bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rosa26 docking sites for investigating genetic circuit silencing in stem cells
Authors: Fitzgerald Michael , Livingston Mark , Gibbs Chelsea , Deans Tara L. 
Published: March 2019

ABSTRACTApproaches in mammalian synthetic biology have transformed how cells can be programmed to have reliable and predictable behaviour, however, the majority of mammalian synthetic biology has been accomplished using immortalized cell lines that are easy to grow and easy to transfect. Genetic circuits that integrate into the genome of these immortalized cell lines remain functional for many generations, often for the lifetime of the cells, yet when genetic circuits are integrated into the genome of stem cells gene silencing is observed within a few generations. To investigate the reactivation of silenced genetic circuits in stem cells, the Rosa26 locus of mouse pluripotent stem cells was modified to contain docking sites for site-specific integration of genetic circuits. We show that the silencing of genetic circuits can be reversed with the addition of sodium butyrate, a histone deacetylase inhibitor. These findings demonstrate an approach to reactivate the function of genetic circuits in pluripotent stem cells to ensure robust function over many generations. Altogether, this work introduces an approach to overcome the silencing of genetic circuits in pluripotent stem cells that may enable the use of genetic circuits in pluripotent stem cells for long-term function.
Loss of ErbB3 redirects Integrin β1 from early endosomal recycling to secretion in extracellular vesicles
Authors: Rodrigues-Junior Dorival Mendes , Saez-Ibanez Ana Rosa , Terabayashi Takeshi , Daubel Nina , Makinen Taija , Idevall-Hagren Olof , Moustakas Aristidis , Ferby Ingvar 
Published: March 2019

ABSTRACTReceptor tyrosine kinases (RTKs) are important cargo of endocytic trafficking, yet the role of RTKs in endocytic sorting and maturation of multivesicular bodies (MVBs) per se remains unclear. Here we show that the ErbB3 receptor, frequently overexpressed in invasive breast cancers, sorts internalized transferrin receptor (TfR) and Integrin β1 for endocytic recycling, in a manner that does not require ligand-induced ErbB3 signaling in breast epithelial cells. Loss of ErbB3 abrogates recycling of Integrin β1, likely from a Rab4-positive compartment, and redirects it towards lysosomal degradation or secretion as cargo of extracellular vesicles (EVs). Depletion of ErbB3 impairs migration of sheets of breast epithelial cells, concomitant with imposing a reduction of Integrin β1 cell surface level and an increase in release of EVs containing Integrin β1. In contrast, EVs secreted from ErbB3-depleted cells enhanced the motility of wild-type cells, potentially counteracting the reduced migration of ErbB3-deficient cells. Mechanistically, ErbB3 facilitates assembly of the Arf6-GGA3-Rabaptin5 endosomal sorting complex to promote early recycling, which consequently suppresses EV release. Therefore, ErbB3 constitutes part of the endosomal trafficking machinery, provoking the notion that RTKs might play a novel and yet unrecognised role in vesicular trafficking.
VIDHOP, viral host prediction with Deep Learning
Authors: Mock Florian , Viehweger Adrian , Barth Emanuel , Marz Manja 
Published: March 2019

