bluuebunny/crossref_metadata_2025_split huggingface dataset:
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
Authors: Morales Joannella , Bowler Emily H. , Buniello Annalisa , Cerezo Maria , Hall Peggy , Harris Laura W. , Hastings Emma , Junkins Heather A. , Malangone Cinzia , McMahon Aoife C. , Milano Annalisa , Welter Danielle , Burdett Tony , Cunningham Fiona , Flicek Paul , Parkinson Helen , Hindorff Lucia A. , MacArthur Jacqueline A. L. 
Published: April 2017

AbstractBackgroundThe accurate description of ancestry is essential to interpret and integrate human genomics data, and to ensure that advances in the field of genomics benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the consistent, unambiguous and standardized description of ancestry. To fill this gap, we provide a framework, designed for the representation of ancestry in GWAS data, but with wider application to studies and resources involving human subjects.ResultHere we describe our framework and its application to the representation of ancestry data in a widely-used publically available genomics resource, the NHGRI-EBI GWAS Catalog. We present the first analyses of GWAS data using our ancestry categories, demonstrating the validity of the framework to facilitate the tracking of ancestry in big data sets. We exhibit the broader relevance and integration potential of our method by its usage to describe the well-established HapMap and 1000 Genomes reference populations. Finally, to encourage adoption, we outline recommendations for authors to implement when describing samples.ConclusionsWhile the known bias towards inclusion of European ancestry individuals in GWA studies persists, African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations, suggesting that analyses including these groups may be more effective at identifying new associations. We believe the widespread adoption of our framework will increase standardization of ancestry data, thus enabling improved analysis, interpretation and integration of human genomics data and furthering our understanding of disease.
Rational Design of Evolutionarily Stable Microbial Kill Switches
Authors: Stirling Finn , Bitzan Lisa , Oliver John WK , Way Jeffrey , Silver Pamela A. 
Published: April 2017

SummaryThe evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One particularly useful but challenging situation is a switch between life and death depending on environment. Here are presented “essentializer” and “cryodeath” circuits, which act as kill switches inEscherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a novel toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable. Both kill switches were shown to maintain functionality in vitro for at least 140 generations. In addition, cryodeath was shown to control the growth environment of a bacterial population, with an escape rate of less than 1 in 105after ten daysin vivo.
Mashona Mole-Rat Automatic Individual Identification Based on the Mating Calls
Authors: Dvorakova Veronika , Ptacek Ladislav , Hrouzkova Ema , Muller Ludek , Sumbera Radim 
Published: April 2017

AbstractIn this study was tested mole-rat vocalization for presence of diverse individually distinctive features. An automatic system based on the GMM-UBM was used for individual recognition. The system distinguishes the recordings of the five mole-rats females. The overall achieved identification accuracy is 76.7%, the lowest 59.2%, and the highest 83.5%. The overall percentage is thus high enough to prove that the mating calls of the Mashona mole-rat can carry information about mole-rat individuality. Our results showed that studied vocal signals in the Mashona mole-rats are individually specific which indicates the possibility of individual vocal recognition in this species.
Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations
Authors: Forester Brenna R. , Lasky Jesse R. , Wagner Helene H. , Urban Dean L. 
Published: April 2017

AbstractIdentifying adaptive loci can provide insight into the mechanisms underlying local adaptation. Genotype-environment association (GEA) methods, which identify these loci based on correlations between genetic and environmental data, are particularly promising. Univariate methods have dominated GEA, despite the high dimensional nature of genotype and environment. Multivariate methods, which analyze many loci simultaneously, may be better suited to these data since they consider how sets of markers covary in response to environment. These methods may also be more effective at detecting adaptive processes that result in weak, multilocus signatures. Here, we evaluate four multivariate methods, and five univariate and differentiation-based approaches, using published simulations of multilocus selection. We found that Random Forest performed poorly for GEA. Univariate GEAs performed better, but had low detection rates for loci under weak selection. Constrained ordinations showed a superior combination of low false positive and high true positive rates across all levels of selection. These results were robust across the demographic histories, sampling designs, sample sizes, and levels of population structure tested. The value of combining detections from different methods was variable, and depended on study goals and knowledge of the drivers of selection. Reanalysis of genomic data from gray wolves highlighted the unique, covarying sets of adaptive loci that could be identified using redundancy analysis, a constrained ordination. Although additional testing is needed, this study indicates that constrained ordinations are an effective means of detecting adaptation, including signatures of weak, multilocus selection, providing a powerful tool for investigating the genetic basis of local adaptation.
Transcription factor activities enhance markers of drug response in cancer
Authors: Garcia-Alonso Luz , Iorio Francesco , Matchan Angela , Fonseca Nuno , Jaaks Patricia , Falcone Fiamenta , Bignell Graham , McDade Simon S. , Garnett Mathew J. , Saez-Rodriguez Julio 
Published: April 2017

