bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence
Authors: Ouyang Ningxin , Boyle Alan P. 
Published: October 2019

AbstractTranscription is tightly regulated by cis-regulatory DNA elements where transcription factors can bind. Thus, identification of transcription factor binding sites is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches for transcription factor binding sites (TFBSs) prediction such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) are widely used but have their drawbacks such as high false positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by investigating chromatin accessibility patterns, but also have their limitations. To improve on these methods, we have developed a footprinting method to predict Transcription factor footpRints in Active Chromatin Elements (TRACE). Trace incorporates DNase-seq data and PWMs within a multivariate Hidden Markov Model (HMM) to detect footprint-like regions with matching motifs. Trace is an unsupervised method that accurately annotates binding sites for specific TFs automatically with no requirement on pre-generated candidate binding sites or ChIP-seq training data. Compared to published footprinting algorithms, TRACE has the best overall performance with the distinct advantage of targeting multiple motifs in a single model.
GAL4/GFP enhancer-trap lines for identification and manipulation of cells and tissues in developing Arabidopsis leaves
Authors: Amalraj Brindhi , Govindaraju Priyanka , Krishna Anmol , Lavania Dhruv , Linh Nguyen Manh , Ravichandran Sree Janani , Scarpella Enrico 
Published: October 2019

AbstractUnderstanding developmental processes requires the unambiguous identification of cells and tissues, and the selective manipulation of the properties of those cells and tissues. Both requirements can most efficiently be satisfied through the use of GAL4/GFP enhancer-trap lines. No such lines are available, however, for the study of leaf development in the Columbia-0 reference genotype of Arabidopsis. Here we address this limitation by identifying and characterizing a set of GAL4/GFP enhancer-trap lines in the Columbia-0 background for the specific labeling of cells and tissues during leaf development, and for the targeted expression of genes of interest in those cells and tissues. By using one line in our set to resolve outstanding problems in leaf vein patterning, we show that these lines can be used to address key questions in plant developmental biology.
Exceptional biostability of paranemic crossover (PX) DNA, crossover-dependent nuclease resistance, and implications for DNA nanotechnology
Authors: Chandrasekaran Arun Richard , Vilcapoma Javier , Dey Paromita , Wong-Deyrup SiuWah , Dey Bijan K. , Halvorsen Ken 
Published: October 2019

AbstractInherent nanometer-sized features and molecular recognition properties make DNA a useful material in constructing nanoscale objects, with alluring applications in biosensing and drug delivery. However, DNA can be easily degraded by nucleases present in biological fluids, posing a considerable roadblock to realizing the full potential of DNA nanotechnology for biomedical applications. Here we investigated the nuclease resistance and biostability of the multi-stranded motif called paranemic crossover (PX) DNA and discovered a remarkable and previously unreported resistance to nucleases. We show that PX DNA has more than an order of magnitude increased resistance to degradation by DNase I, serum, and urine compared to double stranded DNA. We further demonstrate that the degradation resistance decreases monotonically as DNA crossovers are removed from the structure, suggesting that frequent DNA crossovers disrupt either the binding or catalysis of nucleases or both. Further, we show using mouse and human cell lines that PX DNA does not affect cell proliferation or interfere with biological processes such as myogenesis. These results have important implications for building DNA nanostructures with enhanced biostability, either by adopting PX-based architectures or by carefully engineering crossovers. We contend that such crossover-dependent nuclease resistance could potentially be used to add “tunable biostability” to the many features of DNA nanotechnology.
FMRP Links Optimal Codons to mRNA stability in Neurons
Authors: Shu Huan , Donnard Elisa , Liu Botao , Wang Ruijia , Richter Joel D. 
Published: October 2019

AbstractFragile X syndrome (FXS) is caused by inactivation of theFMR1gene and loss of encoded FMRP, an RNA binding protein that represses translation of some of its target transcripts. Here we use ribosome profiling and RNA-seq to investigate the dysregulation of translation in the mouse brain cortex. We find that most changes in ribosome occupancy on hundreds of mRNAs are largely driven by dysregulation in transcript abundance. Many downregulated mRNAs, which are mostly responsible for neuronal and synaptic functions, are highly enriched for FMRP binding targets. RNA metabolic labeling demonstrates that in FMRP-deficient cortical neurons, mRNA downregulation is caused by elevated degradation, and is correlated with codon optimality. Moreover, FMRP preferentially binds mRNAs with optimal codons, suggesting that it stabilizes such transcripts through direct interactions via the translational machinery. Finally, we show that the paradigm of genetic rescue of FXS-like phenotypes in FMRP-deficient mice by deletion of theCpeb1gene is mediated by restoration of steady state RNA levels and consequent rebalancing of translational homeostasis. Our data establish an essential role of FMRP in codon optimality-dependent mRNA stability as an important factor in FXS.
Interplay between cortical actin and E-cadherin dynamics regulates cell shape in theDrosophilaembryonic epidermis
Authors: Greig Joshua , Bulgakova Natalia A. 
Published: October 2019

