bluuebunny/crossref_metadata_2025 huggingface dataset:
Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast
Authors: Geiler-Samerotte Kerry A. , Dion Michael F. , Budnik Bogdan A. , Wang Stephanie M. , Hartl Daniel L. , Drummond D. Allan
Published: December 2010

Evolving lineages face a constant intracellular threat: most new coding sequence mutations destabilize the folding of the encoded protein. Misfolded proteins form insoluble aggregates and are hypothesized to be intrinsically cytotoxic. Here, we experimentally isolate a fitness cost caused by toxicity of misfolded proteins. We exclude other costs of protein misfolding, such as loss of functional protein or attenuation of growth-limiting protein synthesis resources, by comparing growth rates of budding yeast expressing folded or misfolded variants of a gratuitous protein, YFP, at equal levels. We quantify a fitness cost that increases with misfolded protein abundance, up to as much as a 3.2% growth rate reduction when misfolded YFP represents less than 0.1% of total cellular protein. Comparable experiments on variants of the yeast gene orotidine-5′-phosphate decarboxylase (
URA3
) produce similar results. Quantitative proteomic measurements reveal that, within the cell, misfolded YFP induces coordinated synthesis of interacting cytosolic chaperone proteins in the absence of a wider stress response, providing evidence for an evolved modular response to misfolded proteins in the cytosol. These results underscore the distinct and evolutionarily relevant molecular threat of protein misfolding, independent of protein function. Assuming that most misfolded proteins impose similar costs, yeast cells express almost all proteins at steady-state levels sufficient to expose their encoding genes to selection against misfolding, lending credibility to the recent suggestion that such selection imposes a global constraint on molecular evolution.
Unitary response of mouse olfactory receptor neurons
Authors: Ben-Chaim Yair , Cheng Melody M. , Yau King-Wai
Published: December 2010

The sense of smell begins with odorant molecules binding to membrane receptors on the cilia of olfactory receptor neurons (ORNs), thereby activating a G protein, G
olf
, and the downstream effector enzyme, an adenylyl cyclase (ACIII). Recently, we have found in amphibian ORNs that an odorant-binding event has a low probability of activating sensory transduction at all; even when successful, the resulting unitary response apparently involves a single active Gα
olf
–ACIII molecular complex. This low amplification is in contrast to rod phototransduction in vision, the best-quantified G-protein signaling pathway, where each photoisomerized rhodopsin molecule is well known to produce substantial amplification by activating many G-protein, and hence effector-enzyme, molecules. We have now carried out similar experiments on mouse ORNs, which offer, additionally, the advantage of genetics. Indeed, we found the same low probability of transduction, based on the unitary olfactory response having a fairly constant amplitude and similar kinetics across different odorants and randomly encountered ORNs. Also, consistent with our picture, the unitary response of Gα
olf
+/−
ORNs was similar to WT in amplitude, although their Gα
olf
-protein expression was only half of normal. Finally, from the action potential firing, we estimated that ≤19 odorant-binding events successfully triggering transduction in a WT mouse ORN will lead to signaling to the brain.
Antiviral CD8+ T cell effector activities in situ are regulated by target cell type
Authors: Hufford Matthew M. , Kim Taeg S. , Sun Jie , Braciale Thomas J.
Published: December 2010

Cytotoxic T lymphocytes (CTLs) play a prominent role in the resolution of viral infections through their capacity both to mediate contact-dependent lysis of infected cells and to release soluble proinflammatory cytokines and chemokines. The factors controlling these antiviral effector activities in vivo at infection sites are ill defined. Using a mouse model of influenza infection, we observed that the expression of CTL effector activity in the infected lungs is dictated by the target cell type encountered. CD45+ lung infiltrating inflammatory mononuclear cells, particularly CD11chi dendritic cells, trigger both CTL cytotoxicity and release of inflammatory mediators, whereas CD45− influenza-infected respiratory epithelial cells stimulate only CTL cytotoxicity. CTL proinflammatory mediator release is modulated by co-stimulatory ligands (CD80 and CD86) expressed by the CD45+ inflammatory cells. These findings suggest novel mechanisms of control of CTL effector activity and have potentially important implications for the control of excess pulmonary inflammation and immunopathology while preserving optimal viral clearance during respiratory virus infections.
Researching and implementing a new tiered pricing model
Authors: RAPPLE Charlie
Published: December 2010

Tiered pricing can help to arrest the revenue decline associated with the transition from print to online subscriptions. This case study reviews the objectives, challenges, project phases, impact, and key lessons of a project to research and implement a new tiered pricing model for a society publisher. We analysed current sales and profiled institutional subscribers to define, model, and refine appropriate price tiers. This led to the introduction of fair and transparent pricing that encourages usage, is manageable for supply chain stakeholders and minimizes the need for custom licences. We then planned and implemented a segmented communications strategy to increase current customer awareness of and support for the new pricing, and identified prospective customers and segments for potential sales growth.
E‐journals, researchers — and the new librarians
Authors: NICHOLAS David , ROWLANDS Ian , WILLIAMS Peter
Published: December 2010

