bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer
Authors: Urioistegui-Arcos Maritere , Aguayo-Ortiz Rodrigo , Valencia-Morales María del Pilar , Melchy-Pérez Erika , Rosenstein Yvonne , Domínguez Laura , Zurita Mario 
Published: December 2019

AbstractDisruption of the enzymatic activities of the transcription factor TFIIH by Triptolide (TPL) or THZ1 could be used against cancer. Here, we used an oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had an additive effect. TPL affects the interaction between XPB and P52, causing a reduction in the levels of XPB, P52, and P8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
The somatic genetic and epigenetic mutation rate in a wild long-lived perennialPopulus trichocarpa
Authors: Hofmeister Brigitte T. , Denkena Johanna , Colomé-Tatché Maria , Shahryary Yadollah , Hazarika Rashmi , Grimwood Jane , Mamidi Sujan , Jenkins Jerry , Grabowski Paul P. , Sreedasyam Avinash , Shu Shengqiang , Barry Kerrie , Lail Kathleen , Adam Catherine , Lipzen Anna , Sorek Rotem , Kudrna Dave , Talag Jayson , Wing Rod , Hall David W. , Tuskan Gerald A. , Schmutz Jeremy , Johannes Frank , Schmitz Robert J. 
Published: December 2019

ABSTRACTBackgroundPlants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an eco-evolutionary context, particularly in long-lived perennials.ResultsHere, we generated a new high-quality reference genome from the oldest branch of a wildPopulus trichocarpatree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we used a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions.ConclusionTaken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.
Connectomic consistency: a systematic stability analysis of structural and functional connectivity
Authors: Osmanlıoğlu Yusuf , Alappatt Jacob A. , Parker Drew , Verma Ragini 
Published: December 2019

AbstractConnectomics, the study of brain connectivity, has become an indispensable tool in neuroscientific research as it provides insights into brain organization. Connectomes are generated for different modalities such as using diffusion MRI to capture structural organization of the brain or using functional MRI to elaborate brain’s functional organization. Understanding links between structural and functional organizations is crucial in explaining how observed behavior emerges from the underlying neurobiological mechanisms. Many studies have investigated how these two organizations relate to each other; however, we still lack a proper understanding on how much variation should be expected on the two modalities, both between people cross-sectionally and within a single person longitudinally. Notably, connectomes of both modalities were shown to have significant differences depending on how they are generated. In this study, for both modalities, we systematically analyzed consistency of connectomes, that is the similarity between connectomes in terms of individual connections between brain regions or in terms of overall network topology. We present a comprehensive study of consistency in structural and resting-state functional connectomes both for a single subject examined longitudinally and across a large cohort of subjects cross-sectionally. We compared connectomes generated by different tracking algorithms, parcellations, edge weighting schemes, and edge pruning techniques. We evaluated consistency both at the levels of individual edges using correlation and at the level of network topology via graph matching accuracy. We also examined consistency of connectomes that are generated using most commonly applied communication schemes. Our results demonstrate varying degrees of consistency for the two modalities, with structural connectomes showing higher consistency than functional connectomes. Moreover, we observed a wide variation in consistency depending on how connectomes are generated. Our study sets a reference point for consistency of connectome types, which is especially important for structure-function coupling studies in evaluating mismatches between modalities.
In Vivo Dual RNA-Seq Analysis Reveals the Basis for Differential Tissue Tropism of Clinical Isolates of Streptococcus pneumoniae
Authors: Minhas Vikrant , Aprianto Rieza , McAllister Lauren J. , Wang Hui , David Shannon C. , McLean Kimberley T. , Comerford Iain , McColl Shaun R. , Paton James C. , Veening Jan-Willem , Trappetti Claudia 
Published: December 2019

