bluuebunny/crossref_metadata_2025_split huggingface dataset:
VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays
Authors: Allred Adam F. , Renshaw Hilary , Weaver Scott , Tesh Robert B. , Wang David 
Published: October 2012

Abstract
Motivation: Current methods in diagnostic microbiology typically focus on the detection of a single genomic locus or protein in a candidate agent. The presence of the entire microbe is then inferred from this isolated result. Problematically, the presence of recombination in microbial genomes would go undetected unless other genomic loci or protein components were specifically assayed. Microarrays lend themselves well to the detection of multiple loci from a given microbe; furthermore, the inherent nature of microarrays facilitates highly parallel interrogation of multiple microbes. However, none of the existing methods for analyzing diagnostic microarray data has the capacity to specifically identify recombinant microbes. In previous work, we developed a novel algorithm, VIPR, for analyzing diagnostic microarray data.
Results: We have expanded upon our previous implementation of VIPR by incorporating a hidden Markov model (HMM) to detect recombinant genomes. We trained our HMM on a set of non-recombinant parental viruses and applied our method to 11 recombinant alphaviruses and 4 recombinant flaviviruses hybridized to a diagnostic microarray in order to evaluate performance of the HMM. VIPR HMM correctly identified 95% of the 62 inter-species recombination breakpoints in the validation set and only two false-positive breakpoints were predicted. This study represents the first description and validation of an algorithm capable of detecting recombinant viruses based on diagnostic microarray hybridization patterns.
Availability: VIPR HMM is freely available for academic use and can be downloaded from http://ibridgenetwork.org/wustl/vipr.
Contact: davewang@borcim.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
Authors: Liu Binghang , Yuan Jianying , Yiu Siu-Ming , Li Zhenyu , Xie Yinlong , Chen Yanxiang , Shi Yujian , Zhang Hao , Li Yingrui , Lam Tak-Wah , Luo Ruibang 
Published: October 2012

Abstract
Motivation: The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us from better assembling the genome from scratch. New protocols now exist that can generate overlapping pair-end reads. By joining the 3′ ends of each read pair, one is able to construct longer reads for assembling. However, effectively joining two overlapped pair-end reads remains a challenging task.
Result: In this article, we present an efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.
Availability and implementation: COPE is implemented in C++ and is freely available as open-source code at ftp://ftp.genomics.org.cn/pub/cope.
Contact: twlam@cs.hku.hk or luoruibang@genomics.org.cn
MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit
Authors: Fange David , Mahmutovic Anel , Elf Johan 
Published: October 2012

Abstract
Summary: MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make it possible to construct physically consistent models of diffusion-controlled reactions also at fine spatial discretization.
Availability: MesoRD is written in C++ and licensed under the GNU general public license (GPL). MesoRD can be downloaded at http://mesord.sourceforge.net. The MesoRD homepage, http://mesord.sourceforge.net, contains detailed documentation and news about recently implemented features.
Contact: johan.elf@icm.uu.se
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data
Authors: Chen Chong-Jian , Servant Nicolas , Toedling Joern , Sarazin Alexis , Marchais Antonin , Duvernois-Berthet Evelyne , Cognat Valérie , Colot Vincent , Voinnet Olivier , Heard Edith , Ciaudo Constance , Barillot Emmanuel 
Published: October 2012

Abstract
Summary: Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions. The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that sRNA raw data from the three current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) can be analyzed with this pipeline. The ncPRO-seq pipeline can be used to analyze read and alignment data, based on any sequenced genome, including mammals and plants.
Availability: Source code, annotation files, manual and online version are available at http://ncpro.curie.fr/.
Contact: bioinfo.ncproseq@curie.fr or cciaudo@ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Robust design of microbial strains
Authors: Costanza Jole , Carapezza Giovanni , Angione Claudio , Lió Pietro , Nicosia Giuseppe 
Published: October 2012

