bluuebunny/crossref_metadata_2025 huggingface dataset:
Reno: regularized non-parametric analysis of protein lysate array data
Authors: Li Bin , Liang Feng , Hu Jianhua , He and Xuming
Published: March 2012

Motivation: The reverse-phase protein lysate arrays have been used to quantify the relative expression levels of a protein in a number of cellular samples simultaneously. To avoid quantification bias due to mis-specification of commonly used parametric models, a nonparametric approach based on monotone response curves may be used. The existing methods, however, aggregate the protein concentration levels of replicates of each sample, and therefore fail to account for within-sample variability.

Results: We propose a method of regularization on protein concentration estimation at the level of individual dilution series to account for within-sample or within-group variability. We use an efficient algorithm to optimize an approximate objective function, with a data-adaptive approach to choose the level of shrinkage. Simulation results show that the proposed method quantifies protein concentration levels well. We show through the analysis of protein lysate array data from cell lines of different cancer groups that accounting for within-sample variability leads to better statistical analysis.

Availability: Code written in statistical programming language R is available at: http://odin.mdacc.tmc.edu/~jhhu/Reno

Contact:  jhu@mdanderson.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory
Authors: Sparkes Andrew , Clare Amanda
Published: March 2012

Motivation: Modern automated laboratories need substantial data management solutions to both store and make accessible the details of the experiments they perform. To be useful, a modern Laboratory Information Management System (LIMS) should be flexible and easily extensible to support evolving laboratory requirements, and should be based on the solid foundations of a robust, well-designed database. We have developed such a database schema to support an automated laboratory that performs experiments in systems biology and high-throughput screening.

Results: We describe the design of the database schema (AutoLabDB), detailing the main features and describing why we believe it will be relevant to LIMS manufacturers or custom builders. This database has been developed to support two large automated Robot Scientist systems over the last 5 years, where it has been used as the basis of an LIMS that helps to manage both the laboratory and all the experiment data produced.

Availability and implementation: The database schema has been made available as open source (BSD license), so that others may use, extend and improve it to meet their own needs. Example software interfaces to the database are also provided. http://autolabdb.sourceforge.net/

Contact:  afc@aber.ac.uk
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies
Authors: Sun Hokeun , Wang Shuang
Published: March 2012

Motivation: DNA methylation is a molecular modification of DNA that plays crucial roles in regulation of gene expression. Particularly, CpG rich regions are frequently hypermethylated in cancer tissues, but not methylated in normal tissues. However, there are not many methodological literatures of case-control association studies for high-dimensional DNA methylation data, compared with those of microarray gene expression. One key feature of DNA methylation data is a grouped structure among CpG sites from a gene that are possibly highly correlated. In this article, we proposed a penalized logistic regression model for correlated DNA methylation CpG sites within genes from high-dimensional array data. Our regularization procedure is based on a combination of the l1 penalty and squared l2 penalty on degree-scaled differences of coefficients of CpG sites within one gene, so it induces both sparsity and smoothness with respect to the correlated regression coefficients. We combined the penalized procedure with a stability selection procedure such that a selection probability of each regression coefficient was provided which helps us make a stable and confident selection of methylation CpG sites that are possibly truly associated with the outcome.

Results: Using simulation studies we demonstrated that the proposed procedure outperforms existing main-stream regularization methods such as lasso and elastic-net when data is correlated within a group. We also applied our method to identify important CpG sites and corresponding genes for ovarian cancer from over 20 000 CpGs generated from Illumina Infinium HumanMethylation27K Beadchip. Some genes identified are potentially associated with cancers.

Contact:  sw2206@columbia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DeOri: a database of eukaryotic DNA replication origins
Authors: Gao Feng , Luo Hao , Zhang Chun-Ting
Published: March 2012

Summary: DNA replication, a central event for cell proliferation, is the basis of biological inheritance. The identification of replication origins helps to reveal the mechanism of the regulation of DNA replication. However, only few eukaryotic replication origins were characterized not long ago; nevertheless, recent genome-wide approaches have boosted the number of mapped replication origins. To gain a comprehensive understanding of the nature of eukaryotic replication origins, we have constructed a Database of Eukaryotic ORIs (DeOri), which contains all the eukaryotic ones identified by genome-wide analyses currently available. A total of 16 145 eukaryotic replication origins have been collected from 6 eukaryotic organisms in which genome-wide studies have been performed, the replication-origin numbers being 433, 7489, 1543, 148, 348 and 6184 for humans, mice, Arabidopsis thaliana, Kluyveromyces lactis, Schizosaccharomyces pombe and Drosophila melanogaster, respectively.

