bluuebunny/crossref_metadata_2025 huggingface dataset:
Transfection of exogenous rotavirus rearranged RNA segments in cells infected with a WT rotavirus results in subsequent gene rearrangements
Authors: Duponchel Sarah , Troupin Cécile , Vu Lan Trang , Schnuriger Aurélie , Trugnan Germain , Garbarg-Chenon Antoine
Published: June 2014

Group A rotaviruses, members of the family Reoviridae, are a major cause of infantile acute gastroenteritis. The rotavirus genome consists of 11 dsRNA segments. In some cases, an RNA segment is replaced by a rearranged RNA segment, which is derived from its standard counterpart by partial sequence duplication. It has been shown that some rearranged segments are preferentially encapsidated into viral progenies after serial passages in cell culture. Based on this characteristic, a reverse genetics system was used previously to introduce exogenous segment 7 rearrangements into an infectious rotavirus. This study extends this reverse genetics system to RNA segments 5 and 11. Transfection of exogenous rotavirus rearranged RNA segment 5 or 11 into cells infected with a WT helper rotavirus (bovine strain RF) resulted in subsequent gene rearrangements in the viral progeny. Whilst recombinant viruses were rescued with an exogenous rearranged segment 11, the exogenous segment was modified by a secondary rearrangement. The occurrence of spontaneous rearrangements of WT or exogenous segments is a major hindrance to the use of this reverse genetics approach.
Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq
Authors: Gonzàlez-Porta Mar , Brazma Alvis
Published: June 2014

In the past years, RNA sequencing has become the method of choice for the study of transcriptome composition. When working with this type of data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes. However, the number of genes predicted to undergo differential splicing is often high, and further interpretation of the results becomes a challenging task. Here we present SwitchSeq, a novel set of tools designed to help the users in the interpretation of differential splicing events that affect protein coding genes. More specifically, we provide a framework to identify switch events,i.e.,cases where, for a given gene, the identity of the most abundant transcript changes across conditions. The identified events are then annotated by incorporating information from several public databases and third-party tools, and are further visualised in an intuitive manner with the independent R package tviz. All the results are displayed in a self-contained HTML document, and are also stored in txt and json format to facilitate the integration with any further downstream analysis tools. Such analysis approach can be used complementarily to Gene Ontology and pathway enrichment analysis, and can also serve as an aid in the validation of predicted changes in mRNA and protein abundance.

Availability: The latest version of SwitchSeq, including installation instructions and use cases, can be found athttps://github.com/mgonzalezporta/SwitchSeq. Additionally, the plot capabilities are provided as an independent R package athttps://github.com/mgonzalezporta/tviz.
Avoiding test set bias with rank-based prediction
Authors: Patil Prasad , Bachant-Winner Pierre-Olivier , Haibe-Kains Benjamin , Leek Jeffrey T.
Published: June 2014

Background

Prior to applying genomic predictors to clinical samples, the genomic data must be properly normalized. The most effective normalization methods depend on the data from multiple patients. From a biomedical perspective this implies that predictions for a single patient may change depending on which other patient samples they are normalized with. This test set bias will occur when any cross-sample normalization is used before clinical prediction.

Methods

We developed a new prediction modeling framework based on the relative ranks of features within a sample in order to prevent the need for cross-sample normalization, therefore effectively avoiding test set bias. We employed modeling with previously published Top-Scoring Pairs (TSPs) methodology to build the rank-based predictors. We further investigated the robustness of the rank-based models in case of heterogeneous datasets using diverse microarray technologies.

Results

We demonstrated that results from existing genetic signatures which rely on normalizing test data may be unreproducible when the patient population changes composition or size. Using pairwise comparisons of features, we produced a ten gene, platform-robust, and interpretable alternative to the PAM50 subtyping signature and evaluated the robustness of our signature across 6,297 patients samples from 28 curated breast cancer microarray datasets spanning 15 different platforms.

Conclusion

We propose a new approach to developing genomic signatures that avoids test set bias through the robustness of rank-based features. Our small, interpretable alternative to PAM50 produces comparable predictions and patient survival differentiation to the original signature. Additionally, we are able to ensure that the same patient will be classified the same way in every context.
iRAP - an integrated RNA-seq Analysis Pipeline
Authors: Fonseca Nuno A. , Petryszak Robert , Marioni John C. , Brazma Alvis
Published: June 2014

RNA-sequencing (RNA-Seq) has become the technology of choice for whole-transcriptome profiling. However, processing the millions of sequence reads generated requires considerable bioinformatics skills and computational resources. At each step of the processing pipeline many tools are available, each with specific advantages and disadvantages. While using a specific combination of tools might be desirable, integrating the different tools can be time consuming, often due to specificities in the formats of input/output files required by the different programs.