This paper provides the results of a two‐year investigation into the use of e‐journals by the UK research community. Log analysis, questionnaires, interviews, and observation were used to collect the information. The results are presented in a FAQ format to make the key findings accessible. The main findings are that journals have become central to most disciplines, and that the e‐form has become the prime means of access. The results for history suggest that the old scholarly communication mantras (scientists primarily communicate through articles, historians through monographs) are rapidly breaking down. Indeed, all researchers seem addicted to journal content. Research without this resource now seems unthinkable; journals are a researcher's lifeblood. Gateway services, hugely popular in science, are re‐intermediating the broken chain between publisher and reader; they are the new librarians.
Avoiding a Digital Dark Age for data: why publishers should care about digital preservation
Authors: SMIT Eefke , VAN DER HOEVEN Jeffrey , GIARETTA David
Published: December 2010

This paper provides an overview of the needs and threats for digital preservation and summarizes the findings from project PARSE.Insight. This project, co‐funded by the EU, contains one of the first large worldwide surveys about digital preservation including most players of the STM information chain: researchers, libraries, data managers, publishers, and research funders. One of the conclusions is that in the present data deluge, it is extremely important that all players in the information chain work together on proper digital preservation of all research output, to ensure its future usability, understandability, and authenticity. This poses a new role for publishers who can ensure better discoverability and citability via good linking and integration of data and publications.
The ethics of scholarly peer review: a review of the literature
Authors: SOUDER Lawrence
Published: December 2010

This review summarizes the literature of a subset of the published research and commentary on peer review – the ethics of peer review. It attempts to track the various ethical issues that arise among the key participants in peer‐review systems: authors, editors, referees, and readers. These issues include: bias, courtesy, conflict of interest, redundant publication, honesty, transparency, and training. It concludes that debates over such issues as open vs. blind reviews continue unresolved but that new technologies offer some prospects for resolving old issues while they also may create new challenges.
Book Reviews
Authors: THATCHER Sanford G.
Published: December 2010

The Subversive Copy Editor: Advice from Chicago (Or, How to Negotiate Good Relationships with Your Writers, Your Colleagues, and Yourself) Carol Fisher Saller Chicago, University of Chicago Press, 2009, 136pp. ISBN: 9780226734255, £9.00/$10.14
Book Reviews
Authors: SMART Pippa
Published: December 2010

Bookmakers: British Publishing in the Twentieth Century Iain Stevenson London, British Library, 2010, 296pp. ISBN 978‐0‐7123‐0961‐5, £25, hbk
Book Reviews
Authors: SMART Pippa
Published: December 2010

Scholarly Communication in Library and Information Sciences: The Impact of Open Access Journals and e‐Journals on a Changing Scenario Bhaskar Mukherjee Oxford, Chandos Publishing, 2010, 296 pp. ISBN 978‐1‐84334‐626‐5, £49.50 / US$85.00 / E60.00, pbk
Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach
Authors: Xiao Hang , Li Ying , Du Jiulin , Mosig Axel
Published: December 2010

Motivation: Cell tracking is an important method to quantitatively analyze time-lapse microscopy data. While numerous methods and tools exist for tracking cells in 2D time-lapse images, only few and very application-specific tracking tools are available for 3D time-lapse images, which is of high relevance in immunoimaging, in particular for studying the motility of microglia in vivo.

Results: We introduce a novel algorithm for tracking cells in 3D time-lapse microscopy data, based on computing cosegmentations between component trees representing individual time frames using the so-called tree-assignments. For the first time, our method allows to track microglia in three dimensional confocal time-lapse microscopy images. We also evaluate our method on synthetically generated data, demonstrating that our algorithm is robust even in the presence of different types of inhomogeneous background noise.

Availability: Our algorithm is implemented in the ct3d package, which is available under http://www.picb.ac.cn/patterns/Software/ct3d; supplementary videos are available from http://www.picb.ac.cn/patterns/Supplements/ct3d.

Contact:  axel@picb.ac.cn; forestdu@ion.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
A computationally efficient modular optimal discovery procedure
Authors: Woo Sangsoon , Leek Jeffrey T. , Storey John D.
Published: December 2010

Motivation: It is well known that patterns of differential gene expression across biological conditions are often shared by many genes, particularly those within functional groups. Taking advantage of these patterns can lead to increased statistical power and biological clarity when testing for differential expression in a microarray experiment. The optimal discovery procedure (ODP), which maximizes the expected number of true positives for each fixed number of expected false positives, is a framework aimed at this goal. Storey et al. introduced an estimator of the ODP for identifying differentially expressed genes. However, their ODP estimator grows quadratically in computational time with respect to the number of genes. Reducing this computational burden is a key step in making the ODP practical for usage in a variety of high-throughput problems.

