.

Originality/value

The paper presents a valuable overview of new citation‐enhanced databases in the context of research evaluation.
Use of the Universal Decimal Classification
Authors: Slavic Aida
Published: March 2008

Purpose

The purpose of this paper is to present a general overview with up‐to‐date information on the Universal Decimal Classification (UDC) use worldwide.

Design/methodology/approach

The research combined e‐mail interviews with LIS professionals in 208 countries, literature research and information obtained from UDC distributors/publishers (AENOR, BSI, UDC Consortium). The following categorisation of UDC use was offered: A – dominant system; B – used in some kind of libraries only; or C – rarely used.

Findings

The paper finds that, of the 208 countries contacted and researched through the literature in 2004‐2006, the UDC was found to be used in 124 (60 per cent) of these. In 34 (28 per cent) of the countries researched (in Europe, Asia and Africa), UDC is the main classification system used across national information networks. In 45 (36 per cent) of the countries it is used in certain kinds of libraries. In the remaining 45 (36 per cent) of the countries it is used rarely, in only a few libraries or information centres.

Research limitations/implications

It was beyond the scope of this research to provide any information regarding the actual number of institutions using UDC in a given country or to give an estimate of the size and number of document collections organised by it. Although a decline in UDC use since the 1980s was reported from a number of countries, it was not possible to measure this accurately.

Practical implications

The interest shown for using UDC in the organisation of digital collections, information exchange and cross domain and cross collection resource discovery depends on accurate knowledge of its actual usage worldwide. This gives a measure of its global importance and verifies its credentials as an indexing standard. This research, which attempted wider and more systematic coverage than previous surveys, should help clarify the status of UDC and its potential use in the networked environment.

Originality/value

The paper provides up‐to‐date information on the presence of the UDC system across countries and languages.
Author‐rated importance of cited references in biology and psychology publications
Authors: Tang Rong , Safer Martin A.
Published: March 2008

Purpose

The present study aims to investigate how textual features, depth of citation treatment, reasons for citation, and relationships between citers and citees predict author‐rated citation importance.

Design/methodology/approach

A total of 49 biology and 50 psychology authors assessed the importance, reason for citation, and relationship to the cited author for each cited reference in his or her own recently published empirical article. Participants performed their evaluations on individualized web‐based surveys.

Findings

The paper finds that certain textual features, such as citation frequency, citation length, and citation location, as well as author‐stated reasons for citation predicted ratings of importance, but the strength of the relationship often depended on citation features in the article as a whole. The relationship between objective citation features and author‐rated importance also tended to be weaker for self‐citations.

Research limitations/implications

The study sample included authors of relatively long empirical articles with a minimum of 35 cited references. There were relatively few disciplinary differences, which suggests that citation behavior in psychology may be similar to that in natural science disciplines. Future studies should involve authors from other disciplines employing diverse referencing patterns in articles of varying lengths and types.

Originality/value

Findings of the study have enabled a comprehensive, profound level of understanding of citation behaviors of biology and psychology authors. It uncovered a number of unique characteristics in authors' citation evaluations, such as article‐level context effects and rule‐ versus affective‐based judgments. The paper suggests possible implications for developing retrieval algorithms based on automatically predicted importance of cited references.
Students' search process and outcome in Medline in writing an essay for a class on evidence‐based medicine
Authors: Huuskonen Saila , Vakkari Pertti
Published: March 2008

Purpose

The aim of this study is to explore to which extent searching by medical students in Medline produces information items useful for writing an essay measured by precision and relative recall as perceived by the students, the proportion of cited items, and their utilization on four dimensions of the essay writing task evaluated by external assessors. It also aims to study interrelations of search process and outcome.

Design/methodology/approach

The study subjects were 42 third year medical students attending a class on Diagnostic and therapy. Searching in Medline was a part of their assignment of essay writing. The data consist of students' printed logs of Medline searches, students' assessments of the usefulness of the references retrieved, a questionnaire concerning the search process, and evaluation scores of the essays given by the teachers of the class. Pearson correlation coefficients were calculated for answering the research questions.

Findings

The paper finds that precision and relative recall were not associated with evaluation scores in three of the four dimensions assessed. Some of the process variables were associated with precision and with assessment scores in two of the four dimensions assessed. Citing rate was negatively associated with recall. It seems that precision and recall are only weakly, if at all, associated to the use of information in the documents retrieved for writing the essay. Precision and relative recall are not associated to the way information in the retrieved items is used for performing the task. Users evidently look for a sufficient number of documents containing enough information for progressing in their task. Precision and recall are not sufficient measures in evaluating IR systems, but they have to be completed by other measures indicating the impact of the system on users’ task performance.

