bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast and sensitive mapping of bisulfite-treated sequencing data
Authors: Otto Christian , Stadler Peter F. , Hoffmann Steve
Published: May 2012

Motivation: Cytosine DNA methylation is one of the major epigenetic modifications and influences gene expression, developmental processes, X-chromosome inactivation, and genomic imprinting. Aberrant methylation is furthermore known to be associated with several diseases including cancer. The gold standard to determine DNA methylation on genome-wide scales is ‘bisulfite sequencing’: DNA fragments are treated with sodium bisulfite resulting in the conversion of unmethylated cytosines into uracils, whereas methylated cytosines remain unchanged. The resulting sequencing reads thus exhibit asymmetric bisulfite-related mismatches and suffer from an effective reduction of the alphabet size in the unmethylated regions, rendering the mapping of bisulfite sequencing reads computationally much more demanding. As a consequence, currently available read mapping software often fails to achieve high sensitivity and in many cases requires unrealistic computational resources to cope with large real-life datasets.

Results: In this study, we present a seed-based approach based on enhanced suffix arrays in conjunction with Myers bit-vector algorithm to efficiently extend seeds to optimal semi-global alignments while allowing for bisulfite-related substitutions. It outperforms most current approaches in terms of sensitivity and performs time-competitive in mapping hundreds of millions of sequencing reads to vertebrate genomes.

Availability: The software segemehl is freely available at http://www.bioinf.uni-leipzig.de/Software/segemehl.

Contact: E-mail: steve@bioinf.uni-leipzig.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Software support for SBGN maps: SBGN-ML and LibSBGN
Authors: van Iersel Martijn P. , Villéger Alice C. , Czauderna Tobias , Boyd Sarah E. , Bergmann Frank T. , Luna Augustin , Demir Emek , Sorokin Anatoly , Dogrusoz Ugur , Matsuoka Yukiko , Funahashi Akira , Aladjem Mirit I. , Mi Huaiyu , Moodie Stuart L. , Kitano Hiroaki , Le Novère Nicolas , Schreiber Falk
Published: May 2012

Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.

Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net.

Contact:  sbgn-libsbgn@lists.sourceforge.net
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
Authors: Saunders Christopher T. , Wong Wendy S. W. , Swamy Sajani , Becq Jennifer , Murray Lisa J. , Cheetham R. Keira
Published: May 2012

Motivation: Whole genome and exome sequencing of matched tumor–normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity.

Results: We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor–normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests.

Availability: The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/.

Contact:  csaunders@illumina.com

Supplementary information:  Supplementary data are available at Bioinformatics online
Exhaustive database searching for amino acid mutations in proteomes
Authors: Hyatt Doug , Pan Chongle
Published: May 2012

Motivation: Amino acid mutations in proteins can be found by searching tandem mass spectra acquired in shotgun proteomics experiments against protein sequences predicted from genomes. Traditionally, unconstrained searches for amino acid mutations have been accomplished by using a sequence tagging approach that combines de novo sequencing with database searching. However, this approach is limited by the performance of de novo sequencing.

Results: The Sipros algorithm v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spectra by exhaustively enumerating all single non-isobaric mutations for every residue in a protein database. The performance of Sipros for amino acid mutation identification exceeded that of an established sequence tagging algorithm, Inspect, based on benchmarking results from a Rhodopseudomonas palustris proteomics dataset. To demonstrate the viability of the algorithm for meta-proteomics, Sipros was used to identify amino acid mutations in a natural microbial community in acid mine drainage.

Availability: The Sipros algorithm is freely available at\newline http://code.google.com/p/sipros.

Contact:  panc@ornl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online
iFad: an integrative factor analysis model for drug-pathway association inference†
Authors: Ma Haisu , Zhao Hongyu
Published: May 2012

Motivation: Pathway-based drug discovery considers the therapeutic effects of compounds in the global physiological environment. This approach has been gaining popularity in recent years because the target pathways and mechanism of action for many compounds are still unknown, and there are also some unexpected off-target effects. Therefore, the inference of drug-pathway associations is a crucial step to fully realize the potential of system-based pharmacological research. Transcriptome data offer valuable information on drug-pathway targets because the pathway activities may be reflected through gene expression levels. Hence, it is of great interest to jointly analyze the drug sensitivity and gene expression data from the same set of samples to investigate the gene-pathway–drug-pathway associations.

Results: We have developed iFad, a Bayesian sparse factor analysis model to jointly analyze the paired gene expression and drug sensitivity datasets measured across the same panel of samples. The model enables direct incorporation of prior knowledge regarding gene-pathway and/or drug-pathway associations to aid the discovery of new association relationships. We use a collapsed Gibbs sampling algorithm for inference. Satisfactory performance of the proposed model was found for both simulated datasets and real data collected on the NCI-60 cell lines. Our results suggest that iFad is a promising approach for the identification of drug targets. This model also provides a general statistical framework for pathway-based integrative analysis of other types of -omics data.