Abstract
Motivation: Metabolic engineering algorithms provide means to optimize a biological process leading to the improvement of a biotechnological interesting molecule. Therefore, it is important to understand how to act in a metabolic pathway in order to have the best results in terms of productions. In this work, we present a computational framework that searches for optimal and robust microbial strains that are able to produce target molecules. Our framework performs three tasks: it evaluates the parameter sensitivity of the microbial model, searches for the optimal genetic or fluxes design and finally calculates the robustness of the microbial strains. We are capable to combine the exploration of species, reactions, pathways and knockout parameter spaces with the Pareto-optimality principle.
Results: Our framework provides also theoretical and practical guidelines for design automation. The statistical cross comparison of our new optimization procedures, performed with respect to currently widely used algorithms for bacteria (e.g. Escherichia coli) over different multiple functions, reveals good performances over a variety of biotechnological products.
Availability: http://www.dmi.unict.it/nicosia/pathDesign.html.
Contact: nicosia@dmi.unict.it or pl219@cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Patron‐driven e‐book use and users' e‐book perceptions: a snapshot
Authors: McLure Merinda , Hoseth Amy 
Published: October 2012

PurposeThis paper aims to provide a snapshot of student and staff attitudes towards e‐books, collected through a web‐based survey, as well as an analysis of use data for a specific universe of e‐books provided via a patron‐driven purchasing model and accessed during the survey timeframe.Design/methodology/approachThis research analyzed survey responses collected from May 2010 to December 2010 and use data for the universe of e‐books made accessible via PDA, and used by library patrons, during this period.FindingsE‐books are no longer a new phenomenon and the CSU Libraries have provided access to e‐books for many years, yet users' prior experience with e‐books, perspectives on desirable and undesirable e‐book characteristics, and preferences for print versus e‐books as provided by the libraries continue to vary. During the libraries' initial entry into PDA, e‐books made accessible to users via this model received more use through browsing than sustained use or download, but relatively little use overall. The study provides a starting point for the continued analysis of this library's PDA program, now the primary mechanism used to provide its academic user community with book access.Practical implicationsThe authors present a review of the literature and research findings about academic users' interactions with, and preferences for, e‐books. They provide a point‐in‐time analysis of user interactions with e‐book titles made accessible via the libraries' PDA program and a subject‐level study of the use of these titles.Originality/valueThis paper presents point‐of‐use feedback regarding e‐books, from academic users, and detailed information about e‐book titles accessed via a PDA model.
Problematic customers and turnover intentions of customer service employees
Authors: Poddar Amit , Madupalli Ramana 
Published: October 2012

PurposeThe purpose of this paper is to examine the effects of problematic customer behaviors on customer service employee attitudes and subsequent turnover intentions from the organization and also the occupation.Design/methodology/approachData from five semi‐structured depth interviews and 215 quantitative surveys using structured questionnaires were used to develop and test the theoretical model. Customer service employees working in different call center companies serving American customers were approached using an established survey panel.FindingsResults using the partial least squares (PLS) methodology showed that problematic customer behaviors drain customer service employees emotionally. Emotional exhaustion is negatively related to job satisfaction, and subsequently, employees' turnover intentions. The results also show that turnover intentions with organization and occupation are positively related to each other.Research limitations/implicationsAs regards implications, this study provides an understanding of the relationship between problematic customer behaviors and employees' turnover intentions. Future researchers can utilize the findings from this study for investigating other consequences and antecedents of problematic customer behaviors. A limitation of the study is its use of cross‐sectional data.Practical implicationsThis paper provides call center managers with an understanding of the effects of problematic customer behaviors on employee attitudes. It discusses the need for understanding problematic customers and ways to manage the effects of such experiences.Originality/valueThe study investigates an under‐researched phenomenon, i.e. problematic customer behaviors. The study provides evidence of the relationship between problematic customer behaviors and turnover intentions in service employees. This study is also one of very few in marketing to investigate the relationship between organizational and occupational turnover intentions.
Leadership style and team processes as predictors of organisational learning
Authors: Bhat Aruna B. , Verma Neha , Rangnekar S. , Barua M.K. 
Published: October 2012