AbstractTranscriptional dysregulation is a key feature of cancer. Transcription factors (TFs) are the main link between signalling pathways and the transcriptional regulatory machinery of the cell, positioning them as key oncogenic inductors and therefore potential targets of therapeutic intervention. We implemented a computational pipeline to infer TF regulatory activities from basal gene expression and applied it to publicly available and newly generated RNA-seq data from a collection of 1,010 cancer cell lines and 9,250 primary tumors. We show that the predicted TF activities recapitulate known mechanisms of transcriptional dysregulation in cancer and dissect mutant-specific effects in driver genes. Importantly, we show the potential for predicted TF activities to be used as markers of sensitivity to the inhibition of their upstream regulators. Furthermore, combining these inferred activities with existing pharmacogenomic markers significantly improves the stratification of sensitive and resistant cell lines for several compounds. Our approach provides a framework to link driver genomic alterations with transcriptional dysregulation that helps to predict drug sensitivity in cancer and to dissect its mechanistic determinants.
A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps
Authors: Stadler Michael R. , Eisen Michael B. 
Published: April 2017

AbstractInsulator proteins bind to specific genomic loci and have been shown to play a role in partitioning genomes into independent domains of gene expression and chromatin structure. Despite decades of study, the mechanism by which insulators establish these domains remains elusive. Here, we use genome-wide chromatin conformation capture (Hi-C) to generate a high-resolution map of spatial interactions of chromatin fromDrosophila melanogasterembryos. We show that from the earliest stages of development the genome is divided into distinct topologically associated domains (TADs), that we can map the boundaries between TADs to sub-kilobase resolution, and that these boundaries correspond to 500-2000 bp insulator elements. Comparing this map with a detailed assessment of the banding pattern of a region of a polytene chromosome, we show that these insulator elements correspond to low density polytene interbands that divide compacted bands, which correspond to TADs. It has been previously shown that polytene interbands have low packing ratios allowing the conversion of small genomic distances (in base pairs) into a large physical distances. We therefore suggest a simple mechanism for insulator function whereby insulators increase the physical space between adjacent domains via the unpacking and extension of intervening chromatin. This model provides an intuitive explanation for known features of insulators, including the ability to block enhancer-promoter interactions, limit the spread of heterochromatin, and organize the structural features of interphase chromosomes.
Strategic B2B customer experience management: the importance of outcomes-based measures
Authors: Zolkiewski Judy , Story Victoria , Burton Jamie , Chan Paul , Gomes Andre , Hunter-Jones Philippa , O’Malley Lisa , Peters Linda D. , Raddats Chris , Robinson William 
Published: April 2017

Purpose
The purpose of this paper is to critique the adequacy of efforts to capture the complexities of customer experience in a business-to-business (B2B) context using input–output measures. The paper introduces a strategic customer experience management framework to capture the complexity of B2B service interactions and discusses the value of outcomes-based measurement.

Design/methodology/approach
This is a theoretical paper that reviews extant literature related to B2B customer experience and asks fresh questions regarding B2B customer experience at a more strategic network level.

Findings
The paper offers a reconceptualisation of B2B customer experience, proposes a strategic customer experience management framework and outlines a future research agenda.

Research limitations/implications
This paper is conceptual and seeks to raise questions surrounding the under-examined area of B2B customer experience. As a consequence, it has inevitable limitations resulting from the lack of empirical evidence to support the reconceptualisation.

Practical implications
Existing measures of customer experience are problematic when applied in a B2B (services) context. Rather than adopting input- and output-based measures, widely used in a business-to-consumer (B2C) context, a B2B context requires a more strategic approach to capturing and managing customer experience. Focussing on strategically important issues should generate opportunities for value co-creation and are more likely to involve outcomes-based measures.

Social implications
Improving the understanding of customer experience in a B2B context should allow organisations to design better services and consequently enhance the experiences of their employees, their customers and other connected actors.

Originality/value
This paper critiques the current approach to measuring customer experience in a B2B context, drawing on contemporary ideas of value-in-use, outcomes-based measures and “Big Data” to offer potential solutions to the measurement problems identified.
Customer engagement in a Big Data world
Authors: Kunz Werner , Aksoy Lerzan , Bart Yakov , Heinonen Kristina , Kabadayi Sertan , Ordenes Francisco Villarroel , Sigala Marianna , Diaz David , Theodoulidis Babis 
Published: April 2017

Purpose
This paper aims to propose that the literature on customer engagement has emphasized the benefits of customer engagement to the firm and, to a large extent, ignored the customers’ perspective. By drawing upon co-creation and other literature, this paper attempts to alleviate this gap by proposing a strategic framework that aligns both the customer and firm perspectives in successfully creating engagement that generates value for both the customer and the bottom line.

