bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interplay between the epigenetic enzyme lysine (K)-specific demethylase 2B and Epstein-Barr virus infection
Authors: Vargas-Ayala Romina C. , Jay Antonin , Hernandez-Vargas Hector , Diederichs Audrey , Robitaille Alexis , Sirand Cecilia , Ceraolo Maria Grazia , Romero Maria , Cros Marie Pierre , Cuenin Cyrille , Durand Geoffroy , Calvez-Kelm Florence Le , Mundo Lucia , Maroui Mohamed Ali , Leoncini Lorenzo , Manet Evelyne , Herceg Zdenko , Gruffat Henri , Accardi Rosita 
Published: July 2018

AbstractHistone modifier lysine (K)-specific demethylase 2B(KDM2B) plays a role in hematopoietic cells differentiation and its expression appears to be deregulated in certain cancers of hematological and lymphoid origins. We have previously found that KDM2B gene is differentially methylated in cell lines derived from the Epstein-Barr virus (EBV) associated endemic Burkitt’s lymphomas (eBL) compared to EBV negative sporadic BL cells. However, whether KDM2B plays a role in eBL development has never been previously demonstrated. Oncogenic viruses have been shown to hijack the host cell epigenome to complete their life cycle and to promote the transformation process by perturbing cell chromatin organization. Here we investigated whether EBV would alter KDM2B levels to enable its life cycle and promote B-cells transformation. We show that infection of B-cells with EBV leads to down-regulation of KDM2B levels. We also show that LMP1, one of the main EBV transforming proteins, induces increased DNMT1 recruitment to KDM2B gene and augments its methylation. By altering KDM2B levels and performing chromatin immunoprecipitation in EBV infected B-cells, we were able to show that KDM2B is recruited to the EBV gene promoters and inhibits their expression. Furthermore, forced KDM2B expression in immortalized B-cells led to altered mRNA levels of some differentiation-related genes. Our data show that EBV deregulates KDM2B levels through an epigenetic mechanism and provide evidence for a role of KDM2B in regulating virus and host cell gene expression, warranting further investigations to assess the role of KDM2B in the process of EBV-mediated lymphomagenesis.IMPORTANCE. In Africa, Epstein-Barr virus infection is associated with endemic Burkitt lymphoma, a pediatric cancer. The molecular events leading to its development are poorly understood compared to the sporadic Burkitt lymphoma. In a previous study, by analyzing the DNA methylation changes in endemic compared to sporadic Burkitt lymphomas cell lines, we identified several differential methylated genomic positions in proximity of genes with a potential role in cancer, among them the KDM2B gene. KDM2B encodes a histone H3 demethylase already shown to be involved in some hematological disorders. However, whether KDM2B plays a role in the development of Epstein-Barr virus-mediated lymphoma has never been investigated before. In this study we show that Epstein-Barr virus deregulates KDM2B expression and describe the underlying mechanisms. We also reveal a role of the demethylase in controlling viral and B-cells genes expression, thus highlighting a novel interaction between the virus and the cellular epigenome.
Probing chemotaxis activity inEscherichia coliusing fluorescent protein fusions
Authors: Roggo Clémence , van der Meer Jan Roelof 
Published: July 2018