Availability: The R package ‘iFad’ and real NCI-60 dataset used are available at http://bioinformatics.med.yale.edu/group/.

Contact:  hongyu.zhao@yale.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
SRMA: an R package for resequencing array data analysis
Authors: Zhang Nianxiang , Xu Yan , O'Hely Martin , Speed Terence P. , Scharfe Curt , Wang Wenyi
Published: May 2012

Summary: Sequencing by hybridization to oligonucleotides has evolved into an inexpensive, reliable and fast technology for targeted sequencing. Hundreds of human genes can now be sequenced within a day using a single hybridization to a resequencing microarray. However, several issues inherent to these arrays (e.g. cross-hybridization, variable probe/target affinity) cause sequencing errors and have prevented more widespread applications. We developed an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multi-array analysis (SRMA), for rare variant detection with high sensitivity (false negative rate, FNR 5%) and accuracy (false positive rate, FPR 1×10−5). The SRMA package consists of five modules for quality control, data normalization, single array analysis, multi-array analysis and output analysis. The entire workflow is efficient and identifies rare DNA single nucleotide variations and structural changes such as gene deletions with high accuracy and sensitivity.

Availability:  http://cran.r-project.org/, http://odin.mdacc.tmc.edu/~wwang7/SRMAIndex.html

Contact:  wwang7@mdanderson.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Spatio-temporal overlap of hatching in Norwegian spring-spawning herring and the spring phytoplankton bloom at available spawning substrata
Authors: Vikebø Frode B. , Korosov Anton , Stenevik Erling Kåre , Husebø Åse , Slotte Aril
Published: May 2012

Vikebø, F. B., Korosov, A., Stenevik, E. K., Husebø, Å., and Slotte, A. 2012. Spatio-temporal overlap of hatching in Norwegian spring-spawning herring and the spring phytoplankton bloom at available spawning substrata. – ICES Journal of Marine Science, 69: . Analyses of bottom substrata demonstrated that a potential spawning area of 13 490 nautical miles2 is available for Norwegian spring-spawning (NSS) herring on the Norwegian shelf between 59 and 71°N. However, the availability of suitable substrata differed significantly on a latitudinal scale; 60% of the available spawning area was north of 67°N. However, the spatial distribution of larvae indicated that the bulk of the adult population wintering off northern Norway in the period 1998–2007 migrated farther south and upstream to spawn. This suggests benefits attributable to extra costs accompanying the spawning migration. To test whether southern spawning is beneficial with regard to overlap between herring larvae and their prey, remotely sensed chlorophyll a data from SeaWiFS were used as a proxy for the onset of phytoplankton bloom (OSB) in discrete bins along the Norwegian coast and linked to interannual variation in the observed average timing of larval hatching during the years 1998–2007. There was a delay in OSB with increasing latitude of 37 d within the spawning habitat of NSS herring. Overlap between larval hatching and OSB was clearly highest in the south, suggesting that match with prey availability may be an important factor in the selection of spawning grounds by NSS herring.
Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the

Alphaproteobacteria
Authors: Bazylinski Dennis A. , Williams Timothy J. , Lefèvre Christopher T. , Berg Ryan J. , Zhang Chuanlun L. , Bowser Samuel S. , Dean Annette J. , Beveridge Terrence J.
Published: May 2012

Magnetotactic bacteria are a morphologically, metabolically and phylogenetically disparate array of bacteria united by the ability to biomineralize membrane-encased, single-magnetic-domain mineral crystals (magnetosomes) that cause the cell to orientate along the Earth’s geomagnetic field. The most commonly observed type of magnetotactic bacteria is the ubiquitous magnetotactic cocci, which comprise their own phylogenetic group. Strain MC-1T, a member of this group, was isolated from water collected from the oxic–anoxic interface of the Pettaquamscutt Estuary in Rhode Island, USA, and cultivated in axenic culture. Cells of strain MC-1T are roughly spherical, with two sheathed bundles of flagella at a single pole (bilophotrichous). Strain MC-1T uses polar magnetotaxis, and has a single chain of magnetite crystals per cell. Cells grow chemolithoautotrophically with thiosulfate or sulfide as the electron donors, and chemo-organoheterotrophically on acetate. During autotrophic growth, strain MC-1T relies on the reductive tricarboxylic acid cycle for CO2 fixation. The DNA G+C content is 54.2 mol%. The new genus and species Magnetococcus marinus gen. nov., sp. nov. are proposed to accommodate strain MC-1T ( = ATCC BAA-1437T  = JCM 17883T), which is nominated as the type strain of Magnetococcus marinus. A new order (Magnetococcales ord. nov.) and family (Magnetococcaceae fam. nov.) are proposed for the reception of Magnetococcus and related magnetotactic cocci, which are provisionally included in the