Design/methodology/approach
A strategic framework is proposed that includes the necessary firm resources, data, process, timeline and goals for engagement, and captures customers’ motives, situational factors and preferred engagement styles.

Findings
The authors argue that sustainability of data-driven customer engagement requires a dynamic and iterative value generation process involving customers recognizing the value of engagement behaviours and firm’s ability to capture and passing value back to customers.

Originality/value
This paper proposes a dynamic strategic value-creation framework that comprehensively captures both the customer and firm perspectives to data-driven customer engagement.
Innovation as a key to strengthen the effect of relationship benefits on loyalty in retailing
Authors: Ruiz-Molina Maria-Eugenia , Gil-Saura Irene , Servera-Francés David 
Published: April 2017

PurposeThis work aims to attempt an in-depth study of the link between relationship benefits and store loyalty, examining the moderating role of the retailer’s degree of innovation in these relations.Design/methodology/approachAn equations model has been contrasted based on 820 valid individual structured questionnaires administered to consumers of 13 trade names in four retail distribution sectors (food, textile, electronics and household goods).FindingsThe results provide evidence of the positive influence of relationship benefits on store loyalty and in particular the benefits stemming from trust. The links between social and special treatment benefits in relation to loyalty are, however, significantly stronger in the less innovative establishments.Research limitations/implicationsThis paper provides evidence of the moderating role of innovation on the relationship between social benefits and special treatment benefits and loyalty.Practical implicationsTechnology may be used as a differentiation tool. The retailer should concentrate its investments on information and communications technology solutions that contribute to enhance the customer experience at the point of sale without neglecting the social dimension to increase the benefits of trust and ultimately, customer loyalty.Originality/valueThe paper provides an in-depth examination of the retail innovation variable which is scarcely analysed in the literature, offering support for the idea that innovation at the point of sale plays a moderating role in the links between relational benefits and customer loyalty.
The three R’s: reading, (W)Riting, and researching through multi-genre project
Authors: Roberts Kathryn , Brugar Kristy 
Published: April 2017

Purpose
The purpose of this paper is to examine how the authors, two teacher educators, planned for and guided 23 students (teacher candidates) through a multi-genre historical inquiry experience, integrating instruction on the Inquiry Arc and writing process, during a co-taught literacy and social studies methods course. The authors describe the ways in which the students demonstrated both active and passive participation and resistance to this process/project, and the related implications.

Design/methodology/approach
Using an action research approach, this paper reports analysis and interpretation of lesson plans, course materials, debriefing notes, field notes, student response notebooks and intermediate and final inquiry project artifacts.

Findings
All students demonstrated gains in content knowledge through their products, oral presentations, group discussions, or conferences with the authors; and all gained experience with the Inquiry Arc and process writing. Many students saw the benefits of collaboration and social construction of knowledge as they moved toward more central participation.

Practical implications
Instructors cannot mandate full participation in any task, but can influence the conditions (i.e. pedagogy, task, scaffolding) to increase the possibility of positive peer interactions and learning.

Originality/value
This paper contributes to the knowledge of teaching and learning innovation in teacher preparation coursework.
Scaffolded lesson study
Authors: Saye John W. , Kohlmeier Jada , Howell James B. , McCormick Theresa M. , Jones Robert C. , Brush Thomas A. 
Published: April 2017

Purpose
The purpose of this paper is to investigate the effects of scaffolded lesson study on the content knowledge, conceptions of curriculum, and classroom practice of 22 elementary and secondary history teachers in four school districts.

Design/methodology/approach
Teachers, teacher educators, and historians collaborated to design and test research lessons grounded in a theory-based framework for problem-based historical inquiry (PBHI) practice. The authors sought to support consonance between the reform ideas of the formal, professional development, curriculum, and the curriculum as enacted in participants’ classrooms.

Findings
Project participation was associated with significant gains in content knowledge and the conceptualization and implementation of more challenging instruction consistent with the PBHI model and the standards of authentic intellectual work (AIW). Mean AIW instruction scores for research lessons were more than double the scores for participants’ non-lesson study lessons and indicated noteworthy progress in integrating the formal and enacted curricula. Evidence suggested that many teachers developed more nuanced understandings of historical phenomena, gained greater appreciation for the importance of authentic purpose in motivating student engagement in challenging learning, and began to reconsider what is required to facilitate complex learning and to refine their repertoire of learning strategies.