Here we present iRAP, an integrated RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression, testing for differential expression. iRAP also includes multiple tools for gene set enrichment analysis and generates web browsable reports of the results obtained in the different stages of the pipeline. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level. iRAP is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line. Despite this, it also provides more advanced users with the ability to customise the options used by their chosen tools.

iRAP is available under General Public License 3 (GPLv3) and although it should be portable to any POSIX-compliant operating system, several third party programs only run on Linux. iRAP can be obtained fromhttp://code.google.com/p/irap.
Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
Authors: Frazee Alyssa C. , Jaffe Andrew E. , Langmead Ben , Leek Jeffrey T.
Published: June 2014

Motivation

Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially-constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data.

Results

Polyesteris an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user.

Availability and Implementation

Polyesteris freely available from Bioconductor (http://bioconductor.org/).

Contact

jtleek@gmail.com

Supplementary Information

Supplementary figures are available online.
Restriction and recruitment - gene duplication and the origin and evolution of snake venom toxins
Authors: Hargreaves Adam D , Swain Martin T , Hegarty Matthew J , Logan Darren W , Mulley John F
Published: June 2014

Snake venom has been hypothesised to have originated and diversified via a process that involves duplication of genes encoding body proteins with subsequent recruitment of the copy to the venom gland, where natural selection acts to develop or increase toxicity. However, gene duplication is known to be a rare event in vertebrate genomes and the recruitment of duplicated genes to a novel expression domain (neofunctionalisation) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions. Therefore, whilst this hypothesis concerning the evolution of snake venom is therefore very unlikely and should be regarded with caution, it is nonetheless often assumed to be established fact, hindering research into the true origins of snake venom toxins. To critically evaluate this hypothesis we have generated transcriptomic data for body tissues and salivary and venom glands from five species of venomous and non-venomous reptiles. Our comparative transcriptomic analysis of these data reveals that snake venom does not evolve via the hypothesised process of duplication and recruitment of genes encoding body proteins. Indeed, our results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of non-venomous reptiles and that these genes have therefore been restricted to the venom gland following duplication, not recruited. Thus snake venom evolves via the duplication and subfunctionalisation of genes encoding existing salivary proteins. These results highlight the danger of the elegant and intuitive ?just-so story? in evolutionary biology.
Testing the Toxicofera: comparative reptile transcriptomics casts doubt on the single, early evolution of the reptile venom system
Authors: Hargreaves Adam D , Swain Martin T , Logan Darren W , Mulley John F
Published: June 2014

Background

The identification of apparently conserved gene complements in the venom and salivary glands of a diverse set of reptiles led to the development of the Toxicofera hypothesis – the idea that there was a single, early evolution of the venom system in reptiles. However, this hypothesis is based largely on relatively small scale EST-based studies of only venom or salivary glands and toxic effects have been assigned to only some of these putative Toxcoferan toxins in some species. We set out to investigate the distribution of these putative venom toxin transcripts in order to investigate to what extent conservation of gene complements may reflect a bias in previous sampling efforts.

Results

We have carried out the first large-scale test of the Toxicofera hypothesis and found it lacking in a number of regards. Our quantitative transcriptomic analyses of venom and salivary glands and other body tissues in five species of reptile, together with the use of available RNA-Seq datasets for additional species shows that the majority of genes used to support the establishment and expansion of the Toxicofera are in fact expressed in multiple body tissues and most likely represent general maintenance or “housekeeping” genes. The apparent conservation of gene complements across the Toxicofera therefore reflects an artefact of incomplete tissue sampling. In other cases, the identification of a non-toxic paralog of a gene encoding a true venom toxin has led to confusion about the phylogenetic distribution of that venom component.