AbstractPrecise regulation of cell shape is vital for building functional tissues. Here, we study the mechanisms which lead to the formation of highly elongated anisotropic epithelial cells in theDrosophilaepidermis. We demonstrate that this cell shape is the result of two counteracting mechanisms at the cell surface: actomyosin, which inhibits cell elongation downstream of RhoA signalling, and intercellular adhesion, modulated via clathrin-mediated endocytosis of E-cadherin, which promotes cell elongation downstream of the GTPase Arf1. We show that these two mechanisms are interconnected, with RhoA signalling activity reducing Arf1 recruitment to the plasma membrane. Additionally, cell adhesion itself regulates both mechanisms: p120-catenin, a regulator of intercellular adhesion, promotes the activity of both Arf1 and RhoA. Altogether, we uncover a complex network of interactions between cell-cell adhesion, the endocytic machinery, and the actomyosin cortex, and demonstrate how this network regulates cell shape in an epithelial tissuein vivo.
Determinants of switching intention to cloud computing in large enterprises
Authors: Chang Yu-Wei , Hsu Ping-Yu , Huang Shih-Hsiang , Chen Jiahe 
Published: October 2019

Purpose
The purpose of this paper is to investigate switching intention from traditional enterprise information systems (EISs) to private cloud EIS in large enterprises. The authors propose that the factors motivate and inhibit enterprises’ switching intention to private EIS by integrating technology–organization–environment (TOE) framework and two-factor theory.

Design/methodology/approach
A research model draws from TOE framework and two-factor theory. Data were collected from 227 top managers and owners of the enterprises in China and used to analyze 11 hypotheses.

Findings
The results show that the technological context (compatibility), organizational context (financial support) and environmental context (vendor support and industry pressure) significantly influence switching benefits while data security and costs significantly influence switching costs. Switching benefits and switching costs significantly influence switching intention.

Originality/value
Past studies have focused mainly on the adoption of cloud computing. However, few studies have addressed the switching issues, especially in large enterprises. The findings are useful to understand switching issues from traditional EIS to private cloud EIS for both researchers and practitioners.
The coupled lattice Boltzmann simulation of free convection in a finned L-shaped cavity filled with nanofluid
Authors: Zhang Peng , Ashraf Muhammad Aqeel , Liu Zhenling , Peng Wan-Xi , Ross David 
Published: October 2019

Purpose
This paper aims to investigate the free convection, heat transfer and entropy generation numerically and experientially. A numerical/experimental investigation is carried out to investigate the free convection hydrodynamically/thermally and entropy generation.

Design/methodology/approach
The coupled lattice Boltzmann method is used as a numerical approach which keeps the significant advantages of standard lattice Boltzmann method with better numerical stability. On the other hand, the thermal conductivity and dynamic viscosity are measured using modern devices in the laboratory.

Findings
Some correlations based on the temperature at different nanofluid concentration are derived and used in the numerical simulations. In this regard, the results will be accurate with respect to using theoretical properties of nanofluid, and close agreements will be detected between present results and the previous numerical and experimental works. The numerical investigation is done under the effect of Rayleigh number (103 < Ra < 106), volume concentration of nanofluid (?? = 0.5, 1, 1.5, 2, 2.5 and 3%) and thermal configuration of the cavity (Cases A, B, C and D).

Originality/value
The originality of the present work lies in coupling of the lattice Boltzmann method with experimental observations to analyse the free convection in a cavity.
A new agent-based simulation model of bilateral negotiation
Authors: Lempp Frieder 
Published: October 2019

