bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease ecology, health and the environment: a framework to account for ecological and socio-economic drivers in the control of neglected tropical diseases
Authors: Garchitorena A. , Sokolow S. H. , Roche B. , Ngonghala C. N. , Jocque M. , Lund A. , Barry M. , Mordecai E. A. , Daily G. C. , Jones J. H. , Andrews J. R. , Bendavid E. , Luby S. P. , LaBeaud A. D. , Seetah K. , Guégan J. F. , Bonds M. H. , De Leo G. A. 
Published: April 2017

Reducing the burden of neglected tropical diseases (NTDs) is one of the key strategic targets advanced by the Sustainable Development Goals. Despite the unprecedented effort deployed for NTD elimination in the past decade, their control, mainly through drug administration, remains particularly challenging: persistent poverty and repeated exposure to pathogens embedded in the environment limit the efficacy of strategies focused exclusively on human treatment or medical care. Here, we present a simple modelling framework to illustrate the relative role of ecological and socio-economic drivers of environmentally transmitted parasites and pathogens. Through the analysis of system dynamics, we show that periodic drug treatments that lead to the elimination of directly transmitted diseases may fail to do so in the case of human pathogens with an environmental reservoir. Control of environmentally transmitted diseases can be more effective when human treatment is complemented with interventions targeting the environmental reservoir of the pathogen. We present mechanisms through which the environment can influence the dynamics of poverty via disease feedbacks. For illustration, we present the case studies of Buruli ulcer and schistosomiasis, two devastating waterborne NTDs for which control is particularly challenging.
This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications’.
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Authors: Stancu Mircea Cretu , van Roosmalen Markus J. , Renkens Ivo , Nieboer Marleen , Middelkamp Sjors , Ligt Joep de , Pregno Giulia , Giachino Daniela , Mandrile Giorgia , Valle-Inclan Jose Espejo , Korzelius Jerome , Bruijn Ewart de , Cuppen Edwin , Talkowski Michael E. , Marschall Tobias , Ridder Jeroen de , Kloosterman Wigard P. 
Published: April 2017

AbstractStructural genomic variants form a common type of genetic alteration underlying human genetic disease and phenotypic variation. Despite major improvements in genome sequencing technology and data analysis, the detection of structural variants still poses challenges, particularly when variants are of high complexity. Emerging long-read single-molecule sequencing technologies provide new opportunities for detection of structural variants. Here, we demonstrate sequencing of the genomes of two patients with congenital abnormalities using the ONT MinION at 11x and 16x mean coverage, respectively. We developed a bioinformatic pipeline - NanoSV - to efficiently map genomic structural variants (SVs) from the long-read data. We demonstrate that the nanopore data are superior to corresponding short-read data with regard to detection ofde novorearrangements originating from complex chromothripsis events in the patients. Additionally, genome-wide surveillance of SVs, revealed 3,253 (33%) novel variants that were missed in short-read data of the same sample, the majority of which are duplications < 200bp in size. Long sequencing reads enabled efficient phasing of genetic variations, allowing the construction of genome-wide maps of phased SVs and SNVs. We employed read-based phasing to show that allde novochromothripsis breakpoints occurred on paternal chromosomes and we resolved the long-range structure of the chromothripsis. This work demonstrates the value of long-read sequencing for screening whole genomes of patients for complex structural variants.
Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region
Authors: Dubois Adélaïde , Castel Guillaume , Murri Séverine , Pulido Coralie , Pons Jean-Baptiste , Benoit Laure , Loiseau Anne , Lakhdar Latifa , Galan Maxime , Marianneau Philippe , Charbonnel Nathalie 
Published: April 2017

AbstractEcoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole,Myodes glareolus. Despite the continuous distribution of the reservoir in Europe, PUUV occurence is highly fragmented. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions using serological and virological surveys. We used bank vole population genetics to demonstrate the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to establish, circulate and persist in the NE-free region. Immune responsiveness was phenotyped both in the wild and during experimental infections, using serological, virological and immune related gene expression assays. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. In natural populations, antiviral gene expression (TnfandMx2genes) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE endemic region. Altogether, our results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, what might limit PUUV circulation and persistence, and in turn, the risk of NE.Graphical abstract
Epistasis in genomic and survival data of cancer patients
Authors: Matlak Dariusz , Szczurek Ewa 
Published: April 2017