AbstractMotivationZoonosis, the natural transmission of infections from animals to humans, is a far-reaching global problem. The recent outbreaks of Zika virus, Ebola virus and Corona virus are examples of viral zoonosis, which occur more frequently due to globalization. In the case of a virus outbreak, it is helpful to know which host organism was the original carrier of the virus. Once the reservoir or intermediate host is known, it can be isolated to prevent further spreading of the viral infection. Recent approaches aim to predict a viral host based on the viral genome, often in combination with the potential host genome and arbitrarily selected features. These methods have a clear limitation in either the number of different hosts they can predict or the accuracy of their prediction.ResultsHere, we present a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. To ensure a high prediction accuracy, we developed an effective selection approach for the training data to avoid biases due to a highly unbalanced number of known sequences per virus-host combinations. We tested our deep neural network on three different virus species (influenza A, rabies lyssavirus, rotavirus A). We reached for each virus species an AUG between 0.93 and 0.98, outperforming previous approaches and allowing highly accurate predictions while only using fractions (100-400 bp) of the viral genome sequences. We show that deep neural networks are suitable to predict the host of a virus, even with a limited amount of sequences and highly unbalanced available data. The deep neural networks trained for this approach build the core of the virus-host predicting tool VIDHOP (Virus Deep learning HOst Prediction).AvailabilityThe trained models for the prediction of the host for the viruses influenza A, rabies lyssavirus, rotavirus A are implemented in the tool VIDHOP. This tool is freely available under https://github.com/flomock/vidhop.Supplementary informationSupplementary data are available at DOI 10.17605/OSF.IO/UXT7N
Reproductive success of Eastern Bluebirds (Sialia sialis) varies with the timing and severity of drought
Authors: Carleton Reneé E. , Graham John H. , Lee Adel , Taylor Zachary P. , Carleton Jon F. 
Published: March 2019

AbstractDrought affects avian communities in complex ways. We used our own and citizen science-generated reproductive data acquired through The Cornell Lab of Ornithology’s NestWatch Program, combined with drought and vegetation indices obtained from governmental agencies, to determine drought effects on Eastern Bluebird (Sialia sialisL.) reproduction across their North American breeding range for the years 2006–2013. Our results demonstrate that some aspects of bluebird reproductive success varies with the timing and severity of drought. Clutch size was unaffected by drought occurrence or severity during or within one and two months of clutch initiation, but hatching and fledging rates decreased as drought severity increased. Drought conditions occurring one month prior to the month during which eggs should have hatched, and two months prior to the month nestlings should have fledged also reduced the numbers of fledged offspring. We also demonstrate the value of datasets generated by citizen scientists in combination with climate data for examining biotic responses at large temporal and spatial scales.
ARMOR: an Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data
Authors: Orjuela Stephany , Huang Ruizhu , Hembach Katharina M. , Robinson Mark D. , Soneson Charlotte 
Published: March 2019

AbstractThe extensive generation of RNA sequencing (RNA-seq) data in the last decade has resulted in a myriad of specialized software for its analysis. Each software module typically targets a specific step within the analysis pipeline, making it necessary to join several of them to get a single cohesive workflow. Multiple software programs automating this procedure have been proposed, but often lack modularity, transparency or flexibility. We present ARMOR, which performs an end-to-end RNA-seq data analysis, from raw read files, via quality checks, alignment and quantification, to differential expression testing, geneset analysis and browser-based exploration of the data. ARMOR is implemented using the Snakemake workflow management system and leverages conda environments; Bioconductor objects are generated to facilitate downstream analysis, ensuring seamless integration with many R packages. The workflow is easily implemented by cloning the GitHub repository, replacing the supplied input and reference files and editing a configuration file. Although we have selected the tools currently included in ARMOR, the setup is modular and alternative tools can be easily integrated.
The gene annotated by the locus tag At3g08860 encodes a β-alanine/L-alanine aminotransferase in Arabidopsis thaliana
Authors: Parthasarathy Anutthaman , Savka Francisco C. , Hudson André O. 
Published: March 2019

AbstractThe aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes some of which remain uncharacterized. This study elucidates the function of an uninvestigated aminotransferase annotated by the locus tag At3g08860. The cDNA was shown to functionally complement two E. coli mutants auxotrophic for the amino acids β-alanine (non-proteogenic) and L-alanine (proteogenic). The elucidation of At3g08860 activity has the potential to facilitate experiments for the optimization of plant lines involved in nitrogen utilization efficiency, response to hypoxia, osmo-protection, vitamin B5 and coenzyme A metabolism.
Effects of enalapril and paricalcitol treatment on diabetic nephropathy and renal expressions of TNF-α, P53, Caspase-3 and Bcl-2 in STZ-induced diabetic rats
Authors: Ahmed Osama M. , Ali Tarek M. , Abdel Gaid Mohamed A. , Elberry Ahmed A. 
Published: March 2019

