bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene nucleotide composition accurately predicts expression and is linked to topological chromatin domains
Authors: Bessière Chloé , Taha May , Petitprez Florent , Vandel Jimmy , Marin Jean-Michel , Bréhélin Laurent , Lèbre Sophie , Lecellier Charles-Henri 
Published: March 2017

AbstractGene expression is orchestrated by distinct regulatory regions (e.g. promoters, enhancers, UTRs) to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks (e.g. ChIP-seq, methylation, DNase hypersensitivity), with the ultimate goal of identifying driving genomic regions and mutations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, their biological interpretation can be misleading. Finally these methods are not designed to capture potential regulation instructions present at the sequence level, before the binding of regulators or the opening of the chromatin. We develop here a method for predicting mRNA levels based solely on sequence features collected from distinct regulatory regions, which is as accurate as methods based on experimental data. Our approach confirms the importance of nucleotide composition in predicting gene expression and ranks regulatory regions according to their contribution. It also unveils strong influence of gene body sequence, in particular introns. We further provide evidence that the contribution of nucleotide content can be linked to co-regulations associated with genome 3D architecture and to associations of genes within topologically associated domains.
Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers
Authors: Nakamura Hideki , Lee Albert A. , Afshar Ali Sobhi , Watanabe Shigeki , Rho Elmer , Razavi Shiva , Suarez Allison , Lin Yu-Chun , Tanigawa Makoto , Huang Brian , DeRose Robert , Bobb Diana , Hong William , Gabelli Sandra B. , Goutsias John , Inoue Takanari 
Published: March 2017

AbstractNon-membrane bound, hydrogel-like entities, such as RNA granules, nucleate essential cellular functions through their unique physico-chemical properties. However, these intracellular hydrogels have not been as extensively studied as their extracellular counterparts, primarily due to technical challenges in probing these materialsin situ.Here, by taking advantage of a chemically inducible dimerization paradigm, we developed iPOLYMER, a strategy for rapid induction of protein-based hydrogels inside living cells. A series of biochemical and biophysical characterizations, in conjunction with computational modeling, revealed that the polymer network formed in the cytosol resembles a physiological hydrogel-like entity that behaves as a size-dependent molecular sieve. We studied several properties of the gel and functionalized it with RNA binding motifs that sequester polyadenine-containing nucleotides to synthetically mimic RNA granules. Therefore, we here demonstrate that iPOLYMER presents a unique and powerful approach to synthetically reconstitute hydrogel-like structures including RNA granules in intact cells.
A comprehensive approach to understanding cooking behavior
Authors: Wolfson Julia A. , Bostic Stephanie , Lahne Jacob , Morgan Caitlin , Henley Shauna C. , Harvey Jean , Trubek Amy 
Published: March 2017

Purpose
The purpose of this paper is to describe the development of – and need for – an expanded understanding of cooking (skills and knowledge) to inform research on the connection between cooking and health.

Design/methodology/approach
This paper describes a concept of “food agency” and contrasts it with how cooking is commonly conceived in food and nutrition literature. A food agency-based pedagogy and proposals for using it are also introduced.

Findings
Cooking is a complex process that may be crucial for making a difference in the contemporary problems of diet-related chronic diseases. There are two interlinked problems with present research on cooking. First, cooking has yet to be adequately conceptualized for the design and evaluation of effective public health and nutrition interventions. The context within which food-related decisions and actions occur has been neglected. Instead, the major focus has been on discrete mechanical tasks. In particular, recipes are relied upon despite no clear evidence that recipes move people from knowledge to action. Second, given the incomplete theorization and definition of this vital everyday practice, intervention designs tend to rely on assumptions over theory. This creates certain forms of tautological reasoning when claims are made about how behavior changes. A comprehensive theory of food agency provides a nuanced understanding of daily food practices and clarifies how to teach cooking skills that are generalizable throughout varied life contexts.

Originality/value
This commentary is of value to academics studying cooking-related behavior and public health practitioners implementing and evaluating cooking interventions.
The mediating effects of organization-based self-esteem for the relationship between workplace ostracism and workplace behaviors
Authors: Chung Yang Woon , Yang Ji Yeon 
Published: March 2017

