bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional landscape of cell lines and their tissues of origin
Authors: Lopes-Ramos Camila M. , Paulson Joseph N. , Chen Cho-Yi , Kuijjer Marieke L. , Fagny Maud , Platig John , Sonawane Abhijeet R. , DeMeo Dawn L. , Quackenbush John , Glass Kimberly 
Published: October 2016

SummaryCell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. An important question is how well a cell line’s transcriptional and regulatory processes reflect those of its tissue of origin. We analyzed RNA-Seq data from GTEx for 127 paired Epstein-Barr virus transformed lymphoblastoid cell lines and whole blood samples; and 244 paired fibroblast cell lines and skin biopsies. A combination of gene expression and network analyses shows that while cell lines carry the expression signatures of their primary tissues, albeit at reduced levels, they also exhibit changes in their patterns of transcription factor regulation. Cell cycle genes are over-expressed in cell lines compared to primary tissue, and they have a reduction of repressive transcription factor targeting. Our results provide insight into the expression and regulatory alterations observed in cell lines and suggest that these changes should be considered when using cell lines as models.HighlightsCell lines differ from their source tissues in gene expression and regulationDistinct cell lines share altered patterns of cell cycle regulationCell cycle genes are less strongly targeted by repressive TFs in cell linesCell lines share expression with their source tissue, but at reduced levels
Lowest expressing microRNAs capture indispensable information: identifying cancer types
Authors: Rasnic Roni , Linial Nathan , Linial Michal 
Published: October 2016

ABSTRACTThe primary function of microRNAs (miRNAs) is to maintain cell homeostasis. In cancerous tissues miRNAs’ expression undergo drastic alterations. In this study, we used miRNA expression profiles from The Cancer Genome Atlas (TCGA) of 24 cancer types and 3 healthy tissues, collected from >8500 samples. We seek to classify the cancer’s origin and tissue identification using the expression from 1046 reported miRNAs. Despite an apparent uniform appearance of miRNAs among cancerous samples, we recover indispensable information from lowly expressed miRNAs regarding the cancer/tissue types. Multiclass support vector machine classification yields an average recall of 58% in identifying the correct tissue and tumor types. Data discretization has led to substantial improvement reaching an average recall of 91% (95% median). We propose a straightforward protocol as a crucial step in classifying tumors of unknown primary origin. Our counter-intuitive conclusion is that in almost all cancer types, highly expressing miRNAs mask the significant signal that lower expressed miRNAs provide.
Gene regulatory network inference from single-cell data using multivariate information measures
Authors: Chan Thalia E. , Stumpf Michael P.H. , Babtie Ann C. 
Published: October 2016

AbstractWhile single-cell gene expression experiments present new challenges for data processing, the cell-to-cell variability observed also reveals statistical relationships that can be used by information theory. Here, we use multivariate information theory to explore the statistical dependencies between triplets of genes in single-cell gene expression datasets. We develop PIDC, a fast, efficient algorithm that uses partial information decomposition (PID) to identify regulatory relationships between genes. We thoroughly evaluate the performance of our algorithm and demonstrate that the higher order information captured by PIDC allows it to outperform pairwise mutual information-based algorithms when recovering true relationships present in simulated data. We also infer gene regulatory networks from three experimental single-cell data sets and illustrate how network context, choices made during analysis, and sources of variability affect network inference. PIDC tutorials and open-source software for estimating PID are available here:https://github.com/Tchanders/network_inference_tutorials. PIDC should facilitate the identification of putative functional relationships and mechanistic hypotheses from single-cell transcriptomic data.
First report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil
Authors: de Souza Thiara Manuele Alves , de Azeredo Elzinandes Leal , da Silva Jéssica Badolato Corrêa , Damasco Paulo Vieira , Santos Carla Cunha , de Paiva Fabienne Petitinga , Nunes Priscila Conrado Guerra , Barbosa Luciana Santos , Cipitelli Márcio da Costa , Chouin-Carneiro Thaís , Faria Nieli Rodrigues da Costa , Nogueira Rita Maria Ribeiro , de Bruycker-Nogueira Fernanda , dos Santos Flavia Barreto 
Published: October 2016

