bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction
Authors: Menden Michael P , Wang Dennis , Guan Yuanfang , Mason Mike J , Szalai Bence , Bulusu Krishna C , Yu Thomas , Kang Jaewoo , Jeon Minji , Wolfinger Russ , Nguyen Tin , Zaslavskiy Mikhail ,   AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang Sock , Ghazoui Zara , Ahsen Mehmet Eren , Vogel Robert , Neto Elias Chaibub , Norman Thea , Tang Eric KY , Garnett Mathew J , Di Veroli Giovanni , Fawell Stephen , Stolovitzky Gustavo , Guinney Justin , Dry Jonathan R. , Saez-Rodriguez Julio 
Published: October 2017

AbstractThe effectiveness of most cancer targeted therapies is short lived since tumors evolve and develop resistance. Combinations of drugs offer the potential to overcome resistance, however the number of possible combinations is vast necessitating data-driven approaches to find optimal treatments tailored to a patient’s tumor. AstraZeneca carried out 11,576 experiments on 910 drug combinations across 85 cancer cell lines, recapitulatingin vivoresponse profiles. These data, the largest openly available screen, were hosted by DREAM alongside deep molecular characterization from the Sanger Institute for a Challenge to computationally predict synergistic drug pairs and associated biomarkers. 160 teams participated to provide the most comprehensive methodological development and subsequent benchmarking to date. Winning methods incorporated prior knowledge of putative drug target interactions. For >60% of drug combinations synergy was reproducibly predicted with an accuracy matching biological replicate experiments, however 20% of drug combinations were poorly predicted by all methods. Genomic rationale for synergy predictions were identified, including antagonism unique to combined PIK3CB/D inhibition with the ADAM17 inhibitor where synergy is seen with other PI3K pathway inhibitors. All data, methods and code are freely available as a resource to the community.
A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: linking ecological, population genetics and evolutionary processes
Authors: Ponciano José M. 
Published: October 2017

AbstractUsing a nonparametric Bayesian approach Palacios and Minin [1] dramatically improved the accuracy, precision of Bayesian inference of population size trajectories from gene genealogies. These authors proposed an extension of a Gaussian Process (GP) nonparametric inferential method for the intensity function of non-homogeneous Poisson processes. They found that not only the statistical properties of the estimators were improved with their method, but also, that key aspects of the demographic histories were recovered. The authors’ work represents the first Bayesian nonparametric solution to this inferential problem because they specify a convenient prior belief without a particular functional form on the population trajectory. Their approach works so well and provides such a profound understanding of the biological process, that the question arises as to how truly “biology-free” their approach really is. Using well-known concepts of stochastic population dynamics, here I demonstrate that in fact, Palacios and Minin’s GP model can be cast as a parametric population growth model with density dependence and environmental stochasticity. Making this link between population genetics and stochastic population dynamics modeling provides novel insights into eliciting biologically meaningful priors for the trajectory of the effective population size. The results presented here also bring novel understanding of GP as models for the evolution of a trait. Thus, the ecological principles foundation of Palacios and Minin [1]’s prior adds to the conceptual and scientific value of these authors’inferential approach. I conclude this note by listing a series of insights brought about by this connection with Ecology.
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database
Authors: Cotto Kelsy C. , Wagner Alex H. , Feng Yang-Yang , Kiwala Susanna , Coffman Adam C. , Spies Greg , Wollam Alex , Spies Nick , Griffith Obi L. , Griffith Malachi 
Published: October 2017

ABSTRACTThe Drug-Gene Interaction Database (DGIdb,www.dgidb.org) consolidates, organizes, and presents drug-gene interactions and gene druggability information from papers, databases, and web resources. DGIdb normalizes content from more than thirty disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API), and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included twenty-eight sources were updated. Six new resources were added, bringing the total number of sources to thirty-three. These updates and additions of sources have cumulatively resulted in 56,309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and antineoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times, and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes, and drug-gene interactions, including listings of PubMed IDs (PMIDs), interaction type, and other interaction metadata.
Psychosocial factors associated with adolescent substance use: a longitudinal investigation
Authors: Champion Katrina Elizabeth , Barrett Emma Louise , Slade Tim , Teesson Maree , Newton Nicola Clare 
Published: October 2017