Alphaproteobacteria

as the most basal known lineage of this class.
Comamonas guangdongensis sp. nov., isolated from subterranean forest sediment, and emended description of the genus

Comamonas
Authors: Zhang Jun , Wang Yueqiang , Zhou Shungui , Wu Chunyuan , He Jian , Li Fangbai
Published: May 2012

A facultatively anaerobic bacterium, strain CY01T, isolated from subterranean forest sediment collected from Guangdong Province, China, was investigated using a polyphasic taxonomic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CY01T showed highest sequence similarities to

Comamonas thiooxydans

S23T (98.0 %),

Comamonas testosteroni

JCM 5832T (97.9 %),

Comamonas koreensis

KCTC 12005T (97.7 %) and

Comamonas odontotermitis

LMG 23579T (97.0 %). The major respiratory quinone was ubiquinone-8. The major cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain CY01T was clearly distinguishable from all recognized species of the genus

Comamonas

and should be classified as a representative of a novel species of the genus, for which the name Comamonas guangdongensis sp. nov. is proposed. The type strain is CY01T ( = CCTCC AB 2011133T = KACC 16241T).
Paenibacillus vulneris sp. nov., isolated from a necrotic wound
Authors: Glaeser Stefanie P. , Falsen Enevold , Busse Hans-Jürgen , Kämpfer Peter
Published: May 2012

A Gram-positive-staining, aerobic, endospore-forming bacterium, isolated from a necrotic wound of a 35-year-old man was studied in detail to determine its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain CCUG 53270T was grouped into the genus

Paenibacillus

, most closely related to the type strains of

Paenibacillus rigui

(97.2 %),

Paenibacillus xylanisolvens

(96.3 %) and

Paenibacillus chinjuensis

(96.1 %). The 16S rRNA gene sequence similarity to strains of other

Paenibacillus

species was ≤96 %. Chemotaxonomic characterization supported the allocation of the strain to the genus

Paenibacillus

. The major menaquinones were MK-7 (85 %) and MK-6 (15 %). The polar lipid profile contained the major compounds diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The polyamine pattern contained predominantly spermidine. The major fatty acids were iso- and anteiso-branched fatty acids. The results of physiological and biochemical tests allowed phenotypic differentiation of strain CCUG 53270T from closely related species. Thus, strain CCUG 53270T represents a novel species of the genus

Paenibacillus

, for which the name Paenibacillus vulneris sp. nov. is proposed, with CCUG 53270T ( = JCM 18268T) as the type strain.
Spencermartinsiella ligniputridi sp. nov., a yeast species isolated from rotten wood
Authors: Dlauchy Dénes , Lee Ching-Fu , Péter Gábor
Published: May 2012

Four strains of a novel heterothallic yeast species were isolated from rotten wood samples collected at different locations in Hungary. Analysis of sequences of the D1/D2 domain of the large subunit rRNA gene placed the novel species in the genus Spencermartinsiella. The novel species can be distinguished from Spencermartinsiella europaea, the single species of the genus, and from Candida cellulosicola, the only recognized anamorphic species of the Spencermartinsiella clade, on the basis of standard phenotypic characteristics. The relatedness among the four strains of the novel species and two closely related strains representing undescribed yeast species is discussed. The name Spencermartinsiella ligniputridi sp. nov. is proposed to accommodate the four novel strains. The type and isotype strains of Spencermartinsiella ligniputridi sp. nov. are NCAIM Y.01992T ( = CBS 12585T = NRRL Y-48818T) and NCAIM Y.01936I ( = CBS 12586I = NRRL Y-48819I), respectively. Two additional strains are NCAIM Y.01991 and NCAIM Y.01993.
Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment
Authors: Higashioka Yuriko , Kojima Hisaya , Watanabe Miho , Fukui Manabu
Published: May 2012

A novel sulfate-reducing bacterium, strain S28bFT, was isolated from tidal flat sediment from Tokyo Bay, Japan. Cells of strain S28bFT were rod-shaped (0.5–0.6×1.7–3.8 µm), motile and Gram-stain-negative. For growth, the optimum pH was pH 6.8–7.3 and the optimum temperature was 34–42 °C. Strain S28bFT used sulfate and thiosulfate as electron acceptors, but not nitrate. The G+C content of the genomic DNA was 56.6 mol%. The fatty acid profile of strain S28bFT was characterized by the presence of anteiso-C15 : 0 and C16 : 0 as the major components. Phylogenetic analyses based on genes for 16S rRNA, the alpha subunit of dissimilatory sulfite reductase (dsrA) and adenosine-5′-phosphosulfate reductase (aprA) revealed that the isolated strain belonged to the class