AbstractThis study aimed to assess the renopreventive effect of the angiotensin converting enzyme inhibitor (ACEI), enalapril, and/or vitamin D receptor (VDR) activator, paricalcitol, on streptozotocin (STZ) diabetes-induced nephropathy and to elucidate the mechanisms of action through investigation of the effects on renal oxidative stress, antioxidant defense system and expressions of TNF-α, P53, caspase-3, and Bcl-2. Diabetes mellitus was induced in fasting male Wistar rats by single intraperitoneal injection of STZ (45 mg /kg b.w.) dissolved in citrate buffer pH 4.5. Ten days after STZ injection, the diabetic rats were treated with enalapril (25 mg/l of drinking water) and/or paricalcitol (8 µg/kg b.w.per os) dissolved in 5% DMSO daily for 4 weeks. The obtained data revealed that the treatment of diabetic Wistar rats with enalapril and/or paricalcitol led to a significant decrease in the elevated serum urea, uric acid, creatinine and sodium, potassium levels; thereby reflecting improvement of the impaired kidney function. The deteriorated kidney lipid peroxidation, GSH content and GST and catalase activities in diabetic rats were significantly ameliorated as a result of treatment with enalapril and/or paricalcitol. The elevated fasting and post-prandial serum glucose levels and the lowered serum insulin and C-peptide levels were also improved. Moreover, the treatment of diabetic rats successfully prevented the diabetes-induced histopathological deleterious changes of kidney and islets of Langerhans of pancreas. In association, the immunohistochemically detected pro-inflammatory cytokine TNF-α and apoptotic mediators P53 and caspase-3 were remarkably decreased in kidney of diabetic rats as a result of treatment, while the expression of anti-apoptotic protein Bcl-2 was increased. Based on these findings, it can be concluded that enalapril and paricalcitol can prevent STZ diabetes-induced nephropathy though amelioration of the glycemic state and antioxidant defense system together with the suppression of oxidative stress, inflammation and apoptosis.
Channelrhodopsin-1 Phosphorylation Changes with Phototactic Behavior and Responds to Physiological Stimuli inChlamydomonas
Authors: Böhm Michaela , Boness David , Fantisch Elisabeth , Erhard Hanna , Frauenholz Julia , Kowalzyk Zarah , Marcinkowski Nadin , Kateriya Suneel , Hegemann Peter , Kreimer Georg 
Published: March 2019

AbstractThe unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) exhibits oriented movement responses (phototaxis) to light over more than three log units of intensity. Phototaxis thus depends on the cell’s ability to adjust the sensitivity of its photoreceptors to ambient light conditions. In Chlamydomonas, the photoreceptors for phototaxis are the channelrhodopsins (ChR)1 and ChR2; these light-gated cation channels are located in the plasma membrane. Although ChRs are widely used in optogenetic studies, little is known about ChR signaling in algae. We characterized the in vivo phosphorylation of ChR1. Its reversible phosphorylation occurred within seconds as a graded response to changes in the light intensity and ionic composition of the medium and depended on an elevated cytosolic Ca2+ concentration. Changes in the phototactic sign were accompanied by alterations in the phosphorylation status of ChR1. Furthermore, compared with the wild type, a permanently negative phototactic mutant required higher light intensities to evoke ChR1 phosphorylation. C-terminal truncation of ChR1 disturbed its reversible phosphorylation, whereas it was normal in ChR2-knockout and eyespot-assembly mutants. The identification of phosphosites in regions important for ChR1 function points to their potential regulatory role(s). We propose that multiple ChR1 phosphorylation, regulated via a Ca2+-based feedback loop, is an important component in the adaptation of phototactic sensitivity in Chlamydomonas.
Experiential marketing, social judgements, and customer shopping experience in emerging markets
Authors: Ihtiyar Ali , Barut Mehmet , Ihtiyar Hatice Gulsah 
Published: March 2019

Purpose
The purpose of this paper is to examine the influence of experiential marketing modules, service quality and social judgement on experiential values of young customers. The paper also investigates the effects of experiential values on customer satisfaction (CS) and post-purchasing behaviour. In addition, the paper intends to strengthen the shift in marketing paradigm and to provide insightful enhancements to the literature.