PurposeAlcohol and cannabis are the two most commonly used substances by young people in many developed nations. The purpose of this paper is to explore the longitudinal relationships between risky substance use (binge drinking and cannabis use) and psychological distress, emotional and behavioural difficulties, and truancy among Australian adolescents.Design/methodology/approachA total of 527 students (Mage=13.4 years, SD=0.43; 67 per cent female) from seven Australian schools completed an online self-report survey on four occasions over two years (baseline, 6, 12 and 24 months). The survey assessed binge drinking (5+ standard drinks on one occasion), cannabis use in the past six months, psychological distress, emotional and behavioural difficulties (Strength and Difficulties Questionnaire), and truancy. Generalised estimating equations (GEEs) were conducted to examine the longitudinal relationship between the substance use outcomes and each predictor variable.FindingsAt baseline, 3 per cent of students reported binge drinking and 6 per cent had used cannabis in the past six months. Rates of binge drinking significantly increased over time (21.1 per cent at 24 months) however, rates of cannabis use remained relatively stable (8.8 per cent at 24 months). Multivariate GEE analyses indicated that higher levels of hyperactivity/inattention, more days of truancy and being female were independently and consistently associated with binge drinking over time. Conduct problems was the only factor to be independently associated with cannabis use over time.Originality/valueThese findings provide valuable information about psychosocial risk factors for harmful alcohol and cannabis use. A better understanding of these associations is critical for informing substance use prevention efforts in the future.
Trajectories of emotional symptoms in adolescence: impact on alcohol use
Authors: Birrell Louise Elizabeth , Newton Nicola Clare , Stapinski Lexine , Prior Katrina , Champion Katrina Elizabeth , Mackie Clare J. , Teesson Maree , Slade Tim 
Published: October 2017

PurposeThe purpose of this paper is to explore how different trajectories of emotional symptoms relate to alcohol use in adolescence.Design/methodology/approachIn all, 431 participants (majority female), aged approximately 13 years at baseline were followed over three years and reported on their emotional symptoms and alcohol use. Latent class growth analyses explored different trajectories of emotional symptoms and regression models were run to relate these trajectories to alcohol use (full standard drink, and binge drinking) at 36-month follow-up (age 16 years).FindingsWhile the majority of adolescents were best characterised by low-stable emotional symptoms, those with high-stable symptoms were more likely to be have consumed a full standard drink of alcohol and binge drunk when aged 16 years.Research limitations/implicationsFindings highlight the importance of prevention and early intervention, particularly targeting adolescents with elevated stable emotional symptoms who were more likely to be using alcohol at 16 years of age.Originality/valueThe present study is one of the first longitudinal investigations into the use of alcohol by community adolescents with different emotional symptom trajectories.
Time-varying formation finite-time tracking control for multi-UAV systems under jointly connected topologies
Authors: Xiong Tianyi , Pu Zhiqiang , Yi Jianqiang 
Published: October 2017

Purpose
The purpose of this paper is to investigate the time-varying finite-time formation tracking control problem for multiple unmanned aerial vehicle systems under switching topologies, where the states of the unmanned aerial vehicles need to form desired time-varying formations while tracking the trajectory of the virtual leader in finite time under jointly connected topologies.

Design/methodology/approach
A consensus-based formation control protocol is constructed to achieve the desired formation. In this paper, the time-varying formation is specified by a piecewise continuously differentiable vector, while the finite-time convergence is guaranteed by utilizing a non-linear function. Based on the graph theory, the finite-time stability of the close-loop system with the proposed control protocol under jointly connected topologies is proven by applying LaSalle’s invariance principle and the theory of homogeneity with dilation.

Findings
The effectiveness of the proposed protocol is verified by numerical simulations. Consequently, the proposed protocol can successfully achieve the predefined time-varying formation in finite time under jointly connected topologies while tracking the trajectory generated by the leader.

Originality/value
This paper proposes a solution to simultaneously solve the control problems of time-varying formation tracking, finite-time convergence, and switching topologies.
Contesting the austerity and “welfare reform” narrative of the UK Government
Authors: Wiggan Jay 
Published: October 2017

Purpose
The “welfare reform” narrative of successive Conservative-led UK Government emphasises public spending reductions, individual responsibility and strengthening of benefit conditionality. The purpose of this paper is to cast light on how this narrative is challenged and disrupted by the Scottish Government through their articulation of a social democratic welfare state imaginary.

Design/methodology/approach
The study draws together a decentred governance perspective that emphasises ideational tradition for understanding (re)construction of governance (Bevir, 2013, p. 27) with critical discourse analysis to examine how welfare interpretations/representations are carried into the policy and public arena. The Scottish Government documents are deconstructed to interrogate the ideas and form of their emergent discourse and its relation to the independence referendum and welfare governance reform.