Availability: Database of Eukaryotic ORIs (DeOri) can be accessed from http://tubic.tju.edu.cn/deori/

Contact:  ctzhang@tju.edu.cn
Paenibacillus oceanisediminis sp. nov. isolated from marine sediment
Authors: Lee Jina , Shin Na-Ri , Jung Mi-Ja , Roh Seong Woon , Kim Min-Soo , Lee Jung-Sook , Lee Keun Chul , Kim Young-Ok , Bae Jin-Woo
Published: March 2012

A Gram-stain-negative, non-motile, aerobic, endospore forming and rod-shaped bacterium, designated strain L10T, was isolated from marine sediment collected from the South Korean coast. The organism grew optimally under conditions of 30 °C, 1 % (w/v) NaCl and pH 6.0. It was oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain L10T was associated with the genus

Paenibacillus

and most closely related to

Paenibacillus barcinonensis

BP-23T (98.2 % similarity). The major fatty acids of strain L10T were iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0. The cell-wall peptidoglycan was the A1γ type, and the predominant isoprenoid quinone was menaquinone-7. Strain L10T contained two unidentified lipids, an unidentified amino-phospholipid, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The G+C content of the genomic DNA was 44 mol% and the DNA–DNA hybridization values with closely related strains were below 14±2 %. Based on phenotypic, genotypic, and phylogenetic data, strain L10T should be classified as a novel species within the genus

Paenibacillus

. The name Paenibacillus oceanisediminis sp. nov. is proposed. The type strain is L10T ( = KACC 16203T = JCM 17814T).
Marivita geojedonensis sp. nov., isolated from seawater
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Jung-Sook
Published: March 2012

A Gram-negative-staining, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, DPG-138T, was isolated from seawater on the southern coast in Korea. Strain DPG-138T grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DPG-138T fell within the cluster comprising the type strains of four species of the genus

Marivita

(sequence similarity values of 97.8–98.2 %). The DNA G+C content was 59.9 mol%. The predominant ubiquinone of strain DPG-138T was Q-10, typical for the genus

Marivita

. The cellular fatty acid profiles of strain DPG-138T and type strains of four species of the genus

Marivita

were similar with C18 : 1ω7c as the most common fatty acid. The major polar lipids in strain DPG-138T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties and genetic distinctiveness of strain DPG-138T demonstrated that this strain is distinguishable from all four recognized species of the genus

Marivita

. On the basis of the data presented, strain DPG-138T is considered to represent a novel species of the genus

Marivita

, for which the name Marivita geojedonensis sp. nov. is proposed. The type strain is DPG-138T ( = KCTC 23882T = CCUG 62112T).
Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.
Authors: Sheu Shih-Yi , Chou Jui-Hsing , Bontemps Cyril , Elliott Geoffrey N. , Gross Eduardo , dos Reis Junior Fabio Bueno , Melkonian Rémy , Moulin Lionel , James Euan K. , Sprent Janet I. , Young J. Peter W. , Chen Wen-Ming
Published: March 2012

Five strains, JPY461T, JPY359, JPY389, DPU-3 and STM4206 were isolated from nitrogen-fixing nodules on the roots of Mimosa spp. and their taxonomic positions were investigated using a polyphasic approach. All five strains grew at 15–40 °C (optimum, 30–37 °C), at pH 4.0–8.0 (optimum, pH 6.0–7.0) and with 0–1 % (w/v) NaCl [optimum, 0 % (w/v)]. On the basis of 16S rRNA gene sequence analysis, a representative strain (JPY461T) showed 97.2 % sequence similarity to the closest related species

Burkholderia acidipaludis

SA33T, a similarity of 97.2 % to

Burkholderia terrae

KMY02T, 97.1 % to

Burkholderia phymatum

STM815T and 97.1 % to

Burkholderia hospita

LMG 20598T. The predominant fatty acids of the five novel strains were summed feature 2 (comprising C16 : 1 iso I and/or C14 : 0 3-OH), summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c), C16 : 0 , C16 : 0 3-OH, C17 : 0 cyclo, C18 : 1
ω7c and C19 : 0 cyclo ω8c. The major isoprenoid quinone was Q-8 and the DNA G+C content of the strains was 63.0–65.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, an unidentified aminolipid and several unidentified phospholipids. The DNA–DNA relatedness of the novel strain with respect to recognized species of the genus

Burkholderia

was less than 54 %. On the basis of 16S rRNA and recA gene sequence similarities, chemotaxonomic and phenotypic data, the five strains represent a novel species in the genus