AbstractBackgroundChikungunya virus (CHIKV) is an arbovirus that causes an acute febrile illness characterized by severe and debilitating arthralgia. In Brazil, the Asian and East-Central South African (ECSA) genotypes are circulating in the north and northeast of the country, respectively. In 2015, the first autochthonous cases in Rio de Janeiro, Brazil were reported but until now the circulating strains have not been characterized. Therefore, we aimed here to perform the molecular characterization and phylogenetic analysis of CHIKV strains circulating in the 2016 outbreak occurred in the municipality of Rio de Janeiro.MethodsThe cases analyzed in this study were collected at a private Hospital, from April 2016 to May 2016, during the chikungunya outbreak in Rio de Janeiro, Brazil. All cases were submitted to the Real Time RT-PCR for CHIKV genome detection and to anti-CHIKV IgM ELISA. Chikungunya infection was laboratorially confirmed by at least one diagnostic method and, randomly selected positive cases (n=10), were partially sequenced (CHIKV E1 gene) and analyzed.ResultsThe results showed that all the samples grouped in ECSA genotype branch and the molecular characterization of the fragment did not reveal the A226V mutation in the Rio de Janeiro strains analyzed, but a K211T amino acid substitution was observed for the first time in all samples and a V156A substitution in two of ten samples.ConclusionsPhylogenetic analysis and molecular characterization reveals the circulation of the ECSA genotype of CHIKV in the city of Rio de Janeiro, Brazil and two amino acids substitutions (K211T and V156A) exclusive to the CHIKV strains obtained during the 2016 epidemic, were reported.
Chimeric Genes Revealed in the Polyploidy Fish Hybrids ofCarassius cuvieri(Female) ×Megalobrama amblycephala(Male)
Authors: Hu Fangzhou , Wu Chang , Zhou Yunfan , Wang Shi , Xiao Jun , Wu Yanhong , Xu Kang , Ren Li , Liu Qingfeng , Li Wuhui , Wen Ming , Tao Min , Qin Qinbo , Zhao Rurong , Luo Kaikun , Liu Shaojun 
Published: October 2016

AbstractThe genomes of newly formed natural or artificial polyploids may experience rapid gene loss and genome restructuring. In this study, we obtained tetraploid hybrids (4n=148, 4nJB) and triploid hybrids (3n=124, 3nJB) derived from the hybridization of two different subfamily speciesCarassius cuvieri(♀, 2n = 100, JCC) andMegalobrama amblycephala(♂, 2n = 48, BSB). Some significant morphological and physiological differences were detected in the polyploidy hybrids compared with their parents. To reveal the molecular traits of the polyploids, we compared the liver transcriptomes of 4nJB, 3nJB and their parents. The results indicated high proportion chimeric genes (31 > %) and mutated orthologous genes (17 > %) both in 4nJB and 3nJB. We classified 10 gene patterns within three categories in 4nJB and 3nJB orthologous gene, and characterized 30 randomly chosen genes using genomic DNA to confirm the chimera or mutant. Moreover, we mapped chimeric genes involved pathways and discussed that the phenotypic novelty of the hybrids may relate to some chimeric genes. For example, we found there is an intragenic insertion in the K+ channelkcnk5b, which may be related to the novel presence of the barbels in 4nJB. Our results indicated that the genomes of newly formed polyploids experienced rapid restructuring post-polyploidization, which may results in the phenotypic and phenotypic changes among the polyploidy hybrid offspring. The formation of the 4nJB and 3nJB provided new insights into the genotypic and phenotypic diversity of hybrid fish resulting from distant hybridization between subfamilies.
The fitness ofPseudomonas aeruginosaquorum sensing signal cheats is influenced by the diffusivity of the environment
Authors: Mund Anne , Diggle Stephen P. , Harrison Freya 
Published: October 2016