Deltaproteobacteria

. Its closest relative was

Desulfosarcina cetonica

DSM 7267T with a 16S rRNA gene sequence similarity of 93.3 %. Two other strains, S28OL1 and S28OL2 were also isolated from the same sediment. These strains were closely related to S28bFT with 16S rRNA gene sequence similarities of 99 %, and the same physiological characteristics were shared with strain S28bFT. On the basis of phylogenetic and phenotypic characterization, a novel species in a new genus, Desulfatitalea tepidiphila gen. nov., sp. nov., is proposed to accommodate the strains obtained in this study. The type strain is S28bFT ( = NBRC 107166T = DSM 23472T).
BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
Authors: Flockhart Ross J. , Webster Dan E. , Qu Kun , Mascarenhas Nicholas , Kovalski Joanna , Kretz Markus , Khavari Paul A.
Published: May 2012

Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ∼50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of melanomas, 90% of which produce active mutant BRAFV600E protein. To define the impacts of oncogenic BRAF on the melanocyte transcriptome, massively parallel cDNA sequencing (RNA-seq) was performed on genetically matched normal human melanocytes with and without BRAFV600E expression. To enhance potential disease relevance by verifying expression of altered genes in BRAF-driven cancer tissue, parallel RNA-seq was also undertaken of two BRAFV600E-mutant human melanomas. BRAFV600E regulated expression of 1027 protein-coding transcripts and 39 annotated lncRNAs, as well as 70 unannotated, potentially novel, intergenic transcripts. These transcripts display both tissue-specific and multi-tissue expression profiles and harbor distinctive regulatory chromatin marks and transcription factor binding sites indicative of active transcription. Coding potential analysis of the 70 unannotated transcripts suggested that most may represent newly identified lncRNAs. BRAF-regulated lncRNA 1 (BANCR) was identified as a recurrently overexpressed, previously unannotated 693-bp transcript on chromosome 9 with a potential functional role in melanoma cell migration. BANCR knockdown reduced melanoma cell migration, and this could be rescued by the chemokine CXCL11. Combining RNA-seq of oncogene-expressing normal cells with RNA-seq of their corresponding human cancers may represent a useful approach to discover new oncogene-regulated RNA transcripts of potential clinical relevance in cancer.
Analysis of Arabidopsisglucose insensitive growthMutants Reveals the Involvement of the Plastidial Copper Transporter PAA1 in Glucose-Induced Intracellular Signaling
Authors: Lee Shin Ae , Yoon Eun Kyung , Heo Jung-Ok , Lee Mi-Hyun , Hwang Indeok , Cheong Hyeonsook , Lee Woo Sung , Hwang Yong-sic , Lim Jun
Published: May 2012

Sugars play important roles in many aspects of plant growth and development, acting as both energy sources and signaling molecules. With the successful use of genetic approaches, the molecular components involved in sugar signaling have been identified and their regulatory roles in the pathways have been elucidated. Here, we describe novel mutants of Arabidopsis (Arabidopsis thaliana), named glucose insensitive growth (gig), identified by their insensitivity to high-glucose (Glc)-induced growth inhibition. The gig mutant displayed retarded growth under normal growth conditions and also showed alterations in the expression of Glc-responsive genes under high-Glc conditions. Our molecular identification reveals that GIG encodes the plastidial copper (Cu) transporter PAA1 (for P1B-type ATPase 1). Interestingly, double mutant analysis indicated that in high Glc, gig is epistatic to both hexokinase1 (hxk1) and aba insensitive4 (abi4), major regulators in sugar and retrograde signaling. Under high-Glc conditions, the addition of Cu had no effect on the recovery of gig/paa1 to the wild type, whereas exogenous Cu feeding could suppress its phenotype under normal growth conditions. The expression of GIG/PAA1 was also altered by mutations in the nuclear factors HXK1, ABI3, and ABI4 in high Glc. Furthermore, a transient expression assay revealed the interaction between ABI4 and the GIG/PAA1 promoter, suggesting that ABI4 actively regulates the transcription of GIG/PAA1, likely binding to the CCAC/ACGT core element of the GIG/PAA1 promoter. Our findings indicate that the plastidial Cu transporter PAA1, which is essential for plastid function and/or activity, plays an important role in bidirectional communication between the plastid and the nucleus in high Glc.
Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template-Dependent, Nonvascular, Cell-to-Cell Movement
Authors: Liang Dacheng , White Rosemary G. , Waterhouse Peter M.
Published: May 2012