Originality/value

The paper provides useful information on students' information search process.
ANTAEUS “Do mention the war”
Authors: Joint Nicholas
Published: March 2008

Purpose

This paper aims to explore the relationship between library and information management principles and defence and national security.

Design/methodology/approach

An opinion piece based on viewpoints from speakers at the 2007 American Library Association conference held in Washington DC, and on recent US writings on US foreign and defence policy. Findings – That there is a verifiable relationship between library and information management principles and defence and national security. But the exact nature of this relationship is open to dispute, which therefore presents important challenges in professional ethics to librarians. Research limitations/implications – It is impossible to define the moral parameters of professional ethical issue in the abstract. Reflective and sophisticated analysis of ethical issues in the particular contemporary context is an ongoing requirement of LIS research.

Practical implications

It is important for a fully rounded professional to see the relevance of larger moral, political and social issues to the narrower sphere of their professional practice. Originality/value – This paper gives a starting point for the analysis of information principles in terms of the most recent developments in the international political arena.
MLIS program at Kuwait University
Authors: Rehman Sajjad , Marouf Laila
Published: March 2008

Purpose

This study aims to analyze the perceptions of the graduates of Master in Library and Information Science (MLIS) program at Kuwait University about coursework, faculty, instructional methods, instructional facilities, fieldwork, comprehensive examination, and research component.

Design/methodology/approach

A survey instrument was used for electronic administration. Eighty graduates of the MLIS program of Kuwait University were identified as population of the study. Sixty‐seven alumni (86.3 per cent) participated in the survey.

Findings

Based on the analysis of 61 usable responses, it was found that the faculty and core courses received highest mean scores for satisfaction whereas elective coursework, fieldwork, and comprehensive examinations received the lowest. Qualitative analysis of the participants revealed that the alumni wished broadening the breadth of the elective coursework and fundamental changes in fieldwork and comprehensive examination. Many of them were quite critical of instructional methods and facilities.

Research limitations/implications

Results cannot be generalized to other graduate programs. Yet, these provide procedural guidance and insights about the way these studies of perception can be conducted.

Practical implications

This input can be meaningfully applied in further development of the MLIS program.

Originality/value

It is original research that carries value for the assessment of graduate programs of library and information studies.
Enticing teenagers into the library
Authors: Snowball Clare
Published: March 2008

Purpose

Children and teenagers are the future adult users of libraries, and how they are treated in our libraries, particularly school and public libraries, can cement lifelong memories and habits in these young people. This paper aims to address this issue.

Design/methodology/approach

The following paper is a review of the literature on young people's, particularly teenagers’ use (or lack thereof) of libraries, the importance of library use and methods to encourage library use in young people.

Findings

Despite the findings from some of the literature that teenagers are less likely to visit libraries, there were many services and programmes in libraries that aim to reverse this trend.

Research limitations/implications

Some of the literature is peer‐reviewed, but selected pieces were written by librarians in the field about their interactions with young people in their libraries. Although the latter cannot be generalised to all young people, they are important in providing examples of what occurs in some cases and what might be replicated in other settings.

Originality/value

Encouraging young people to visit and enjoy libraries can be a rewarding experience and is important in creating the next generation of library users.
Why should not they benefit from rare books?
Authors: Torre Meredith E.
Published: March 2008

Purpose

Special collections departments are predominately portrayed or perceived as a place for researchers rather than as a means for enhancing the learning experience for the undergraduate student. The very nature of rare books and manuscripts means that arguments to discourage their heavy use prevail. The purpose of this paper is to address this issue.

Design/methodology/approach

This paper reviews these perceptions, considers why such perceptions continue to thrive, and provides examples in which the image of special collections departments can be refashioned into a more inclusive environment for the undergraduate student.

Findings

There are extraordinary barriers that face the average undergraduate experience with rare books at most academic institutions. Librarians of special collections departments and other primary resource collections can play a fundamental role in making these collections accessible to the undergraduate student.

Originality/value

This paper reexamines the notion that special collections should have limited use due to conservation concerns and demonstrates that using fragile materials may serve as a good opportunity to reflect on the collection's conservational health.
Periodical literature use by the pre‐final and final undergraduate students in Nigerian universities
Authors: Isaac Ajala Olugbenga
Published: March 2008

Purpose

The main objective of this study is to discuss the needs and the information utilization patterns of periodical literature amongst the pre‐final and final year undergraduate students in Nigerian universities. As a result, the study attempts to solve the following problems: What are the information needs of undergraduate students in relation to periodical literature? How do they go about seeking such information needed in periodical literature? How do they make valuable use of the information available to them in such periodical literature? What should the university libraries do to meet the information needs of these students in relation to periodical literature?