ABSTRACTExperiments examining the social dynamics of bacterial quorum sensing (QS) have focused on mutants which do not respond to signals, and the role of QS-regulated exoproducts as public goods. The potential for QS signal molecules to themselves be social public goods has received much less attention. Here, we analyse how signal-deficient (lasI−) mutants of the opportunistic pathogenPseudomonas aeruginosainteract with wild-type cells in an environment where QS is required for growth. We show that when growth requires a ‘private’ intracellular metabolic mechanism activated by the presence of QS signal,lasI−mutants act as social cheats and outcompete signal-producing wild-type bacteria in mixed cultures, because they can use the signals produced by wild type cells. However, reducing the ability of signal molecules to diffuse through the growth medium, results in signal molecules becoming less accessible to mutants, leading to reduced cheating. Our results indicate that QS signal molecules can be considered as social public goods in a way that has been previously described for other exoproducts, but that spatial structuring of populations reduces exploitation by non-cooperative signal cheats.ImportanceBacteria communicate via signaling molecules to regulate the expression of a whole range of genes. This process, termed quorum sensing (QS), moderates bacterial metabolism in many environmental conditions, from soil and water (where QS-regulated genes influence nutrient cycling) to animal hosts (where QS-regulated genes determine pathogen virulence). Understanding the ecology of QS could therefore yield vital clues as to how we might modify bacterial behaviour for environmental or clinical gains. Here, we demonstrate that QS signals act as shareable public goods. This means that their evolution, and therefore population-level responses to interference with QS, will be constrained by population structure. Further, we show that environmental structure (constraints on signal diffusion) alters the accessibility of QS signals and demonstrates that we need to consider population and environmental structure to help us further our understanding of QS signaling systems.
Potent optogenetic inhibition of behavior with anion channelrhodopsins
Authors: Mohammad Farhan , Stewart James C. , Ott Stanislav , Chlebikova Katarina , Chua Jia Yi , Koh Tong-Wey , Ho Joses , Claridge-Chang Adam 
Published: October 2016

AbstractOptogenetics employs light exposure to manipulate physiology in genetically modified organisms. There are abundant tools for optogenetic excitation of neuronal activity, but the limitations of current activity photo-inhibitors present an obstacle to demonstrating the necessity of specific neuronal circuits. Here we show that anion channelrhodopsins can be used to specifically and rapidly inhibit a range of systems involved inDrosophilalocomotion, wing expansion, memory retrieval and gustation, demonstrating their broad utility to the circuit analysis of behavior.
normR: Regime enrichment calling for ChIP-seq data
Authors: Helmuth Johannes , Li Na , Arrigoni Laura , Gianmoena Kathrin , Cadenas Cristina , Gasparoni Gilles , Sinha Anupam , Rosenstiel Philip , Walter Jörn , Hengstler Jan G. , Manke Thomas , Chung Ho-Ryun 
Published: October 2016

AbstractChIP-seq probes genome-wide localization of DNA-associated proteins. To mitigate technical biases ChIP-seq read densities are normalized to read densities obtained by a control. Our statistical framework “normR” achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics. Here, we demonstrate normR’s suitability in three studies: (i) calling enrichment for high (H3K4me3) and low (H3K36me3) signal-to-ratio data; (ii) identifying two previously undescribed H3K27me3 and H3K9me3 heterochromatic regimes of broad and peak enrichment; and (iii) calling differential H3K4me3 or H3K27me3-enrichment between HepG2 hepatocarcinoma cells and primary human Hepatocytes. normR is readily available onhttp://bioconductor.org/packages/normr
Striking differences in patterns of germline mutation between mice and humans
Authors: Lindsay Sarah J. , Rahbari Raheleh , Kaplanis Joanna , Keane Thomas , Hurles Matthew E. 
Published: October 2016

