bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
Authors: Wu George , Yustein Jason T. , McCall Matthew N. , Zilliox Michael , Irizarry Rafael A. , Zeller Karen , Dang Chi V. , Ji Hongkai 
Published: March 2013

Abstract
Motivation: Although chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip) is increasingly used to map genome-wide–binding sites of transcription factors (TFs), it still remains difficult to generate a quality ChIPx (i.e. ChIP-seq or ChIP-chip) dataset because of the tremendous amount of effort required to develop effective antibodies and efficient protocols. Moreover, most laboratories are unable to easily obtain ChIPx data for one or more TF(s) in more than a handful of biological contexts. Thus, standard ChIPx analyses primarily focus on analyzing data from one experiment, and the discoveries are restricted to a specific biological context.
Results: We propose to enrich this existing data analysis paradigm by developing a novel approach, ChIP-PED, which superimposes ChIPx data on large amounts of publicly available human and mouse gene expression data containing a diverse collection of cell types, tissues and disease conditions to discover new biological contexts with potential TF regulatory activities. We demonstrate ChIP-PED using a number of examples, including a novel discovery that MYC, a human TF, plays an important functional role in pediatric Ewing sarcoma cell lines. These examples show that ChIP-PED increases the value of ChIPx data by allowing one to expand the scope of possible discoveries made from a ChIPx experiment.
Availability: http://www.biostat.jhsph.edu/∼gewu/ChIPPED/
Contact: hji@jhsph.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Resolving Whistleblowing Disputes in the Public Interest: Is Tribunal Adjudication the Best that Can be Offered?
Authors: Lewis David 
Published: March 2013

Abstract
This article argues that employment tribunal adjudication may be both a difficult and ineffective mechanism for resolving whistleblowing disputes. The author asserts that, if disclosures of serious wrongdoing are to be encouraged, both the law and dispute resolution mechanisms need to be improved. Ideally, employers should have whistleblowing procedures which provide for conciliation, mediation and arbitration as alternative forms of redress for those who feel that their disclosures have not been dealt with properly or have allegedly suffered retaliation. Recognising that a legal obligation to have effective whistleblowing arrangements is unlikely to be imposed by law, the author suggests that alternative dispute resolution mechanisms should be made available where whistleblowing claims are lodged with employment tribunals.
Hardness Changes and Endosperm Modification During Sorghum Malting in Grains of Varying Hardness and Malt Quality
Authors: Chiremba Constance , Siwela Muthulisi , Rooney Lloyd W. , Taylor John R. N. 
Published: March 2013

ABSTRACTThis study examined the interaction between sorghum grain hardness and sorghum malt quality in terms of diastatic power and free amino nitrogen with endosperm modification during malting. The changes in kernel hardness during malting of four commercial sorghum cultivars of differing quality in terms of endosperm texture and potential malt quality were measured using tests for hardness and density, and endosperm modification was followed by scanning electron microscopy. The general pattern of modification during sorghum malting was confirmed to start at the endosperm–scutellum interface and then continue into the floury endosperm toward the kernel distal end. Significantly, a cultivar of intermediate hardness and low malting quality remained harder and modified more slowly than a harder cultivar of high malting quality. It appeared that intrinsic grain hardness and malt amylase and protease activity both affected malt hardness and endosperm modification, but amylase and protease activity had a greater effect because of their degradation of endosperm starch and protein. Of the hardness and density tests studied, the tangential abrasive dehulling device (TADD) gave the best measure of hardness throughout malting; maximum range was 24–100% kernel removed over five days of malting. Also, the data agreed with the observed malt modification rates. Thus, the TADD may have application as a simple and rapid test for estimating sorghum malt quality.
Autophagy Contributes to Nighttime Energy Availability for Growth in Arabidopsis
Authors: Izumi Masanori , Hidema Jun , Makino Amane , Ishida Hiroyuki 
Published: March 2013