Burkholderia

, for which the name Burkholderia diazotrophica sp. nov. is proposed with the type strain, JPY461T ( = LMG 26031T = BCRC 80259T = KCTC 23308T).
Current View on Phytoplasma Genomes and Encoded Metabolism
Authors: Kube Michael , Mitrovic Jelena , Duduk Bojan , Rabus Ralf , Seemüller Erich
Published: April 2012

Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘CandidatusPhytoplasma’ genomes that include those of ‘Ca.P. asteris’ strains OY-M and AY-WB, ‘Ca.P. australiense,’ and ‘Ca.P. mali’. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca.P. mali’ is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.
Complex Tasks Force Hand Laterality and Technological Behaviour in Naturalistically Housed Chimpanzees: Inferences in Hominin Evolution
Authors: Mosquera M. , Geribàs N. , Bargalló A. , Llorente M. , Riba D.
Published: April 2012

Clear hand laterality patterns in humans are widely accepted. However, humans only elicit a significant hand laterality pattern when performing complementary role differentiation (CRD) tasks. Meanwhile, hand laterality in chimpanzees is weaker and controversial. Here we have reevaluated our results on hand laterality in chimpanzees housed in naturalistic environments at Fundació Mona (Spain) and Chimfunshi Wild Orphanage (Zambia). Our results show that the difference between hand laterality in humans and chimpanzees is not as great as once thought. Furthermore, we found a link between hand laterality and task complexity and also an even more interesting connection: CRD tasks elicited not only the hand laterality but also the use of tools. This paper aims to turn attention to the importance of this threefold connection in human evolution: the link between CRD tasks, hand laterality, and tool use, which has important evolutionary implications that may explain the development of complex behaviour in early hominins.
Estimating Annual CO2Flux for Lutjewad Station Using Three Different Gap-Filling Techniques
Authors: Dragomir Carmelia M. , Klaassen Wim , Voiculescu Mirela , Georgescu Lucian P. , van der Laan Sander
Published: April 2012

Long-term measurements of CO2flux can be obtained using the eddy covariance technique, but these datasets are affected by gaps which hinder the estimation of robust long-term means and annual ecosystem exchanges. We compare results obtained using three gap-fill techniques: multiple regression (MR), multiple imputation (MI), and artificial neural networks (ANNs), applied to a one-year dataset of hourly CO2flux measurements collected in Lutjewad, over a flat agriculture area near the Wadden Sea dike in the north of the Netherlands. The dataset was separated in two subsets: a learning and a validation set. The performances of gap-filling techniques were analysed by calculating statistical criteria: coefficient of determination (R2), root mean square error (RMSE), mean absolute error (MAE), maximum absolute error (MaxAE), and mean square bias (MSB). The gap-fill accuracy is seasonally dependent, with better results in cold seasons. The highest accuracy is obtained using ANN technique which is also less sensitive to environmental/seasonal conditions. We argue that filling gaps directly on measured CO2fluxes is more advantageous than the common method of filling gaps on calculated net ecosystem change, because ANN is an empirical method and smaller scatter is expected when gap filling is applied directly to measurements.
A dual role of linker histone H1.4 Lys 34 acetylation in transcriptional activation
Authors: Kamieniarz Kinga , Izzo Annalisa , Dundr Miroslav , Tropberger Philipp , Ozretić Luka , Kirfel Jutta , Scheer Elisabeth , Tropel Philippe , Wiśniewski Jacek R. , Tora Laszlo , Viville Stephane , Buettner Reinhard , Schneider Robert
Published: March 2012

The linker histone H1 is a key player in chromatin organization, yet our understanding of the regulation of H1 functions by post-translational modifications is very limited. We provide here the first functional characterization of H1 acetylation. We show that H1.4K34 acetylation (H1.4K34ac) is mediated by GCN5 and is preferentially enriched at promoters of active genes, where it stimulates transcription by increasing H1 mobility and recruiting a general transcription factor. H1.4K34ac is dynamic during spermatogenesis and marks undifferentiated cells such as induced pluripotent stem (iPS) cells and testicular germ cell tumors. We propose a model for H1.4K34ac as a novel regulator of chromatin function with a dual role in transcriptional activation.
Endosomal sorting by Semaphorin 4A in retinal pigment epithelium supports photoreceptor survival
Authors: Toyofuku Toshihiko , Nojima Satoshi , Ishikawa Takako , Takamatsu Hyota , Tsujimura Tohru , Uemura Akiyoshi , Matsuda Junko , Seki Takaharu , Kumanogoh Atsushi
Published: March 2012