SummaryRecent whole genome sequencing (WGS) studies have estimated that the human germline mutation rate per basepair per generation (∼1.2−10−8)1,2is substantially higher than in mice (3.5-5.4−10−9)3,4, which has been attributed to more efficient purifying selection due to larger effective population sizes in mice compared to humans.5,6,7. In humans, most germline mutations are paternal in origin and the numbers of mutations per offspring increase markedly with paternal age2,8,9and more weakly with maternal age10. Germline mutations can arise at any stage of the cellular lineage from zygote to gamete, resulting in mutations being represented in different proportion and types of cells, with the earliest embryonic mutations being mosaic in both somatic and germline cells. Here we use WGS of multi-sibling mouse and human pedigrees to show striking differences in germline mutation rate and spectra between the two species, including a dramatic reduction in mutation rate in human spermatogonial stem cell (SSC) divisions, which we hypothesise was driven by selection. The differences we observed between mice and humans result from both biological differences within the same stage of embryogenesis or gametogenesis and species-specific differences in cellular genealogies of the germline.
The selfie phenomenon – consumer identities in the social media marketplace
Authors: Kedzior Richard , Allen Douglas E. , Schroeder Jonathan 
Published: October 2016

PurposeThe purpose of this paper is to outline the contributions presented in this special section on the selfie phenomenon and its significance for marketing practice and scholarship.Design/methodology/approachThe significance of the topic is reviewed and themes related to the selfie phenomenon and marketplace issues are discussed in connection with extant research. The contributions of each paper are briefly highlighted and discussed.FindingsAlthough the selfie is a relatively new phenomenon, both marketing practice and scholarship have noticed its prominence in consumer lives and potential for generating marketplace insights. Despite its frequently presumed triviality, the selfie is a multifaceted phenomenon of significance to key marketing areas such as branding, consumer behavior or market research. Possible avenues for future research are outlined.Originality/valueKey issues relating to research into the selfie phenomenon for marketing scholars are illuminated.
Agency and empowerment in consumption in relation to a patriarchal bargain
Authors: Lindridge Andrew , Peñaloza Lisa , Worlu Onipreye 
Published: October 2016

Purpose
This research aims to explore how female immigrants use consumption to challenge and support their husband's position within the context of their patriarchal bargain.

Design/methodology/approach
The sample group (n = 20) consisted of ten first-generation Nigerian immigrant married couples living in Britain, who were interviewed together, with the married female then re-interviewed separately.

Findings
This paper demonstrates how women transition from being a wife in a consanguine family in Nigeria, which they describe as patriarchal, to becoming one within a nuclear family in the UK, a society to which they attribute gender equality. Nigerian immigrant women alter their ways of thinking and consuming, with implications to their agency and empowerment. In particular, consumption choices demonstrated the limits of these women’s willingness to challenge their patriarchal bargain and instead often colluded with their husbands to maintain his position as the head of the family.

Practical implications
Immigrant women should not be seen as passive receptors of their male partner’s wishes or demands, but instead active participators in purchasing and consumption decisions. Although marketing encourages direct targeting of customers, this approach raises a number of ethical issues for female African immigrants.

Originality/value
Previous research on the consumption behaviour of immigrants is limited in scope and tends to focus on male immigrants, with female immigrants either invisible or stereotyped. Compounding this problem are disciplinary, geographical and linguistic barriers that hinder social scientists' research into the consumption of female migration. This paper works to address these omissions.
Beauty blogger selfies as authenticating practices
Authors: Gannon Valerie , Prothero Andrea 
Published: October 2016

PurposeThe purpose of this paper is to consider the use of beauty blogging selfies in conveying consumer authenticity. The authors used an under-researched consumer-based authenticity approach.Design/methodology/approachThe authors adopt a practice theory approach to selfies as both objects and practices. The study combines depth-interviews with a review of the participants’ blogs and selfies.FindingsThis research shows that bloggers use selfies as records of product trial, success and failure via specific sub-types. These selfies function as authenticating consumer acts, intertwined with key life narratives and as records of communal events, where bloggers identify as a community.Research limitations/implicationsThis research is limited to beauty bloggers. Further research on consumer authenticity could be extended to other product categories and other media channels. The widened definition of selfies proposed enables further research on self-representational practices in consumption contexts. Likewise, the practice theory approach could be extended to other online contexts.Practical implicationsAs social media and peer endorsement become ever more important to marketers, brands are seeking to leverage bloggers as brand ambassadors as well as the authenticity they convey. Maintaining this authenticity and credibility among peer networks and audiences is crucial for influencers and for marketers.Originality/valueThis study contributes to the understanding of consumer-based authenticity, self-representational practices using selfies and beauty blogging communities. Practice theories are applied in an online context, suggesting an opening for further research into mediated practices.
Heterotopian selfies: how social media destabilizes brand assemblages
Authors: Rokka Joonas , Canniford Robin 
Published: October 2016