PurposeThe purpose of this paper is to investigate the mediating effects of organization-based self-esteem (OBSE) for the relationship between workplace ostracism with helping behavior, voicing behavior, in-role behavior, and deviant behavior. The workplace has now become a social context where ostracism occurs and the study emphasizes how ostracism can affect workplace behaviors.Design/methodology/approachThe study was designed using a three-wave self-reported survey. Confirmatory factor analysis, structural equation modeling, and bootstrapping for indirect effects were conducted to test the study’s hypotheses.FindingsThe study found OBSE to fully mediate the relationship between workplace ostracism and helping behavior, voicing behavior, and in-role behavior, while OBSE partially mediated workplace ostracism and deviant behavior as workplace ostracism was found to have a direct effect on deviant behavior.Originality/valueThe study explores and empirically tests the mediating effects of OBSE with helping behavior, voicing behavior, in-role behavior, and deviant behavior. Therefore, the study extends research on workplace ostracism by investigating beyond the direct effects of workplace ostracism on workplace behaviors.
A neural network identifier for electromagnetic thermotherapy systems
Authors: Tai Cheng-Chi , Wang Wei-Cheng , Hsu Yuan-Jui 
Published: March 2017

Purpose
This study aims to establish a dynamic process model of an electromagnetic thermotherapy system (ETS) to predict the temperature of a thermotherapy needle.

Design/methodology/approach
The model is used for real-time predicting the static and dynamic responses of temperature and can therefore provide a valuable analysis for system monitoring.

Findings
The electromagnetic thermotherapy process is a nonlinear problem in which the system identification is implemented by a neural network identifier. It can simulate the input/output relationship of a real system with an excellent approximation ability to uncertain nonlinear system. A system identifier for an ETS is analyzed and selected with recurrent neural networks models to deal with various treatment processes.

Originality/value
The Elman neural network (ENN) prediction model on ETS proposed in this study is an easy and feasible method. Comparing two situations of inputs with more and fewer data, both are trained to present low mean squared error, and the temperature response error appears within 15 per cent. The ENN, with the advantages of simple design and stable efficacy, is useful for establishing the temperature prediction model to ensure the security in the thermotherapy.
Lattice Boltzmann modelling for multiphase bubble flow in electroconducting liquids
Authors: Tatulcenkovs Andrejs , Jakovics Andris , Baake Egbert , Nacke Bernard 
Published: March 2017

Purpose
The purpose of this paper is to the study the multiphase bubbles flow motion in a vertical channel with an electroconducting liquid without and under the influence of a magnetic field.

Design/methodology/approach
For numerical calculations, the lattice Boltzmann method (LBM) is used, which is based on the kinetic theory for solving fluid mechanics and other physical problems. The phase-field lattice Boltzmann model is developed to simulate the behaviour of multiphase bubble–bubble interaction while rising in the fluid with high density ratios.

Findings
The behaviour of the rising bubble flow in a rectangular column of two phases is investigated with the two-dimensional LBM.

Originality/value
The multiphase flow in electroconducting liquids with high ratio of density is studied using the LBM.
Transactive knowledge from communities of practice to firms
Authors: Longo Maria Cristina , Narduzzo Alessandro 
Published: March 2017

PurposeThe purpose of this paper is to analyze to what extent and under which conditions R&D projects benefit from team members’ participation in spontaneous and work-related communities of practice (CoPs).Design/methodology/approachThis is a quantitative empirical study. R&D projects are the unit of analysis. Data are collected through interviews to 121 informants who are members of 60 R&D projects and participants in 195 CoPs.FindingsThe participation of project team members in work-related CoPs positively affects the R&D project performance. This positive effect applies also to radically innovative projects. The diversity in the institutional affiliation of CoPs members is also highly significant and positively correlated with the project performance.Research limitations/implicationsThe paper considers only work-related CoPs, thus neglecting the knowledge transacted through other types of CoPs.Practical implicationsPractitioners should support the autonomous participation of project team members to spontaneous and work-related CoPs that cut across the organizational boundaries. Team leaders may enhance team innovative capabilities and performance by ensuring diversity of knowledge and skills from CoPs whose members work for institutions that differ from each other.Originality/valueFirst, this study provides quantitative evidence of the CoPs ability to support innovation. Second, this research is focused on spontaneous and work-related CoPs within business environments. Third, this study does not analyze CoPs performance, but it postulates a connection between innovative organizational units (i.e. R&D projects) and spontaneous CoPs that cut across the firms’ boundaries.
Organizational service orientation and job satisfaction
Authors: Bellou Victoria , Andronikidis Andreas 
Published: March 2017