Photoreceptor cell death is the hallmark of a group of human inherited retinal degeneration. Although the causative genetic mutations are often known, the mechanisms leading to photoreceptor degeneration remain poorly defined. Here, we show that Semaphorin 4A (Sema4A), a member of axonal guidance molecule semaphorin, plays a role in Rab11/FIP2-mediated endosomal sorting in retinal pigment epithelial cells to support photoreceptor function. In response to oxidative stress, Sema4A switches the endosomal sorting of the lysosomal precursor protein prosaposin from the lysosome to the exosomal release, which prevents light-induced photoreceptor apoptosis. In the absence of oxidative stress, Sema4A sorts retinoid-binding proteins with retinoids between the cell surface and endoplasmic reticulum, by which 11-cis-retinal, a chromophore for phototransduction, is regenerated and transported back to photoreceptors. Owing to defects in these processes, Sema4A-deficient mice exhibit marked photoreceptor degeneration. Our findings therefore indicate that Sema4A regulates two distinct endosomal-sorting pathways that are critical for photoreceptor survival and phototransduction during the transition between daylight and darkness.
Regulation of SIRT1 activity by genotoxic stress
Authors: Yuan Jian , Luo Kuntian , Liu Tongzheng , Lou Zhenkun
Published: March 2012

SIRT1 regulates a variety of cellular functions, including cellular stress responses and energy metabolism. SIRT1 activity is negatively regulated by DBC1 (Deleted in Breast Cancer 1) through direct binding. However, how the DBC1–SIRT1 interaction is regulated remains unclear. We found that the DBC1–SIRT1 interaction increases following DNA damage and oxidative stress. The stress-induced DBC1–SIRT1 interaction requires the ATM-dependent phosphorylation of DBC1 at Thr 454, which creates a second binding site for SIRT1. Finally, we showed that the stress-induced DBC1–SIRT1 interaction is important for cell fate determination following genotoxic stress. These results revealed a novel mechanism of SIRT1 regulation during genotoxic stress.
Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
Authors: Sun Mai , Schwalb Björn , Schulz Daniel , Pirkl Nicole , Etzold Stefanie , Larivière Laurent , Maier Kerstin C. , Seizl Martin , Tresch Achim , Cramer Patrick
Published: March 2012

To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4–Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation.
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
Authors: Statham Aaron L. , Robinson Mark D. , Song Jenny Z. , Coolen Marcel W. , Stirzaker Clare , Clark Susan J.
Published: March 2012

The complex relationship between DNA methylation, chromatin modification, and underlying DNA sequence is often difficult to unravel with existing technologies. Here, we describe a novel technique based on high-throughput sequencing of bisulfite-treated chromatin immunoprecipitated DNA (BisChIP-seq), which can directly interrogate genetic and epigenetic processes that occur in normal and diseased cells. Unlike most previous reports based on correlative techniques, we found using direct bisulfite sequencing of Polycomb H3K27me3-enriched DNA from normal and prostate cancer cells that DNA methylation and H3K27me3-marked histones are not always mutually exclusive, but can co-occur in a genomic region-dependent manner. Notably, in cancer, the co-dependency of marks is largely redistributed with an increase of the dual repressive marks at CpG islands and transcription start sites of silent genes. In contrast, there is a loss of DNA methylation in intergenic H3K27me3-marked regions. Allele-specific methylation status derived from the BisChIP-seq data clearly showed that both methylated and unmethylated alleles can simultaneously be associated with H3K27me3 histones, highlighting that DNA methylation status in these regions is not dependent on Polycomb chromatin status. BisChIP-seq is a novel approach that can be widely applied to directly interrogate the genomic relationship between allele-specific DNA methylation, histone modification, or other important epigenetic regulators.
Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
Authors: Adey Andrew , Shendure Jay
Published: March 2012

We have adapted transposase-based in vitro shotgun library construction (“tagmentation”) for whole-genome bisulfite sequencing. This method, Tn5mC-seq, enables a >100-fold reduction in starting material relative to conventional protocols, such that we generate highly complex bisulfite sequencing libraries from as little as 10 ng of input DNA, and ample useful sequences from 1 ng of input DNA. We demonstrate Tn5mC-seq by sequencing the methylome of a human lymphoblastoid cell line to ∼8.6× high-quality coverage of each strand.
Histidine Kinase Activity of the Ethylene Receptor ETR1 Facilitates the Ethylene Response in Arabidopsis
Authors: Hall Brenda P. , Shakeel Samina N. , Amir Madiha , Haq Noor Ul , Qu Xiang , Schaller G. Eric
Published: March 2012