ABSTRACTChemotaxis is based on ligand-receptor interactions that are transmitted via protein-protein interactions to the flagellar motors. Ligand-receptor interactions in chemotaxis can be deployed for the development of rapid biosensor assays, but there is no consensus as to what the best readout of such assays would have to be. Here we explore two potential fluorescent readouts of chemotactically activeEscherichia colicells. In the first, we probed interactions between the chemotaxis signaling proteins CheY and CheZ by fusing them individually with non-fluorescent parts of a ‘split’-Green Fluorescent Protein. Wild-type chemotactic cells but not mutants lacking the CheA kinase produced distinguishable fluorescence foci, two-thirds of which localize at the cell poles with the chemoreceptors and one-third at motor complexes. Cells expressing fusion proteins only were attracted to serine sources, demonstrating measurable functional interactions between CheY~P and CheZ. Fluorescent foci based on stable split-eGFP displayed small fluctuations in cells exposed to attractant or repellent, but those based on an unstable ASV-tagged eGFP showed a higher dynamic behaviour both in the foci intensity changes and the number of foci per cell. For the second readout, we expressed the pH-sensitive fluorophore pHluorin in the cyto- and periplasm of chemotactically activeE. coli. Calibrations of pHluorin fluorescence as a function of pH demonstrated that cells accumulating near a chemo-attractant temporally increase cytoplasmic pH while decreasing periplasmic pH. Both readouts thus show promise as proxies for chemotaxis activity, but will have to be further optimized in order to deliver practical biosensor assays.IMPORTANCEBacterial chemotaxis may be deployed for future biosensing purposes with the advantages of its chemoreceptor ligand-specificity and its minute-scale response time. On the downside, chemotaxis is ephemeral and more difficult to quantitatively read out than, e.g., reporter gene expression. It is thus important to investigate different alternative ways to interrogate chemotactic response of cells. Here we gauge the possibilities to measure dynamic response in theEscherichia colichemotaxis pathway resulting from phosphorylated CheY-CheZ interactions by using (unstable) split-fluorescent proteins. We further test whether pH differences between cyto- and periplasm as a result of chemotactic activity can be measured with help of pH-sensitive fluorescent proteins. Our results show that both approaches conceptually function, but will need further improvement in terms of detection and assay types to be practical for biosensing.
Phenogenon: Gene to Phenotype Associations for Rare Genetic Diseases
Authors: Murphy Cian , Moghul Ismail , Pontikos Nikolas ,   Phenopolis consortium, UK Inherited Retinal Dystrophy consortium, UCLex consortium, Yu Jing 
Published: July 2018

AbstractAs genome sequencing is increasingly applied to molecular diagnosis of rare Mendelian disorders, large number of patients with diverse phenotypes have their genomic and phenotypic data pooled together to uncover new genotype - phenotype relations. We introduce Phenogenon, a method that combines: the power of Human Phenotype Ontology for describing patient phenotypes, gnomAD for estimating rare variant population frequency, and CADD for variant pathogenicity prediction. By using a divide and conquer approach, we demonstrate here that Phenogenon is able to uncover true gene to phenotype relations, such as “ABCA4 – Macular dystrophy” and “SCN1A – Seizures”. Additionally, it accurately infers mode of inheritance, such as a recessive mode of inheritance in the case of the “ABCA4 – Macular dystrophy” relationship and a dominant mode of inheritance with the “SCN1A – Seizures” relationship. We also found that CADD has more power to detect early-onset rare genetic diseases than late-onset diseases. In this study, we ran Phenogenon against a diverse cohort of 3288 patients. Among the top 13 gene-phenotype relations, seven were previously known. We also highlight four potentially novel gene – phenotype relations such as “SIPA1L3 – Abnormal electroretinogram”.
A molecular phylogeny of bedbugs elucidates the evolution of host associations and sex-reversal of reproductive trait diversification
Authors: Roth Steffen , Balvín Ondřej , Di Iorio Osvaldo , Siva-Jothy Michael T. , Benda Petr , Calva Omar , Faundez Eduardo I. , McFadzen Mary , Lehnert Margie P. , Anwarali Khan Faisal Ali , Naylor Richard , Simov Nikolay , Morrow Edward H. , Willassen Endre , Reinhardt Klaus 
Published: July 2018