AbstractAutophagy is an intracellular process leading to the vacuolar degradation of cytoplasmic components. Autophagic degradation of chloroplasts is particularly activated in leaves under conditions of low sugar availability. Here, we investigated the importance of autophagy in the energy availability and growth of Arabidopsis (Arabidopsis thaliana). autophagy-deficient (atg) mutants showed reduced growth under short-day conditions. This growth inhibition was largely relieved under continuous light or under short-day conditions combined with feeding of exogenous sucrose, suggesting that autophagy is involved in energy production at night for growth. Arabidopsis accumulates starch during the day and degrades it for respiration at night. Nighttime energy availability is perturbed in starchless mutants, in which a lack of starch accumulation causes a transient sugar deficit at night. We generated starchless and atg double mutants and grew them under different photoperiods. The double mutants showed more severe phenotypes than did atg or starchless single mutants: reduced growth and early cell death in leaves were observed when plants were grown under 10-h photoperiods. Transcript analysis of dark-inducible genes revealed that the sugar starvation symptoms observed in starchless mutants became more severe in starchless atg double mutants. The contents of free amino acids (AAs) increased, and transcript levels of several genes involved in AA catabolism were elevated in starchless mutant leaves. The increases in branched-chain AA and aromatic AA contents were partially compromised in starchless atg double mutants. We conclude that autophagy can contribute to energy availability at night by providing a supply of alternative energy sources such as AAs.
AGAMOUS-Like15 Promotes Somatic Embryogenesis in Arabidopsis and Soybean in Part by the Control of Ethylene Biosynthesis and Response
Authors: Zheng Qiaolin , Zheng Yumei , Perry Sharyn E. 
Published: March 2013

AbstractMany of the regulatory processes occurring during plant embryogenesis are still unknown. Relatively few cells are involved, and they are embedded within maternal tissues, making this developmental phase difficult to study. Somatic embryogenesis is a more accessible system, and many important regulatory genes appear to function similar to zygotic development, making somatic embryogenesis a valuable model for the study of zygotic processes. To better understand the role of the Arabidopsis (Arabidopsis thaliana) MADS factor AGAMOUS-Like15 (AGL15) in the promotion of somatic embryogenesis, direct target genes were identified by chromatin immunoprecipitation-tiling arrays and expression arrays. One potential directly up-regulated target was At5g61590, which encodes a member of the ethylene response factor subfamily B-3 of APETALA2/ETHYLENE RESPONSE FACTOR transcription factors and is related to Medicago truncatula SOMATIC EMBRYO-RELATED FACTOR1 (MtSERF1), which has been shown to be required for somatic embryogenesis in M. truncatula. Here, we report confirmation that At5g61590 is a directly expressed target of AGL15 and that At5g61590 is essential for AGL15’s promotion of somatic embryogenesis. Because At5g61590 is a member of the ETHYLENE RESPONSE FACTOR family, effects of ethylene on somatic embryogenesis were investigated. Precursors to ethylene stimulate somatic embryogenesis, whereas inhibitors of ethylene synthesis or perception reduce somatic embryogenesis. To extend findings to a crop plant, we investigated the effects of ethylene on somatic embryogenesis in soybean (Glycine max). Furthermore, we found that a potential ortholog of AGL15 in soybean (GmAGL15) up-regulates ethylene biosynthesis and response, including direct regulation of soybean orthologs of At5g61590/MtSERF1 named here GmSERF1 and GmSERF2, in concordance with the M. truncatula nomenclature.
International responsiveness of entrepreneurial new ventures from three leading emerging economies
Authors: Khavul Susanna , Prater Edmund , Swafford Patricia M. 
Published: March 2013

PurposeThe purpose of this paper is to answer the question, “How do international new ventures (INVs) from emerging economies become responsive to the demands of their international customers?”Design/methodology/approachThe authors propose a model of international responsiveness that incorporates founding team experience, international firm experience, international strategic orientation, and investment in international supply chain and test the model using data from 293 INVs from three leading emerging economies: China, India, and South Africa.FindingsResults show that for INVs from emerging economies international strategic orientation mediates the relationship between international firm experience, investment in international supply chain, and international responsiveness. In addition, the authors identify a significant difference in the effects of international strategic orientation on international responsiveness among subgroups of INVs.Practical implicationsGiven the specific context of the sample, this study provides unique managerial insights for entrepreneurs planning to internationalize their new ventures from emerging economies.Originality/valueThe paper adds originality and value by extending research on international responsiveness, bridging two disciplines, and using a unique international, multi‐country sample.
Influence of total quality management on human resource management practices
Authors: Wickramasinghe Vathsala 
Published: March 2013