In Arabidopsis (Arabidopsis thaliana), ethylene is perceived by a receptor family consisting of five members. Subfamily 1 members ETHYLENE RESPONSE1 (ETR1) and ETHYLENE RESPONSE SENSOR1 (ERS1) have histidine kinase activity, unlike the subfamily 2 members ETR2, ERS2, and ETHYLENE INSENSITIVE4 (EIN4), which lack amino acid residues critical for this enzymatic activity. To resolve the role of histidine kinase activity in signaling by the receptors, we transformed an etr1-9;ers1-3 double mutant with wild-type and kinase-inactive versions of the receptor ETR1. Both wild-type and kinase-inactive ETR1 rescue the constitutive ethylene-response phenotype of etr1-9;ers1-3, restoring normal growth to the mutant in air. However, the lines carrying kinase-inactive ETR1 exhibit reduced sensitivity to ethylene based on several growth response assays. Microarray and real-time polymerase chain reaction analyses of gene expression support a role for histidine kinase activity in eliciting the ethylene response. In addition, protein levels of the Raf-like kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1), which physically associates with the ethylene receptor ETR1, are less responsive to ethylene in lines containing kinase-inactive ETR1. These data indicate that the histidine kinase activity of ETR1 is not required for but plays a modulating role in the regulation of ethylene responses. Models for how enzymatic and nonenzymatic regulation may facilitate signaling from the ethylene receptors are discussed.
Automated packaging is a big hit at PackExpo
Authors: Bloss Richard
Published: March 2012

Purpose

The purpose of this paper is to review the PackExpo Show (packaging technology) with emphasis on automation innovations for better and more cost effective packaging.

Design/methodology/approach

In‐depth interviews with exhibitors of packaging automation of all types at the PackExpo Show.

Findings

Suppliers of packaging automation continue to innovate with faster, more effective and cost cutting systems.

Practical implications

Packaging customers now have more automation innovations to address packaging requirements with faster and smarter product handling technologies to increase productivity and decrease packaging costs.

Originality/value

For packaging customers who could not attend PackExpo, they now have an opportunity to see and learn about some of packaging automation innovations that were on display.
A dynamic assembly model for assembly sequence planning of complex product based on polychromatic sets theory
Authors: Xu Zhijia , Li Yuan , Zhang Jie , Cheng Hui , Jiang Shoushan , Tang Wenbin
Published: March 2012

Purpose

Assembly Sequence Planning integrating assembly Resources (ASPR) is a trend in industry. Because of the introduction of resource, the complexity of ASPR for complex product increases drastically; besides, the dynamic property of resource and the co‐existence of assembly sequence and disassembly sequence (ASDS) make the problems in ASPR more difficult. The dynamic assembly model (DAM) based on polychromatic sets (PS) theory was proposed to address these issues.

Design/methodology/approach

First, a strategy was presented to simplify ASPR, taking advantage of assembly sequence generated in the phase of assembly design which considers no resource. Secondly, the concept of DAM was discussed, and some principles/criteria for DAM modeling were generalized from experience. Then, the DAM was modeled by formalizing its incidence relations as PS matrix, and refined based on the formalized criteria, which were expressed as PS locating and collision relation models. Finally, an application case was studied to demonstrate the effectiveness of the method.

Findings

The approach could reduce the complexity of ASPR significantly, and was able to identify dynamic resource, model DAM and handle the co‐existence of ASDS effectively.

Practical implications

The method may change the manual pattern of ASPR in simulation environment, and become a potential tool to change the pattern of traditional ASP which comes to work from scratch, by utilizing the upstream information of product design.

Originality/value

Different from traditional assembly model, DAM was a local model which consists of partial components of product and resource, and the DAM‐based ASPR approach would make the computational complexity of product assembly become more linear than exponential.
Ontology‐based context‐sensitive computing for FMS optimization
Authors: Kamal Uddin Mohammad , Puttonen Juha , Scholze Sebastian , Dvoryanchikova Aleksandra , Luis Martinez Lastra Jose
Published: March 2012

Purpose

The purpose of this paper is to present an ontology‐based approach of context‐sensitive computing for the optimization of flexible manufacturing systems (FMS).

Design/methodology/approach

A context‐sensitive computing approach is presented, integrated on top of FMS control platform. The approach addresses how to extract manufacturing contexts at source, how to process contextual entities by developing an ontology‐based context model and how to utilize this approach for real time decision making to optimize the key performance indicators (KPIs). A framework for such an optimization support system is proposed. A practical FMS use case within SOA‐based control architecture is considered as an illustrative example and the implementation of the core functionalities to the use case is reported.

Findings

Continuous improvement of the factory can be enhanced utilizing context‐sensitive support applications, which provides an intelligent interface for knowledge acquisition and elicitation. This can be used for improved data analysis and diagnostics, real time feedback control and support for optimization.