Results: Here, we propose a new estimate of the ODP called the modular ODP (mODP). The existing ‘full ODP’ requires that the likelihood function for each gene be evaluated according to the parameter estimates for all genes. The mODP assigns genes to modules according to a Kullback–Leibler distance, and then evaluates the statistic only at the module-averaged parameter estimates. We show that the mODP is relatively insensitive to the choice of the number of modules, but dramatically reduces the computational complexity from quadratic to linear in the number of genes. We compare the full ODP algorithm and mODP on simulated data and gene expression data from a recent study of Morrocan Amazighs. The mODP and full ODP algorithm perform very similarly across a range of comparisons.

Availability: The mODP methodology has been implemented into EDGE, a comprehensive gene expression analysis software package in R, available at http://genomine.org/edge/.

Contact:  jstorey@princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A sub-pathway-based approach for identifying drug response principal network
Authors: Chen Xiujie , Xu Jiankai , Huang Bangqing , Li Jin , Wu Xin , Ma Ling , Jia Xiaodong , Bian Xiusen , Tan Fujian , Liu Lei , Chen Sheng , Li Xia
Published: December 2010

Motivation: The high redundancy of and high degree of cross-talk between biological pathways hint that a sub-pathway may respond more effectively or sensitively than the whole pathway. However, few current pathway enrichment analysis methods account for the sub-pathways or structures of the tested pathways. We present a sub-pathway-based enrichment approach for identifying a drug response principal network, which takes into consideration the quantitative structures of the pathways.

Result: We validated this new approach on a microarray experiment that captures the transcriptional profile of dexamethasone (DEX)-treated human prostate cancer PC3 cells. Compared with GeneTrail and DAVID, our approach is more sensitive to the DEX response pathways. Specifically, not only pathways but also the principal components of sub-pathways and networks related to prostate cancer and DEX response could be identified and verified by literature retrieval.

Contact:  chenxiujie@ems.hrbmu.edu.cn; lixia@hrbmu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure
Authors: Olechnovič Kliment , Margelevičius Mindaugas , Venclovas Česlovas
Published: December 2010

Summary: We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure.

Availability: Voroprot is available for Windows, Linux and Mac OS X operating systems and can be downloaded from http://www.ibt.lt/bioinformatics/voroprot/.

Contact:  venclovas@ibt.lt
PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification
Authors: Yu Guoqiang , Li Huai , Ha Sook , Shih Ie−Ming , Clarke Robert , Hoffman Eric P. , Madhavan Subha , Xuan Jianhua , Wang Yue
Published: December 2010

Summary: Phenotypic Up-regulated Gene Support Vector Machine (PUGSVM) is a cancer Biomedical Informatics Grid (caBIG™) analytical tool for multiclass gene selection and classification. PUGSVM addresses the problem of imbalanced class separability, small sample size and high gene space dimensionality, where multiclass gene markers are defined by the union of one-versus-everyone phenotypic upregulated genes, and used by a well-matched one-versus-rest support vector machine. PUGSVM provides a simple yet more accurate strategy to identify statistically reproducible mechanistic marker genes for characterization of heterogeneous diseases.

Availability:  http://www.cbil.ece.vt.edu/caBIG-PUGSVM.htm.

Contact:  yuewang@vt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Catch-at-age assessment in the face of time-varying selectivity
Authors: Linton Brian C. , Bence James R.
Published: December 2010

Linton, B. C., and Bence, J. R. 2011. Catch-at-age assessment in the face of time-varying selectivity. – ICES Journal of Marine Science, 68: . Age-based fishery selectivity represents the relative vulnerability of specific ages of fish to a fishery, whereby age classes that are highly selected tend to be overrepresented in the catch compared with their relative abundance in the population. Statistical catch-at-age analysis (SCAA) results can be sensitive to misspecification of selectivity, which can occur when changes in selectivity over time are not accounted for properly in the assessment model. Four approaches for modelling time-varying selectivity were evaluated within SCAA using Monte Carlo simulations: double-logistic functions with one, two, and all four of the function parameters varying over time, and age-specific selectivity parameters that all varied over time. None of these estimation approaches outperformed the others always. In addition, methods of model selection were compared to identify good estimation models, i.e. those accurately matching the true fish population. The degree of retrospectivity, the best selection method, was based on a retrospective analysis of errors in model estimates as the data time-series for estimation is sequentially shortened. This selection method performed about as well as knowing the correct selectivity model and led to substantial benefits over misspecifying the selectivity model.
Phytoplankton size structure, distribution, and primary production as the basis for trophic analysis of Caribbean ecosystems
Authors: Forget Marie-Hélène , Platt Trevor , Sathyendranath Shubha , Fanning Paul
Published: December 2010