PurposeThe purpose of this paper is to explore changes occurring in the human resource (HR) function and human resource management (HRM) practices due to the implementation of total quality management (TQM) in Sri Lanka.Design/methodology/approachQuality managers and HR managers from 77 export‐based firms with ISO 9001 certification that have implemented a formal TQM programme, running for at least three years, participated in the survey. Factor analysis, correlation and regression were used for the data analysis.FindingsIt was found that firms introduce process improvement initiatives within the HR department by upgrading the role of the HR function, and by redesigning HRM practices of performance management, competence development and career planning, rewards and recognition, recruitment and selection, HR planning, and satisfaction and well‐being to bring those in line with TQM requirements.Originality/valueAlthough QM literature is extensive, it is difficult to find studies that investigated to what extent TQM practices have been adopted by export‐driven organisations in developing economies and what are the changes occurring in the HR function and HRM practices due to TQM initiatives. Understanding these is important to the development of QM theory in the international context. It is expected that the paper's findings will be able to establish baseline data to stimulate further research in this area.
Selection of single sampling attribute plan for given AQL and LQL involving minimum risks using weighted Poisson distribution
Authors: Subramani Kandasamy , Haridoss Venugopal 
Published: March 2013

PurposeThe purpose of this paper is to present the single sampling attribute plan for given acceptance quality level (AQL) and limiting quality level (LQL) involving minimum sum of risks using weighted Poisson distribution.Design/methodology/approachFor the given AQL and LQL, sum of producer's and consumer's risks have been attained. Based on weighted Poisson distribution, the sum of these risks has been arrived at, along with the acceptance number and the rejection number. Also, the operating characteristic function for the single sampling attribute sampling plan, using weighted Poisson distribution, has been derived.FindingsIn the final inspection, the producer and the consumer represent the same party. So, the sum these two risks should be minimized. In this paper, the sum of risks has been tabulated using weighted Poisson distribution for different operating ratios. These tabulated values are comparatively less than the sum of risks derived using Poisson distribution.Originality/valueThe sampling plan presented in this paper is particularly useful for testing the quality of finished products in shop floor situations.
Inter-firm opportunism: a meta-analytic review and assessment of its antecedents and effect on performance
Authors: Wang Xuehua , Yang Zhilin 
Published: March 2013

Purpose
– This meta-analysis aims to aggregate empirical findings from extant inter-firm opportunism literature.

Design/methodology/approach
– First, a quantitative summary on the bivariate relationships between the antecedents and the consequences of opportunism is offered. Second, a multivariate analysis is employed to identify significant antecedents of opportunism and the process variables that mediate the relationship between inter-firm opportunism and organizational performance.

Findings
– Results reveal that goal congruence has the largest influence on inter-firm opportunism, followed by cultural sensitivity, communication, and environmental volatility, norms, governance emphasis, and relative dependence. These important antecedents represent significant research directions for inter-firm opportunism. In addition, inter-firm opportunism affects organizational performance through a mediating process including commitment, functional conflict, overall satisfaction, and trust. Commitment is found to act as a major moderating construct between inter-firm opportunism and its other significant consequences in the revised model.

Originality/value
– This study widens the horizon on inter-firm opportunism research by examining a much greater number of effect sizes and by employing a more complex framework of the mechanism mediating the inter-firm opportunism-organizational performance relationship and does so more effectively than any individual research work.
Market power and relational conflicts in Russian retailing
Authors: Radaev Vadim 
Published: March 2013

PurposeThe purpose of this paper is to examine new rules of exchange in retailer‐supplier relationships imposed by the retail chains, to analyse factors facilitating this institutional change and to reveal the links between channel power and relational conflicts.Design/methodology/approachSurvey data were collected from 500 managers of retail chains and their suppliers in five Russian cities. The sample includes firms of different sizes that sell food and home electronic appliances. After the diffusion of new contract arrangements is examined, logistic regression models are constructed to evaluate major sources of relational conflicts.FindingsThe findings indicate that power‐advantaged firms disseminate new rules of exchange effectively. However, relational conflicts largely originate not from these new demands but from the frequent contract infringements by both exchange parties.Research limitations/implicationsThe study is confined to two sectors of retail trade in one country. Further research is required to determine the effects on channel relationships of the financial crisis and of the adoption of restrictive federal legislation.Practical implicationsPractitioners should recognise the need to provide socio‐political legitimacy for the new rules of exchange. Otherwise, they may face relational conflicts and provoke restrictive state regulations. Public officials should know that relational conflicts may originate largely from opportunistic behaviour by exchange parties rather than from abuse of market power.Originality/valueThis paper presents the first systematic quantitative study of retailer‐supplier relationships in Russia. It investigates institutional change and relational conflicts as perceived by both exchange parties.
Customer flow: evaluating the long‐term impact of marketing on value creation
Authors: Tretyak Olga A. , Sloev Igor 
Published: March 2013