Research limitations/implications

The performance of context‐sensitive computing increases with the extraction, modeling and reasoning of as much contexts as possible. However, more computational resources and processing times are associated to this. Hence, the trade‐off should be in between the extent of context processing and the required outcome of the support applications.

Practical implications

This paper includes the practical implications of context‐sensitive applications development in manufacturing, especially in the dynamic operating environment of FMS.

Originality/value

Reported results provide a modular approach of context‐sensitive computing and a practical use case implementation to achieve context awareness in FMS. The results are seen extendable to other manufacturing domains.
Effect of system compliance and workpiece dynamics on machining error
Authors: Vishnupriyan S.
Published: March 2012

Purpose

Source errors in a workpiece fixture system include the compliance of the workpiece fixture system and workpiece dynamics. The purpose of this paper is to study the relative significance of these two. The findings would help to achieve computational economy in optimization of fixture layout and/or clamping forces.

Design/methodology/approach

Different layouts are generated with the help of a reconfigurable fixture set up and a slot is end milled on the workpiece. Using these data and the finite element software ANSYS, the machining error due to system compliance is computed. The machining error due to workpiece dynamics is obtained using a data acquisition system with the LabView software. These steps are repeated for different clamping forces and the relative contribution of these two sources to the overall machining error is studied.

Findings

Results show that the system compliance is much smaller in magnitude compared to workpiece dynamics and hence does not contribute appreciably to the overall machining error. This leads to the conclusion that, for bulky and stiff parts, evaluation of the machining error due to compliance can be done away with.

Originality/value

The paper's originality lies in comparing the two sources of machining error using experimental work and finite element models. To the author's knowledge such a comparison has not been reported in the literature.
Analysing user's queries for cross‐language image retrieval from digital library collections
Authors: Petrelli Daniela , Clough Paul
Published: March 2012

Purpose

This paper aims to describe a study of the queries generated from a user experiment for cross‐language information retrieval (CLIR) from a historic image archive.

Design/methodology/approach

A controlled lab‐based user study was carried out using a prototype Italian‐English image retrieval system. Participants were asked to carry out searches for 16 images provided to them, a known‐item search task. Italian speaking users generated 618 queries for a set of known‐item search tasks. User's interactions with the system were recorded and queries were analysed manually quantitatively and qualitatively. The queries generated by user's interaction with the system were analysed and the results used to suggest recommendations for the future development of cross‐language retrieval systems for digital image libraries.

Findings

Results highlight the diversity in requests for similar visual content and the weaknesses of machine translation for query translation. Through the manual translation of queries the authors show the benefits of using high‐quality translation resources. The results show the individual characteristics of users while performing known‐item searches and the overlap obtained between query terms and structured image captions, highlighting the use of user's search terms for objects within the foreground of an image.

Research limitations/implications

This research looks in depth into one case of interaction and one image repository. Despite this limitation, the discussed results are likely to be valid across other languages and image repositories.

Practical implications

To develop effective systems requires studying user's search behaviours, particularly in digital image libraries.

Originality/value

The growing quantity of digital visual material in digital libraries offers the potential to apply techniques from CLIR to provide cross‐language information access services. The value of this paper is in the provision of empirical evidence to support recommendations for effective cross‐language image retrieval system design.
Exploration and study of multilingual thesauri automation construction for digital libraries in China
Authors: Zeng Wen
Published: March 2012

Purpose

The paper aims to explore multilingual thesauri automation construction based on the freely available digital library resources. The key methods and study results are presented in the paper. It also proposes a way that terms are automatically extracted from multilingual parallel corpus.

Design/methodology/approach

The study adopted the technology of natural language processing to analyze the linguistics characteristics of terms, and combined this with statistical analyses to extract the terms from technological documents. The methods consist of automatically extracting and filtering terms, judging and building relationship among terms, building the multilingual parallel corpus, and extracting term pairs between Chinese and foreign languages through calculating their associated probability. The experiments run on the Java test platform.

Findings

The study obtains the following conclusions: finding the similarities and differences between the Chinese thesaurus standard and international thesaurus standard. The methods for automatically extracting terms and building relationships among them are presented. Eventually the multilingual terms' translation sets are generated based on real corpora. The results of the study show that the proposed methods can obtain better performance. The effect of automatic terms' translation alignment method is better than that of traditional IBM model method.

Practical implications

The study results can provide references for further study and application of multilingual thesauri automation construction using Chinese as a pivot.