Forget, M-H., Platt, T., Sathyendranath, S., and Fanning, P. 2011. Phytoplankton size structure, distribution, and primary production as the basis for trophic analysis of Caribbean ecosystems. – ICES Journal of Marine Science, 68: 751–765. An oceanographic survey was conducted in Caribbean waters in April and May 2006 to assess the marine ecosystem in the context of a trophic analysis of the foodweb. Analyses of pigment and absorption data revealed that the phytoplankton community was dominated by pico- and nanophytoplankton, particularly at the deep chlorophyll maximum. Based on cluster analysis of remotely sensed data, three dynamic provinces were defined for the region. A 5-year time-series of sea surface temperature and chlorophyll concentration provided information on the annual cycle of these properties. To implement the computation of primary production on a synoptic scale, parameters characterizing the biomass profiles and photosynthesis–irradiance relationships were assigned using four protocols: two regional approaches, a regression with surface chlorophyll, and the nearest-neighbour method (NNM), which has the advantage of assigning parameters on a pixel-by-pixel basis. Monthly images of primary production were computed over an annual cycle using MODIS chlorophyll a concentration. The NNM and the use of dynamic provinces emerged as the methods of choice for parameter assignment. Finally, a new approach from remotely sensed data was developed to estimate production-to-carbon ratios, a key input to Ecopath models. The results contribute to ecotrophic analysis of the Lesser Antilles Pelagic Ecosystem project.
Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil
Authors: Männistö Minna K. , Rawat Suman , Starovoytov Valentin , Häggblom Max M.
Published: December 2010

Two aerobic bacterial strains, designated SP1PR4T and SP1PR5, were isolated from tundra soil samples collected from Saana fjeld, North-western Finland (69° 03′ N 20° 50′ E). Cells of both strains were Gram-negative, non-motile rods. Phylogenetic analysis indicated that the strains belong to the genus Terriglobus in subdivision 1 of the phylum Acidobacteria. Strains SP1PR4T and SP1PR5 shared identical BOX and ERIC fingerprints and 99.7 % 16S rRNA gene similarity indicating that, together with their identical physiological features, these strains are members of the same species. The 16S rRNA gene sequence similarity of SP1PR4T and SP1PR5 with Terriglobus roseus DSM 18391T was 97.1 %. A low DNA–DNA hybridization value (<20 %) and rpoB gene sequence similarity (83.6 %) with T. roseus DSM 18391T indicated that the tundra soil isolates represent novel members of the genus Terriglobus. Strains SP1PR4T and SP1PR5 grew at pH 4.5–7.5 and 4–30 °C. Sugars were the preferred growth substrates. The major cellular fatty acids were iso-C15 : 0, C16 : 1ω7c, iso-C13 : 0 and C16 : 0. The DNA G+C content of strain SP1PR4T was 57.3 mol%. Based on phylogenetic, chemotaxonomic and physiological analyses, the name Terriglobus saanensis sp. nov. is proposed to accommodate the two strains; the type strain is SP1PR4T ( = DSM 23119T  = ATCC BAA-1853T).
Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi
Authors: Moretti Chiaraluce , Hosni Taha , Vandemeulebroecke Katrien , Brady Carrie , De Vos Paul , Buonaurio Roberto , Cleenwerck Ilse
Published: December 2010

Three endophytic bacterial isolates were obtained in Italy from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position for these isolates in the genera Erwinia or Pantoea, and revealed two other strains with highly similar 16S rRNA gene sequences (>99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial atpD, gyrB, infB and rpoB gene sequences indicated that the strains constituted a single novel species in the genus Erwinia. The strains showed general phenotypic characteristics typical of the genus Erwinia and whole genome DNA–DNA hybridization data confirmed that they represented a single novel species of the genus Erwinia. The strains showed DNA G+C contents ranging from 54.7 to 54.9 mol%. They could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, l-rhamnose and d-arabitol, but not glycerol, inositol or d-sorbitol. The name Erwinia oleae sp. nov. (type strain DAPP-PG 531T = LMG 25322T = DSM 23398T) is proposed for this novel taxon.
Reclassification of Aurantimonas altamirensis (Jurado et al. 2006), Aurantimonas ureilytica (Weon et al. 2007) and Aurantimonas frigidaquae (Kim et al. 2008) as members of a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov., Aureimonas ureilytica comb. nov. and Aureimonas frigidaquae comb. nov., and emended descriptions of the genera Aurantimonas and Fulvimarina
Authors: Rathsack K. , Reitner J. , Stackebrandt E. , Tindall B. J.
Published: December 2010

Members of the genera Aurantimonas and Fulvimarina have largely been described on the basis of 16S rRNA gene sequence analyses, biochemical tests and limited chemotaxonomic data. Examination of the polar lipid compositions of members of these two genera indicated that although the patterns were similar with regards the phospholipid and amino lipid compositions, there were clear differences in the presence or absence of the glycolipid sulfoquinovosyldiacylglycerol (SQDG). This glycolipid was absent in members of the species Aurantimonas coralicida and Fulvimarina pelagi but was present in Aurantimonas altamirensis, Aurantimonas ureilytica and Aurantimonas frigidaquae. These results are also consistent with the 16S rRNA sequence-based grouping. We therefore propose that the genus Aurantimonas be divided further to reflect this additional information. Thus, it is recommended that Aurantimonas altamirensis, Aurantimonas ureilytica and Aurantimonas frigidaquae are transferred to a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov. (type strain S21BT  = CECT 7138T  = CIP 109525T  = KCTC 22106T  = LMG 23375T  = DSM 21988T), Aureimonas ureilytica comb. nov. (type strain 5715S-12T  = KACC 11607T  = DSM 18598T  = CIP 109815T) and Aureimonas frigidaquae comb. nov. (type strain CW5T  = KCTC 12893T  = JCM 14755T  = DSM 21987T). The type species of the new genus is Aureimonas altamirensis. Additionally, emended descriptions of the genera Aurantimonas and Fulvimarina are provided.
Flavobacterium phragmitis sp. nov., an endophyte of reed (Phragmites australis)
Authors: Liu Min , Li Yan Hong , Liu Yang , Zhu Jing Nan , Liu Qun Fang , Liu Yin , Gu Jin Gang , Zhang Xiao Xia , Li Chun Li
Published: December 2010