PurposeGiven the polyphony around service orientation related constructs coming from both Marketing and Organizational Behavior researchers, the first purpose of this paper is to delineate the construct of service orientation, and second, recognizing the focal role of employees for offering services of high quality, it investigates the complex relationship between service orientation and job satisfaction.Design/methodology/approachThis paper draws upon theories and arguments from marketing and organizational behavior to identify “organizational service orientation” (OSO) as a common basis for both scholarships. Grounded on the review of the impact of OSO and job satisfaction constructs to each other, the authors develop research propositions, and discuss implications of the proposed relationships for both.FindingsThe paper explicates the positive impact of OSO on job satisfaction but also puts forward a positive influence of job satisfaction on OSO, suggesting hence a reciprocal relationship between the two.Originality/valueFirst, this paper offers construct clarification for OSO, bridging disciplinary and audience divides. Second, it argues over the reciprocal relationship between OSO and job satisfaction, indicating the necessity to invest on maximizing both constructs in order to ultimately optimize the service experience of customers.
Success factors in university sport partnerships: a case study
Authors: Franco Mário , Haase Heiko 
Published: March 2017

PurposeFrom a resource-based perspective, the purpose of this paper is to analyse the key success factors underlying inter-organisational partnerships in the university sport sector.Design/methodology/approachTo attain this objective, the paper uses a qualitative approach, performing an exploratory case study in a Portuguese higher education institution. Four interviews with key informants and documentary analysis served for data collection.FindingsBased on the case evidence, five generic success factors emerged: relationships, partner selection, complementarity, sporting performance and organisation, which are likely to determine the success of partnerships in the field of university sport.Practical implicationsUniversity sport managers and other actors in the field should bear the major success factors in mind when taking strategic decisions. Specifically, relational capital and the complementarity of resources seem to be important in initiating and managing sport partnerships.Originality/valueThis exploratory study contributes to advancing knowledge of inter-organisational partnerships in a particular area: sport in higher education. More precisely, this research outlines which success factors are relevant in sport partnerships and deserve further investigation with other research designs.
A supply chain framework for characterizing indirect vulnerability
Authors: Gotangco Charlotte Kendra , Favis Abigail Marie , Guzman Ma. Aileen Leah , Tan Marion Lara , Quintana Carissa , Josol Jairus Carmela 
Published: March 2017

Purpose
Climate vulnerability assessments are often operationalized by the analysis of indicators defined by the spatial boundaries of the community under study. These, however, sometimes fail to capture interdependency among communities for basic resources. This paper aims to propose a framework for characterizing vulnerability caused by interdependency by adapting a supply chain lens.

Design/methodology/approach
The paper proposes a definition for “indirect vulnerability” that recognizes the transboundary and teleconnected nature of vulnerability arising from resource networks among cities and communities. A conceptual framework using a supply chain approach is presented for climate hazards in particular. This approach is then demonstrated through a rapid appraisal of the rice, energy and water supply chains and the waste management chains of Metro Manila.

Findings
The application of the supply chain lens to assessing the indirect vulnerability of Metro Manila brings to fore issues extending beyond the decision-making boundaries of local government units. Addressing these will require vertical government coordination and horizontal inter-sectoral collaboration. Thus, this supply chain-based indirect vulnerability assessment can be complementary to traditional vulnerability assessments in providing a larger systems perspective.

Originality/value
Innovative tools are needed to make community vulnerability assessments both holistic and tractable. Existing methods in the private sector can be adapted rather than reinventing the wheel. This supply chain framework can be a useful decision support and planning tool across governance levels to comprehensively address vulnerability.
Corporate governance structure and capital adequacy: implications to bank risk taking
Authors: Abou-El-Sood Heba 
Published: March 2017

PurposeThe purpose of this paper is to show the importance of policy discussions on the role of governance in limiting excessive risk-taking at times of turmoil.Design/methodology/approachCorporate governance measures are regressed on measures of risk taking using a sample of US bank holding companies (BHCs) during 2002-2014.FindingsResults show that BHCs with more concentrated shareholders, more managerial ownership, smaller boards, and less outside directors undertake less risky investments with respect to total assets, loans, and off-balance-sheet items. Capital adequacy effect is overpowering pushing for more risky positions. Finally, banks with good governance push for less risky positions, even with larger capital ratios, during the financial crisis period relative to the precrisis boom.Practical implicationsThis paper extends research on the association between bank ownership structure and risk taking. It adds to prior research by examining a key feature of banks, namely, their bank-specific capital adequacy. The relevance of this study stems from recent initiatives undertaken by the Basel Committee, the Group of Thirty (G30), and bank regulators to address deficient corporate governance structures that led to bank breakdowns.Originality/valueOne of the innovations of this paper is the use of risk-weighted measures to proxy for risk taking in banks, using risk weights used by bank regulators to adjust for operational risk, credit risk, and market risk.
Family ownership and free cash flow
Authors: Sitthipongpanich Thitima 
Published: March 2017

Purpose
The purpose of this paper is to investigate the effect of family ownership on investment-cash flow sensitivity and on firm performance.