ABSTRACTStreptococcus pneumoniae is a genetically diverse human-adapted pathogen commonly carried asymptomatically in the nasopharynx. We have recently shown that a single nucleotide polymorphism (SNP) in the raffinose pathway regulatory gene rafR accounts for a significant difference in the capacity of clonally-related strains to cause localised versus systemic infection. Here we have used dual RNA-seq to show that this SNP extensively impacts both bacterial and host transcriptomes in infected lungs. It affects expression of bacterial genes encoding multiple sugar transporters, and fine-tunes carbohydrate metabolism, along with extensive rewiring of host transcriptional responses to infection, particularly expression of genes encoding cytokine and chemokine ligands and receptors. The dual RNA-seq data predicted a crucial role for differential neutrophil recruitment in the distinct virulence profiles of the infecting strains and single cell analysis revealed that while reduced expression of the RafR regulon driven by a single rafR SNP provides a clear advantage for pneumococci to colonize the ear, in the lung it leads to massive recruitment of neutrophils and bacterial clearance. Importantly, the observed disease outcomes were confirmed by in vivo neutrophil depletion showing that early detection of bacteria by the host in the lung environment is crucial for effective clearance. Thus, dual RNA-seq provides a powerful tool for understanding complex host-pathogen interactions and revealed how a single bacterial SNP can drive differential disease outcomes.
Arabidopsis CPR5 regulates ethylene signaling via interacting with ETR1 N-terminus and controlling mRNAs nucleocytoplasmic transport
Authors: Chen Jiacai , Yu Yanchong , Sui Xinying , Qiao Longfei , Dong Chun-Hai 
Published: December 2019

AbstractETR1 is the major ethylene receptor in Arabidopsis thaliana. Previous studies showed that RTE1 and CPR5 can bind to ETR1 and play regulatory roles in ethylene signaling. RTE1 has been suggested to promote ETR1 signal transduction by influencing the conformation of ETR1, but little is known about the mechanism of CPR5 on the regulation of ETR1 signaling. In this study, we showed that both CPR5 and RTE1 could interact with the N-terminal transmembrane domains of ETR1, and CPR5 needs at least three transmembrane domains of ETR1 while RTE1 needs only two for the binding. As CPR5 has also been shown to be localized in the nuclear membrane and might act as a nucleoporin, we analyzed the effects of CPR5 on the nucleocytoplasmic transport of ethylene-related mRNAs using poly(A)-mRNA in situ hybridization and real-time quantitative PCR (qPCR), and the results indicated that CPR5 could selectively regulate the nucleocytoplasmic transport of mRNAs in ethylene signaling pathway. In contrast, the nucleoporin mutants (nup160, nup96-1 and nup96-2) dramatically accumulated all the examined mRNAs in the nucleus. In conclusion, the present study provides evidence demonstrating that CPR5 regulates ethylene signaling through interacting with the ETR1 receptor and controlling the mRNAs nucleocytoplasmic transport in ethylene signaling pathway.Key messageThis study reveals that CPR5 is involved in the regulation of ethylene signaling via two different ways: interacting with the N-terminal domains of ERT1 and controlling the nucleocytoplasmic transport of mRNAs in ethylene signaling pathway.
Expanding the Chinese hamster ovary cell long non-coding RNA transcriptome using RNASeq
Authors: Motheramgari Krishna , Valdés-Bango Curell Ricardo , Tzani Ioanna , Gallagher Clair , Rivadeneyra Marina Castro , Zhang Lin , Barron Niall , Clarke Colin 
Published: December 2019

AbstractOur ability to study Chinese hamster ovary (CHO) cell biology has been revolutionised over the last decade with the development of next generation sequencing and the publication of reference DNA sequences for CHO cells and the Chinese hamster. RNA sequencing has not only enabled the association of transcript expression with bioreactor conditions and desirable bioprocess phenotypes but played a key role in the characterisation of protein coding and small non-coding RNAs. The annotation of long non-coding RNAs, and therefore our understanding of their role in CHO cell biology, has been limited to date. In this manuscript, we use high resolution RNASeq data to more than double the number of annotated lncRNA transcripts for the CHOK1 genome. In addition, the utilisation of strand specific sequencing enabled the identification of more than 1,000 new lncRNAs located antisense to protein coding genes. The utility of monitoring lncRNA expression is demonstrated through an analysis of the transcriptomic response to a reduction of cell culture temperature and identification of simultaneous sense/antisense differential expression for the first time in CHO cells. To enable further studies of lncRNAs, the transcripts annotated in this study have been made available for the CHO cell biology community.
Global energy and geopolitical risk: behavior of oil markets
Authors: Alqahtani Abdullah , Taillard Michael 
Published: December 2019