Design/methodology/approach

The researcher aimed at studying periodical literature use by the pre‐final and final year undergraduate students in Nigerian universities. It is impossible to sample the entire population hence a cross‐sectional descriptive Survey design was employed as the most suitable because the population under study was fairly large and heterogeneous. A questionnaire was designed to know the attitude, interest and value of the pre‐final and final year undergraduate students. In order to have an accurate assessment, questionnaire was designed and distributed to collect vital information from the undergraduate students. Also, observation and direct oral interviews were also employed to supplement the information provided through the questionnaires collected.

Findings

Findings show that 70 per cent respondents used the library once every week, undergraduate students need and utilize periodical literature materials for their information needs, the general purpose of using periodical literature was mainly for research among others.

Originality/value

Useful in determining the periodical use by students as well as assisting serials librarian in planning.
Changing the way we look at libraries?
Authors: Rooney‐Browne Christine
Published: March 2008

Purpose

The current financial and political climate means that libraries are more accountable to their stakeholders and are under increasing pressure to justify their place and value in an ever‐changing information society. The purpose of this report is to discuss how one local library and information service has adapted to changes in cultural demands and user expectations to deliver a concept that communicates its social value to all of its stakeholders.

Design/methodology/approach

The report combines quantitative and qualitative research techniques to determine the outputs and outcomes of the project and to assess if key objectives have been achieved.

Findings

The results of this evaluation confirm that the Look at Libraries Festival has been embraced by event attendees, staff, participants and the community. The research also illustrates that the demands and expectations of two communities can vary dramatically, posing the question: is it right to judge libraries so heavily on their outputs? The emerging impact of the festival also supports the argument that the local library service can support its parent body to achieve overall community objectives.

Research limitations/implications

The research was conducted during a four week academic placement period within East Renfrewshire Council Library and Information Service. The depth of the research has been challenged by limitations associated with time and resources. Therefore, the findings must be viewed as preliminary and suggestive rather than exhaustive.

Originality/value

The case study reveals an innovative approach by a public library and information service to challenge perceptions, communicate changes in service provision, market public libraries, attract new members and establish an effective brand extension for the service.
New landmarks in Brontë bibliography
Authors: Duckett Bob
Published: March 2008

Purpose

The purpose of this paper is to alert students, scholars and librarians to the many recently published works of reference on the life and works of the Brontë family. The paper aims to present an account of new major reference works, which are transforming the nature of Brontë scholarship, giving an insight into the development of literary studies in a field which has reached maturity and provides a benchmark for studies with other classic authors.

Design/methodology/approach

The paper takes the form of a literature review set against developing scholarship.

Findings

After 150 years of scholarship, Brontë studies have reached a peak of maturity in the areas of biography, bibliography and textual transcription.

Research limitations/implications

The greater reliability of recent texts necessitates a re‐evaluation of biographical and critical studies on the Brontë family. The paper indicates the rigorous standards required in author bibliography.

Practical implications

Librarians need to update their reference collections.

Originality/value

The paper brings together disparate sources to provide a coherent overview.
Market entry decisions of US small and medium‐sized software firms
Authors: Ojala Arto , Tyrväinen Pasi
Published: March 2008

Purpose

The purpose of this paper is to investigate market entry decisions of the US software SMEs by analyzing the impact of the most obvious factors (cultural distance, geographical distance, country risk, and three market size variables) in traditional internationalization theories to target country selection. By investigating the influence of these commonly cited macro‐level factors, this study proposes the best indicator for market entry decisions of the US small and medium‐sized software firms.

Design/methodology/approach

This study uses a quantitative research approach applied to a sample of 100 US small and medium‐sized software firms.

Findings

Empirical findings in this study indicate that vertical (software) market size in a target country is the best single indicator for market entry decision and in themselves explain 63 percent of market entries. Thus, the findings in this study suggest that the vertical market size gives a better explanation for market entry decisions of software SMEs than the earlier widely used variables.

Research implications/limitations

Integrating earlier findings related to firm‐level factors with findings of macro‐level factors will help theory development and will facilitate obtaining a more holistic view of internationalization of knowledge‐intensive SMEs.

Practical implications

Findings in this study imply that managers should take an active role when they develop network relationships for the market entry. If a firm takes a passive role in networking, it might lose market opportunities available in the leading markets and end up in countries where the real market potential is low.

Originality/value

This paper highlights vertical market size, which has been largely ignored in earlier studies, as the most important indicator for international market entry decision.