bluuebunny/crossref_metadata_2025_split huggingface dataset:
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies
Authors: Sun Hokeun , Wang Shuang 
Published: March 2012

AbstractMotivation: 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.eduSupplementary 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

Abstract
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
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

Abstract
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

PurposeThe 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/approachIn‐depth interviews with exhibitors of packaging automation of all types at the PackExpo Show.FindingsSuppliers of packaging automation continue to innovate with faster, more effective and cost cutting systems.Practical implicationsPackaging 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/valueFor 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

PurposeAssembly 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/approachFirst, 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.FindingsThe 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 implicationsThe 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/valueDifferent 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

PurposeThe 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/approachA 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.FindingsContinuous 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/implicationsThe 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 implicationsThis paper includes the practical implications of context‐sensitive applications development in manufacturing, especially in the dynamic operating environment of FMS.Originality/valueReported 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

PurposeSource 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/approachDifferent 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.FindingsResults 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/valueThe 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

PurposeThis 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/approachA 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.FindingsResults 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/implicationsThis 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 implicationsTo develop effective systems requires studying user's search behaviours, particularly in digital image libraries.Originality/valueThe 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

PurposeThe 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/approachThe 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.FindingsThe 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 implicationsThe study results can provide references for further study and application of multilingual thesauri automation construction using Chinese as a pivot.Originality/valueThe 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

PurposeAs 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/approachA 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.FindingsThe 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/implicationsThe OMIR system is currently implemented for medical resources from the CDC. The developed method may also be applied to other domain areas.Originality/valueThis 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

PurposeThe 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/approachTerms 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.FindingsAmong 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 implicationsThe 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/valueThe 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

PurposeThis 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/approachThe 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.FindingsThe 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/implicationsThe 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 implicationsThe 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/valueThe 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

PurposeThis 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/approachA 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.FindingsRelational 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 implicationsThe 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/valueBy 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?