Originality/value

The paper proposes new ideas on thesaurus automation construction in the digital age. The presented method based on linguistics and statistics is a new attempt. According to the experimental results, this exploration and study is innovative and valuable. In addition, these ideas and methods give a good start for improving information services of the PRC's National Science and Technology Digital Library.
Effective medical resources searching using an ontology‐driven medical information retrieval system
Authors: Yi Myongho
Published: March 2012

Purpose

As international users increase rapidly, multilingual systems have become a very important service for global users. The purpose of this paper is to design and implement an ontology‐driven medical information retrieval (OMIR) system by building a medical ontology based on the Centers for Disease Control and Prevention's (CDC) medical records.

Design/methodology/approach

A traditional cataloging scheme is used as a navigation menu in the CDC system. This traditional cataloging scheme is transformed to a unique medical ontology for global users in the OMIR system. An experimental study was conducted on both an ontology‐driven medical information system (OMIR) and the CDC system.

Findings

The medical ontology can be used to filter out unsuitable resources based on semantic relationships. In addition, the recommended resources can be categorized and provide the patron with different languages to access resources. The OMIR system provides better relevancy and shorter search times compared with alternative systems.

Research limitations/implications

The OMIR system is currently implemented for medical resources from the CDC. The developed method may also be applied to other domain areas.

Originality/value

This paper represents a practical method of building a multilingual medical information retrieval system and explains the functional use of ontological knowledge. This study provides insights into medical information seeking performance on the medical database systems.
Mapping multilingual lexical semantics for knowledge organization systems
Authors: Chen Shu‐jiun , Chen Hsueh‐hua
Published: March 2012

Purpose

The study aims to investigate, through mapping analysis, the operation of knowledge organization systems (KOS) in different languages (English and Chinese), the types of term equivalence and the degree of similarity between different conceptual structures, and issues related thereto.

Design/methodology/approach

Terms are selected from the Art & Architecture Thesaurus developed by Getty Research Institute in the USA (source language) and the National Palace Museum in Taiwan participating in Taiwan e‐Learning and Digital Archives Program (target language). In respect of data analysis, mapping analysis and content analysis are both adopted.

Findings

Among the six types of term equivalence, “exact equivalence” appears most frequently. The degree of similarity between different conceptual structures can be divided into four types: similar structure, transferring part of the structure of source language into the system of target language by modeling; similar structure, but the structure of source language needs to be expanded or revised; dissimilar structure, the term in target language can be partially mapped to the term in source language; lack of structure, no matches between target language and source language.

Practical implications

The next step is to develop a more comprehensive conceptual structure that can incorporate multicultural perspectives. If the “partial equivalence” terms are further identified as important concepts, the problems of non‐exact equivalence terms and dissimilar conceptual structures can be solved by addressing the needs of English users in searching for Chinese art collections.

Originality/value

The study serves as a pilot study applicable to the development of multilingual KOS in the domain of Chinese fine arts, building the first demonstration model for the interoperability of KOS in Chinese and English.
An empirical inquiry into marketing Islamic mortgages in the UK
Authors: Tameme Mohammed , Asutay Mehmet
Published: March 2012

Purpose

This paper aims to explore public perceptions on marketing‐related issues of Islamic mortgages, which can help to identify the contents of the best marketing strategies for financial institutions wishing to promote Islamic mortgages among the Muslim community in the UK. In doing so, the access issues of the Islamic mortgages and how to effectively raise awareness among the Muslim community is discussed. The paper also aims to discuss the integration of the Islamic mortgage and to investigate the importance of staff confidence and the acceptability of promoting the Islamic mortgage by a non‐Muslim sales person. Furthermore, the role of religion, the Muslim households' consumer preferences and the prospect of Islamic mortgage providers' cross‐selling Islamic mortgage products to the Muslim customers are also discussed.

Design/methodology/approach

The principal method used to gather primary data is a questionnaire survey conducted with Muslim households in East London. From a total of 350 questionnaires distributed, 270 were returned, of which 250 were fully completed, thereby yielding a response rate of about 77 per cent.

Findings

The findings indicate that wider social factors and lifestyle choices may be increasing the demand for Islamic mortgages. The paper also argues that there is scope in the UK to expand the market for Islamic products and services to non‐Muslims as well if effective and sound marketing strategies are implemented.

Research limitations/implications

The sample size can be extended to have more reliable results. In addition, future research should consider other geographical locations in the UK to provide diversity in terms of participants.

Practical implications

The findings of the research can provide valuable information for the Islamic mortgage market in the UK but also render information for Islamic finance service providers in shaping their marketing strategy in relation to Islamic mortgages.