Conclusions

Venom has evolved multiple times in reptiles. In addition, the misunderstanding regarding what constitutes a toxic venom component, together with the misidentification of genes and the classification of identical or near-identical sequences as distinct genes has led to an overestimation of the complexity of reptile venoms in general, and snake venom in particular, with implications for our understanding of (and development of treatments to counter) the molecules responsible for the physiological consequences of snakebite.
A comparison of the gobiid fauna between a shoal and an island habitat in the central Visayas (Philippines)
Authors: Stiefel Klaus M. , Merrifield Alistair , Reed Matt , Joyce David B.
Published: June 2014

We surveyed the marine gobies of Malapascua island (Philippines), the surrounding islets and the nearby Monad shoal. We found 59 species in 19 genera, including 2 undescribed species of the genusTrimma, and 3 geographic and 6 depth range expansions. Furthermore we describe a new type of mimicry between the gobyKoumasetta hectoriand the cardinalfishApogon nigrofasciatus. The comparison of the island versus shoal goby fauna showed a lesser species richness of shrimp-associated gobies at the shoal. This likely reflects the fact that hydrodynamic features of the environment play a dominant role in selecting which gobiid species, or their symbiotic shrimp, will be found in a certain location. We also observed a bias towards hovering species (of the genusTrimma) and away from shrimp-associated gobies at greater depths. These findings are in accord with the suspected shift of gobies towards planctotrophy with increasing depth.

We furthermore compare this study to previous surveys of goby faunas, and plot the recorded species numbers against the survey areas. This species-area plot provides support for the notion of high speciation rates in gobies due to their low mobility.
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function
Authors: Mulley John F , Hargreaves Adam D , Hegarty Matthew J , Heller R. Scott , Swain Martin T
Published: June 2014

Background

Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles, although the lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their “unusual” energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes we have carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark,Scyliorhinus canicula.

Results

We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissue based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to published mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in vertebrates, although the peptide diversity of the early vertebrate pancreas has been overestimated as a result of the use of cross-reacting antisera in earlier studies. A three hormone islet organ is therefore the basal vertebrate condition, later elaborated upon only in the tetrapod lineage.

Conclusions

The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of “model organism”.
Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins
Authors: Fujita Toshitsugu , Fujii Hodaka
Published: June 2014

Background

Comprehensive understanding of mechanisms of genome functions requires identification of molecules interacting with genomic regions of interestin vivo. We have developed the insertional chromatin immunoprecipitatin (iChIP) technology to isolate specific genomic regions retaining molecular interactions and identify their associated molecules. iChIP consists of locus-tagging and affinity purification. The recognition sequences of an exogenous DNA-binding protein such as LexA are inserted into a genomic region of interest in the cell to be analyzed. The exogenous DNA-binding protein fused with a tag(s) is expressed in the cell and the target genomic region is purified with antibody against the tag(s). In this study, we developed the iChIP system using recombinant DNA-binding proteins to make iChIP more straightforward.

Results

In this system, recombinant 3xFNLDD-D (r3xFNLDD-D) consisting of the 3xFLAG-tag, a nuclear localization signal, the DNA-binding domain plus the dimerization domain of the LexA protein, and the Dock-tag is used for isolation of specific genomic regions. 3xFNLDD-D was expressed using a silkworm-baculovirus expression system and purified by affinity purification. iChIP using r3xFNLDD-D could efficiently isolate the single-copy chickenPax5(cPax5) locus, in which LexA binding elements were inserted, with negligible contamination of other genomic regions. In addition, we could detect RNA associated with the cPax5locus using this form of the iChIP system combined with RT-PCR.

Conclusions

The iChIP system using r3xFNLDD-D can isolate specific genomic regions retaining molecular interactions without expression of the exogenous DNA-binding protein in the cell to be analyzed. iChIP using r3xFNLDD-D would be more straightforward and useful for analysis of specific genomic regions to elucidate their functions.
Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
Authors: Shi Weibing , Moon Christina D. , Leahy Sinead C. , Kang Dongwan , Froula Jeff , Kittelmann Sandra , Fan Christina , Deutsch Samuel , Gagic Dragana , Seedorf Henning , Kelly William J. , Atua Renee , Sang Carrie , Soni Priya , Li Dong , Pinares-Patiño Cesar S. , McEwan John C. , Janssen Peter H. , Chen Feng , Visel Axel , Wang Zhong , Attwood Graeme T. , Rubin Edward M.
Published: June 2014

Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4mitigation at the levels of microbiota composition and transcriptional regulation.
Polyamine Oxidase5 Regulates Arabidopsis Growth through Thermospermine Oxidase Activity
Authors: Kim Dong Wook , Watanabe Kanako , Murayama Chihiro , Izawa Sho , Niitsu Masaru , Michael Anthony J. , Berberich Thomas , Kusano Tomonobu
Published: June 2014