PurposeThis paper aims to explore the independent and interactive leadership style and team processes on organisational learning in an Indian context.Design/methodology/approachThe methodology used is survey based. Primary data were collected from 36 Indian manufacturing sector executives and in total there were three teams (n=11, n=13 and n=12).FindingsIt was found that overall leadership style and transactional leadership had significant positive impact on organisational learning. Furthermore, team processes like cohesion and support and confrontation and problem solving were also found to be important predictors of organisational learning. The interactive effect of independent variables on dependent variable was also positive and significant.Research limitations/implicationsDiscussions are performed and conclusions are drawn in the light of existing literature. The study bears implications for researchers to take on similar research in other contexts.Practical implicationsThe study bears significant implications for executives working in manufacturing organisations. It is suggested that transactional leadership style should be employed to contribute towards organisational learning in such firms. Moreover, the use of team processes will also help in enhancing learning at the team and organisational levels.Originality/valueThis paper identifies two significant criterion variables to predict organisational learning. It is a pioneering effort to use team processes and leadership style together as predictors of organisational learning in Indian context.
Conflict management and effectiveness in virtual teams
Authors: Pazos Pilar 
Published: October 2012

PurposeThis paper aims to explore the role of goal‐oriented attitudes and behaviors as antecedents of conflict management and the subsequent impact of conflict management on team outcomes in virtual teams. Of particular interest is the role of “commitment to team goals” as a predictor of successful conflict management and the subsequent impact of conflict management on team outcomes.Design/methodology/approachThis paper describes the results from a quasi‐experimental study examining the relationships among commitment to team goals, conflict management and team outcomes in virtual teams. First, it provides an in depth review of relevant empirical findings. Next, it describes a study examining the relationships between three sets of variables: commitment to team goals; conflict management; and team outcomes (performance and attitudinal) in the context of virtual teams. Data were collected from 141 students grouped in 39 teams size 3 to 4 that were part of four cohorts of an Engineering Management course.FindingsThe results provide some preliminary evidence that conflict management mediated the relationships between goal commitment and team outcomes. Results suggest that commitment to team goals is a significant predictor of successful conflict management. Findings also suggest that teams that are more actively involved in preventing and solving their conflict experience a significant increase in the relationship between commitment to team goals and team performance, suggesting that use of effective conflict management can support team effectiveness in the context of virtual teams. Finally, limitations and suggestions for future research are presented.Originality/valueThis paper sheds some light into the role conflict as a mediator on the relationship between goal commitment and virtual team effectiveness. It provides preliminary evidence that conflict management plays a critical role in enhancing virtual team effectiveness.
Intellectual capital transformation evaluating model
Authors: Molodchik Mariya , Shakina Elena , Bykova Anna 
Published: October 2012

PurposeThe purpose of this paper is to present a framework that is developed for analysis of intellectual capital transformation into companies’ value, including an identification of the key factors of this process.Design/methodology/approachThe paper employs intellectual capital on the intersection of value‐based management (VBM) and the resource‐based view (RBV). Starting from a review of the results provided in the literature regarding intellectual capital (IC) evaluation and its link with firm performance, a system of proxy indicators related to IC transformation in both concepts has been designed. The evaluation ability of the developed model was justified using regression analyses.FindingsA detailed algorithm for intellectual capital evaluation in terms of input‐outcome transformation. The intellectual capital transformation evaluating model (ICTEM) provides a holistic view of intellectual resources as companies’ strategic investments.Research limitations/implicationsThe paper emphasizes that the ICTEM framework could be mostly applied for the analysis of a firm as a typical representative of the industry or the country. In that sense it is not applicable for specific feature analysis of a company.Practical implicationsThe paper highlights the ICTEM as a tool of investment decisions, mostly taking into account common trends, the prospects of industries, and economies’ development.Originality/valueThe ICTEM provides the ostensive framework of intellectual capital transformation analysis using a statistical approach.
Intellectual capital as competitive advantage in emerging clusters in Latin America
Authors: Jardon Carlos M. , Susana Martos Maria 
Published: October 2012