Upward long-distance mobile silencing has been shown to be phloem mediated in several different solanaceous species. We show that the Arabidopsis (Arabidopsis thaliana) seedling grafting system and a counterpart inducible system generate upwardly spreading long-distance silencing that travels not in the phloem but by template-dependent reiterated short-distance cell-to-cell spread through the cells of the central stele. Examining the movement of the silencing front revealed a largely unrecognized zone of tissue, below the apical meristem, that is resistant to the silencing signal and that may provide a gating or protective barrier against small RNA signals. Using a range of auxin and actin transport inhibitors revealed that, in this zone, alteration of vesicular transport together with cytoskeleton dynamics prevented or retarded the spread of the silencing signal. This suggests that small RNAs are transported from cell to cell via plasmodesmata rather than diffusing from their source in the phloem.
Barley Metallothioneins: MT3 and MT4 Are Localized in the Grain Aleurone Layer and Show Differential Zinc Binding
Authors: Hegelund Josefine Nymark , Schiller Michaela , Kichey Thomas , Hansen Thomas Hesselhøj , Pedas Pai , Husted Søren , Schjoerring Jan Kofod
Published: May 2012

Metallothioneins (MTs) are low-molecular-weight, cysteine-rich proteins believed to play a role in cytosolic zinc (Zn) and copper (Cu) homeostasis. However, evidence for the functional properties of MTs has been hampered by methodological problems in the isolation and characterization of the proteins. Here, we document that barley (Hordeum vulgare) MT3 and MT4 proteins exist in planta and that they differ in tissue localization as well as in metal coordination chemistry. Combined transcriptional and histological analyses showed temporal and spatial correlations between transcript levels and protein abundance during grain development. MT3 was present in tissues of both maternal and filial origin throughout grain filling. In contrast, MT4 was confined to the embryo and aleurone layer, where it appeared during tissue specialization and remained until maturity. Using state-of-the-art speciation analysis by size-exclusion chromatography inductively coupled plasma mass spectrometry and electrospray ionization time-of-flight mass spectrometry on recombinant MT3 and MT4, their specificity and capacity for metal ion binding were quantified, showing a strong preferential Zn binding relative to Cu and cadmium (Cd) in MT4, which was not the case for MT3. When complementary DNAs from barley MTs were expressed in Cu- or Cd-sensitive yeast mutants, MT3 provided a much stronger complementation than did MT4. We conclude that MT3 may play a housekeeping role in metal homeostasis, while MT4 may function in Zn storage in developing and mature grains. The localization of MT4 and its discrimination against Cd make it an ideal candidate for future biofortification strategies directed toward increasing food and feed Zn concentrations.
Non‐destructive surface analysis of accelerated corroded copper alloys
Authors: Papandreopoulos Panayiotis , Koui Maria , Yfantis Dimitrios , Theophanides Theophilos
Published: May 2012

Purpose

The purpose of this paper is to investigate the surface corrosion products of copper alloys by non‐destructive techniques (NDT) and correlate them with their bulk composition.

Design/methodology/approach

Specimens of copper alloys, whose compositions were close to those of ancient copper‐based artefacts, were left to be corroded in simulated soil solution containing ammoniacal buffering solution of pH =10 in 1:1 ratio, in order to accelerate the corrosion rate. The elemental compositions of the surface corrosion products were determined versus time using X‐Ray Fluorescence Spectroscopy, and the surface morphology by Scanning Electron Microscopy with Energy Dispersive X‐Ray Micro‐detector methods, and the results were compared to the bulk composition, as measured by Atomic Absorption Spectroscopy and Inductively Coupled Plasma Atomic Emission Spectroscopy.

Findings

During the corrosion evolution of the copper alloys in the corrosive solution, transitional phenomena were observed such as an initial decrease of the copper concentration with a simultaneous increase of the concentrations of the secondary alloying metals (Sn, Zn and Pb). After 30‐60 immersion days, the alloy concentrations were stabilised.

Originality/value

The results of this research could contribute to the non‐destructive characterisation of copper‐based ancient artefacts (from which the taking of samples is not allowed).
Modeling cathodic prevention for unconventional concrete in salt‐laden environment
Authors: Liu Yajun , Shi Xianming
Published: May 2012

Purpose

The purpose of this paper is to provide a modeling perspective relevant to the use of cathodic prevention (CPre) for unconventional concrete in salt‐laden environment.

Design/methodology/approach

Based on the experimentally obtained concrete resistivity and chloride diffusion coefficient data, numerical studies with the Nernst‐Planck equations were conducted to investigate the influence of applied voltage (magnitude, direction, and interruption), surface chloride concentration, and concrete mix design on the effectiveness of cathodic prevention and the distribution of ionic species in protected concrete.