The major plant polyamines (PAs) are the tetraamines spermine (Spm) and thermospermine (T-Spm), the triamine spermidine, and the diamine putrescine. PA homeostasis is governed by the balance between biosynthesis and catabolism; the latter is catalyzed by polyamine oxidase (PAO). Arabidopsis (Arabidopsis thaliana) has five PAO genes, AtPAO1 to AtPAO5, and all encoded proteins have been biochemically characterized. All AtPAO enzymes function in the back-conversion of tetraamine to triamine and/or triamine to diamine, albeit with different PA specificities. Here, we demonstrate that AtPAO5 loss-of-function mutants (pao5) contain 2-fold higher T-Spm levels and exhibit delayed transition from vegetative to reproductive growth compared with that of wild-type plants. Although the wild type and pao5 are indistinguishable at the early seedling stage, externally supplied low-dose T-Spm, but not other PAs, inhibits aerial growth of pao5 mutants in a dose-dependent manner. Introduction of wild-type AtPAO5 into pao5 mutants rescues growth and reduces the T-Spm content, demonstrating that AtPAO5 is a T-Spm oxidase. Recombinant AtPAO5 catalyzes the conversion of T-Spm and Spm to triamine spermidine in vitro. AtPAO5 specificity for T-Spm in planta may be explained by coexpression with T-Spm synthase but not with Spm synthase. The pao5 mutant lacking T-Spm oxidation and the acl5 mutant lacking T-Spm synthesis both exhibit growth defects. This study indicates a crucial role for T-Spm in plant growth and development.
An Uncharacterized Apocarotenoid-Derived Signal Generated in ζ-Carotene Desaturase Mutants Regulates Leaf Development and the Expression of Chloroplast and Nuclear Genes inArabidopsis
Authors: Avendaño-Vázquez Aida-Odette , Cordoba Elizabeth , Llamas Ernesto , San Román Carolina , Nisar Nazia , De la Torre Susana , Ramos-Vega Maricela , Gutiérrez-Nava María de la Luz , Cazzonelli Christopher Ian , Pogson Barry James , León Patricia
Published: June 2014

In addition to acting as photoprotective compounds, carotenoids also serve as precursors in the biosynthesis of several phytohormones and proposed regulatory signals. Here, we report a signaling process derived from carotenoids that regulates early chloroplast and leaf development. Biosynthesis of the signal depends on ζ-carotene desaturase activity encoded by the ζ-CAROTENE DESATURASE (ZDS)/CHLOROPLAST BIOGENESIS5 (CLB5) gene in Arabidopsis thaliana. Unlike other carotenoid-deficient plants, zds/clb5 mutant alleles display profound alterations in leaf morphology and cellular differentiation as well as altered expression of many plastid- and nucleus-encoded genes. The leaf developmental phenotypes and gene expression alterations of zds/clb5/spc1/pde181 plants are rescued by inhibitors or mutations of phytoene desaturase, demonstrating that phytofluene and/or ζ-carotene are substrates for an unidentified signaling molecule. Our work further demonstrates that this signal is an apocarotenoid whose synthesis requires the activity of the carotenoid cleavage dioxygenase CCD4.
The Receptor-Like Kinase SIT1 Mediates Salt Sensitivity by Activating MAPK3/6 and Regulating Ethylene Homeostasis in Rice
Authors: Li Chen-Hui , Wang Geng , Zhao Ji-Long , Zhang Li-Qing , Ai Lian-Feng , Han Yong-Feng , Sun Da-Ye , Zhang Sheng-Wei , Sun Ying
Published: June 2014

High salinity causes growth inhibition and shoot bleaching in plants that do not tolerate high salt (glycophytes), including most crops. The molecules affected directly by salt and linking the extracellular stimulus to intracellular responses remain largely unknown. Here, we demonstrate that rice (Oryza sativa) Salt Intolerance 1 (SIT1), a lectin receptor-like kinase expressed mainly in root epidermal cells, mediates salt sensitivity. NaCl rapidly activates SIT1, and in the presence of salt, as SIT1 kinase activity increased, plant survival decreased. Rice MPK3 and MPK6 function as the downstream effectors of SIT1. SIT1 phosphorylates MPK3 and 6, and their activation by salt requires SIT1. SIT1 mediates ethylene production and salt-induced ethylene signaling. SIT1 promotes accumulation of reactive oxygen species (ROS), leading to growth inhibition and plant death under salt stress, which occurred in an MPK3/6- and ethylene signaling-dependent manner in Arabidopsis thaliana. Our findings demonstrate the existence of a SIT1-MPK3/6 cascade that mediates salt sensitivity by affecting ROS and ethylene homeostasis and signaling. These results provide important information for engineering salt-tolerant crops.
Weaving a web of control
Authors: Ladva Puja , Andrew Jane
Published: June 2014

Purpose

– The purpose of this paper is to explore the relationship between management controls and the work-life balance (WLB) of junior accountants working in four multinational accounting firms using semi-structured interviews.