PurposeThe purpose of this paper is to introduce a new agent-based simulation model of bilateral negotiation based on a synthesis of established theories and empirical studies of negotiation research. The central units of the model are negotiators who pursue goals, have attributes (trust, assertiveness, cooperativeness, creativity, time, etc.) and perform actions (proposing and accepting offers, exchanging information, creating value, etc).Design/methodology/approachMethodologically, the model follows the agent-based approach to modeling. This approach is chosen because negotiations can be described as complex, non-linear systems involving autonomous agents (i.e. the negotiators), who interact with each other, pursue goals and perform actions aimed at achieving their goals.FindingsThis paper illustrates how the model can simulate experiments involving variables such as negotiation strategy, creativity, reservation value or time in negotiation. An example simulation is presented which investigates the main and interaction effects of negotiators’ reservation value and their time available for a negotiation. A software implementation of the model is freely accessible athttps://tinyurl.com/y7oj6jo8.Research limitations/implicationsThe model, as developed at this point, provides the basis for future research projects. One project could address the representation of emotions and their impact on the process and outcome of negotiations. Another project could extend the model by allowing negotiators to convey false information (i.e. to bluff). Yet another project could be aimed at refining the routines used for making and accepting offers with a view to allow parties to reach partial settlements during a negotiation.Practical implicationsDue to its broad scope and wide applicability, the model can be used by practitioners and researchers alike. As a decision-support system, the model allows users to simulate negotiation situations and estimate the likelihood of negotiation outcomes. As a research platform, it can generate simulation data in a cost- and time-effective way, allowing researchers to simulate complex, large-N studies at no cost or time.Originality/valueThe model presented in this paper synthesizes in a novel way a comprehensive range of concepts and theories of current negotiation research. It complements other computational models, in that it can simulate a more diverse range of negotiation strategies (distributive, integrative and compromise) and is applicable to a greater variety of negotiation scenarios.
Corporate social responsibility and hospital brand advocacy
Authors: Limbu Yam B. , Pham Long , Mann Manveer 
Published: October 2019

PurposeThis study aims to examine relationships between corporate social responsibility (CSR) toward two key stakeholder groups – patients and society and hospital brand advocacy, and the mediating role of trust and patient-hospital identification (PHI) and the moderating role of hospital type on these associations.Design/methodology/approachThe sample of 455 hospital patients was surveyed in Vietnam.FindingsThe results suggest that both CSR toward society and patients are positively related to brand advocacy. The influence of CSR toward patients on brand advocacy was stronger for private hospitals than public hospitals. Trust and PHI independently and partially mediate relationships between both stakeholder groups of CSR and brand advocacy with the exception of the trust, which fully mediates the relationship between CSR toward society and brand advocacy. Trust and PHI serve as serial mediators.Practical implicationsHospitals can promote patients’ organic word of mouth through CSR initiatives and focusing on the reliability, safety and quality of care.Originality/valueThis study examines the mediation effects of trust and PHI and moderating role of hospital type in the relationships between two components of CSR effort and hospital brand advocacy.
Optimization of dynamic properties of hybrid composite shaft with newly developed resin (NDR) using grey relational analysis
Authors: Patil Sagar Dnyandev , Bhalerao Yogesh J. 
Published: October 2019

Purpose
The purpose of this paper is to find the impact of various design variables on the composite shaft, and also the effect of newly developed resin (NDR) on the strength of the fibers of the composite shaft.

Design/methodology/approach
The Taguchi method is used to optimize the design variables. Also, GRG approach is used to validate the result.

Findings
NDR improves the bonding strength of fiber than the epoxy resin. With the grey relational analysis (GRA) method, the initial setting (A1B4C4D1) was having grey relational grade 0.957. It was enhanced by using a new optimum combination (A2B2C4D2) to 0.965. It indicates that there is an enhancement in the grade by 0.829 percent. Thus, using the GRA approach of analysis, design variables have been successfully optimized to achieve improved dynamic properties of hybrid composite shaft.

Originality/value
The findings of this research are helping to optimize the design variables for the composite shaft. Also, the NDR gives the good bonding strength of carbon/glass fibers in dynamic loading condition than the epoxy resin.
Remaining useful life prediction for lithium-ion batteries using particle filter and artificial neural network
Authors: Qin Wei , Lv Huichun , Liu Chengliang , Nirmalya Datta , Jahanshahi Peyman 
Published: October 2019

Purpose
With the promotion of lithium-ion battery, it is more and more important to ensure the safety usage of the battery. The purpose of this paper is to analyze the battery operation data and estimate the remaining life of the battery, and provide effective information to the user to avoid the risk of battery accidents.

Design/methodology/approach
The particle filter (PF) algorithm is taken as the core, and the double-exponential model is used as the state equation and the artificial neural network is used as the observation equation. After the importance resampling process, the battery degradation curve is obtained after getting the posterior parameter, and then the system could estimate remaining useful life (RUL).

Findings
Experiments were carried out by using the public data set. The results show that the Bayesian-based posterior estimation model has a good predictive effect and fits the degradation curve of the battery well, and the prediction accuracy will increase gradually as the cycle increases.

Originality/value
This paper combines the advantages of the data-driven method and PF algorithm. The proposed method has good prediction accuracy and has an uncertain expression on the RUL of the battery. Besides, the method proposed is relatively easy to implement in the battery management system, which has high practical value and can effectively avoid battery using risk for driver safety.
The role of executive functions in academic performance and behaviour of university students
Authors: Ramos-Galarza Carlos , Acosta-Rodas Pamela , Bolaños-Pasquel Mónica , Lepe-Martínez Nancy 
Published: October 2019

Purpose
The purpose of this paper is fourfold: first, to analyse the relationship between executive functions and academic performance; second, to identify the level of prediction executive functions have on academic performance; third, to determine the correlation between executive functions and academic performance; and fourth, to compare executive functions based on the level of academic performance.