AbstractAll 100+ bedbug species (Cimicidae) are obligate blood-sucking parasites and well-known for their habit of traumatic insemination but the evolutionary trajectory of these characters is unknown. Our new, fossil-dated, molecular phylogeny estimates that ancestral Cimicidae evolved ca. 115MYA as hematophagous specialists on an unidentified host, 50MY before bats, switching to bats and birds thereafter. Humans were independently colonized three times and our phylogeny rejects the idea that the divergence of the two current urban pests (Cimex lectulariusandC. hemipterus) 47MYA was associated with the divergence ofHomo sapiensandH. erectus(1.6MYA). The female’s functional reproductive tract is unusually diverse and heterotopic, despite the unusual and strong morphological stasis of the male genitalia. This sex-reversal in genital co-variation is incompatible with current models of genital evolution. The evolutionary trait diversification in cimicids allowed us to uncover fascinating biology and link it to human pre-history and current activity.
Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC
Authors: Greathouse K. Leigh , Robert White James , Padgett R. Noah , Perrotta Brittany G , Jenkins Gregory D , Chia Nicholas , Chen Jun 
Published: July 2018

AbstractObesity is a risk factor for colorectal cancer (CRC), accounting for more than 14% of CRC incidence. Microbial dysbiosis and chronic inflammation are common characteristics in both obesity and CRC. Human and murine studies, together, demonstrate the significant impact of the microbiome on governing energy metabolism and CRC development; yet, little is understood about the contribution of the microbiome to development of obesity-associated CRC as compared to non-obese individuals. In this study, we conducted a meta-analysis using five publicly available stool and tissue-based 16S rRNA and whole genome sequencing (WGS) data sets of CRC microbiome studies. High-resolution analysis was employed for 16S rRNA data using Resphera Insight, which allowed us to achieve species-level information to compare with WGS. Characterization of the confounders between studies, 16S rRNA variable region, and sequencing method, did not reveal any significant effect on alpha diversity in CRC prediction. Both 16S rRNA and WGS were equally variable in their ability to predict CRC. Results from community structure and composition analysis confirmed lower diversity in obese individuals without CRC; however, no universal differences were found in diversity between obese and non-obese individuals with CRC. When examining taxonomic differences, the probability of being classified as CRC did not change significantly in obese individuals for all taxa tested. However, random forest classification was able to distinguish CRC and non-CRC stool when body mass index was added to the model. Overall, microbial dysbiosis was not a significant factor in explaining the higher risk of colon cancer among individuals with obesity.
Attraction in buyer–supplier relationships
Authors: Patrucco Andrea S. , Luzzini Davide , Moretto Antonella , Ronchi Stefano 
Published: July 2018

PurposeThe purpose of this paper is to shed light on the dynamics of buyer–supplier industrial relationships and the role of customer attractiveness—a requisite to obtain best efforts from suppliers involved in collaborative initiatives.Design/methodology/approachThe paper develops a theoretical framework tested through an international survey with a structured equation modeling approach.FindingsResults confirm that customer attractiveness positively affects both innovation and cost performance ensured by suppliers. Moreover, several direct and indirect antecedents of customer attractiveness are identified, including characteristics of the buying firm’s procurement department (i.e. procurement knowledge and procurement status) and supply chain relationship characteristics (i.e. proficiency of supplier collaboration and visibility).Research limitations/implicationsBecause of the survey approach, the research results are limited to the data collected.Practical implicationsFindings support the relevance of collaborative relationships in improving performance, and the key role procurement department could play in managing the multifaceted aspects of supplier collaboration.Originality/valueThis paper investigates, on the one hand, why customer attractiveness is relevant for supply chain management, and what are the effects on innovation and cost performance ensured by suppliers; on the other hand, antecedents of customer attractiveness are considered, with a main focus on organizational and relational procurement variables.
UAV rendezvous based on Nash bargain
Authors: Jiang Wanyue , Wang Daobo , Wang Yin 
Published: July 2018

Purpose
The purpose of this paper is to find a solution for the unmanned aerial vehicle (UAV) rendezvous problem, which should be feasible, optimal and not time consuming. In the existing literatures, the UAV rendezvous problem is always presented as a matter of simultaneous arrival. They focus only on the time consistency. However, the arrival time of UAVs can vary according to the rendezvous position. The authors should determine the best rendezvous position with considering UAVs’ maneuver constraint, so that UAVs can construct a formation in a short time.