A Gram-staining-negative bacterium, designated strain BLN2T, was isolated from within the roots of reeds (Phragmites australis) in Beijing Cuihu Wetland (China) and characterized using a polyphasic taxonomic approach. The cells were yellow-pigmented, rod-shaped, strictly aerobic and devoid of flagella, but showed gliding motility. Strain BLN2T produced yellow, translucent, circular and convex colonies, with optimal growth at 30 °C and pH 7.0. The major respiratory quinone was menaquinone 6 (MK-6) and the predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 3-OH, C16 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The G+C content of the genomic DNA was 34.8 mol%. The 16S rRNA gene sequence analysis showed that strain BLN2T belonged to the genus Flavobacterium and was most closely related to Flavobacterium anhuiense CGMCC 1.6859T (97.0 % sequence similarity). The DNA–DNA relatedness between strain BLN2T and F. anhuiense CGMCC 1.6859T was 25.7 %. Based on the phenotypic data and phylogenetic inference presented, it is concluded that strain BLN2T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium phragmitis sp. nov. is proposed. The type strain is BLN2T ( = DSM 23314T = CGMCC 1.10370T).
Nonomuraea maritima sp. nov., isolated from coastal sediment
Authors: Xi Lijun , Zhang Limin , Ruan Jisheng , Huang Ying
Published: December 2010

A novel actinomycete, strain FXJ7.203T, was isolated from a coastal sediment sample collected in Bohai Bay, China. In 16S rRNA gene sequence analyses, strain FXJ7.203T always formed a unique monophyletic line within the genus Nonomuraea and was most closely related to Nonomuraea turkmeniaca (97.9 %), Nonomuraea candida (97.8 %), Nonomuraea helvata (97.7 %) and Nonomuraea rubra (97.5 %). Morphological and chemotaxonomic characteristics supported the allocation of the strain to the genus Nonomuraea. The polar lipid profile showed that its phospholipid type was PIV. The major fatty acids were iso-C16 : 0, C17 : 1ω6c, iso-C16 : 1 G, 10-methyl C17 : 0 and iso-C15 : 0. The major menaquinone was MK-9(H4) with minor amounts of MK-9(H2), MK-9(H0) and MK-9(H6). The results of physiological and biochemical tests allowed differentiation of strain FXJ7.203T from closely related species. Based on the genotypic and phenotypic data, strain FXJ7.203T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea maritima sp. nov. is proposed, with strain FXJ7.203T ( = CGMCC 4.5681T  = NBRC 106687T) as the type strain.
Flavobacterium chungbukense sp. nov., isolated from soil
Authors: Lim Chae-Sung , Oh Yong-Sik , Lee Jae-Kwan , Park A-Rum , Yoo Jae-Soo , Rhee Sung-Keun , Roh Dong-Hyun
Published: December 2010

A yellow-pigmented, Gram-staining-negative, non-motile, strictly aerobic and rod-shaped bacterium, designated CS100T, was isolated from soil in Chungbuk, Korea. Phylogenetic analysis and comparative studies based on the 16S rRNA gene sequence showed that strain CS100T belonged to the genus Flavobacterium in the family Flavobacteriaceae. Strain CS100T showed the highest sequence similarities to Flavobacterium glaciei JCM 13953T (97.6 %) and Flavobacterium johnsoniae KACC 11410T (97.1 %). Sequence similarity to other members of the genus Flavobacterium was 91.5–97.0 %. Growth occurred at 4–30 °C, at pH 5.0–9.0 and in the presence of 0–2 % (w/v) NaCl. Flexirubin-type pigments were produced. Menaquinone-6 (MK-6) was the major respiratory quinone and the major fatty acids were iso-C15 : 0 (17.3 %), summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c, 15.5 %) and C16 : 0 (11.8 %). The DNA G+C content was 36.4 mol%. Strain CS100T hydrolysed skimmed milk and gelatin, but not chitin or pectin, and showed oxidase and catalase activities. DNA–DNA relatedness was 3.0 % with F. glaciei JCM 13953T and 11.5 % with F. johnsoniae KACC 11410T. On the basis of the evidence from this study, strain CS100T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium chungbukense sp. nov. is proposed. The type strain is CS100T ( = KACC 15048T = JCM 17386T).
Luteimonas lutimaris sp. nov., isolated from a tidal flat
Authors: Park Youn-Je , Park Moon Su , Lee Seung Hyeon , Park Woojun , Lee Kangseok , Jeon Che Ok
Published: December 2010

