7,762 research outputs found

    Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data

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    Determining where transcription factors (TFs) bind in genomes provides insight into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these data sets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF-binding preferences, or motifs, to identify TF-binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here, we compare four motif-mapping tools widely used in the Arabidopsis (Arabidopsis thaliana) research community and evaluate their performance using chromatin immunoprecipitation data sets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of Find Individual Motif Occurrences, one of the most frequently used motif-mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a protocol is presented to effectively derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression data sets. This approach will pave the way to increase our understanding of GRNs in different cellular conditions

    The promise and pitfalls of globalisation

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    Investigating English Language Teachers’ Beliefs and Stated Practices Regarding Bottom-up Processing Instruction for Listening in L2 English

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    In a survey of teachers’ beliefs and stated practices, sourced mainly through Twitter, it was found that instruction in bottom-up processing for L2 listening in English language teaching, as recommended by research literature, is stated as being carried out although not to a very large or regular extent. It also found that most teachers stated that they do not base their listening instruction upon L1-L2 phonological differences. Additionally it was found that teachers stating they taught at the single-sound level also correlated strongly with stating that they taught at the single-word level

    A celebrity chef goes global : the business of eating

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    Purpose &ndash; This paper examines the internationalization strategy of Gordon Ramsay Holdings Ltd (GRH) from its base in London. While a substantial body of research on the strategic prerequisites for successful internationalization already exists, little attention has been given within this literature to the international growth of small, informally organized and entrepreneurially-driven firms. The discussion also identifies the challenges facing GRH as it strives to continue its international expansion. Design/methodology/approach &ndash; The paper utilizes various published sources from the general press, business press and trade journals to examine the international expansion of GRH on the back of the personal brand the charismatic Gordon Ramsay has achieved in culinary and media circles. The growth of the GRH organization is interpreted through a theoretical framework of strategic capabilities and relationships. Findings &ndash; The analysis illustrates how critical resources and capabilities, branded reputation, and strategic relationships established in GRH\u27s home market have been leveraged effectively overseas. The most fundamental challenge facing GRH going forward is balancing the opportunities and pressures for growth against the need to maintain the highest levels of quality in existing establishments. This &ldquo;balancing act&rdquo; has to unfold within an empire in which the entrepreneur-emperor (Ramsay) has less and less time to devote to any particular activity or establishment. Originality/value &ndash; The case illustrates the importance of developing and leveraging strategic capabilities and relationships in support of successful international expansion. Some of the unique challenges associated with the internationalization of small, informally organized and entrepreneurially-driven (and branded) firms are addressed in terms of both problems and solutions.<br /

    Preface to the Special Issue on the Fairy Tale in Japan

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    Non-market strategy and the \u27race to the bottom\u27: lessons from the Baywatch experience

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    This article examines how international firms operate strategically in the non-market environment to secure advantages which improve their cost and/or revenue structures and, hence, their economic performance. It centres on a detailed case study of the globally popular Baywatch television show\u27s efforts during 1999 to secure attractive locational subsidies by placing the states of New South Wales, Queensland (both in Australia) and Hawaii into competition with each other in a \u27race to the bottom\u27. The article is organized into three main sections: the first briefly reviews the concept of non-market strategy; the second examines the Baywatch case in detail; and the conclusion presents some lessons for various stakeholders involved in this and similar non-market contexts.<br /

    Methods of Repression in Bahrain during the 20th and 21st Century: From the Civil List to Social Media

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    Despite being afflicted by cyclical bouts of unrest over the past century, repression in Bahrain as a concept has not been the focus of considerable academic attention. This is the first interpretive historical and contemporary study of repression in Bahrain. It addresses the limitations of regime-type analysis and quantitative studies of repression, which tend to focus on the co-variation between repression and demobilization. Using a template analysis, a virtual ethnography and framing theory, this thesis offers a new conceptualisation of repression. Several episodes of contention in Bahrain are analysed, including; tribal resistance to the British reforms of the 1920s, the rise of the Higher Executive Committee in the 1950s, the leftist agitation of the 1970s, the 1990s Intifada, and the 2001 Uprising. Using evidence from multiple sources, including recently released Foreign and Commonwealth Office files, social media, and historical records, this thesis argues that Bahrain's protecting powers have had a marked impact on the severity, nature and type of repression in Bahrain, as well as the structure of the repressive apparatus. While the British mitigated the excesses of Al Khalifa's treatment of political opposition, their declining influence following Independence saw the rise of a Saudi-Al Khalifa dual authority structure that created a new approach to repressive choices. Crucially, Bahrain's protecting powers influenced the nature and type of repression that was applied to political opposition. Yet despite this meta-narrative of outside influence, this research complicates generalisable theories of repression, showing that repressive choices are often contingent on a complex mix of the availability of resources, elite attitudes, strategic objectives of power holders, and the nature of threat. For this reason, the research sheds light on repression in Bahrain, but also highlights the value of conducting case studies and long term studies that allow researchers to compare and contrast the reasons motivating repressive choices. The new conceptualisation also emphasises the rising importance of social media and rhizomatic actors as tools of repression
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