Design/methodology/approach

– The authors interviewed junior accountants, asking them about their firms’ time budgeting process, their views on organisational culture and their experience of WLB.

Findings

– Time budgeting controls and the dominant discourses of “efficiency” and “career” form a web of control within these firms that sustain the long-hours culture. Drawing on the work of Foucault, the authors argue that the web of control is particularly strong because it is not imposed externally by a clearly identifiable source of power. Instead, the interviews revealed how junior accountants actively produce the web of control in order to secure their identity. This is particularly apparent when they speak of their career.

Research limitations/implications

– This research sheds light on the relationship between management controls and WLB. Management controls are effective in large multinational accounting firms because they work through the emergent identity of young professionals.

Originality/value

– The link between management control systems and WLB has received little attention from accounting academics. This research offers important insights into the way management control systems and organisational culture may impact the lived experience of WLB within multinational accounting firms.
The rise and fall of the UK operating and financial review
Authors: Rowbottom N. , Schroeder M.A.S.
Published: June 2014

Purpose

– The purpose of this paper is to analyse the controversial repeal of legislation requiring UK companies to disclose an Operating and Financial Review (OFR). After a lengthy period of consultation and the preparation of a reporting standard, legislation was passed in March 2005 requiring UK listed companies to disclose a separate statement of management commentary, an OFR. In November 2005 the Chancellor unexpectedly and controversially announced the repeal of the OFR during a speech to the largest business lobbying group in the UK.

Design/methodology/approach

– The analysis draws upon internal, private governmental documents prepared by the Treasury ministry to brief the Chancellor, publicly disclosed as a result of a legal challenge against the repeal decision.

Findings

– The paper describes how Treasury officials were motivated to seek deregulatory opportunities in order to gain political support for their head, Prime Minister-in-waiting, Gordon Brown. The analysis reveals how the repeal of the OFR was identified as an example of corporate deregulation, and how this perception proved to be misplaced following the reaction to the repeal decision which led to the government reinstating many OFR requirements in an enhanced Business Review in 2006.

Originality/value

– The paper draws on the conception of “3-D” power to analyse how a political ideology prevalent in the pre-financial crisis environment came to influence accounting technology with unexpected consequences. Using data rarely disclosed in the public domain, it illuminates the “black boxed” processes underlying regulatory decision making. The paper details how the Treasury were politically motivated to influence corporate reporting policy in the absence of concerted political lobbying, and why this episode of government intervention led to an unanticipated regulatory outcome.
Polarisation in political Twitter conversations
Authors: Gunnarsson Lorentzen David
Published: June 2014

Purpose

– The purpose of this paper is to describe and analyse relationships and communication between Twitter actors in Swedish political conversations. More specifically, the paper aims to identify the most prominent actors, among these actors identify the sub-groups of actors with similar political affiliations, and describe and analyse the relationships and communication between these sub-groups.

Design/methodology/approach

– Data were collected during four weeks in September 2012, using Twitter API. The material included 77,436 tweets from 10,294 Twitter actors containing the hashtag #svpol. In total, 916 prominent actors were identified and categorised according to the main political blocks, using information from their profiles. Social network analysis was utilised to map the relationships and the communication between these actors.

Findings

– There was a marked dominance of the three main political blocks among the 916 most prominent actors: left block, centre-right block, and right-wing block. The results from the social network analysis suggest that while polarisation exists in both followership and re-tweet networks, actors follow and re-tweet actors from other groups. The mention network did not show any signs of polarisation. The blocks differed from each other with the right-wingers being tighter and far more active, but also more distant from the others in the followership network.

Originality/value

– While a few papers have studied political polarisation on Twitter, this is the first to study the phenomenon using followership data, mention data, and re-tweet data.
Global social media, local context
Authors: Cheng Yu-Chung , Chen Pai-Lin
Published: June 2014

Purpose

– Social media connect individuals in different geographical location and allow people of different political and cultural backgrounds to discuss and participate in events that occur in distant corners of the globe. But, this does not suggest that social media promote homogeneous globalization. Rather, the local and its interactions with the global or regional views remain a powerful force in the realm of social media. The purpose of this paper is to take on the local/global factors in the social media service Twitter and analyzed the keyword-captured Chinese language tweets relating to the 2012 presidential election in Taiwan.