A Gram-staining-negative, strictly aerobic bacterium, designated strain G3T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were moderately halotolerant and non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain G3T was observed between 15 and 40 °C (optimum 30 °C) and between pH 5.5 and 9.0 (optimum pH 6.5–7.5). Strain G3T contained Q-8 as the predominant lipoquinone and iso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0 and iso-C11 : 0 as the major fatty acids. The G+C content of the genomic DNA was 69.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain G3T formed a tight phylogenetic lineage with Luteimonas mephitis B1953/27.1T within the genus Luteimonas and was most closely related to L. mephitis B1953/27.1T with 98.0 % 16S rRNA gene sequence similarity. The DNA–DNA relatedness between strain G3T and L. mephitis B1953/27.1T was 35.2±3.3 %. On the basis of chemotaxonomic data and molecular properties, strain G3T represents a novel species of the genus Luteimonas, for which the name Luteimonas lutimaris sp. nov. is proposed. The type strain is G3T ( = KACC 14929T = JCM 16916T).
Coordinated Activation of Cellulose and Repression of Lignin Biosynthesis Pathways in Rice
Authors: Ambavaram Madana M.R. , Krishnan Arjun , Trijatmiko Kurniawan R. , Pereira Andy
Published: December 2010

Cellulose from plant biomass is the largest renewable energy resource of carbon fixed from the atmosphere, which can be converted into fermentable sugars for production into ethanol. However, the cellulose present as lignocellulosic biomass is embedded in a hemicellulose and lignin matrix from which it needs to be extracted for efficient processing. Here, we show that expression of an Arabidopsis (Arabidopsis thaliana) transcription factor, SHINE (SHN), in rice (Oryza sativa), a model for the grasses, causes a 34% increase in cellulose and a 45% reduction in lignin content. The rice AtSHN lines also exhibit an altered lignin composition correlated with improved digestibility, with no compromise in plant strength and performance. Using a detailed systems-level analysis of global gene expression in rice, we reveal the SHN regulatory network coordinating down-regulation of lignin biosynthesis and up-regulation of cellulose and other cell wall biosynthesis pathway genes. The results thus support the development of nonfood crops and crop wastes with increased cellulose and low lignin with good agronomic performance that could improve the economic viability of lignocellulosic crop utilization for biofuels.
The campus‐wide laptop loan service and the library's role
Authors: Gu Fang
Published: December 2010

Purpose

This paper aims to present a successful partnership between the library and other campus units of California State University Sacramento in the program of campus‐wide laptop loan service. As an integral part of university resources, the library staff and systems play an exceptional role in collaborating with other university units in the campus‐wide program.

Design/methodology/approach

Three campus units worked together to create a model of support in innovation, cooperation and sharing of the campus resources, technology and expertise. Introducing the establishment of the campus‐wide loan service program and sharing service feedback retrieved from multiple service units in the project contributed to the success of this new program in the campus resource‐sharing practice.

Findings

Collaboration, cooperation, and teamwork are fundamental in sharing campus resources, and creating staffing synergies and delivering an ever‐increasing range of university services, especially in an environment of budget constraints and economic difficulties.

Originality/value

There are many academic libraries now providing laptop loan service, but campus‐wide laptop loan service needs more collaboration, cooperation and communication for the program crew to embrace differences in serving a common‐interest group.
Strategic repositioning in a dynamic environment
Authors: Chan Diana L.H. , Soong Samson C.
Published: December 2010

Purpose

The main purpose of this paper is to discuss the strategic repositioning of an academic library using the dynamic capability framework.

Design/methodology/approach

The discussion is based on the re‐organizational process of the Hong Kong University of Science and Technology Library. Three stages are focused, illustrating how the library managed to be dynamically capable, including: sensing the environmental impacts; realigning and reconfiguring its resources; and implementing effective strategies to respond to these challenges.

Findings

The library adopted a multitude of channels and media in sensing environmental challenges. By going through a strategic reorganization, the library has realigned and redeployed its staff resources to better prepare for incoming changes. The reformed organization moved ahead with renewed culture and values, including better internal communication, team spirit, collective learning mechanisms, and effective user communication.

Research limitations/implications

Reorganization is complex and can be highly stressful. Participative culture and effective communication seem to be successful mechanisms.

Practical implications

Cross‐training on work procedures and routines in other units provided organizational learning mechanisms. This collective learning broadened staff's work knowledge, enlightened their understanding of complex processes, fostered good team spirit, and improved overall effectiveness, as more staff become aware of the overall performance implications of their actions.