AbstractCancer aggressiveness and its effect on patient survival depends on mutations in the tumor genome. Epistatic interactions between the mutated genes may guide the choice of anticancer therapy and set predictive factors of its success. Inhibitors targeting synthetic lethal partners of genes mutated in tumors are already utilized for efficient and specific treatment in the clinic. The space of possible epistatic interactions, how-ever, is overwhelming, and computational methods are needed to limit the experimental effort of validating the interactions for therapy and characterizing their biomarkers. Here, we introduce SurvLRT, a statistical likelihood ratio test for identifying epistatic gene pairs and triplets from cancer patient genomic and survival data. Compared to established approaches, SurvLRT performed favorable in predicting known, experimentally verified synthetic lethal partners ofPARP1from TCGA data. Our approach is the first to test for epistasis between triplets of genes to identify biomarkers of synthetic lethality-based therapy. SurvLRT proved successful in identifying the known geneTP53BP1as the biomarker of success of the therapy targeting PARP inBRCA1deficient tumors. Search for other biomarkers for the same interaction revealed a region whose deletion was a more significant biomarker than deletion ofTP53BP1. With the ability to detect not only pairwise but twelve different types of triple epistasis, applicability of SurvLRT goes beyond cancer therapy, to the level of characterization of shapes of fitness landscapes.Author SummaryGenomic alterations in tumors affect the fitness of tumor cells, controlling how well they replicate and survive compared to other cells. The landscape of tumor fitness is shaped by epistasis. Epistasis occurs when the contribution of gene alterations to the total fitness is non-linear. The type of epistatic genetic interactions with great potential for cancer therapy is synthetic lethality. Inhibitors targeting synthetic lethal partners of genes mutated in tumors can selectively kill tumor and not normal cells. Therapy based on synthetic lethality is, however, context dependent, and it is crucial to identify its biomarkers. Unfortunately, the space of possible interactions and their biomarkers is overwhelming for experimental validation. Computational pre-selection methods are required to limit the experimental effort. Here, we introduce a statistical approach called SurvLRT, for the identification of epistatic gene pairs and triplets based on patient genomic and survival data. First, we show that using SurvLRT, we can deliver synthetic lethal interactions of pairs of genes that are specific to cancer. Second, we demonstrate the applicability of SurvLRT to identify biomarkers for synthetic lethality, such as mutational status of other genes that can alleviate the synthetic effect.
Supplier collaboration practices: implications for focal firm innovation performance
Authors: Kähkönen Anni-Kaisa , Lintukangas Katrina , Ritala Paavo , Hallikas Jukka 
Published: April 2017

PurposeDue to the increasing complexity in supply chains and networks, several key practices have been highlighted as beneficial for supply chain performance. However, it is less known whether adopting such practices affects the innovation performance of the focal firm. This study hypothesises that supplier collaboration practices in four specific areas (green and ethical supply management, early supplier involvement, systemic purchasing and inter-firm learning) may lead to higher focal firm innovation performance, as they require the firm to adopt new business models, processes and product features.Design/methodology/approachThe hypotheses drawn from previous research are tested with a quantitative survey study of 165 Finnish firms and analysed by means of regression analysis.FindingsThe results show that two examined practices are positively related to focal firm innovation performance: systemic purchasing and green and ethical supply management. Interestingly, early supplier involvement and inter-firm learning did not influence innovation performance.Originality/valueLittle is known about whether adopting certain practices in supply management affects the innovation performance of the firm. In fact, among the performance indicators of supply management, innovation is rarely studied, and more studies using innovation as a performance indicator are called for. Thus, this study focuses on supplier collaboration practices and their relation to the focal firm’s innovation performance.
Human-oriented corporate entrepreneurship
Authors: Elia Gianluca , Li Xiaoyang , Margherita Alessandro , Petti Claudio 
Published: April 2017

PurposeThe generation of new ventures within established companies, also known as corporate entrepreneurship (CE), is a process influenced by a set of individual and organizational factors. This paper aims to focus on creativity and human resource management enablers of CE, with the purpose to define an integrative framework and draw a set of related research propositions.Design/methodology/approachThe paper relies on a multidisciplinary literature review in the fields of CE, creativity and organizational innovation.FindingsThe effectiveness of CE depends on a set of individual factors, distinguished into professional and psychological characteristics, and organizational factors, which include the system of values of the organization and the management practices applied in the same.Research limitations/implicationsFrom a theoretical point of view, the paper develops an integrative framework of conditions that impact on CE and outlines a set of propositions and alternative research methods to test.Practical/implicationsFrom a practitioner perspective, the study provides managers with a comprehensive set of factors enabling CE by leveraging the creativity of individuals and make it flourish through consistent human resource management practices.Originality/valueThe value of the paper stays in the integration of individual-related and organizational-related determinants of entrepreneurial performance.
An adaptive methodology for multi-GPU programming in OpenCL
Authors: Cavalcanti Bueno Andre Luis , de La Rocque Rodriguez Noemi , Dominguez Sotelino Elisa 
Published: April 2017

Purpose
The purpose of this work is to present a methodology that harnesses the computational power of multiple graphics processing units (GPUs) and hides the complexities of tuning GPU parameters from the users.