Design/methodology/approach

– Language code usage was used to sort out the community origins of Chinese language tweets relating to the election, given that distinct types and codes of Chinese characters are used within each political border. Community-specific patterns of communication were identified by cross-correlating language styles, tweeting frequency and participating users. Social network analysis was used to further characterize the local factors in the global social media.

Findings

– The authors found that the language styles and character types can be used to identify the regions to which the users belong. The authors were able to identify community-specific patterns of communication and reconstruct a social network that exhibits local characteristics.

Originality/value

– The results demonstrate that language code can be used to identify the community origin of Chinese tweets. This will enable fine-grain content-based analysis of the Chinese language social media.
Understanding the role of networking in organizations
Authors: Gibson Carter , H. Hardy III Jay , Ronald Buckley M.
Published: June 2014

Purpose

– The purpose of this paper is to review and synthesize research and theory on the definition, antecedents, outcomes, and mechanisms of networking in organizations.

Design/methodology/approach

– Descriptions of networking are reviewed and an integrated definition of networking in organizations is presented. Approaches for measuring and studying networking are considered and the similarities and differences of networking with related constructs are discussed. A theoretical model of the antecedents and outcomes of networking is presented with the goal of integrating existing networking research. Mechanisms through which networking leads to individual and organizational outcomes are also considered.

Findings

– Networking is defined as goal-directed behavior which occurs both inside and outside of an organization, focussed on creating, cultivating, and utilizing interpersonal relationships. The current model proposes that networking is influenced by a variety of individual, job, and organizational level factors and leads to increased visibility and power, job performance, organizational access to strategic information, and career success. Access to information and social capital are proposed as mechanisms that facilitate the effects of networking on outcomes.

Originality/value

– Networking is held to be of great professional value for ambitious individuals and organizations. However, much of the research on networking has been spread across various disciplines. Consequentially, consensus on many important topics regarding networking remains notably elusive. This paper reviews and integrates existing research on networking in organizations and proposes directions for future study. A comprehensive definition and model of networking is presented and suggestions to researchers are provided.
Keeping the peace
Authors: L. Kisamore Jennifer , W. Liguori Eric , Muldoon Jeffrey , Jawahar I.M.
Published: June 2014

Purpose

– The purpose of this paper is to investigate the interaction between self-reported proactive personality, competence, and interpersonal conflict in the prediction of supervisor ratings of organizational citizenship behaviors directed at individuals (OCBI) and organizations (OCBO).

Design/methodology/approach

– Data were obtained from 165 full-time subordinate-supervisor dyads. Employees self-reported personality and control variable information in wave 1 and competence and interpersonal conflict information in wave 2. Data regarding employee OCB performance were collected from supervisors in wave 3.

Findings

– Results suggest that OCBs are performed less frequently in stressful circumstances but that proactive personality appears to assuage the effects of stress. Significant two- and three-way interactions suggest the interplay of personal and situational characteristics are more complex in predicting OCBO than OCBI, likely due to its more distal nature.

Practical implications

– Results of the current study suggest steps managers may want to take to increase employee performance of OCBs, specifically, selecting proactive individuals, creating training programs to bolster employees’ competence, and minimizing interpersonal conflict at work.

Originality/value

– The current study confirms and extends extant research. The current study goes beyond previous work to consider a more complex interaction of factors that are related to employee engagement in OCBs.
Product recalls and product-harm crises
Authors: Tariq Anwar Syed
Published: June 2014

Purpose

– The aim of this study is to investigate and analyze product recalls and product-harm crises in the US toy industry, which is a major area in marketing and firms' competitiveness.

Design/methodology/approach

– By using longitudinal data from the US Consumer Product Safety Commission (CPSC), the paper uses content analysis to compare and contrast toy recalls, product hazards and country of origin issues of 721 toy recalls in the US market between 1974 and 2008, covering 270 million recalled toys.

Findings

– Findings of this work reveal that most of the recalled toys were manufactured in China, although a wide variety of toy brands were designed in the USA. Major hazards of toy recalls included choking, lead poisoning, aspiration, fire/burn and other injuries.