Originality/value

The paper shares various reorganization concerns and how they were handled. The benefits of a large‐scale cross‐training program are outlined.
Singing in harmony: statistical benchmarking for academic libraries
Authors: Jilovsky Cathie
Published: December 2010

Purpose

This paper aims to describe the design and implementation of a pilot project for the benchmarking of library statistics for Asian academic libraries.

Design/methodology/approach

The project was facilitated through the development, set‐up and management of an online statistics service for a group of 22 academic libraries in Hong Kong, Malaysia, Singapore and Thailand. CAVAL, an Australian library consortium, managed the project with sponsorship provided by the iGroup, Asia. The objectives were to develop and provide an online statistics web site, to improve the collection processes for the individual libraries and to develop a sustainable service for statistical benchmarking.

Findings

The pilot project provided an opportunity for libraries in the region to participate in the creation and usage of a shared statistical database. At this point in time the utility and value of cumulative statistical collections are not generally recognized in Asian libraries. Hence, participation in the project was an opportunity for library staff to gain some experience with the practicalities, and to raise their awareness of the need for a critical mass of centralized data in order to benchmark.

Practical implications

CAVAL will maintain the Asian Online Statistics web site into the future. Some of the participating libraries are keen to continue to contribute data and to grow the database. However, for this to happen further funding will be required. Discussions are ongoing as to how this can be achieved.

Originality/value

This project was the first opportunity for libraries in this region to gain experience with contributing to and benchmarking with a shared statistical collection.
From library stacks to library‐in‐a‐pocket: will users be around?
Authors: Cheong Choy Fatt
Published: December 2010

Purpose

As libraries move their focus from print collections to digital resources residing in the “cloud”, the library‐user relationship has also changed dramatically. Power has clearly shifted from the library to the user and the dependence relationship has been inverted. The library‐user relationship is fundamental and defines what libraries are, and therefore their future. It is therefore important to think about how to ensure that users continue to use and value libraries. The purpose of this paper is to discuss the changing relationship between libraries and their users and to suggest critical factors to consider when designing and planning library services in order to sustain a viable library‐user relationship.

Design/methodology/approach

The paper sets the context for discussing the importance of maintaining high levels of library use by considering key changes in the information environment and the behavior of users. It is argued that the abundant choices available to information users today cause them to make usage decisions that are not based only on the usefulness and quality of information resources and services, but more on expediency and other factors.

Findings

It is not sufficient to provide useful, high quality and innovative library resources and services. The acid test for their success is whether they will be used frequently. Four factors are suggested – convenience, attention, awareness, and perception of value, that are likely to influence future use of libraries.

Originality/value

The paper serves as a reminder for librarians to pay attention to the common sense factors when designing, planning, implementing and reviewing library facilities, resources and services.
Bibliobabble?
Authors: Storey Colin
Published: December 2010

Purpose

The purpose of this paper is to address the dangers for a highly trained group of professionals – academic librarians – in responding to the challenge of divesting their libraries of a very large amount of printed material.

Design/methodology/approach

The approach takes the form of a general view of the current state‐of‐play in library managementvis‐à‐visthe e‐revolution, in terms of the corresponding preservation of printed materials.

Findings

Traditionally, the majority stock of any library, rarely used printed books and journals seem to have become a liability and a burden in this web‐spun, e‐raddled world. Academic librarians are becoming active participants in the rush to achieve a “print→less” heaven. For the first time in history on such a scale and in any period of war or peace, the next 20 years could witness a huge and deliberate global dispersal and even destruction of a substantial portion of the printed word in university, college and research libraries. ThisFahrenheit 451‐equivalent event would be carefully planned not by ruthless despots and capricious censors riding roughshod over the bodies of librarians to re‐write historical records, but by … the librarians themselves. This is not just “bibliobabble” – defined here as the reactionary ravings of the bibliophile against a tidal wave of e‐books and digital content. Given librarians' innate professional ability for organized thoroughness, a series of small local projects, largely unremarked in the wider world, would be very speedily executed, leading to global and possibly uncoordinated weeding. This sustained dispersal or destruction of printed material from the protective walls of universities and colleges, without the usual finesse or adequate time or resources, will re‐classify “ordinary” works into titles of “relative” or even “absolute” rarity worldwide. Academic librarians will have created a new profession for themselves – “rare book engineers” – by massively reducing the number of copies held in the world's libraries and relying on private book collectors (if they still exist in 2060) to acquire any of the millions of discarded titles and preserve them for posterity.

Practical implications

Librarians need to consider carefully how and where lesser‐used printed materials will be disposed of and sent.

Originality/value

Using practical examples from many years of experience in librarianship, the author states some strong personal opinions on this matter.
Library 2.0 or Library III: returning to leadership
Authors: Nesta Frederick , Mi Jia
Published: December 2010

Purpose

This paper aims to present a critical review of “Web 2.0” and “Library 2.0” applications and proposal of a redirection of resources towards semantic web developments.

Design/methodology/approach

This paper is based on a historical review of library development and new technology.

Findings

The paper finds that acceptance by the public of “Library 2.0” applications has been low and that social networking tools do not contribute to the core mission of libraries.