Design/methodology/approach
A methodology for auto-tuning OpenCL configuration parameters has been developed.

Findings
This described process helps simplify coding and generates a significant gain in time for each method execution.

Originality/value
Most authors develop their GPU applications for specific hardware configurations. In this work, a solution is offered to make the developed code portable to any GPU hardware.
Cricket South Africa’s Protea Fire brand
Authors: Mazinter Luisa , Goldman Michael M. , Lindsey-Renton Jennifer 
Published: April 2017

Subject area
Marketing, Sports marketing and Social media marketing.

Study level/applicability
Graduate level.

Case overview
This case, based on field research and multiple secondary sources, documents the 12-month period since early 2014 during which Cricket South Africa (CSA) developed the Protea Fire brand for their national men’s cricket team, known as the Proteas. In mid-2014, Marc Jury, the Commercial and Marketing manager of CSA set up a project team to take the previously in-house Protea Fire brand public. With the 2015 Cricket World Cup in Australia and New Zealand less than a year away, Jury worked with a diverse project team of Proteas players, cricket brand managers and external consultants to build a public brand identity for the national team, to nurture greater fan affinity and to mobilize South Africans behind their team for the World Cup. The project team developed a range of Protea Fire multimedia content as the core of the campaign. These included video diaries, scripts which were written by the Proteas players themselves, player profile videos, motivational team-talk videos and good luck video messages featuring ordinary and famous South Africans. Having invested in creating this content, the project team faced the difficult task of allocating a limited media budget to broadcast and amplify the content. Another significant challenge was to ensure that the Proteas team values were authentically communicated across all content, including via the social media strategy using Twitter, Instagram and YouTube. As the World Cup tournament kicked off on February 14th 2015, South Africa was well placed to overcome their previous inability to reach a final, although Jury wondered whether another exit in the knockout round would weaken the strong and positive emotions the Protea Fire campaign had ignited. With the last two balls remaining in South Africa’s semi-final game against New Zealand on March 24th 2015, and the home team requiring just five runs to win, Jury joined 60 million South Africans hoping that Protea Fire was strong enough. The case concludes with South Africa losing the semi-final game and Jury turning his attention to how the #ProteaFire campaign should respond.

Expected learning outcomes
This study aimed to analyse the development of a sport team brand and a megaevent campaign; to assess the efficiency and effectiveness of a marketing campaign; and to consider appropriate brand responses to the team’s failure to deliver on expectations.

Subject code
CSS 8: Marketing.
Using flow diagrams to improve tobacco cessation programs
Authors: Dziadkowiec Oliwier , Jenniges Reese 
Published: April 2017

Purpose
The purpose of this paper is to understand how the Wyoming Quit Tobacco Program (WQTP) is used by its subscribers and to better understand how WQTP might be connected to WQTP outcomes.

Design/methodology/approach
Provider intake and program use data corresponding to the May 2010 to March 2012 enrollment period (n=6,168) were used. All program flows were constructed using frequencies and crosstabs, based on an initial theoretical model prepared by the program provider. Data were adjusted based on analysis that explored all possible uses beyond those specified by the provider’s theoretical model.

Findings
Although the authors could replicate the structure – the theoretical model constructed by the provider – the authors were not able to replicate all relationships between program components. The authors also found that most individuals signed up and used web-based services. Only a few individuals finished their treatment regimens in the way they were designed to be used by the program.