PurposeEmerging clusters, formed by small to medium‐sized enterprises (SMEs) of slow growth and embryonic management systems present a different competitive advantage scheme. The purpose of this paper is to analyze relationships among components of intellectual capital within a model of competitive advantages in emerging clusters in a region of Latin America.Design/methodology/approachAn intellectual capital model in a competitive advantage scheme is defined. A sequential method based in PLS technique is suggested to select the model and estimate the parameters. A sample of 113 wood manufacturing SMEs in a region of Argentina was selected.FindingsThe competitive advantage scheme in emerging clusters of SMEs proposes that resources affect organizational capabilities; territory and organizational capabilities affect strategic factors which improve performance. In this scheme, human capital affects structural capital and structural capital generates relational capital. SMEs organize tangible resources and relational capital to build organizational capabilities.Research limitations/implicationsThe sample is a cross‐section. The performance is subjectively measured by the satisfaction of the entrepreneurs with different items.Practical implicationsThe paper establishes suggestions to strategies of the SMEs in emerging clusters and politics of developing countries. This paper enables practitioners and scholars to comprehend and make legitimate decisions and conclusions that can foster business growth.Originality/valueThe authors tested the impact of dimensions of intellectual capital on performance in emerging clusters of developing countries within a competitive advantage scheme, showing relationships among intellectual capital dimensions and competitive advantages. The analysis differentiates between intellectual capital dimension and organizational capabilities.
Use of IC information in Japanese financial firms
Authors: Holland John , Henningsson Johan , Johanson Ulf , Koga Chitoshi , Sakakibara Shigeki 
Published: October 2012

PurposeThe purpose of this paper is to explore the perceptions of: how Japanese financial firms (JFF) acquire and use company intellectual capital (IC) information in their common routine equity investment decisions, how this activity contributes to knowledge creation in the JFFs, and how investee company knowledge creation is affected by the JFFs.Design/methodology/approachThe research employed a multi‐case design, using four JFF cases. The investigation was performed in terms of Nonaka and Toyama's “theory of the knowledge creating firm”.FindingsIC information contributed to earnings estimates and company valuation. Emotional information contributed to JFF feelings and confidence in their information use and valuation. JFF knowledge was an important component of the key interacting and informed contexts used by JFFs. This generated opportunities to improve disclosure and accountability between JFFs and their investee companies. Common patterns of behaviour across the JFFs were counterbalanced by variety and differences noted in JFF behaviour.Practical implicationsThe findings provide important insights into how JFF knowledge creating patterns could limit or progress a common language of communication between companies and markets on the subject of IC. This could impact on the quality of corporate disclosure and accountability processes.Originality/valueThe paper demonstrates that there is a need for further use of qualitative studies of financial market behavior. Especially in the area of understanding the communication of IC between firms and financial markets, the potential of using sociology of finance approaches appears to be considerable.
Intellectual capital disclosures by Indian and Australian information technology companies
Authors: Joshi Mahesh , Singh Ubha Dharminder , Sidhu Jasvinder 
Published: October 2012

PurposeThe purpose of this paper is to investigate and compare the voluntary reporting of intellectual capital (IC) by the top 20 software and technology sector companies in a developing nation, India, and a developed nation, Australia. The paper aims to highlight the differences in IC disclosure practices of the companies operating in two different economies.Design/methodology/approachThe study investigates the top 20 firms by market capitalisation listed on the Bombay Stock Exchange in India and the Australian Stock Exchange in Australia in the year 2007‐2008. Using the content analysis method, the paper reviews the annual reports of these firms to determine IC disclosure trends in India and Australia. Statistical tools and graphs have been used to compare and contrast ICD disclosures in two countries.FindingsThe study has identified IC disclosure differences between Indian and Australian firms, and reports disclosures by Indian companies are on a higher scale than Australian Software and Technology Sector companies. However, Levels of voluntary IC disclosure are found to be low in both the nations and most of the disclosures are declarative in nature.Research limitations/implicationsThis lack of consistency in reporting practices makes comparisons across countries difficult. The paper emphasises the need for a uniform and consistent framework for the reporting of intellectual capital items.Practical implicationsThe results of this exploratory study on the knowledge based industrial sector can be used by researchers to explore different types of IC reporting initiatives pursued across specifically knowledge based industrial sectors.Originality/valueThis study offers insights into comparative trends in IC disclosure practices of software and technology sector companies operating in a developed and a developing country.