PurposeThe question being assessed is whether changes in the degree of global geopolitical risk (GPR), as defined by the framework developed by Iacoviello (2018), can be used to improve allocative efficiency, thereby increasing investment returns on oil commodities.Design/methodology/approachUsing the linear and nonlinear model, this paper analyzes the impact of GPR on returns of oil prices (BRENT, WTI and Organization of Petroleum Exporting Countries), as well as the short- and long-run relationship between GPR and oil prices.FindingsThe results of the impulse response function indicates that oil prices do not respond to shocks in GPR. The results of the Granger causality test show that oil returns are not caused by GPR. The regression analysis and autoregressive distributed lag results show that there is no significant impact of GPR on the returns of oil.Originality/valueThis is unique among the literature in that it identifies and isolates the relationship between GPR and oil market pricing. Insight into the lag in market response and the degree to which GPR can be used to estimate oil prices using curvilinear models are derived from the analysis.
Explicating the influence of shared goals and hope on knowledge sharing and knowledge creation in an emerging economic context
Authors: Goswami Anil Kumar , Agrawal Rakesh Kumar 
Published: December 2019

PurposeThe purpose of this study is to empirically investigate the influence of shared goals and hope on knowledge sharing and knowledge creation in organizations. Furthermore, it examines the mediating role of hope in the relationship between shared goals and knowledge sharing and between shared goals and knowledge creation.Design/methodology/approachThis study has used quantitative research methodology wherein the data have been collected from 221 employees of information technology (IT) companies in India using survey questionnaire. Structural equation modelling has been applied to test the hypotheses of the study.FindingsThe findings of the study reveal that shared goals and hope positively influence knowledge sharing and knowledge creation. Shared goals also affects hope positively. Further, hope acts as a mediator between shared goals and knowledge sharing and between shared goals and knowledge creation.Research limitations/implicationsThis study is a cross-sectional study conducted in IT companies in India. It can be supplemented by future studies through qualitative approaches and longitudinal data collection.Practical implicationsThe study makes a significant contribution to literature by considering shared goals and hope as antecedents of knowledge sharing and knowledge creation. It provides directions to managers to focus on various interventions to strengthen shared goals and hope amongst employees to motivate them to share and create knowledge that can help the organization to get sustainable competitive advantage.Originality/valueTo the best of authors’ knowledge, this study is an early study conducted to examine the influence of shared goals and hope on knowledge sharing and knowledge creation. Further, hardly any study has examined the mediating role of hope in the relationship between shared goals and knowledge sharing and between shared goals and knowledge creation.
Three-echelon supply chain inventory model for growing items
Authors: Sebatjane Makoena , Adetunji Olufemi 
Published: December 2019

Purpose
The purpose of this paper is to formulate a coordinated inventory control model for growing items in a supply chain with farming, processing and retail operations. The farmer grows newborn items and then delivers them to a processor once the items mature. At the processing plant, the items are slaughtered, cut and packaged at a specified rate. The processor then delivers a certain number of equally sized shipments of processed items to a retailer who satisfies customer demand.

Design/methodology/approach
A cost minimisation inventory model describing the problem at hand is formulated with the number of shipments and the cycle time being the decision variables. A solution algorithm for solving the problem is presented and applied to a numerical example.

Findings
Opting for an integrated policy is favourable to all supply chain members. When the proposed model is compared to equivalent independent and equal-cycle time replenishment policies, the total cost savings amount to 3 and 14 per cent, respectively.

Social implications
The model can serve as a guideline for procurement managers dealing with growing items to better their inventory management practices. Considerable cost savings in food production chains can be achieved through improved inventory control, and these savings can be used to cushion consumers against rising food prices.

Originality/value
Most previously published models on inventory management for growing items were formulated under the assumption that the items are grown and then sold to consumers instantaneously. In real food production systems, the items need to be transformed and packaged into a consumable form before customer demand is met. The model presented in this paper accounts for this and is therefore more realistic.
Making investment decisions in stock markets using a forecasting-Markowitz based decision-making approaches
Authors: Moeini Najafabadi Zahra , Bijari Mehdi , Khashei Mehdi 
Published: December 2019