Originality/value

The paper proposes that the concept of a second era of libarianship and the term “Library II” should apply to the revolution in library services that occurred with the development of the MARC format in the 1960s and that librarians should be looking towards “Library III” by developing new linkages with semantic web tools.
Collaboration and co‐operation in Asian library resource collections
Authors: Hall Michelle
Published: December 2010

Purpose

This paper aims to discuss how collaboration between institutions, especially smaller collections, can result in increased access to materials and specialist staff for researchers and students.

Design/methodology/approach

ALIM (Asian Libraries in Melbourne, consisting of the University of Melbourne and Monash University) has already undertaken a number of collaborative projects. Several of these projects are introduced and the most recent example of ALIM collaboration is discussed. In total, 22 university libraries worldwide were surveyed on their respective Asian language collections, staffing levels, budget and holdings. ALIM libraries – both singly and together – were compared with the institutions surveyed.

Findings

Preliminary findings suggest that collaboration helps smaller collections to assist their primary customer base and supports the achievement of greater outcomes than would be the case if each operated independently.

Research limitations/implications

Thus far, only a small sample has been analysed. Deeper follow‐up analysis is planned for late 2010.

Practical implications

The study demonstrates that staff at smaller, specialized libraries benefit from the opportunity to work collaboratively, share their expertise both locally and internationally, and expand their professional networks.

Originality/value

This paper provides possible solutions to managers of specialized libraries who are facing budget cuts and staff shortages. By collaborating with their counterparts in local institutions, individual librarians expand their networks and the breadth of assistance that can be offered to researchers.
Organisational quality and organisational change
Authors: Smith Ian
Published: December 2010

Purpose

Which comes first – quality or change? Managing change is inherent in organisational quality enhancement. Managing organisational change and managing organisational quality go hand‐in‐hand. This paper seeks to look into quality enhancement initiatives to achieve organisational fitness for purpose.

Design/methodology/approach

This discussion focuses first on organisational quality – what quality means, why it is important and the means for achieving quality. The focus then shifts to effective management of organisational change including the nature of change and the high failure rate of change initiatives. Many models, approaches and prescriptions for understanding, and effectively managing, change are available. Two are discussed here: Kotter's eight‐step model of change and Doppelt's seven‐point “wheel of change”. Commonalities and differences of the two approaches are examined and pointers to “green” and “red” lights for change managers are highlighted. A large‐scale organisational reform program at La Trobe University (Australia) provides a case study of complex change in progress. Kotter and Doppelt's frameworks are used to reflect on aspects of that organisation's experience of working with change.

Findings

The discussion concludes by returning to the theme expressed in the title of this paper – quality and change go hand‐in‐hand. Libraries and librarians operating in an environment of rapid and complex change should add to their managerial “toolkits” an understanding of the intersecting issues of organisational quality and organisational change, and a proactive approach to managing both.

Originality/value

Managers and leaders seeking to make change and achieve organisational quality may be well served by keeping these basic green and red lights as markers and check points along the path to reaching change and/or quality objectives.
The use of pneumatic artificial muscles in robot construction
Authors: Palko Anton , Smrček Juraj
Published: December 2010

Purpose

Recent requirements for drive systems in robotic technology, mainly for their performance, performance and weight ratio, compactness with minimal internal structure and with the integration of main functional parts, lead to intensive application of new, non‐traditional solutions. One of the possible approaches to a non‐traditional solution of drive systems in robotic technology is the application of pneumatic artificial muscle (PAM). The purpose of this paper is to review the designs and applications of the under‐pressure artificial muscle (UPAM) and the creation of non‐standard modules for robotic technology based on PAM.

Design/methodology/approach

Certain part of the disadvantages of an over‐pressure PAM can be solved by the use of an UPAM. As a performance output, UPAM principle guarantees linear movement along the axis with relevant traction force. This UPAM demonstration is evaluated as the drive in mechanic constructions.

Findings

Theoretical calculations, which have been performed, as well as experimental tests and evaluations of the model of this muscle have confirmed an agreement with theoretical relationships valid for PAM generally. The module TMPAM with lengthening action element is principally based on the change of input pressure energy, shape and volume change of action element into output mechanical (power, kinetic) energy. The analysis of the results of measurements (set of measurements, four samples of action element) of the given relationships allows to say that the tractive power F and the lift grow with the change of geometric arrangement of the action element in the box of the driving unit. The output parameters of the TMPAM can be regulated by the number of action elements integrated in the unit (creating two‐element and more‐elemnet parallel sets).

Practical implications

The UPAM maintains all advantages of the principle and recent constructions of the PAM, as well as lightness and compactness of the design. The results confirm that this construction principle of the translation modules is suitable mainly for small lifts, lower load and movements, where even, soft motion is required.

Originality/value

On the basis of author's own solutions of the underpressure artificial muscle (UPAM, original patent) and non‐traditional translation module (TMPAM, original design), the paper evaluates and generalizes the findings obtained from the use of PAM in robot construction.