Findings

The modeling results revealed that the direction of applied electric voltage has significant effect on the distributions of electrical potential and hydroxyl ions in the reinforced concrete, confirming the benefits of cathodic prevention in significantly increasing hydroxyl concentration near rebar and in slowing down the ingress of chloride ingress into concrete. The performance of intermittent CPre was found to be constrained by the variations in concrete resistance from the anode to the cathode. The model was also useful in illustrating the temporal and spatial evolutions on rebar surface in terms of oxygen, hydroxyl and chloride concentrations and electrical potential of top rebar, as well as such evolutions in concrete domain in terms of concrete resistivity and current density for each mix design.

Originality/value

The results reported herein shed light on the fundamental processes defining the performance of CPre for new unconventional concrete in salt‐laden environment.
Corrosion behaviour of dual‐phase and galvanized steels in concrete
Authors: Ismail Mohammad , Muhammad Bala , Hamzah Esah , Keong TanWui
Published: May 2012

Purpose

The purpose of this paper is to present results of an evaluation of dual‐phase and galvanized steel reinforcements in corrosive environments.

Design/methodology/approach

Low carbon steels were intercritically annealed at 740°C followed by water quenching to obtain dual‐phase structures with 37 per cent volume fraction of martensite dispersed in ferrite matrix. Dual‐phase and galvanized steel rebars were embedded in concrete cubes and immersed in 5 per cent NaCl solution for up to 100 days. Corrosion rate, tensile and macro as well as microhardness tests were performed. The dual‐phase and galvanized zinc layers were observed under scanning electron microscopy (SEM).

Findings

From all of the tests carried out it was found that dual‐phase steels exhibited better corrosion resistant properties and superior strength compared to galvanized steels.

Originality/value

The results reported show that dual‐phase steel can be a good candidate for reinforcement in concrete especially in aggressive and corrosive environments.
High performance protective coatings for non‐ferrous metals
Authors: Emira Hassan S. , Shakour Alia A. , Abd El Rehim Sayed S. , Saleh Inas A. , El‐Hashemy Mohammed A.
Published: May 2012

Purpose

The purpose of this paper is to report the use of zinc phosphate pigment as a chromate substitute for coatings on non‐ferrous metals (galvanized steel, pure aluminum, α‐brass and pure copper).

Design/methodology/approach

Paint systems based on zinc chromate and zinc phosphate pigments were prepared. The paints were tested for their physico‐mechanical properties. Testing of the anticorrosive properties of the zinc phosphate pigment in comparison with zinc chromate pigment was carried out by accelerated corrosion exposure, i.e. immersion in 3.5 percent salt solution and exposure for one year at five outdoor stations.

Findings

The possibility of replacing chromate pigment was assessed and the “gap“ observable between the performance of zinc chromate and zinc phosphate pigments was noted.

Originality/value

The non‐toxic inhibitive pigment, zinc phosphate, incorporated into a plasticized‐chlorinated rubber binder, could be applied successfully for the protection of non‐ferrous substrates.
Libraries atwitter: trends in academic library tweeting
Authors: Del Bosque Darcy , Leif Sam A. , Skarl Susie
Published: May 2012

Purpose

This paper aims to present an overview of how libraries are using Twitter in an academic setting.

Design/methodology/approach

This study analyzed the current state of 296 Twitter accounts from a random sample of academic libraries. A total of 19 different criteria were explored, with an emphasis on the following three categories: layout and design, content and number of tweets, and account followers.

Findings

Only 34 per cent of libraries in the study had a Twitter account and characteristics varied widely among libraries, however it is evident that it is possible to successfully communicate with patrons via Twitter.

Research limitations/implications

A primary limitation for this study is the frequency with which Twitter can change.

Practical implications

This paper provides a snapshot of how libraries are currently using Twitter, which can be of assistance to libraries seeking to implement a Twitter presence.

Originality/value

The paper presents an overview of trends in academic library Twitter accounts, which could be useful to librarians who are considering launching a Twitter account for their library.
To tweet, or not to tweet?
Authors: Jennings Susan
Published: May 2012

Purpose

The purpose of this article is to address the question “To Tweet or Not to Tweet” – using the social networking application “Twitter” as a communication channel for academic libraries.

Design/methodology/approach

As lead librarian for Desk Services at Appalachian State University's (ASU's) Belk Library and Information Commons, this article shares the author's experiences and lessons learned as the library's “Tweeter.”

Findings

The article finds that Belk Library and Information Commons says “Yes, by all means, tweet” due to the positive response that received from both Twitter as well as Facebook.

Practical implications

Provided in this article are ten helpful tips learned as the program developed at ASU. The tips are a good place to begin thinking about the implications for those libraries contemplating or beginning a social networking program.

Originality/value

The article focuses on lessons learned as social networking policies evolve over time.
Just the right tweet at just the right time
Authors: Doshi Ameet
Published: May 2012

Purpose

This article looks at the function and the value of this Twitter as a form of communication within an academic library.