Design/methodology/approach
The authors present a decentralized method in which UAVs negotiate with each other for the best rendezvous positions by using Nash bargain. The authors analyzed the constraints of the rendezvous time and the UAV maneuver, and proposed an objective function that allows UAVs to get to their rendezvous positions as fast as possible. Bezier curve is adopted to generate smooth and feasible flight trajectories. During the rendezvous process, UAVs adjust their speed so that they can arrive at the rendezvous positions simultaneously.

Findings
The effectiveness of the proposed method is verified by simulation experiments. The proposed method can successfully and efficiently solve the UAV rendezvous problem.

Originality/value
As far as the authors know, it is the first time Nash bargain is used in the UAV rendezvous problem. The authors modified the Nash bargain method and make it distributed, so that it can be computed easily. The proposed method is much less consuming than ordinary Nash bargain method and ordinary swarm intelligence based methods. It also considers the UAV maneuver constraint, and can be applied online for its fast calculation speed. Simulations demonstrate the effectiveness of the proposed method.
Researching accounting
Authors: Mustafa Hasri 
Published: July 2018

Purpose
The purpose of this paper is to engage, cooperate and communicate for a more visible form of research accounting in early research settings, especially by those in non-native English speaking and developing nations.

Design/methodology/approach
The paper highlights four early research settings: in writing a research undertaking, in gaining acceptance of a research undertaking, in situating the self in the research context and in the renegotiation of the research context.

Findings
The paper finds that although organisations offer a forum for a discussion of socialising form of accounting, organisational communication inverts many of the norms of academic etiquettes. It interrupts, takes statements out of context and challenges the academic claim of accounting as a language of business.

Practical implications
The paper alerts corporations, managers, supervisors and researchers that communicating accounting is distinct from communication skills, though both emphasise that communications comprise behaviours which can be learned. Inexperienced researchers are not the only potential readers of the paper. The study is an attempt to provide accounting researchers with a resource for making informed decisions concerning the communication type they face and by placing their research agenda within the appropriate accounting characterisations.

Originality/value
The paper broadens the view of what constitutes knowledge of accounting and the knowledge about accounting and the ways to attain them. The key topics explored in the study provide “hands-on” methodological issues that could be adapted for use on similar programmes.
Do entrepreneur-focused facility incentives create economic impacts? Evidence from Indiana
Authors: Hicks Michael , Faulk Dagney G. 
Published: July 2018

Purpose
As a component of a benefit-cost analysis into the efficacy of publicly funded facility incentives, the purpose of this paper is to examine the county-wide impact of business incubators, makerspaces and co-working spaces on employment, proprietor’s employment and the average wage per job. The period under analysis is 1971 through 2015 across Indiana’s 92 counties.

Design/methodology/approach
Using a unique data set on facility incentives in Indiana, a spatial panel model, which includes a unique identification strategy to account for underlying conditions identified as a source of incubator success in earlier studies, is developed.

Findings
This study finds no statistically significant impact of these facilities on total employment or average wage per job during this period. There is a statistically meaningful impact of co-working spaces on proprietor’s employment, but the effect is an economically insignificant one-time increase of 2.3 jobs in the typical county, which can be interpreted as shifting employment from traditional employment to proprietorship employment.

Originality/value
This is the first empirical estimate of the contribution of modern facility incentives on measures of local economic activity.
Public response to the implementation of clean and healthy living behavior (PHBS) in coastal community in Rokan Hilir Regency
Authors: Rizal Yose 
Published: July 2018

Purpose
This paper aims to find in-depth information related the activities of “clean and healthy behavior” in household regulations, starting from assessment, planning, mobilization, implementation monitoring and assessment.

Design/methodology/approach
Data analysis was used for quantitative and qualitative approaches (mixing method). The qualitative approach was used to understand the individual phenomena in terms of finding, obtaining and describing the community behavior, which is related to health problems. The data obtained through the approach were then analyzed using interactive model.