Findings
Responding to changing socio-economic contexts and welfare governance, the Scottish Government has developed a discourse of modernisation rooted in British and Scandinavian social democratic traditions. Fusing (civic) nationalism with social wage and social investment concepts, they conjure up imaginaries of a prosperous, solidaristic, egalitarian welfare state as a feasible future reality, recuperating “welfare” as a collective endeavour and positioning a maldistribution of power/resources between groups and constituent countries of the UK as the “problem”.

Originality/value
The paper is of value to those interested in how changes to centralised-hierarchical welfare governance can open new spaces for actors at different levels of government to articulate counter-hegemonic discourses and practices. Its originality lies in the analysis of how the Scottish Government has reworked social democratic traditions to weave together a welfare imaginary that directly contests the problem-solution narrative of successive Conservative-led UK Governments.
Virtual world global collaboration: an educational quest
Authors: Hill Valerie , Knutzen K. Brant 
Published: October 2017

Purpose
This research case study shares the partnership between librarians and educators to create a live digital literacy experience at The Quest (Camelot Project), a virtual world medieval simulation. The purpose of the partnership was to gain understanding of the learning elements addressed with a group of participants from across the globe, working at various skill levels and interacting with an immersive virtual world simulation.

Design/methodology/approach
Using field notes, machinima and interviews (participatory action research), the study identifies learning elements within three contexts: technological, pedagogical and content. Learners cycle toward intended learning outcomes in a virtual-world treasure hunt game from the perspective of both designers and participants.

Findings
Findings of the case study illustrate the value of collaboration in a digital game-based learning (DGBL) environment through scaffolding of knowledge and skills in a virtual world. Findings exemplify the experiential learning cycle within a virtual world for constructing learning, and support a proposed new theoretical framework of technology-mediated learning which may help educators in both design and implementation.

Originality/value
As virtual worlds and immersive learning opportunities continue to expand for learners and educators, this study shares the value of experiential learning from the perspective of both the teacher and the learner. Socially constructing knowledge and acquiring skills across distance with a team of librarians and educators are innovative examples of DGBL in an alternative reality setting.
Mobile technologies make education a part of everyday life
Authors: Shyshkanova Ganna , Zaytseva Tetyana , Frydman Oleksandr 
Published: October 2017

Purpose
The purpose of this paper is to show the effectiveness of innovative mobile technologies in learning, to develop a new testing system with a mobile application and to investigate the influence of its use on the level of students’ knowledge.

Design/methodology/approach
Modern information assessment methods of knowledge, testing, including application of mobile devices and statistical analysis tools were used in the present research.

Findings
In recent times, students are motivated to use mobile technologies in education. This paper offers one of the approaches for achieving the effective integration of mobile technologies into the learning process. The software is developed for in-class testing as a client-server and its mobile application.

Practical implications
The practical research verified many advantages of mobile device usage during testing. It contributes to higher academic performance; in addition, it is economically advantageous as it does not require special equipment in classrooms and is psychologically comfortable for students who are accustomed to constantly using their mobile devices.

Social implications
Well-educated people play a role in the development of modern society. Mobile technologies can transform education into a seamless part of the ordinary life so that a person does not recognize it as training at all. The learning process will become more natural and easier and that will improve its quality.

Originality/value
This paper demonstrates how mobile devices can satisfy the learning expectations of students who frequently use mobile services on the Web and can attract their study interest implementing the created testing system in full-time education process.
75 lessons learned for enhancing information literacy programs
Authors: Uribe-Tirado Alejandro , Pinto María 
Published: October 2017

PurposeThe purpose of this study has the aim of expanding lessons learned that were originally detected for information literacy (INFOLIT) programs in Ibero-American universities (from Latin America, Spain and Portugal), this paper presents lessons learned for enhancing equivalent programs offered by other universities around the world.Design/methodology/approachAs this paper is a comparative literature review, the methodology involved three stages. Initially, a documentary analysis was carried out to identify the texts published during the past five years – since 2013 – reporting a categorization of experiences and cases of international INFOLIT programs and their corresponding lessons learned. Second, we conducted a content analysis of these publications to uncover the classification, identification and frequency of the lessons learned. A third comparative step consisted of analyzing the similarities of these lessons when compared to those reported in similar research on Ibero-American universities (Uribe-Tirado, 2013).FindingsFrom the 75 lessons learned from INFOLIT programs in Ibero-American universities, 65 lessons (87 per cent) were identified as also present in universities elsewhere. These similarities give an account of the possibilities for collaborative learning and benchmarking that INFOLIT programs could achieve with regard to content, pedagogy, learning objects and evaluation if there were more networking and more common participation in sharing experiences, with appropriate adaptations to contextual, technological and idiomatic variations.Originality/valueAs a comparative literature review, this paper makes a significant contribution to the international advancement of INFOLIT in higher education, as it correlates the lessons learned from INFOLIT programs in Ibero-American universities with those from other countries. This provides a global view of the lessons learned about INFOLIT, which to date have not been reported with such a wide scope and number of lessons.
Art galleries in the library
Authors: Massis Bruce 
Published: October 2017

