bluuebunny/crossref_metadata_2025_split huggingface dataset:
Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data
Authors: Wymant Chris , Blanquart François , Gall Astrid , Bakker Margreet , Bezemer Daniela , Croucher Nicholas J. , Golubchik Tanya , Hall Matthew , Hillebregt Mariska , Ong Swee Hoe , Albert Jan , Bannert Norbert , Fellay Jacques , Fransen Katrien , Gourlay Annabelle , Grabowski M. Kate , Gunsenheimer-Bartmeyer Barbara , Günthard Huldrych F. , Kivelä Pia , Kouyos Roger , Laeyendecker Oliver , Liitsola Kirsi , Meyer Laurence , Porter Kholoud , Ristola Matti , van Sighem Ard , Vanham Guido , Berkhout Ben , Cornelissen Marion , Kellam Paul , Reiss Peter , Fraser Christophe ,   The BEEHIVE Collaboration
Published: December 2016

AbstractNext-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of rapid between- and within-host evolution may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions.De novoassembly avoids this bias by effectively aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the toolshiverto preprocess reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We useshiverto reconstruct the consensus sequence and minority variant information from paired-end short-read data produced with the Illumina platform, for 65 existing publicly available samples and 50 new samples. We show the systematic superiority of mapping toshiver’s constructed reference over mapping the same reads to the standard reference HXB2: an average of 29 bases per sample are called differently, of which 98.5% are supported by higher coverage. We also provide a practical guide to working with imperfect contigs.
Integration of social protection and climate change adaptation in Brazil
Authors: S. Mesquita Patricia , Bursztyn Marcel 
Published: December 2016

Purpose
Social protection (SP) and climate change adaptation (CCA) are two subjects highly debated when discussing social vulnerabilities and food insecurity in rural areas of developing countries. Both fields address matters related to socioeconomic vulnerabilities and thus present opportunities for integration. However, many studies have stated the lack of interaction within the study areas. When dealing with CCA and SP in Brazil, the two offer an opportunity for integration since some SP programmes (such as food-based safety nets) can both affect adaptation and be impacted by expected changes in climate. Impacts from CC are projected to be extreme in the Brazilian semi-arid Northeast, a region where social programmes of assistance and aid are historically crucial during periods of drought. Thus, the purpose of this paper is to address the interaction of CCA and SP in a conceptual level on policies and programmes in Brazil.

Design/methodology/approach
A desk review of government documents (policies, plans, decrees) related to food security, food-based programmes and CC.

Findings
Based on the results the authors highlight the limited integration between CC and SP in Brazil and the potential for interaction in many of the programmes already in place.

Originality/value
The authors attribute findings to the segmented governmental structure and the weak interaction between sectors, and the only recent discussion of linkages between CC and poverty, development and food insecurity. Discussion on the challenges and benefits of this interaction are provided in a context of CC in Brazil, still not very debated in the academic literature.
Building psychological contract: the role of leader member exchanges
Authors: Kasekende Francis , Munene John C. , Ntayi Joseph M. , Ahiauzu Augustine 
Published: December 2016

PurposeThe purpose of this paper is to address the building blocks for psychological contract among public institutions in Uganda by investigating the mediation effect of leader-member exchanges (LMX) in the relationship between perceived environmental dynamism and psychological contract.Design/methodology/approachThe authors use structural equation modelling (AMOS) to investigate the hypotheses.FindingsLMX is a significant mediator in the association between generational work values and psychological contract and technological advancement and psychological contract among employees in public institutions in Uganda.Practical implicationsAt commissions and agencies level, generational work values and technological advancement seem to create better effects on employee-employer unwritten expectations and obligations when they go through LMX. This has important implications for the investment in and outcomes of these LMX endeavours from both the employer and the employee.Originality/valueThe study is one of the pioneers to demonstrate that the presence of LMX reflected in the form of a dyadic relationship helps to extend the positive effects generational work values and technological advancement have on psychological contract.
E-books usage by agricultural, engineering and social science students in selected universities of Pakistan
Authors: Khan Amjid , Bhatti Rubina , Khan Asad 
Published: December 2016

Purpose
The purpose of this paper is to compare the usage patterns of e-books among the students of social, agricultural, and engineering sciences; demonstrate how e-books are used by students for various purposes; explore the main reasons for using e-books; and uncover the major issues being encountered by students while using e-books in Pakistani Universities.

