bluuebunny/crossref_metadata_2025_split huggingface dataset:
The State of Software in Evolutionary Biology
Authors: Darriba Diego , Flouri Tomáš , Stamatakis Alexandros 
Published: November 2015

AbstractWith Next Generation Sequencing Data (NGS) coming off age and being routinely used, evolutionary biology is transforming into a data-driven science.As a consequence, researchers have to rely on a growing number of increasingly complex software. All widely used tools in our field have grown considerably, in terms of the number of features as well as lines of code. In addition, analysis pipelines now include substantially more components than 5-10 years ago.A topic that has received little attention in this context is the code quality of widely used codes. Unfortunately, the majority of users tend to blindly trust software and the results it produces. To this end, we assessed the code quality of 15 highly cited tools (e.g., MrBayes, MAFFT, SweepFinder etc.) from the broader area of evolutionary biology that are used in current data analysis pipelines.We also discuss widely unknown problems associated with floating point arithmetics for representing real numbers on computer systems. Since, the software quality of the tools we analyzed is rather mediocre, we provide a list of best practices for improving the quality of existing tools, but also list techniques that can be deployed for developing reliable, high quality scientific software from scratch.Finally, we also discuss journal and science policy as well as funding issues that need to be addressed for improving software quality as well as ensuring support for developing new and maintaining existing software.Our intention is to raise the awareness of the community regarding software quality issues and to emphasize the substantial lack of funding for scientific software development.
Towards a study of gene regulatory constraints to morphological evolution of theDrosophilaocellar region
Authors: Aguilar-Hidalgo D. , Becerra-Alonso D. , García-Morales D. , Casares F. 
Published: November 2015

ABSTRACTThe morphology and function of organs depend on coordinated changes in gene expression during development. These changes are controlled by transcription factors, signaling pathways and their regulatory interactions, which are represented bygene regulatory networks(GRNs). Therefore, the structure of an organ GRN restricts the morphological and functionalvariationsthat the organ can experience –its potential morphospace. Therefore, two important questions arise when studying any GRN: what is the predicted available morphospace and what are the regulatory linkages that contribute the most to control morphological variation within this space. Here, we explore these questions by analyzing a small “3-node” GRN model that captures the Hh-driven regulatory interactions controlling a simple visual structure: the ocellar region ofDrosophila.Analysis of the model predicts that random variation of model parameters results in a specific non-random distribution of morphological variants. Study of a limited sample of Drosophilids and other dipterans finds a correspondence between the predicted phenotypic range and that found in nature. As an alternative to simulations, we apply Bayesian Networks methods in order to identify the set of parameters with the largest contribution to morphological variation. Our results predict the potential morphological space of the ocellar complex, and identify likely candidate processes to be responsible for ocellar morphological evolution using Bayesian networks. We further discuss the assumptions that the approach we have taken entails and their validity.
The human side of economic development in Africa: a paradigm shift
Authors: Kuada John 
Published: November 2015

Purpose
– This editorial builds on the distinction between soft and hard economics and discusses dominant explanations for the development challenges of Sub-Sahara African (SSA) countries. It also seeks to offer a backdrop for the papers in the present volume of AJEMS. The paper aims to discuss these issues.

Design/methodology/approach
– It is based on a review of a selection of literature that highlights the dominant perspectives in neoclassical economics and competing streams of research that provide alternative perspectives.

Findings
– The review suggests the emergence of a competing paradigm that focuses attention on the human factor in economic growth process – i.e. the development of human capability as a foundation of sustainable inclusive growth. The competing streams of research seem to co-exist today, but there are potentials for paradigmatic criss-crossing in future research.

Originality/value
– It provides directions for future research into issues of economic growth and poverty alleviation in SSA.
Social protection for poor, vulnerable and disadvantaged groups
Authors: Brzeska Joanna , Das Mousumi , Fan Shenggen 
Published: November 2015