PurposeThis study aims to make investment decisions in stock markets using forecasting-Markowitz based decision-making approaches.Design/methodology/approachThe authors’ approach offers the use of time series prediction methods including autoregressive, autoregressive moving average and artificial neural network, rather than calculating the expected rate of return based on distribution.FindingsThe results show that using time series prediction methods has a significant effect on improving investment decisions and the performance of the investments.Originality/valueIn this study, in contrast to previous studies, the alteration in the Markowitz model started with the investment expected rate of return. For this purpose, instead of considering the distribution of returns and determining the expected returns, time series prediction methods were used to calculate the future return of each asset. Then, the results of different time series methods replaced the expected returns in the Markowitz model. Finally, the overall performance of the method, as well as the performance of each of the prediction methods used, was examined in relation to nine stock market indices.
Relationship between corporate identity, place architecture and identification
Authors: Foroudi Mohammad M. , Balmer John M.T. , Chen Weifeng , Foroudi Pantea 
Published: December 2019

PurposeHow organizations view, value and manage their place architecture in relation to identification and corporate identity has received little research attention. The main goal of this paper is to provide an integrative understanding of the relationships between corporate identity, place architecture, and identification from a multi-disciplinary approach. It is assumed that the characteristics of the organization and of the way a corporate identity and place architecture are managed will affect employees’ and consumers’ identification.Design/methodology/approachThe paper uses a theory-building case study within the phenomenological/qualitative research tradition. The data were gathered through 15 in-depth interviews with top management who were working at a London-Based Business School. In addition, six focus groups were conducted with a total of 36 academics, and new empirical insights are offered. NVivo software was used to gain insight into the various influences and relationships.FindingsDrawing on one case study, the findings confirm that firms are using the conceptualizations of corporate identity and place architecture, including the leveraging of tangible and intangible forms of consumers’/employees’ identification, toward a university business school. The insights from a single, exploratory, case study might not be generalizable.Originality/valueThe relationships between corporate identity, place architecture and identification have received little research attention and have hardly been studied at all from the perspective of this paper. This paper has value to researchers in the fields of marketing, corporate identity, place architecture, design, as well as professionals involved in managing a company’s architecture. Drawing on the marketing/management theory of identity and architecture alignment, managers and policy advisors should devote attention to each element of the corporate identity and place architecture and ensure that they are meaningful, as well as in dynamic alignment.
Evaluating the factors of corporate website favorability: a case of UK and Russia
Authors: Ageeva Elena , Melewar T.C. , Foroudi Pantea , Dennis Charles 
Published: December 2019

PurposeThis study aims to evaluate the significance of the corporate website favorability notion and examines its factors in developing competitive advantage in the context of retail and service settings in the UK and Russia.Design/methodology/approachBased on the attribution, social identity and signaling theories, this study adopted the qualitative exploratory approach by conducting 14 interviews with retail experts and eight focus groups with retail users in the UK and Russia, combined with experts in website design, communication and marketing.FindingsThe study findings indicated that it is crucial to build and maintain a favorable corporate website that reveals the corporate identity as part of the overall company strategy. The study suggests that navigation, visual, information, usability, customization, security, availability, website credibility, customer service, perceived corporate social responsibility and perceived corporate culture are the factors of corporate website favorability that contribute to the company’s competitive advantage. The findings show that consumers from Russia as well as from the UK found the significance of a favorable corporate website (i.e. corporate website favorability), as well as the factors affecting corporate website favorability. However, consumers in the UK are more critical and demanding in the level of expectation of the website overall and put more weight than consumers from Russia on the perceived corporate social responsibility, perceived corporate culture, customer service and website credibility.Practical implicationsCorporate website favorability should be adopted by the companies, as part of the overall corporate identity management. Furthermore, it is advised to take into consideration the variations in the level of importance of the factors of corporate website favorability in different countries. The findings of this study suggest that this investigation will make a considerable managerial contribution to the understanding of a company’s decision-makers, communication professionals and website specialists about the building of a favorable corporate website in line with corporate identity strategy of the company.Originality/valueThere has been little systematic study of the effect of corporate websites on consumer evaluations of the websites; also, there is a lack of research with regard to the factors that contribute to the development of a favorable corporate website (i.e. corporate website favorability). This is the first study of its kind to find the effect of corporate website favorability in Russia, representing a non-western country, and the UK, representing a western country. Therefore, it contributes to the corporate visual identity literature by presenting the corporate website favorability construct and demonstrating the factors that influence corporate website favorability.