Design/methodology/approach
An instrument was developed to measure how strategic experiential module (Schmitt, 1999), social judgement module (Rosenberg et al., 1968) and service quality perceptions of customers influence functional and emotional values. Primary data were gathered through surveying 402 respondents in order to diagnose young customers’ experiences in popular coffee stores in Phnom Penh, Cambodia. The constructs and their interrelationships were examined based on partial least square-structural equation modelling (PLS-SEM).

Findings
The results of PLS-SEM were found to be adequate in terms of validity and reliability. The results revealed that some of experiential modules and service quality have positive stimuli on experiential values. These contributions postulate an impetus for potential exploration in numerous service settings.

Originality/value
The study assesses the effect of shopping experiences of young customers on experiential values, social judgement, CS and post-purchase shopping attitudes. It is anticipated that by filling this gap, this study will assist in strengthening marketing strategies, which requires an alteration in the existing business atmosphere. The suggestions and results for future research are discussed in detail accordingly.
The impact of pioneer adopter characteristics and perceptions on the perceived costs of switching to a follower product
Authors: Parry Mark Edward , Sarma Sumita 
Published: March 2019

Purpose
The purpose of this paper is to propose and test a model in which the perceived post-purchase monetary costs and time costs of switching from a pioneer product are a function of the perceived difficulty of comparing follower products with the pioneer product, the variety of ways in which the pioneer product is used by an adopter, pioneer adopter satisfaction with the pioneer, the familiarity of the pioneer adopter with follower products and the anticipated reactions to switching of other household members who use the pioneer product.

Design/methodology/approach
The authors test this model with data collected from 518 Japanese iPad owners. Hypotheses are evaluated using structural equation modeling.

Findings
The authors find that each of the hypothesized independent variables is related in the hypothesized direction with one or both types of switching costs.

Research limitations/implications
Findings indicate that the variety of pioneer product use, the perceived negative reaction of other household users of the pioneer product and comparison difficulties between the pioneer and follower product have an important influence on the perceptions of the perceived costs of switching from a pioneer to a follower product.

Practical implications
Findings suggest that managers responsible for launching follower products can lower the perceived costs of switching from a pioneer product through specific product design and communication decisions.

Originality/value
In contrast with prior switching-cost research, this paper focuses on switching costs as perceived by pioneer adopters and examining the importance of pioneer-follower product comparison difficulties, the variety of pioneer product use and the negative reactions of other household users of the pioneer product.
Consumers’ perceptions regarding questionable consumption practices in China
Authors: Chang Hsiu-Hua , Vitell Scott J. , Lu Long-Chuan 
Published: March 2019

Purpose
Since East Asian Confucian societies are relational societies that view harmonious relationships with others as important, the issue of consumer ethics has received considerable attention in the quest to improve the effectiveness of business transactions. This is especially true of China, a large developing country with many business investment opportunities. The purpose of this paper is to examine the relationships between consumer ethical beliefs and the personality traits of consumer relationship proneness, religiousness, attitude toward business and love of money, which are seldom explored in the literature.

Design/methodology/approach
The sample is collected by systematic sampling in China and a sample of 434 individuals is surveyed. This study performs confirmatory factor analysis to examine the reliability and validity and then uses the evaluation of the structural equation model exhibited a good fit between the model and the observed data to test the hypotheses via LISREL 8.7.