Purpose– The purpose of this paper is to identify the pathways through which social protection policies in China and India can address the key challenges facing poor, vulnerable, and disadvantaged groups under rapid transformation in both countries.Design/methodology/approach– This paper reviews the main social protection policies in China and India and analyzes the challenges that they are facing. This analysis is based on an evaluation of poverty and food security trends in both countries among vulnerable and disadvantaged groups followed by an overview of major experiences and gaps in social protection policies in the two emerging Asian giants.Findings– Improving the coverage and targeting of social protection systems is vital, and will require a multi-faceted reform portfolio that promotes more integrated and horizontally equitable systems. Emphasis should be placed on developing productive, cross-sectoral social protection programs that combine short-term social safety support with long-term tools to enhance productivity, paying special attention to nutrition, health, and human capital development. More efficient coverage and targeting should bridge the rural and urban divide and be grounded in transparent criteria and procedures that govern program implementation at all levels of the government. As both countries become more urbanized, social protection programs need to give equal attention to emerging food insecurity and nutrition issues within urban areas without detracting from food security and nutrition efforts in rural areas.Originality/value– Faced with a sizable population of undernourished and poor people, India and China have applied rather different approaches to address food insecurity. The originality and value of this paper lie in an in-depth parallel analysis of how China and India can better use their social protection systems to address food insecurity and undernutrition among poor, vulnerable, and disadvantaged groups.
The role of translation in cross-cultural knowledge transfer within a MNE’s business networks
Authors: Zhong Weihe , Chin Tachia 
Published: November 2015

Purpose
– The purpose of this paper is to explore how translation activities influence knowledge transfer across cultures in Chinese multinational enterprises (MNEs). Although translation is recognized as a critical instrument for MNEs to enhance cross-national knowledge flow, scholars have not put much emphasis on the importance of translation in international business research.

Design/methodology/approach
– This paper proposes a novel hierarchical framework to delineate the five major boundary-spanning functions regarding translation for knowledge transfer in China (i.e. exchanging, linking, manipulating, facilitating and intervening). Due to the paucity of relevant literature, the authors used exploratory case studies investigating two large Chinese MNEs to illustrate how individuals as boundary spanners handle the translation requirements associated with cross-cultural knowledge transmission within a MNE’s business network. The data coding approach was used to examine the assumed model.

Findings
– The findings demonstrate that translators indeed play a vital role in cross-border knowledge exchanging, linking people with crucial knowledge, manipulating the flow of knowledge for protecting confidentiality, facilitating the cross-cultural interaction of various knowledge sources and intervening to prevent the occurrence of misunderstanding in MNE contexts. The authors also reveal how translators overcome the three constraints of language interpretation concerning knowledge transfer (i.e. lack of equivalence, cultural interference and ambiguity). The proposed research framework was fully supported.

Research limitations/implications
– The results provide insightful implications for MNEs to treat translation as a significant “re-codification” rather than a mundane task. Knowledge transfer within MNEs involves not only knowledge regarding products, technology and operations but also involves “whole organizations” including business models, organizational visions, missions and strategies.

Originality/value
– The main value of this paper is to propose a novel model regarding the role of translation in cross-cultural knowledge transfer in China. Language is a container of contexts; the translation procedure in MNEs is actually dynamic and contingent in nature and can be seen as an act of knowledge creation per se.
Knowledge creation and application in technology collaboration portfolio
Authors: Liu Yang , Ying Ying , Fagerlin Wen Pan 
Published: November 2015

Purpose– This study aims at developing a better understanding of the different mechanisms that affect technology collaboration portfolio management. How do firms manage their technology collaboration portfolio? Despite some thoughtful scholars have advanced the understanding of the phenomenon of technology collaboration portfolio, there is not much research that has been done in terms of understanding the endeavors of firms when they collectively use a range of actors for the best interests of the firms. Additionally, little attention has been paid to the trade-offs and managing mechanisms for the collaborations between different partners from a portfolio-level perspective, especially in emerging markets.Design/methodology/approach– A multiple-case study of two Chinese high-tech firms, an inductive approach.Findings– The authors identified three primary mechanisms that underlie successful knowledge creation and application in technology collaboration portfolio context: informally mobilizing boundary-spanning brokers for domestic academic collaborations, formally institutionalizing learning activities for industry collaborations and integrating formal and informal mechanisms for technology collaborations between focused firms and foreign organizations.Originality/value– The authors extend the line of organizational ambidexterity literature with a focus on strategic alliance, proposing that firms need to balance academic and industry collaborations from a portfolio level. Moreover, the authors intend to extend the literature of alliance portfolio by suggesting three different learning mechanisms of managing different technology collaborations for the purpose of balancing successful knowledge creation and application.
Cross-organizational knowledge creation theory from the perspective of I-Ching
Authors: Yao Wei , Han Xu , Li Yuxiang 
Published: November 2015