Originality/value
Evidence from the first year of this project offers hope for the potential of collaborative communities of practice to facilitate a shared professional knowledge base of wise practice that brings the formal, intended, and enacted curriculum into greater alignment. These results also emphasize the evolutionary process of conceptual change.
High rate of systemic corticosteroid prescription among outpatient visits for psoriasis: A population‐based epidemiological study using the Korean National Health Insurance database
Authors: Eun Sang Jun , Jang Sihyeok , Lee Jin Yong , Do Young Kyung , Jo Seong Jin 
Published: April 2017

AbstractThe use of systemic corticosteroids (SC) for the treatment of psoriasis is not recommended according to textbooks and guidelines. In clinical practise, however, many physicians frequently prescribe SC for patients with psoriasis. To determine the magnitude of SC prescription for outpatients with psoriasis in Korea and identify factors associated with the use of SC, we used the 2010–2014 nationwide claims data of the Health Insurance Review and Assessment Service of Korea. In frequency analysis for the full scale of prescribed SC, oral methylprednisolone was the most frequently prescribed SC, followed by dexamethasone and betamethasone injections. The prescription rate of SC was 26.4% in outpatient visit episodes for psoriasis. The prescription rate of SC was higher in older patients, Medical Aid recipients, patients who visited office‐based physician practices and hospitals, and patients living in non‐metropolitan areas. In multiple logistic regression analyses, the older age group and smaller health‐care institutions were more associated with the SC prescription. In conclusion, SC were widely prescribed for patients with psoriasis in Korea despite the current guidelines. Both patients’ individual and institutional characteristics were associated with the SC prescription.
Severe primary autoimmune thrombocytopenia in pregnancy: a national cohort study
Authors: Care A , Pavord S , Knight M , Alfirevic Z 
Published: April 2017

ObjectiveTo quantify the incidence of severe autoimmune thrombocytopenia (ITP) in pregnancy in the UK, determine current treatment strategies, and establish maternal and neonatal morbidity and mortality associated with severe ITP in pregnancy.DesignA prospective national cohort study.SettingUK.PopulationWomen with severe ITP, defined as platelets <50 × 109/L in pregnancy or antenatal treatment of isolated low platelets.MethodsData collected via the UK Obstetric Surveillance System (UKOSS) between 1 June 2013 and 31 January 2015 from all UK consultant‐led obstetric units.Main outcome measureIncidence of severe ITP in pregnancy.ResultsThe estimated incidence of severe ITP in pregnancy is 0.83 per 10 000 maternities (95% CI 0.68–1.00). A total of 22 pregnant women (21%) did not receive any antenatal therapy, and 85 pregnant women (79%) received therapy. There was no difference between asymptomatic treated and untreated cohorts in severity of disease or outcome. Postpartum haemorrhage (51%) and severe postpartum haemorrhage (21%) was reported more frequently than the rate reported in the general pregnant population (5–10%). No neonates required treatment for thrombocytopenia and there were no cases of neonatal intracranial bleeding.ConclusionsCurrent UK management of severe ITP in pregnancy results in an exceptionally low morbidity and mortality for the neonate. Mothers with ITP remain at increased risk of severe postpartum haemorrhage, and should be delivered at units that have the capacity to manage severe PPH effectively. Whilst balancing the risks for pregnancy from prophylactic antenatal treatment in asymptomatic women against observed low disease morbidity, we may be over treating asymptomatic patients.Tweetable abstractUKOSS study of severe ITP in pregnancy shows exceptionally low neonatal morbidity with current UK management.
Medical students’ perceptions of the importance of exercise and their perceived competence in prescribing exercise to older people
Authors: Jadczak Agathe Daria , Tam Khai Loon , Yu Solomon , Visvanathan Renuka 
Published: April 2017

ObjectiveTo determine the effects of a 4.5‐week geriatric medicine course on fifth year medical students’ perception of the importance of and their competence in prescribing exercise to older people.MethodsThe modified Exercise and Physical Activity Competence Questionnaire was administered to 81 students before and after the course. Scores ranged from 0 to 6. One open‐ended question about perceived barriers to exercise prescription was asked.ResultsStudents’ perceptions of the importance of designing an exercise prescription (P= 0.038), determining the training heart rate (P= 0.021), determining the body mass index (P> 0.001), referring an older person to an exercise program (P> 0.001) and identifying age‐related limitations (P= 0.029) improved significantly after the course. Students’ self‐perceived competence improved significantly across all items (P> 0.001). Barriers to exercise prescription included lack of: knowledge (57%), patient compliance (39%) and time (33%).ConclusionA geriatric medicine course contributes to improved senior medical students’ perceptions of importance of and their competence in prescribing exercise to older people.