Findings
Findings show that individuals with stronger relationship proneness and high religiousness tend to more strongly consider many questionable consumer practices as unacceptable. Attitude toward business and love of money partially impact consumer unethical beliefs.

Originality/value
While there cultural differences between East Asian and western societies, consumer relationship proneness and the three other constructs featuring Chinese characteristics should be considered a vital personality in Chinese society. The results of this study offer findings which are not fully consistent with the findings of studies conducted in other countries and can improve friendly relationship marketing practices with Chinese consumers. More research is necessary to understand consumer ethical behavior in the varied cultures of Asia.
The temporal effects of social and business networks on international performance of South Korean SMEs
Authors: Jeong So Won , Jin Byoungho Ellie , Jung Sojin 
Published: March 2019

PurposeDrawing on the resource-based view, the purpose of this paper is to investigate the link between resource capabilities and performance by incorporating two network dimensions (i.e. social and business networks), a moderator (i.e. international experience) and a mediator (i.e. marketing capabilities).Design/methodology/approachSME data were collected via surveys. A sampling frame of 3,000 exporting manufactures was developed based on a database sourced from the Korea Chamber of Commerce and Industry. The authors first contacted the managers of each firm in the sampling frame through e-mail or phone to receive permission, and then sent a paper questionnaire. The authors analyzed 392 valid cases using a path analysis.FindingsThe findings largely confirmed the hypotheses in the proposed framework based on the RBV. While social networks only enhanced marketing capabilities and did not directly lead to international performance, business networks enhanced both. Also, unlike social networks, the influence of SME business networks on international performance was weakened as international experience increased. This study found that marketing capabilities mediated the path from business networks to international performance.Research limitations/implicationsThe study explained the distinctive roles played by social and business networks in international performance, extending our knowledge of the RBV by showing how firm resources can turn into sustainable competitive advantages. More importantly, the integration of time into the discussion on networks and international performance extended the business network internationalization process model.Practical implicationsThe authors suggest that Korean SMEs focus on developing their own marketing capabilities by capitalizing on their social and business networks, which could directly enhance international performance. Governments can also offer assistance to SMEs for developing their own marketing capabilities during the initial stages of internationalization, since the benefit of business networks diminishes as international experience increases.Originality/valueBy testing the proposed link between resource capabilities and performance, this study suggested how SME networks can contribute to international performance, extending our understanding of RBV. This study further confirmed the dynamic impact of business networks on international performance, such that it changes over the course of the internationalization process.
Factors influencing agents’ bargaining power and collaborative innovation
Authors: Lee Yung-Heng , Yan Min-Ren 
Published: March 2019

Purpose
The purpose of this paper is to identify the factors influencing bargaining decisions and systematically develop a framework to support collaborative innovation within a strategic alliance. This framework can help companies resolve bargaining problems and facilitate cooperation and effective negotiation of strategic alliances to build successful business relationships.

Design/methodology/approach
The study considers Taiwanese agents’ bargaining power during negotiations with suppliers, using decision analysis to identify the variables affecting judgment. It uses Delphi–AHP methods to evaluate and develop a multi-criteria model explaining the critical factors to increase agents’ bargaining power and collaborative capability in the negotiation process.

Findings
Two significant differences between supply chain management practices and managerial specialty are found. Results suggest that better supply chain management practices of agents could assist suppliers in reducing their stock and processing delivery costs, and suppliers could offer more of their marketing planning and strategies to agents to increase confidence in each other’s products.

Research limitations/implications
It is hoped that this study will encourage more academics in the supply chain management field to investigate the extent to which other bargaining considerations act as facilitating or constraining factors in other Asian and non-Asian economies and other industries.

Practical implications
This study focuses on collaborative thinking and cooperation to develop and improve positive and relational outcomes in agent–supplier relationships.

Originality/value
The study analyzed the bargaining power of agents and collaborative innovation in the semiconductor industry from three major perspectives: professional competence, managerial competence and channel efficiency. The study provides effective suggestions for enhancing profits in agency-based cooperation.