Purpose– This paper aims to refine cross-organizational knowledge creation theory by exploring the knowledge conversion process of University-Industry (U-I) collaboration in Chinese aerospace industry. An ancient Chinese philosophy named I-Ching is also introduced to illustrate dynamics of knowledge creation to achieve enlightenment.Design/methodology/approach– To describe the knowledge conversion tendency, a theoretical framework is developed by reference to Boisot’s (1995) Information Space. The application of the framework is described in the in-depth case study of micro-electrode manufacturing for aerospace vehicles. The dynamics of each stage in knowledge conversion is investigated with the implications from I-Ching.Findings– Analysis of the results suggests that seven certain stages can be especially indicative of cross-organizational knowledge creation, namely: demand codification; knowledge gain; knowledge digestion; knowledge sharing; knowledge propagation; knowledge spillover and knowledge degeneration. A knowledge gain, digestion, sharing and propagation (GDSP) knowledge creation theory is developed accordingly. The form of knowledge in different stages is variable, the change among various forms is effectively explained by I-Ching.Research limitations/implications– There is clearly a strong requirement to test the framework further with other cases, such as sampling cases from different industries and of different firm scales. Besides, the knowledge creation processes on the organizational level and the individual level are quite different, which call for further study.Practical implications– First, the theory helps firms to get a better understanding of the nature of U-I collaboration, that is to say, knowledge creation. That will, in turn, power the firm to take the initiative to participate in knowledge creation activities. Second, the illustration through I-Ching provides reasonable and easily understandable interpretations for Chinese corporate managers and executives. Traditional Chinese culture will be beneficial to make U-I collaborations more efficient and effective in China.Originality/value– A new “GDSP knowledge creation theory” which enriches and advances the typical socialization, externalization, combination and internalization (SECI) knowledge creation theory in some aspects is proposed. The theory is deeply grounded in Chinese culture. Furthermore, the conversion of different knowledge forms in the theory is considered from a totally new perspective of ancient Chinese philosophy: I-Ching.
Achieving digital literacy through game development: an authentic learning experience
Authors: Frydenberg Mark 
Published: November 2015

Purpose
– This paper aims to argue that the process of making an original game develops digital literacy skills and provides an authentic learning experience as students create, publish and deploy interactive games. Teaching students to create computer games has become common in both K-12 and tertiary education to introducing programming concepts, increase student engagement and recruit majors and minors in technology fields. This study describes a project where first-year college students in an introductory technology concepts course use a visual game creation tool to develop original games to play on their computers and mobile devices.

Design/methodology/approach
– The author created a game development exercise which was implemented in three different sections of an introductory technology course. Students who participated were surveyed about their experiences. In addition, the author considers information technology (IT) skills and aspects of authentic learning which are achieved through this assignment.

Findings
– Initial findings suggest that students found the gaming assignment offers an opportunity for students with no prior programming skills to create software within a controlled and supportive environment. It allows them to demonstrate their understanding of coding principles, including identifying objects and interactions, and that creating software requires a developer to specify exact instructions for the computer to follow.

Research limitations/implications
– This study is limited to results from one semester and a small number of students participating. In addition, student frustration with the complicated process of publishing games online may have influenced student attitudes toward the assignment.

Practical implications
– Challenges of implementing this study on a larger scale are discussed.

Social implications
– Creating games encourages collaborative learning through trial and error, and students who share their games with friends to play on their devices achieve a sense of pride.

Originality/value
– While most studies of game development emphasize the programming skills that are developed through creating computer games, this paper looks at a larger scope of digital literacy and IT skills achieved, as well as opportunities to perform tasks often completed by IT professionals.
Learning through telepresence with iPads: placing schools in local/global communities
Authors: Meyer Bente 
Published: November 2015

Purpose– This study aims to present findings from an ongoing study in three rural schools in Denmark where videoconferences are used as part of the teaching at lower secondary level. The research focuses on how students learn from videoconferences that are both one-to-many and peer-to-peer. Videoconferencing, conceptualized by the schools in question as telepresence, is performed in a unique combination of desktop interaction through mobile devices (iPads) and studio-based large screen lectures and interaction.Design/methodology/approach– Data have been collected through multi-sited ethnography, which has contributed to mapping relationships between schools and studying their collaboration through telepresence. As collaboration between schools is built into the project, multi-sited ethnography has followed telepresence as a phenomenon that emerges within these collaborations, i.e. the idea is that looking at it from one locality is only seeing it partially.Findings– Preliminary results from the project suggest that schools need to work more on organizational frameworks for collaboration and that synchronous connections could be extended through asynchronous communication to support the potential of collaboration via telepresence with iPads.Research limitations/implications– The study has followed schools for two years in the initial development phase, but can be further qualified by following the next phase of the project, which will be initiated in the Autumn of 2015.Practical implications– The study has implications for the development of telepresence practices in which mobile devices are used in home classrooms and combined with stationary devices in auditoriums. In addition to this, the study provides examples of how schools can collaborate through telepresence activities in which both teacher-driven and student-driven activities are involved.Originality/value– The study fulfils a need for knowledge about ways in which telepresence and videoconferencing is used in elementary education and for different educational goals.
Sporting memories
&
the social inclusion of older people experiencing mental health problems
Authors: Clark Michael , Murphy Charlie , Jameson-Allen Tony , Wilkins Chris 
Published: November 2015