Findings
In principle, this research exactly determines the responses of officers and the community to the process of “clean and healthy living behavior” activities. In general, the health facility used first is self-treatment, before seeking medical treatment or non-drug treatment. It proves that humans are always experimenting. From the research result, there are respondents who do not use medical treatment at 16 per cent; and the remaining 84 per cent are using medical treatment, despite being preceded by self-treatment (S) and non-medical treatment (N).

Originality/value
Currently, there have not been many studies related to the implementation of clean and healthy behavior although the information about it is very important to know. The managers of the “clean and healthy behavior” program need to know such information.
Understanding internet addiction: a comprehensive review
Authors: Bisen Shilpa Suresh , Deshpande Yogesh M. 
Published: July 2018

PurposeThe purpose of this paper is to delineate the overall theoretical framework on the topic of internet addiction through the comprehensive narrative review to make readers aware of the conceptual growth and development in the respective field. The paper evolves theoretically from the historical foundation, phenomenology, clinical feature, etiological model to the treatment outcome of internet addiction. Multiple studies have been done in the field of mental health but dearth of work given head to toe theoretical overview for understanding of this trendsetter research area in mental health.Design/methodology/approachExtensive review of literature has been carried out to make a systematic layout for conceptual paper.FindingsThe internet has been a source of gratification for several behavioral addictions as well as psychiatric disorders. Mainly because of the lack of established diagnostic criteria and a dearth of large sample surveys, the prevalence of problematic internet use (PIU) in general population has not been established. Still, from all the consolidated data, PIU seems to have a male preponderance and manifests itself in late adulthood. Symptoms of PIU can easily be masked with signs of dependence, tolerance and withdrawal which is quite similar to the phenomenology of substance addiction. Psychiatric co-morbidities are more of a norm than the exception in case of PIU. Even though the clinical status of PIU is doubtful, still there is a significant demand for its treatment all over the world. Overall, the excessive use of internet has been strongly debated in literature from PIU to a positive addiction. Only time will tell how it affects our civilization as a phenomenon of evolutionary significance.Originality/valueThe paper is providing a general conceptual framework for internet addiction/PIU to enable readers to know about the topic in depth from the evolution of the concept to the recent developments in the area.
A reflection on knowledge sharing research: patterns and trends
Authors: Goswami Anil Kumar , Agrawal Rakesh Kumar 
Published: July 2018

Purpose
The purpose of this study is to bring to the fore the identity and image of knowledge sharing (KS) research in terms of the patterns and trends of its growth and its intellectual structure by systematically and objectively extracting various information from extant literature published in KS research area.

Design/methodology/approach
This study is based on the counting technique and bibliometric approach (citations and co-citations analysis) applied in extant literature published in the KS research area.

Findings
The study finds that KS research area is evolving and has immense potential to grow in the future. It elaborates upon the publications and collaborative research patterns and identifies the works, authors and journals that have significant theoretical influence in KS research area. The analysis reveals four major themes in KS research, namely, behaviour-oriented perspective of KS, understanding, frameworks and models of KS, technology-oriented perspective of KS and KS barriers.

Research limitations/implications
This study is based on research papers, published in KS research area, that have been extracted from selected journals by mining their titles with “knowledge sharing” as a keyword. Future studies may enhance the search space by including the abstracts in addition to the title while extracting papers in the search.

Practical implications
This study renders all stakeholders an extensive understanding about the direction of KS research. It will help future researchers to identify their areas of interest before venturing into a deeper search. Thus, it will be a significant resource and a quick reference for researchers in KS research area. The study can also help practitioners to focus on key aspects of KS and, further, apply appropriate organizational interventions to enhance KS in promoting innovation and gaining competitive advantage for their organizations.

Originality/value
This is one of the very few and early studies conducted to extract patterns and trends of growth and provide the intellectual structure with KS as a domain of research.