Design/methodology/approach
During May to July 2014, a convenient sample technique was adopted, and a close-ended questionnaire was used as a survey tool for 300 graduates (BSc honor) and postgraduate (masters and MS) students in the age group of 21-60 years. In this study, the respondents’ gender, age, educational level and major disciplines were individual contextual variables. The data collection process was successfully completed with a 100 per cent response rate. SPSS-19 was utilized for testing the reliability of the instrument, as well as descriptive and inferential statistics (Chi-square test).

Findings
The results show that the adoption of e-books has reached a level where they have become an integral component of academic library services. The results of this study verify the previous findings that the students are relying on e-book adoption for various academic and research purposes. Comparatively, male students, postgraduate students and those between the ages of 21 and 40 years are more frequently e-book users. In addition, the percentage of e-book readership among engineering students on a “daily basis” is greater than the students of agricultural and social sciences. They prefer reading e-books because of the following reasons: to support research endeavors and improve academic performance; and the e-format is quick to read and easy to manage. Insufficient e-contents, lack of personal computers and the variety of e-book formats are the major constraints in the effective utilization of e-books for learning, education and research needs. The study has concluded that e-books have a key role in the set-up of academic libraries and information resources in Pakistan, though further development of e-book readership capabilities and building of e-book collections are required to support users’ needs, and a parallel investigation into their most effective usage is also required.

Originality/value
This empirical research is a first and unique study that systematically and quantitatively compares the relationship between respondents’ e-books usage with their individual contextual variables in the perspective of academic libraries in Pakistan.
Heuristic production line balancing problem solution with MATLAB software programming
Authors: Türkmen Aysun , Yesil Yalcin , Kayar Mahmut 
Published: December 2016

Purpose
The purpose of this paper is to find the most efficient assembly line balancing solution across many heuristic line balancing methods, in assistance with a developed computer program.

Design/methodology/approach
In this paper, assembly line balancing problem was analyzed using t-shirt and knitted pants data. A computer program using MATLAB software for the solution of assembly line balancing problems has been developed. In this study, following heuristic assembly line balancing methods were applied: Hoffman method; position weight method; COMSOAL method; and Kilbridge and Wester method. A MATLAB program has been developed by taking into account of theoretical solution of all these methods. Later the program is developed further by analyzing solutions made manually and is made to verify the developed program.

Findings
Pre-studies which were conducted in order to decide which programming language would be the best choice for line balancing methods’ application came out with the result that MATLAB, from between C, C++, C# and Java, would be the best software choice. The main reason for this choice is that MATLAB is a powerful matrix operation software with a powerful user interface designing tool and has the tools to make development program to be used universally in every computer.

Originality/value
When the researches were investigated, it is clearly seen that, this study is the first research on using computer program for solving assembly line balancing problem.
Adopting Agile software development: the project manager experience
Authors: Taylor Katie Jane 
Published: December 2016

Purpose
Early research into Agile approaches explored particular practices or quantified improvements in code production. Less well researched is how Agile teams are managed. The project manager (PM) role is traditionally one of “command and control” but Agile methods require a more facilitative approach. How this changing role plays out in practice is not yet clearly understood. The purpose of this paper is to provide insight into how adopting Agile techniques shape the working practices of PMs and critically reflect on some of the tensions that arise.

Design/methodology/approach
An ethnographic approach was used to surface a richer understanding of the issues and tensions faced by PMs as Agile methods are introduced. Ethnographic fiction conveys the story to a wider audience.

Findings
Agile approaches shift responsibility and spread expert knowledge seeming to undermine the traditional PM function. However, the findings here show various scenarios that allow PMs to wrest control and become more of a “gate-keeper”. Ethnographic fiction communicates a sense of the PMs frustration with the conflict between the need to control and the desire for teams to take more responsibility.