Design/methodology/approach
The sample composed of 175 university students aged between 18 and 36 years (M=21.49, SD=3.22). The EFECO scale, the average student grade and a scale based on the diagnostic criteria for ADHD were used as measurement instruments.

Findings
Difficulties in executive functions: Difficulties in working memory (r=−0.30, p=<0.01) and difficulties in conscious supervision of behaviour (r=−0.29, p⩽0.01) have an inversely proportional relationship to academic performance (the greater the deficit of executive functions, the lower the academic performance). The regression analysis showed that executive functions explain 31 per cent of the variance of academic performance (χ2(25)=43.81, p <0.001). The study found that there is a relationship between all the executive functions and students’ behaviour in a medium to large magnitude.

Research limitations/implications
A limitation of this study was the size of the sample as it is not representative of the country. Nevertheless, the correlation among the variables studied here has the necessary magnitude for the proposed correlations to be found. Nonetheless, it is necessary that we perform a study with a larger number of participants in order to achieve adequate extrapolation of the results.

Practical implications
Data found in this study suggest that low academic performance of university students is related to a lower functionality of their executive functions.

Originality/value
The originality of the research lies in relating specific concepts of neuropsychology to explain the academic performance of university students. The research findings allow us to project new studies to improve the executive functions for the benefit of the university student.
Prioritizing the vaccine supply chain issues of developing countries using an integrated ISM-fuzzy ANP framework
Authors: Chandra Dheeraj , Kumar Dinesh 
Published: October 2019

PurposeDelivering vaccines to the children who need them requires a supply chain that is efficient and effective. In most of the developing countries, however, the unknown and unresolved supply chain issues are causing inefficiencies in distributing vaccines. There is, therefore, a great need in such countries to recognize the issues that cause delays in vaccine delivery. With this purpose, the present study aims to identify and analyze the key issues in the supply chain of basic vaccines required to immunize children in developing countries.Design/methodology/approachBased on a field survey of three states of India, in-depth review of relevant literature and experts’ opinions, 25 key issues were recognized as factors of the vaccine supply chain (VSC) and categorized into five main domains. Using integrated interpretive structural modeling and fuzzy analytic network process approaches, the issues have been prioritized to determine their relative importance in the VSC. In addition, a sensitivity analysis has been performed to investigate the priority stability of the issues.FindingsThe results of the analysis show that among the five domains of VSC issues, the economic domain with a weight of 0.4262 is the most important domain, followed by the management (0.2672), operational (0.2222), environmental (0.0532) and social (0.0312).Research limitations/implicationsThis study focuses on the prioritization of VSC issues; therefore, the results of the present study can provide direction to the decision-makers of immunization programs of developing countries in driving their efforts and resources on eliminating the most important obstacles to design successful vaccination programs.Originality/valueTo the authors’ knowledge, this paper is first to provide a direction to the decision-makers in identifying and managing important issues through the use of an analytical approach.
Audit committee gender diversity and financial reporting: evidence from restatements
Authors: Oradi Javad , Izadi Javad 
Published: October 2019

PurposeThe purpose of this paper is to investigate the association between gender diversity on the audit committees and the incidence of financial restatements.Design/methodology/approachUsing a sample of 683 firm-year observations from Iranian listed companies for the period 2013 to 2017, this paper uses a logistic regression model to examine a research hypothesis related to the association between the presence of female members on the audit committee and the incidence of financial restatements.FindingsAfter controlling for other restatement-related factors, the authors find that the presence of at least one female member on audit committees reduces the likelihood of the incidence of financial restatements. Robustness tests also confirmed this result. Moreover, the additional analyses show that independent and financial expert female members on audit committees are more strongly associated with a reduction in financial restatements. Further, the results suggest that the presence of female members on the audit committee can increase the likelihood of hiring higher quality auditors. Generally, the findings are consistent with the literature on gender diversity which suggests that women perform better in a monitoring role, are more conservative and make more ethical decisions.Practical implicationsThe findings of this study could help with the understanding of broader participation of female directors on company boards and subgroups such as the audit committee, and of the improvement in corporate governance. Moreover, the findings can be of particular interest to monitoring authorities and policy makers in developing countries and send positive signals to them regarding the recommendation or requirement of gender diversity as a part of corporate governance mechanisms.Originality/valueThe present study contributes to the extant literature by providing empirical evidence on the effect of audit committee gender diversity on financial restatements. Furthermore, this study provides evidence on the more effective oversight and greater ability of independent and financial expert female directors, which has been significantly disregarded in the previous studies.