Originality/value

The paper utilises primary data from a particular case, which provides valuable findings in relation to participants' perceptions on Islamic mortgage and its marketing‐related issues. It also provides the elements of an effective marketing strategy for the marketing of Islamic mortgages in the UK. Therefore, in addition to being an academic paper appealing to academic inquiry, it has practical implications for the industry as well.
Do ongoing relationships buffer the effects of service recovery on customers' trust and loyalty?
Authors: Pizzutti dos Santos Cristiane , Basso Kenny
Published: March 2012

Purpose

This study aims to fill an important gap in the literature by exploring the moderating role of client‐company relationship type on the impact of service recovery judgments on clients' trust and loyalty intentions.

Design/methodology/approach

A sample of 216 Brazilian banks clients who made a complaint to their bank within the previous 12 months answered the survey. Data collection took place at a major Brazilian international airport. In terms of relationship type, the authors segmented their sample in two groups: relational and transactional clients. They used multi‐group structural equation modeling to test their hypotheses.

Findings

Relational clients showed higher switching costs, trust, and loyalty intentions than transactional clients. The client‐company relationship type also moderated the impact of distributive justice on satisfaction, satisfaction on trust in the management policies and practices (MPP trust), and switching costs on repurchase intentions. MPP trust fully mediated the effects of trust in frontline employees (FLE trust) on loyalty (repurchase and WOM intentions).

Practical implications

The findings suggest that stronger client‐company relationships may limit the impact of service and recovery failures on customer trust and loyalty. This is a critical piece of information for banks as they could customize their recovery strategies to fit the different types of relationships they have with their clients.

Originality/value

By exploring the impact of the type of relationship on the service recovery process and their consequences, this study answers the following important research question: do ongoing client‐company relationships buffer the impact of service recovery on trust and loyalty intentions?
Adopting a specific innovation type versus composition of different innovation types
Authors: Baba Yusif
Published: March 2012

Purpose

Although several types of innovation are identified in the extant literature, researchers have not resolved conflicting theoretical predictions about the implication of adopting innovation types. Following the conceptualization of Damanpouret al., this paper aims to distinguish between three innovation types (i.e. services, technological process, and administrative process) and make suggestions for banks on whether to focus their innovation efforts on a specific type or composition of different types in order to optimize the returns to innovation.

Design/methodology/approach

Based on an empirical case study of a large multinational bank in Ghana (name withheld for anonymity), data were collected with questionnaire instruments from 51 bank managers. Two regression equations were estimated and analyzed using the Statistical Package for the Social Sciences (SPSS).

Findings

The paper finds evidence that focus on adopting a specific innovation type seems to contribute more to performance than adopting bundles of different types of innovation. As the bank focuses on adopting only administrative process innovation it enjoys higher growth in market share than when it adopts services innovation and technological process innovation in conjunction with administrative process innovation.

Practical implications

It seems that even when resources are in abundance, and complementary changes or innovations are found to be necessary, there is less need to introduce different types of innovation with a more balanced rate simultaneously.

Originality/value

The study proposes to resolve conflicting theoretical predictions and ongoing policy disputes about the effects on business performance (i.e. market share) of the adoption of a specific innovation type versus composition of different innovation types.
Sequential testing for two exponential distributions at arbitrary risks
Authors: Michlin Yefim H. , Kaplunov Vladimir , Ingman Dov
Published: March 2012

Purpose

This paper aims to propose a methodology for planning of a truncated sequential probability ratio test (SPRT) in which two systems with exponentially distributed times between failures (TBFs) are compared. The study is concerned with tests with arbitrary probabilities of I‐ and II‐type errors.

Design/methodology/approach

The study methodology, based on the proposed optimality criteria for these tests, permitted comparison of different modes of truncation and obviated the drawbacks of discreteness and multidimensionality of their characteristics.

Findings

The solution permits planning of a heavily‐truncated test with an average sample number exceeding its counterpart for the optimal (non‐truncated) test by at most a specified percentage. Relationships are outlined for optimal selection of the truncated test boundaries. So are optimality estimation criteria for the constructed test. The superiority of the SPRTs, truncated by the proposed methodology, over their counterparts, processed according to current practices, is demonstrated.

Research limitations/implications

The solution refers to the case where the compared systems have exponentially distributed TBFs (or times to failure (TTFs) for non‐repairable cases).

Practical implications

The proposed algorithm and relationships for planning the tests in question can be used by developers of tests for reliability. A planning example from the semiconductor industry is given.

Originality/value

This paper presents a novel approach to planning of truncated SPRTs with arbitrary probabilities of I‐ and II‐type errors. The methodology is also applicable for truncated binomial SPRTs.