Research limitations/implications

– The study relied on the CPSC's data that seemed representative of the toy industry in the US market, but missed other markets of Europe and Asia. Also, there was availability of detailed data in sub-categories of the toy industry.

Practical implications

– The paper provides useful academic and managerial implications that can help us understand the issues of product recalls and product-harm crises.

Social implications

– Toys are one of the most widely available products in the world; the industry is a $50 billion industry and has transformed itself from a small-scale business sector into a well-established industry.

Originality/value

– This investigation is particularly important in the areas of firm-specific competitiveness, business ethics and regulatory and societal issues.
The role of the upper echelon in the value chain management
Authors: Agnihotri Arpita
Published: June 2014

Purpose

– The purpose of this study was to analyze the impact of top management teams on firms' value chain action intensity and value chain activity heterogeneity.

Design/methodology/approach

– The study was conducted from an emerging market perspective. The sample was based on the secondary data collected from three fast-growing industries in India: automobile, pharmaceutical and fast-moving consumer goods over the three-year period from 2009 to 2012. The Panel Poisson and Tobit regression have been used to conduct this study.

Findings

– Drawing upon the upper echelon theory, the author found that a top management team's educational level, functional heterogeneity and total organizational tenure influence value chain action intensity and value chain activity heterogeneity.

Originality/value

– The author introduces the concept of value chain action intensity and value chain action heterogeneity and investigates the role of the upper echelon in influencing intensity and heterogeneity.
Competitiveness of Spanish foreign subsidiaries
Authors: Miravitlles Paloma , Guitart-Tarrés Laura , Nuñez-Carballosa Ana
Published: June 2014

Purpose

– The purpose of this study was to approach issues such as what type of value chain activities are carried on by the subsidiaries of multinationals located in Spain, where and how their resources and capabilities are generated and how these are transferred within the multinational. Creating resources and capabilities within a subsidiary of a multinational company enables it to gain competitiveness and therefore greater power of decision within the corporation.

Design/methodology/approach

– This research conducts a descriptive analysis of the value chain in Spanish subsidiaries. A population of 1,072 firms has been identified. To gather primary data, a questionnaire was designed based on international value chain and resources and capabilities literature.

Findings

– Analysis of the data gathered from 125 subsidiaries has enabled researchers to map out the profile of the value chain in these companies. The results indicate that the principal source of resources and capabilities is the subsidiary itself. Moreover, the experience built up over time is basic to the creation of skills in all the activities in the value chain.

Practical implications

– This is a matter of the subsidiaries identifying new opportunities to attain a new position or broaden their existing one.

Social implications

– Subsidiaries should benefit from favourable local policies to help them develop and strengthen their capabilities to obtain major international competitiveness.

Originality/value

– Although numerous studies assess the country's foreign direct investment flows, works concentrating on the presence of foreign capital in Spain are scarce. The growing interest in the international literature on the subsidiary as a unit of analysis makes this study interesting.
How to recover trust in the banking industry? A game theory approach to empirical analyses of bank and corporate customer relationships
Authors: Dahlstrom Robert , Nygaard Arne , Kimasheva Maria , M. Ulvnes Arne
Published: June 2014

Purpose

– Trust is a crucial element of a viable banking industry. In the corporate market though, the characteristics of the relationships between each corporate customer and the bank is a double-sided problem. Both parties might trust the other or choose to behave opportunistically. The paper aims to discuss these issues.

Design/methodology/approach

– The authors have analyzed the effects of inter-organizational trust and opportunism on the perception of risk. The paper presents a structural equations model based on a prisoner's dilemma logic to analyze the unique effects of trust between corporate customers and their banks and its corporate customers.

Findings

– The results based on 252 bank – corporate bank customers relationships reveal an intriguing mixed strategy between trust from one party and opportunism from the other.

Research limitations/implications

– The implication is that mutual trust seems to reduce the perception of risk in the market while bank opportunism significantly escalates perceived risk. The analyses also show that when the corporate customer trusts the bank, perceived risk is significantly reduced.

Practical implications

– The findings emphasize the role of relationship marketing in the banking industry.

Originality/value

– Despite the fact that inter-organizational trust is a crucial dyadic variable, few empirical studies have previously analyzed both sides of the relationship. This investigation is a preliminary analysis of how both sides of the same relationship affects the outcome. When trust erodes from one side of the relationship, it may lead to the same process on the other side of the relationship.
Making quality improvement programs more effective
Authors: Shaw-Taylor Yoku
Published: June 2014

Purpose

– In the past 25 years, and as recent as 2011, all external evaluations of the Quality Improvement Organization (QIO) Program have found its impact to be small or difficult to discern. The QIO program costs about $200 million on average to administer each year to improve quality of healthcare for people of 65 years or older. The program was created to address questionable quality of care. QIOs review how care is provided based on performance measures. The paper aims to discuss these issues.