PurposeThe purpose of this paper is to construct a system of indicators that will allow firms to evaluate the long‐term results of their marketing activities along the value chain.Design/methodology/approachThe paper integrates the concepts of network relationships, value chain management, and customer lifetime value (CLV). The authors use participative inquiry and case studies to validate and clarify the model.FindingsThe authors develop the customer flow conceptual model and propose a sequence of actions to translate it into measures and indicators that will allow firms to understand their role in the creation of sustainable value. Using this model, the authors conduct comparative analyses of the acquisition and retention strategies of a multinational firm in the European and Russian markets. The results provide a crucial justification for new directions in future long‐term marketing activities.Research limitations/implicationsThe model is validated in two cases in different industries. Further research is required to examine the implementation of suggested tools in different industries.Practical implicationsThe model was simplified for a practical application and indicators for future monitoring process and customer flow management were developed.Originality/valueThe authors developed the concept of customer flow to assess the long‐term results of marketing activities and to emphasize the difference between managing new and existing customers. New performance metrics are proposed based on customer flow and its structural characteristics. This allowed comparing of acquisition and retention strategies of the same company in different markets and reveals the crucial differences between the marketing strategies prevailing in Russia and those in Europe. The authors have demonstrated how the concept may help firms to develop and implement successful strategies.
Knowledge city and urban economic resilience
Authors: Huston Simon , Warren Clive 
Published: March 2013

PurposeThe purpose of this paper is to investigate the limitations and potential usefulness of a “knowledge city” concept as diversification vehicle for property investors.Design/methodology/approachThe paper first dissects the “knowledge city” concept and then investigates whether it inoculates against economic turbulence as measured by growth and jobs recovery. The paper also looks at the protection offered by middle class population growth.FindingsThe idea of the “knowledge city” comes from earlier economic constructs but concentrated at the urban scale. There are two versions – a technical and one enriched with institutional and social dimensions. The limited analysis of selective secondary data suggests that “knowledge city” and strong middle class population growth provide some protection from economic and, presumably, property market instability.Research limitations/implicationsStatistical limitations include arbitrary sample frames; lack of data and unclear spatial resolution, short time frames for aggregate analysis. Further research requires, first, a structured grading of knowledge precincts and, second, randomised sampling of individual properties to investigate any links between total risk‐adjusted performance is measured over a decade.Practical implicationsTo mitigate risk, investors should consider re‐weighting their portfolios to increase exposure to knowledge cities and second‐tier but fast growing cities in emerging countries.Social implicationsA knowledge‐city cannot be imposed by infrastructure, technology or place configuration alone. It involves multiple precinct configurations and subsidiarity. Institutions and people matter. A broader knowledge‐city conceptualisation helps inform planning, management and oversight for regional second‐tier cities.Originality/valueDissecting, noting the limits and drawing out the practical implications of the “knowledge city” concept.
Hedonic modelling of high street retail properties: a quality design perspective
Authors: Nase Ilir , Berry Jim , Adair Alastair 
Published: March 2013

PurposeThe purpose of this paper is to investigate the relationship between urban design quality and the real estate value of high street retail properties. Quantitative research on the added value of quality design has seen little advancement during the past two decades and hedonic analysis of the high street retail sector remains embryonic. This paper bridges this gap by providing empirical evidence on the added value of quality design.Design/methodology/approachThe study uses a unique dataset of 301 Belfast City Centre retail transactions during the period 1994‐2009. Ordinary least squares (OLS) regression analysis is used to estimate a hedonic pricing model that utilises a composite range of variables. These variables were designed employing quantitative and qualitative approaches complementarily to strengthen the value of the empirical research.FindingsThe findings suggest that aspects of quality design such as connectivity, frontage continuity and variety, material quality and massing appropriateness add to real estate value. These findings supplement those on sector‐specific value determinants that emphasise the high impact of location, tenant characteristic and Zone‐A price calculations.Practical implicationsIn analysing high street retail rent determinants this paper focuses on the impact of various aspects of quality design to inform investors and developers about those aspects that are highly valued by city centre retail tenants. Policy makers benefit from the findings through empirically justified built environment benchmarks for improving the quality of life in our cities.Originality/valueThis study provides a quantitative model for measuring urban design quality which uses data from a UK city but has a wider application range. It bridges a significant gap in the literature related to hedonic investigation of the added value of quality design by providing a holistic approach to quality.