Purpose
The purpose of this study is to report that the library has recognized the benefit to the community of including art gallery space in the library.

Design/methodology/approach
This paper is a literature review and commentary on this topic that has been addressed by professionals, researchers and practitioners.

Findings
Exposure to art in the library can open and expand worlds that might never have been available to some and can provide the populace with greater access directly in their own community.

Originality/value
The value in exploring this topic is to provide libraries that may not have considered including an art gallery in their libraries to consider the possibility of doing so.
Introducing web components into the LIS graduate curriculum
Authors: Wusteman Judith 
Published: October 2017

Purpose
This paper introduces web components, one of the most exciting and potentially transformative of the technologies that comprise HTML5. Web components provide a standardised method of creating and sharing custom HTML elements.

Design/methodology/approach
This paper is a viewpoint.

Findings
The paper proposes that the web development curriculum in library and information science (LIS) graduate programs needs to expand to cover this important topic.

Originality/value
Despite the potentially seismic impact of web components on Web development, up until this point, there has not been a discussion of this technology within the LIS literature.
Investigating work and learning through complex adaptive organisations
Authors: Lizier Amanda Louise 
Published: October 2017

PurposeThe purpose of this paper is to outline an empirical study of how professionals experience work and learning in complex adaptive organisations. The study uses a complex adaptive systems approach, which forms the basis of a specifically developed conceptual framework for explaining professionals’ experiences of work and learning.Design/methodology/approachSemi-structured interviews were conducted with 14 professionals from a variety of organisations, industry sectors and occupations in Sydney, Australia. The transcripts were subjected to an adapted phenomenographic analysis, and an analysis using the complex adaptive organisations conceptual framework (CAOCF).FindingsThe findings indicated that professionals experienced learning mainly through work, where work was experienced as fluid and influenced by varying degrees of emergence, agency, complex social networks and adaptation. Further, the greater the degree of work fluidity, the greater the impetus towards learning through work, empirically indicating that the experience of learning in contemporary organisations is entwined with work.Originality/valueThis study used the concept of complex adaptive organisations as a conceptual framework, coupled with an adapted phenomenographic methodology, to investigate individual professionals’ experiences of work and learning. The adoption of the concept of complex adaptive organisations provided a rigorous way to adopt a complexity approach. In particular, the concept of emergence provides insights into how organisational complexity influences work and, subsequently, learning and adaptation.
Sociomaterial perspectives on work and learning: sites of emergent learning
Authors: Reich Ann , Rooney Donna , Hopwood Nick 
Published: October 2017

Purpose
This paper aims to introduce, explain and illustrate the concept of “sites of emergent learning” (SEL), which pinpoints particular instances of learning in everyday practice. This concept is located within contemporary practice-oriented and sociomaterial approaches to understanding workplace learning.

Design/methodology/approach
This conceptual development has been resourced by a secondary analysis of data from three workplace learning studies. These were: an ethnographic study of a residential parenting service; a case study of learning among engineers working on a railway construction site; and a case study of a multicultural unit that aims to enhance health services for a diverse community. All were based in the Sydney metropolitan area. The secondary analysis was undertaken by identifying regular practices within each setting where professionals discuss past and future work. These were then subjected to theoretical scrutiny, identifying common and distinctive features.

Findings
SEL were identified within the handover, site-walks and catch-up meeting practices. They arise through and are constituted in relationships between social practices and the materialities of work. SEL involve negotiating, exploring and questioning practice and knowledge associated with it; they are instances within work practices in which work is done about how work gets done, developing new understandings of the past to reshape visions for the future. Alongside these commonalities, each site of emergent learning displayed distinctive features shaped by the particularities of the practices and materialities of each site.

Originality/value
This concept is presented as a valuable tool to assist researchers of workplace learning. It elucidates particular learning-intensive features of practice, extending sociomaterial conceptualisations of professional and workplace learning.