Design/methodology/approach

– In 2012, the author supported the production of quarterly reports and reviewed internal monitoring and evaluation protocols of the program. The task also required reviewing all previous program evaluations. The task involved many conversations about the complexities of the program, why impact is difficult to discern and possible ways for eventual improvement. Process flow charts were created to simulate the data life cycle and discrete event models were created based on the sequence of data collection and reporting to identify gaps in data flow.

Findings

– The internal evaluation uncovered data gaps within the program. The need for a system of specification rules for data conceptualization, collection, distribution, discovery, analysis and repurposing is clear. There were data inconsistencies and difficulty of integrating data from one instance of measurement to the next. The lack of good and reliable data makes it difficult to discern true impact.

Practical implications

– The prescription is for a formal data policy or data governance structure to integrate and document all aspects of the data life cycle. The specification rules for governance are exemplified by the Data Documentation Initiative and the requirements published by the Data Governance Institute. The elements are all in place for a solid foundation of the data governance structure. These recommendations will increase the value of program data.

Originality/value

– The model specifies which agency units must be included in the governance authority and the data team. The model prescribes in detail a data governance model to address gaps in the life cycle. These prescriptive measures will allow the program to integrate all of its data. Without this formal data governance structure, the QIO program will be undetermined by the persistent lack of good data for monitoring and evaluation.
Moving to patient reported collection of race and ethnicity data
Authors: Berry Carolyn , A. Kaplan Sue , Mijanovich Tod , Mayer Andrea
Published: June 2014

Purpose

– The purpose of this paper is to examine the feasibility of collecting standardized, patient reported race and ethnicity (RE) data in hospitals, and to assess the impact on data quality and utility.

Design/methodology/approach

– Part of a larger evaluation that included a comprehensive assessment. Sites documented RE data collection procedures before and after program implementation. Primary data collected through qualitative interviewing with key respondents in ten hospitals to assess implementation. Nine hospitals provided RE data on the same patients before and after implementation new data collection procedures were implemented to assess impact.

Findings

– Implementation went smoothly in nine of ten hospitals and had substantial effects on the hospital staff awareness on the potential for disparities within their hospitals. New procedures had minimal impact on characterization of readmitted patients.

Practical implications

– This study demonstrated that it is feasible for staff in a diverse group of hospitals to implement systematic, internally standardized methods to collect self-reported RE data from patients.

Originality/value

– Although this study found little impact patients’ demographic characterizations, other benefits included greater awareness of and attention to disparities, uncovering small pockets of minorities, and dramatically increased RE data use in quality improvement efforts.
Why is your patient sedated?
Authors: Murphy Olwen , King Graham , Callanan Ian , W. Butler Marcus
Published: June 2014

Purpose

– The purpose of this paper is to examine the recording of clinical indication for prescribed sedative/hypnotic (SH) medications in a large, acute tertiary referral hospital.

Design/methodology/approach

– All hospital inpatients’ medications (n=367) were audited for prescription details regarding SH medications. Medical notes were then examined for evidence of a recorded indication for such medications.

Findings

– SH medications were prescribed to many hospital inpatients (42.5 per cent) during admission. An indication was documented in the nursing or medical records for 24.4 per cent of patients who were prescribed such medications. Nurses rather than by doctors prescribed most SH medications (74 vs 26 per cent, respectively, p=0.003). Some patients receiving SH medications were both over 65 and impaired in their mobility (19.2 per cent). The treatment indication was documented in 47 per cent.

Practical implications

– Most patients prescribed SH medications have nothing in their medical record explaining why these drugs are being used, including half of the elderly, less mobile patients. All health professionals dealing with SH medications and doctors in particular need to justify the use of such medications in the medical record. For the particularly high-risk groups where SH medications are potentially more dangerous, explicit guidance on why and how such medications are to be used must be provided by prescribers.

Originality/value

– For the first time, data are presented on documentation rates for clinical indication of prescribed SH medications across a large acute hospital, and highlights significant shortcomings in practice. This study should inform other organisations of the need to be mindful of facilitating greater compliance with good prescribing practice.