Originality/value
Stories provide insight and communicate the experiential feel behind issues faced by PMs adopting Agile to surface useful knowledge. The objective is not how to measure knowledge, but how to recognize it. These reflections are valuable to fellow researchers as well as practitioners and contribute to the growing literature on Agile project management.
Health beliefs and the valence framework in health information seeking behaviors
Authors: Mou Jian , Shin Dong-Hee , Cohen Jason 
Published: December 2016

Purpose
The purpose of this paper is to help understand consumer acceptance of online health information services by integrating the health belief model and extended valence framework.

Design/methodology/approach
A laboratory-based, experimental-scenarios research design is used to collect data, and the structural equation modeling technique is used to test the research model.

Findings
The model explains 47.6 percent of the variance in intentions to use online health information services. Trust appeared to have the strongest effect on acceptance. Perceived risk also had a significant impact on acceptance. Furthermore, health belief variables are confirmed as important factors for consumer acceptance. Self-efficacy was found to moderate the effect of perceived severity on acceptance.

Research limitations/implications
This study helped identify the relative salience of the health belief model and extended valence framework in consumer acceptance of online health information services.

Practical implications
This study can help practitioners better understand the development of trust and the profiles of consumers who may browse their sites. When online health service providers promote their information to encourage potential online health information seekers, they should use countermeasures against risk perceptions.

Originality/value
This study attempted to extend the valence framework to the non-commercial service context. Moreover, health beliefs and the valence framework are two fundamental aspects that health information seekers consider when making decisions about online health services.
How user personality and social value orientation influence avatar-mediated friendship
Authors: Chesney Thomas , Chuah Swee-Hoon , Hoffmann Robert , Hui Wendy , Larner Jeremy 
Published: December 2016

PurposeThe purpose of this paper is to study the influence of user personality and vlaues on the number of connections users make, the number of requests for connections that users give out, and the number of connections invitations users receive.Design/methodology/approachThis is a field study of 179 participants interacting in a novel virtual world. The world’s server logs are used to capture sociometrics about the users and their interaction.FindingsFindings suggest that personality and values influence the number of friends users make and the number of friendship requests users give out, but not the number of friendship invitations users receive. Only one personality trait – conscientiousness – exhibits homophily.Originality/valuePerosnality and social value orientation have rarely been studied together in information systems (IS) research, despite research showing the two have an impact on IS relevant constructs. The use of server logs for data capture is novel. Avatar friendship is an under-researched concept in IS.
Healthcare resource allocation decisions affecting uninsured services
Authors: Harrison Krista Lyn , Taylor Holly A. 
Published: December 2016

Purpose
Using the example of community access programs (CAPs), the purpose of this paper is to describe resource allocation and policy decisions related to providing health services for the uninsured in the USA and the organizational values affecting these decisions.

Design/methodology/approach
The study used comparative case study methodology at two geographically diverse sites. Researchers collected data from program documents, meeting observations, and interviews with program stakeholders.

Findings
Five resource allocation or policy decisions relevant to providing healthcare services were described at each site across three categories: designing the health plan, reacting to funding changes, and revising policies. Organizational values of access to care and stewardship most frequently affected resource allocation and policy decisions, while economic and political pressures affect the relative prioritization of values.

Research limitations/implications
Small sample size, the potential for social desirability or recall bias, and the exclusion of provider, member or community perspectives beyond those represented among participating board members.

Practical implications
Program directors or researchers can use this study to assess the extent to which resource allocation and policy decisions align with organizational values and mission statements.

Social implications
The description of how healthcare decisions are actually made can be matched with literature that describes how healthcare resource decisions ought to be made, in order to provide a normative grounding for future decisions.

Originality/value
This study addresses a gap in literature regarding how CAPs actually make resource allocation decisions that affect access to healthcare services.
To downsize or not to downsize – what does the empirical evidence suggest?
Authors: Carriger Michael 
Published: December 2016