PurposeDigital technologies are changing the ways in which the meanings and identity of both consumers and brands are constructed. This research aims to extend knowledge of how consumer-made “selfie” images shared in social media might contribute to the destabilization of brands as assemblages.Design/methodology/approachInsights are drawn from a critical visual content analysis of three popular champagne brand accounts and consumer-made selfies featuring these brands in Instagram.FindingsThis study shows how brands and branded selves intersect through “heterotopian selfie practices”. Accentuated by the rise of attention economy and “consumer microcelebrity”, the authors argue that these proliferating selfie images can destabilize spatial, temporal, symbolic and material properties of brand assemblages.Practical implicationsThe implications include a consideration of how selfie practices engender new challenges for brand design and brand management.Originality/valueThis study illustrates how a brand assemblage approach can guide investigations of brands at multiple scales of analysis. In particular, this paper extends knowledge of visual brand-related user-generated content in terms of how consumers express, visualize and share selfies and how the heterotopian quality of this sharing consequently shapes brand assemblages.
Consumer anger: a label in search of meaning
Authors: Antonetti Paolo 
Published: October 2016

Purpose
The paper aims to propose a new conceptualisation of consumer anger directed against a company.

Design/methodology/approach
In this paper, an integrative review of the literature on anger in marketing has been conducted.

Findings
Anger at the firm is experienced in two forms: vengeful anger or problem-focused anger. The motivational goals associated with each differentiate between the two types and lead to different relational consequences: vengeful anger implies a desire to hurt the culprit, whereas problem-focused anger solely requires the attainment of a thwarted goal. The two types are associated with different patterns of appraisals, levels of intensity and emotion expression. These differences, documented in the literature, are not universal but shaped by contextual and personal variables. Although marketers conflate these two types of anger under the same label, only vengeful anger represents a threat to marketing relationships, whereas problem-focused anger has positive consequences if managed appropriately.

Research limitations/implications
Studies that examine anger will benefit from a more nuanced understanding of this concept. This paper raises important implications for the measurement of this emotion, as existing scales are not able to measure the goals associated with the two types of anger.

Practical implications
The insights presented help managers form strategies to address consumer anger in contexts such as service failures and/or crisis communications.

Originality/value
The paper extends scholars’ understanding of consumer anger. It offers an improved conceptualisation of this emotion, opening new avenues for future research.
Mobilizing hegemonic practices in trajectories of conspicuous resistance
Authors: Mamali Elizabeth , Nuttall Peter 
Published: October 2016

Purpose
Focusing on a community organisation, the purpose of this paper is to unravel the process through which infringing contested practices that threaten or compromise the community’s sense of distinction are transformed into acceptable symbolic markers.

Design/methodology/approach
An ethnographic study comprising participant observation, in-depth interviews and secondary data was conducted in the context of a non-profit community cinema.

Findings
Taking a longitudinal approach and drawing from practice theory, this paper outlines how member-driven, customer-driven and necessity-imposed infringing practices settle in new contexts. Further, this paper demonstrates that such practices are filtered in terms of their ideological “fit” with the organisation and are, as a result, rejected, recontextualised or replaced with do-it-yourself alternatives. In this process, authority shifts from the contested practice to community members and eventually to the space as a whole, ensuring the singularisation of the cinema-going experience.

Practical implications
This paper addresses how the integration of hegemonic practices to an off-the-mainstream experience can provide a differentiation tool, aiding resisting organisations to compensate for their lack of resources.

Originality/value
While the appropriation practices that communities use to ensure distinction are well documented, there is little understanding of the journey that negatively contested practices undergo in their purification to more community-friendly forms. This paper theorises this journey by outlining how the objects, meanings and doings that comprise hegemonic practices are transformed by and transforming of resisting organisations.