Design/methodology/approach

The article is anecdotal and based on the author's experience at Georgia Tech library.

Findings

In the author's opinion, there are two recipes for mediocre tweets: first, everyone in the library gets to tweet (i.e. tweet by committee), and, second, the “I only do social media because I have to” librarian tweeting on behalf of the library. Not to be overly prescriptive, but the author feels strongly that social media, and especially Twitter, just does not work well by committee.

Research limitations/implications

This is an essay based on experiential and anecdotal evidence, and not based on a thorough research study.

Practical implications

It would be practical to increase library presence on Twitter in a meaningful way.

Social implications

There should be increased engagement with library users.

Originality/value

How libraries should be organizing their social media efforts is an important and valuable question.
Beyond broadcasting
Authors: Gunton Lyndelle , Davis Kate
Published: May 2012

Purpose

The purpose of this paper is to contribute to discourse around use of Twitter in libraries, and in particular to highlight the value of using Twitter beyond broadcast of marketing messages.

Design/methodology/approach

This paper is an opinion piece designed to initiate conversations about the applications of Twitter for customer service and community building, as well as its role as a ground for information experience.

Findings

The authors suggest that libraries should look to other industries for examples of Twitter as a channel for customer service delivery. Further, they suggest that social media can aid in community building, which is a fundamental role for libraries of all types. Finally, they suggest that social media spaces are sites for information experience, and that libraries must seek to understand the nature of those information experiences if they are to harness the full potential of social media.

Originality/value

The paper highlights the value of libraries using Twitter beyond the broadcasting of marketing messages.
User perceptions of ebooks versus print books for class reserves in an academic library
Authors: Rojeski Mara
Published: May 2012

Purpose

The purpose of this paper is to present the results of a pilot program at Dickinson College where select reserve books for a class were purchased as ebooks and linked through the course management system. The paper aims to shares the results of survey data, a focus group session, and usage statistics to evaluate the pilot.

Design/methodology/approach

The study uses mixed methods with survey, focus group, and usage analysis.

Findings

The study found a much higher use of ebooks over print reserves. The survey and focus group responses also found a relatively high student satisfaction with the use of ebooks, despite some reported use problems.

Practical implications

The results of this study offer academic libraries a new idea to consider for ebook purchases. The paper also highlights important issues to consider if purchasing ebooks to replace print reserve books.

Originality/value

This is the first study to evaluate student attitudes and use of ebook “reserve” materials.
Information literacy on Facebook: an analysis
Authors: Witek Donna , Grettano Teresa
Published: May 2012

Purpose

This analysis, being part one of a two‐part study, aims to illustrate the attitudes and patterns users are being habituated to through the functionality of Facebook, relate them to information literate practices and behaviors, and speculate their application to information literacy instruction within an academic context. It also aims to lay the groundwork for part two, which is to be reported on in a later issue of this journal.

Design/methodology/approach

For this first part of the study, the Association of College & Research Libraries (ACRL) Information Literacy Competency Standards for Higher Education have been aligned with common behaviors on Facebook, examining each standard, performance indicator, and outcome for possible parallels in common Facebook tools and behaviors. These behaviors have then been connected to the process of conducting research in an academic context.

Findings

Three Facebook functions – Feeds, Share, and Comment – emerged as the primary means by which information literate practices and behaviors are developed and exhibited on Facebook. In addition, information literacy in the age of social media requires a “meta‐literacy”: a critical awareness of why we do what we do with information.

Research limitations/implications

This analysis (part one) presents the conceptual framework on which the data collection portion of the study (part two) is based. In doing so, it lays the groundwork for a reexamination of what it means to be information literate in light of social media practices and behaviors.

Originality/value

This paper is valuable to information literacy instructors and researchers because it offers the first extended analysis that deliberately reads Facebook through the lens of the ACRL Standards.
Engaging undergraduates in discipline‐based research
Authors: Gauder Heidi , Jenkins Fred
Published: May 2012

Purpose

This article aims to describe the standards‐based approach used to build the International Studies Research Methods (INS250) course, a discipline‐specific, credit‐based class taught by librarians. This writing‐intensive course emphasizes information literacy and critical thinking skills, which were developed using written assignments, class presentations, multiple assessment methods, and web‐based applications.

Design/methodology/approach

This paper will review the literature about discipline‐specific, credit‐based information literacy (IL) courses and outcomes. It will also analyze the INS250 course structure and map ACRL Information Literacy Competency Standards for Higher Education to learning outcomes for the course.

Findings

The paper finds that, in the absence of discipline‐specific information literacy standards, the ACRL Information Literacy Competency Standards for Higher Education can serve as a starting point for International Studies course outcomes and assessment. Other assessment approaches, specifically student workshops and concept maps, promote student engagement and provide ample evidence of student learning.