Design/methodology/approach
The author uses panel data to examine the relationship between investment and cash flow and between family ownership and the firm performance of Thai listed firms from 2001 to 2008. To account for the endogeneity of the lagged dependent variable, the investment equation is estimated by the generalized method of moments, following Arellano and Bond (1991).

Findings
The presence of family owners reduces the sensitivity of investment and cash flow. At low and high levels of family ownership, an increase in family shareholding leads to lower investment-cash flow sensitivity. In contrast, firms with medium family ownership levels have higher investment-cash flow sensitivity. Only at high levels of family ownership is firm performance positively related to family shareholding.

Originality/value
The ownership levels of family shareholders affect the investment-cash flow sensitivity in an S-shaped relation, supporting the interest alignment and entrenchment effects. When family shareholders have high ownership incentives, their interest alignment reduces the agency costs of free cash flow problems and leads to higher firm performance.
Corporate financial policy and the value of cash under uncertainty
Authors: Chakraborty Atreya , Baum Christopher F. , Liu Boyan 
Published: March 2017

PurposeThe purpose of this paper is to provide evidence on how firm-specific and macroeconomic uncertainty affects shareholders’ valuation of a firm’s cash holdings. This extends previous work on this issue by highlighting the importance of the source of uncertainty. The findings indicate that increases in firm-specific risk generally increase the value of cash while increases in macroeconomic risk generally decrease the value of cash. These findings are robust to alternative definitions of the unexpected change in cash. The authors extend the analysis to financially constrained and unconstrained firms.Design/methodology/approachThe authors test the hypothesis that the marginal effect of cash holdings on excess stock returns is sensitive to uncertainty. To compute this marginal effect, the authors adopt and extend the approach of Faulkender and Wang (2006) to the authors’ more elaborate model.FindingsThe findings indicate that different sources of uncertainty affect the value of cash holdings differently. Findings indicate that increases in firm-specific risk generally increase the value of cash while increases in macroeconomic risk generally decrease the value of cash. These findings are robust to alternative definitions of the unexpected change in cash. The authors also extend the findings to financially constrained and unconstrained firms.Originality/valueThe findings indicate that the source of uncertainty firm-specific vs macroeconomic risk matters. The two sources of risk may have quite different effects on shareholders’ valuation of a firm’s cash holdings. Results from alternative sources of findings are new. These new findings are robust to alternative definitions of the unexpected change in cash.
Cross-enterprise value stream assessment
Authors: Oberhausen Christof , Plapper Peter 
Published: March 2017

Purpose
In most cases, the conventional assessment of value streams is based on key performance indicators (KPIs) like the share of added value, the degree of flow or a comprehensive lead time analysis. To evaluate cross-enterprise value streams of manufacturing, business or service processes in detail, a holistic methodology is needed. The paper aims to discuss this issue.

Design/methodology/approach
In this research paper, the assessment of value streams within complex cross-company networks is described. After a presentation of relevant KPIs in the fields of value stream management (VSM) and supply chain management (SCM), an approach for a cross-enterprise evaluation of value streams on different levels of detail is shown. In addition, the use of an absolute VSM evaluation, in contrast to a relative VSM assessment, is examined.

Findings
Based on a uniform and well-balanced set of KPIs and other VSM and SCM parameters, a performance assessment on different levels of value stream detail is enabled. Further investigations reveal the advantages of a relative compared with an absolute VSM assessment.

Research limitations/implications
In addition to a comprehensive overview of existing KPIs for a value stream assessment beyond company borders, a holistic and multi-level VSM approach is presented in this paper. In contrast to existing VSM approaches, the described method allows an evaluation and subsequent improvement of value streams within supply chain networks. Up to now, the presented approach for the assessment of cross-enterprise value streams has only been tested in specific industrial environments. In future, the proposed methodology shall also be validated for other process types like business, service or further manufacturing processes.

Practical implications
The described cross-company performance measurement approach shows a high practical relevance for organizations operating in supply chain networks. Due to the integrated use of different VSM parameters, the evaluation of highly interconnected value streams across corporate boundaries is facilitated. By means of a case study, the proposed methodology is validated under real industry conditions and proves its practical applicability.

Originality/value
One of the novel features of this research is the extension of the traditional VSM method with respect to a relative evaluation of value streams based on a set of significant KPIs. In addition, the allocation of these KPIs to different value stream layers and categories leads to an innovative approach for a multi-level assessment according to the needs of the specific VSM application, e.g. a more standardized use of VSM in complex supply chain networks.