PurposeThere has been much written about the effects of downsizing on the financial health and the valuation of companies that engage in this practice. But this literature is fragmented, focusing on various aspects of companies, various reasons for downsizing, and various financial and market outcome measures. The purpose of this paper is to try and address some of this fragmentation by comparing those companies that downsized in 2008, whether financially healthy or not, with those companies that did not downsize.Design/methodology/approachThe impact of the downsizing event was assessed by using various financial measures as well as a measure of company valuation over the short term (2009-2011) and long term (2009-2014).FindingsFindings indicate that across all financial measures, except return on equity, downsizing makes no difference to the financial health of a company either in the short term (up to three years after the downsizing) or in the long term (up to six years after the downsizing). And with regards to return on equity, downsizing companies did more poorly immediately after the downsizing in efficiently using their equity.Originality/valueThe hope is that this work will better inform, not only scholars, but also senior leaders faced with a decision to downsize or not to downsize.
Using Primo for undergraduate research: a usability study
Authors: Kliewer Greta , Monroe-Gulick Amalia , Gamble Stephanie , Radio Erik 
Published: December 2016

Purpose
The purpose of this paper is to observe how undergraduate students approach open-ended searching for a research assignment, specifically as it affected their use of the discovery interface Primo.

Design/methodology/approach
In total, 30 undergraduate students were provided with a sample research assignment and instructed to find resources for it using web tools of their choice, followed by the Primo discovery tool. Students were observed for 30 minutes. A survey was provided at the end to solicit additional feedback. Sources students found were evaluated for relevance and utility.

Findings
Students expressed a high level of satisfaction with Primo despite some difficulty navigating through more complicated tasks. Despite their interest in the tool and previous exposure to it, it was usually not the first discovery tool students used when given the research assignment. Students approached the open-ended search environment much like they would with a commercial search engine.

Originality/value
This paper focused on an open-ended search environment as opposed to a known-item scenario in order to assess students’ preferences for web search tools and how a library discovery layer such as Primo was a part of that situation. Evaluation of the resources students found relevant were also analyzed to determine to what degree the students understood the level of quality they exhibited and from which tool they were obtained.
The application of social media in outreach of academic libraries’ resources and services
Authors: Zhu Qiandong 
Published: December 2016

Purpose
The purpose of this paper is to introduce the implementation of the official WeChat account, the most popular mobile social media site in China, to share Jinan University Library collections and services to students, faculty and staff. The implementation, experience and issues have implications for academic libraries and other institutions to run and improve social media tools.

Design/methodology/approach
This paper is a case study, which elaborates on the implementation process of the official WeChat account, including project group establishment, account application and management, users’ needs analysis, WeChat secondary development and model of development.

Findings
The official WeChat account has already engaged a population of followers who are able to directly access library resources and service via their mobile device. The social media tool is an effective approach to promote library services and to enhance relationships between the library and its users. The issues appear during the process of WeChat implementation and promotion, which requires WeChat’s provider, third-party application vendors and the library to work together to solve.

Originality/value
The implementation of official WeChat account has practical implications for academic libraries and other institutions to conduct it and similar social media tools, such as Sina Weibo, Facebook and Line. In particular, it is beneficial for academic libraries outside China which desire to use WeChat to engage Chinese international students. Additionally, it provides insight into the future effort on social media promotion, secondary development and cooperation within the social networking industry.
The different relations of extrinsic, introjected, identified regulation and intrinsic motivation on employees’ performance
Authors: Zhang Jian , Zhang Ying , Song Yahui , Gong Zhenxing 
Published: December 2016

PurposeFollowing self-determination theory, the purpose of this paper is to investigate the impact of four motivational profiles (external, introjected, identified regulation, and intrinsic motivation) on work performance (interpersonal, adaptive, task, and dedicative performance). The authors also examined the proposed relations with longitudinal data.Design/methodology/approachParticipants in Studies 1 and 2 were from several companies in China. Employees completed the questionnaires to measure their work motivation, and managers completed the questionnaires to assess the subordinates’ work performance.FindingsIn Study 1, the authors found that identified regulation significantly predicted interpersonal performance and adaptive performance. External regulation, introjected regulation, and intrinsic motivation had no significant impacts on interpersonal, adaptive, task, or dedicative performance. In Study 2, the results revealed that identified regulation significantly predicted dedicative and interpersonal performance, but external regulation, introjected regulation, and intrinsic motivation had no significant impacts on the four types of performance. These two studies concluded that only identified regulation strongly predicts work performance.Originality/valueThe study has contributed to the body of knowledge by clarifying that identified regulation is an important type of motivation in the workplace. Managers might therefore focus on supporting employees for identifying with the organizational goals in order to promote better performance.