Originality/value
This is the first case study to use a program flow method to investigate an entire comprehensive tobacco cessation program structure and delivery.
R&D investment behavior of US pharmaceutical firms
Authors: Jirásek Michal 
Published: April 2017

PurposeThe behavioral theory of the firm (BTOF) has been used to explain the research and development (R&D) investment behavior of firms in numerous multi industry studies. However, their partially contradictory results point to the possible need for a single industry perspective that would reduce heterogeneity of business trends, models and other characteristics. This study aims to test this theoretical assumption within the challenging context of the US pharmaceutical industry.Design/methodology/approachThe research uses data from 20 firms, which number among the largest in the US pharmaceutical industry, over the period 2002-2014. These data are analyzed using fixed- and random-effect panel models.FindingsThe findings generally support the need for a thorough understanding of the industry under study and its specific characteristics. The firms analyzed in this research behave slightly differently from theoretical assumptions, and it is argued that this is caused by industry specific factors. Moreover, the use of two separate aspiration measures – for historical and social aspirations – is supported as it provides more in-depth insight into the firms’ behavior.Originality/valueThis paper, which is based on research presented at the 4th International Conference on Innovation and Entrepreneurship, represents the first inquiry into the R&D investment behavior of pharmaceutical firms using the BTOF. It also represents an argument for conducting single-industry rather than multi industry studies when using this theory.
Prison health service directors’ views on research priorities and organizational issues in conducting research in prison: outcomes of a national deliberative roundtable
Authors: Simpson Paul Leslie , Guthrie Jill , Butler Tony 
Published: April 2017

Purpose
Given that prisoners have significant health needs across most areas, the paucity of prisoner health research, and the difficulties involved in the conduct of research in this setting, there is a need to develop research priorities that align with key stakeholder groups. One such group are those responsible for health service provision in prisons – prison health service directors. The paper aims to discuss these issues.

Design/methodology/approach
Prison health service directors in each Australian state and territory were invited to participate in a national (deliberative) roundtable where the consensus building nominal group technique was utilized. This involved the identification of research priorities and organizational issues in conducting research with prisoners, and ranking research priorities. A thematic analysis was conducted on organizational issues.

Findings
In total, 13 participants attended the roundtable. Participants identified 28 research priorities and 12 organizational issues. Top ranked research priorities were mental health, cognitive and intellectual disability, post-release health maintenance, ageing prisoners, chronic health conditions and Aboriginal and Torres Strait Islander health. Themes identified from the organizational issues included prisoner access to research participation, health and research literacy of custodial staff, and institutional protectionism in response to research that may discover negative information about the custodial setting.

Research limitations/implications
These findings should inform future efforts to improve research infrastructures to undertake research to improve the health of people in Australian prisons, and help to align researchers’ efforts with those of a key organizational stakeholder.

Originality/value
This is the first paper to determine the research priorities and organizational issues in conducting research in prisons of prison health service directors.
Understanding loyalty in multichannel retailing: the role of brand trust and brand attachment
Authors: Frasquet Marta , Mollá Descals Alejandro , Ruiz-Molina Maria Eugenia 
Published: April 2017

Purpose
The purpose of this paper is to understand loyalty in the multichannel retail context. The paper analyses the interplay between offline and online loyalty and the direct and indirect effects on loyalty of brand trust and brand attachment, in a cross-cultural study.

Design/methodology/approach
Online survey answered by 761 multichannel apparel shoppers in two countries (UK and Spain). Structural equation model multigroup analysis is performed to test the hypothesized relations and the role of culture as a moderating variable.

Findings
Online loyalty is largely driven by offline loyalty, which is also positively affected by brand trust and brand attachment. These relationships hold across the two different cultures.

Research limitations/implications
The findings confirm the validity of applying the theory of cognitive dissonance to explain multichannel shopping behaviours. The authors did not find culture that affects the relationships in the model; however, the validity of these findings should be tested considering other cultural variables different from nationality.

Practical implications
Multichannel retailers should focus on building trust and attachment towards the brand if they want to get online and offline loyalty. The efforts to build stronger bonds between the customer and the retail brand translate into higher loyalty, particularly towards the offline channels.

Originality/value
This paper extends the literature on the interactions between online and offline behaviour by focussing on the power of the brand to build strong customer bonds. The model considers the role of brand attachment together with brand trust in offline and online loyalty simultaneously.
Effect of the stadium occupancy rate on perceived game quality and visit intention
Authors: Oh Taeyeon , Sung Hojun , Kwon Kisung Dennis 
Published: April 2017

Purpose
The purpose of this paper is to examine the impact of the stadium occupancy rate on television viewers’ game quality perception and stadium visit intention (VI).

Design/methodology/approach
An experiment was conducted in which two groups were asked to watch video clips of professional soccer games with low- and high-stadium occupancy rates.

Findings
The results indicate that the higher the stadium occupancy, the higher is perceived game quality and the greater is stadium VI.

Originality/value
The paper provides useful information on the effect of the stadium occupancy rate on perceived game quality and VI.