Purpose
– Social exclusion and isolation of older people and their mental health are likely to be more significant, interlinked issues for society as countries experience an ageing demographic profile. The authors urgently need to identify effective ways of addressing these challenges that can be easily mobilised to meet diverse needs in different settings. The purpose of this paper is to explore the impact of sporting memories (SM) work as one approach to help meet this need. This SM work entails the use of sports-based reminiscence to engage with older people experiencing mental health problems. To date this has especially focused on people living with dementia in institutional and in community settings.

Design/methodology/approach
– The paper sets out the SM idea and discusses lessons learnt from case studies of its application to meet the inclusion and mental health needs of different older people in institutional and community settings.

Findings
– The evidence from the application of SM work to date is that it is an effective and flexible means of engaging people to improve their social inclusion and mental well-being. It can be readily deployed in various care and community settings.

Research limitations/implications
– The evidence to date is of case studies of the use of SM work, and, although these are now extensive case studies, further research is needed on the costs and impacts of SM work.

Practical implications
– SM work is a flexible and readily adoptable intervention to engage older people and help improve their social inclusion and mental well-being.

Social implications
– SM work can be an important part of meeting some of the challenges society faces with an ageing population profile.

Originality/value
– This is the first paper to set out the SM work.
“Broken homes and violent streets”: are there common factors which predispose girls and young women to become street sex workers?
Authors: Collinson Susan , Ash Anny 
Published: November 2015

Purpose
– Street-based sex workers in the London Borough of Hackney have high levels of physical and mental ill-health, antisocial behaviour and substance misuse. This study interviewed sex workers at a local drop-in, in an attempt to understand the women’s family, social and educational backgrounds, and whether there were common factors that contributed to them becoming sex workers. The paper aims to discuss these issues.

Design/methodology/approach
– In total, 17 street sex workers were interviewed using semi-structured questions. The transcripts were examined methodologically using a conceptual content analysis approach in order to identify dominant themes.

Findings
– The women had very similar narratives of early physical and sexual abuse, negative parenting, poor impulse control and low levels of educational attainment, suggestive of conduct disorder, the aetiology of which involves an interaction of genetic, familial and social factors. Research suggests that multi-factorial early intervention to promote social and environmental development can significantly improve a child’s life chances and opportunities.

Research limitations/implications
– This study involved a very small number of women from a very defined inner-city area. Nearly all the women were UK born and local, and thus would have been through the local schools, social services and care system. These factors mean that it is not possible to generalise findings to a whole population.

Originality/value
– This study was the first piece of qualitative work carried out in the confidential drop-in setting used by this hard to reach group of women. Their narratives are valuable in terms of their impact, and that there were so many common themes, especially in relation to their early life experiences.
Epistemic asymmetries in psychotherapy interaction: therapists' practices for displaying access to clients' inner experiences
Authors: Weiste Elina , Voutilainen Liisa , Peräkylä Anssi 
Published: November 2015

AbstractThe relationship between a psychotherapist and a client involves a specific kind of epistemic asymmetry: in therapy sessions the talk mainly concerns the client's experience, which is unavailable, as such, to the therapist. This epistemic asymmetry is understood in different ways within different psychotherapeutic traditions. Drawing on a corpus of 70 audio‐recorded sessions of cognitive psychotherapy and psychoanalysis and using the method of conversation analysis, the interactional practices of therapists for dealing with this epistemic asymmetry are investigated. Two types of epistemic practices were found to be employed by therapists while formulating and interpreting the client's inner experience. In the formulations, the therapists and clients co‐described the client's experience, demonstrating that the client's inner experience was somewhat similarly available to both participants. In the interpretations, the therapists constructed an evidential foundation for the interpretation by summarising the client's talk and using the same descriptive terms as the client. Clients held therapists accountable for this epistemic work: if they failed to engage in such work, their right to know the client's inner experience was called into question.