Originality/value

This article will identify research skills needed by International Studies majors and students in similar multidisciplinary programs. It will serve as a model of how to build a credit‐based course with application to other fields such as political science, sustainability, human rights and international business. The course is student‐focused and responsive to new disciplines and areas, with an emphasis on disciplinary databases, search skills, and citation skills.
Fore‐cite: tactics for evaluating citation management tools
Authors: Marino William
Published: May 2012

Purpose

The purpose of this paper is to explore a general set of criteria that can be used by librarians and information professionals for the evaluation of citation management tools.

Design/methodology/approach

Collection development practices found in the library world are combined with software selection criteria from the corporate sector and applied to the citation management environment. A discussion of these practices identifies general criteria, or best practices, that can be used in the evaluation of various types of citation management tools.

Findings

Eight criteria are discussed. Key questions are raised that can assist librarians and information professionals in the evaluation process. Additional resources that may assist with evaluation efforts are highlighted, where applicable.

Originality/value

Existing attempts to evaluate citation management tools have employed an approach centering on the features and functionality of a limited set of tools. While effective, these studies neglect new developments in the citation management environment, run the risk of missing other criteria that may be important to both users and libraries, and have short life‐cycles due to the mutable nature of software updates. This study explores the larger environment in which these tools operate, and develops a macro‐assessment of the field, not tied to update schedules or specific software options.
iBIRA – integrated bioinformatics information resource access
Authors: Ram Shri , Laxman Rao N.
Published: May 2012

Purpose

Bioinformatics is an emerging discipline where the interdisciplinary research holds great promise for the advancement of research and development in many complex areas. The research output generates a huge amount of data and information. Because of the heterogeneous nature of bioinformatics resources, difficulty in accessing pertinent information is the biggest challenge for the bioinformatics community. The integration of bioinformatics resources in a comprehensive manner is advocated by the bioinformatics user community as well as by information scientists serving this community. There are have already been some efforts made for integration of bioinformatics resources by the discrete bioinformatics community, but these are based on the requirement of their own area and arena. This paper aims to discuss the design and development of a tool for the integration of various heterogeneous bioinformatics information resources available over the internet.

Design/methodology/approach

The authors have developed a tool with the acronym “iBIRA” (Integrated Bioinformatics Information Resource Access) that associates the bioinformatics community with the bioinformatics “resourceome” (the term suggested for the “full set of bioinformatics resources” by Cannataet al.). Available over the internet.iBIRA (www.ibiranet.in) integrates bioinformatics resources in a way such that it is possible to locate, connect and communicate different categories of resources in a cohesive manner. A software engineering and database‐driven approach was used for the integration and organization of bioinformatics resources. Computational programming such as Hypertext Preprocessor (PHP), a server‐side dynamic web programming language, and MySQL as a database management system have been used. Dublin Core Metadata Standards have been used for the design of metadata for bioinformatics resources..

Findings

The term “resource” in the area of bioinformatics covers various entities such as journals, molecular biology databases, online annotation tools, patents, published documents (articles, books, etc), protocols, software tools, and web servers. It has been found that bioinformatics resources are heterogeneous in nature and available over the internet in different forms and formats. The fact that bioinformatics resources are scattered over the internet makes resource discovery difficult for the bioinformatics community, and there is need for a system that reorganizes these resources. The integration of all the resources of bioinformatics at a single platform (called “iBIRA”) provides significant “value added” to the bioinformatics community, those serving this population.

Originality/value

TheiBIRA tool is a meta‐server developed to provide information service about the availability of various bioinformatics resources to the bioinformatics community. This will provide a value‐added benefit to the population in helping them to locate relevant resources for their education, research and training.
The flexibility and benefits of operating a diverse fleet: an analysis using real options
Authors: Treanor Stephen D.
Published: May 2012

Purpose

The purpose of this paper is to develop a simple model illustrating the benefits of operating a diverse fleet of aircraft.

Design/methodology/approach

The paper is theoretical. It describes how real options are beneficial to the firm in both capital budgeting and risk management. It illustrates the use of real options in the airline industry, and how real options are used as a risk management tool. Then the model is developed which illustrates how a diverse fleet can provide an airline protection against fuel price risk.

Findings

The results of the model show that a diverse fleet is value enhancing to an airline during periods when fuel prices are high or uncertain. Furthermore, this paper shows that a diverse fleet provides an airline with an operational hedge to jet fuel prices. Though the paper focuses on the airline industry, the results are applicable to those industries vulnerable to volatile input costs, and prohibitive abandonment and re‐entry costs.

Originality/value

The paper uses real option analysis to show the benefits for an airline deriving from operating a diverse fleet of aircraft.