bluuebunny/crossref_metadata_2025_split huggingface dataset:
To include or not to include: The impact of gene filtering on species tree estimation methods
Authors: Molloy Erin K. , Warnow Tandy 
Published: June 2017

AbstractSpecies tree estimation from loci sampled from multiple genomes is now common, but is challenged by the heterogeneity across the genome due to multiple processes, such as gene duplication and loss, horizontal gene transfer, and incomplete lineage sorting. Although methods for estimating species trees have been developed that address gene tree heterogeneity due to incomplete lineage sorting, many of these methods operate by combining estimated gene trees and are hence vulnerable to gene tree quality. There is also the added concern that missing data, which is frequently encountered in genome-scale datasets, will impact species tree estimation.Our study addresses the impact of gene filtering on species trees inferred from multi-gene datasets. We address these questions using a large and heterogeneous collection of simulated datasets both with and without missing data. We compare several established coalescent-based methods (ASTRAL, ASTRID, MP-EST, and SVDquartets within PAUP*) as well as unpartitioned concatenation using maximum likelihood (RAxML).Our study shows that gene tree error and missing data impact all methods (and some methods degrade more than others), but the degree of incomplete lineage sorting and gene tree estimation error impacts the absolute and relative performance of methods as well as their response to gene filtering strategies. We find that filtering genes based on the degree of missing data is either neutral or else reduces the accuracy of all five methods examined, and so is not recommended. Filtering genes based on gene tree estimation error shows somewhat different trends. Under low levels of incomplete lineage sorting, removing genes with high gene tree estimation errorcanimprove the accuracy of summary methods, but only if not too many genes are removed. Otherwise, filtering genes tends to increase error, especially under high levels of incomplete lineage sorting. Hence, while filtering genes based on missing data is not recommended, there are conditions under which removing high error gene trees can improve species tree estimation. This study provides insights into prior studies and suggests approaches for analyzing phylogenomic datasets.
Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient
Authors: Ryan Sean F. , Fontaine Michael C. , Scriber J. Mark , Pfrender Michael E. , O’Neil Shawn T. , Hellmann Jessica J. 
Published: June 2017

AbstractHybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone betweenPapilio glaucusandPapilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.
DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability
Authors: Lugowski Andrew , Nicholson Beth , Rissland Olivia S. 
Published: June 2017

SUMMARYControl of messenger RNA (mRNA) stability is an important aspect of gene regulation. The gold standard for measuring mRNA stability transcriptome-wide uses metabolic labeling, biochemical isolation of labeled RNA populations, and high-throughput sequencing. However, difficult normalization procedures and complex computational algorithms have inhibited widespread adoption of this approach. Here, we present DRUID (for Determination of Rates Using Intron Dynamics), a computational pipeline that is robust, easy to use, and freely available. Our pipeline uses endogenous introns to normalize time course data and yields more reproducible half-lives than other methods, even with datasets that were otherwise unusable. DRUID can handle datasets from a variety of organisms, spanning yeast to humans, and we even applied it retroactively on published datasets. We anticipate that DRUID will allow broad application of metabolic labeling for studies of mRNA stability.
Value conflicts and organizational commitment of internal construction stakeholders
Authors: Panahi Babak , Moezzi Elena , Preece Christopher Nigel , Wan Zakaria Wan Normeza 
Published: June 2017

PurposeThe possible effect of conflicts as the consequence of differences between personal and organizational values (OV) on organizational commitment (OC) of internal construction stakeholders was an unclear issue in the areas of organizational behaviour in the construction industry, especially in Malaysia. Therefore, the purpose of this paper is to focus on this issue in the Malaysian construction industry.Design/methodology/approachThis paper targeted professional project consultants, who are identified as architects, engineers, and quantity surveyors, as the internal construction stakeholders. The personal-OV and the level of OC of the stakeholders were evaluated through a questionnaire survey. To achieve the research objective, comparative and hierarchical regression analyses were performed.FindingsThe results generated by the analyses indicated a high level of value conflicts in the construction organizations which significantly and negatively affected commitment of the internal stakeholders.Originality/valueValue conflicts in construction organizations are the agenda of this paper while not many empirical studies have been conducted on this issue in Malaysia. This paper through investigating the potential effect of value conflicts on the stakeholders’ commitment reveals the importance of interaction between personal and OV in construction organizations which contributes to the extant literature of organizational behaviour as to the construction literature.
Total factor productivity measurement with carbon reduction
Authors: Hu Xiancun , Liu Chunlu 
Published: June 2017

PurposeThe purpose of this paper is to present an approach for productivity measurement that considers both construction growth and carbon reduction.Design/methodology/approachThe approach applied is a sequential Malmquist-Luenberger productivity analysis based on a directional distance function and sequential benchmark technology using the data envelopment analysis (DEA) technique. The sequential Malmquist-Luenberger productivity change index is decomposed into pure technical efficiency, scale efficiency, and technological change indices, in order to investigate the driving forces for productivity change.FindingsThe construction industries of the Australian states and territories were selected implement the new approach. The results indicate that construction growth and carbon reduction can be achieved simultaneously through the learning of techniques from benchmarks.Practical implicationsCurrent research on total factor productivity (TFP) in construction generally neglects carbon emissions. This does not accurately depict the nature of construction and therefore yields biased estimation results. TFP measurement should consider carbon reduction, which is beneficial for policymakers to promote sustainable productivity development in the construction industry.Originality/valueThe approach developed here is generic and enhances productivity and DEA research levels in construction. This research can be used to formulate policies for evaluating performance in worldwide construction projects, organizations and industries by considering undesirable outputs and desirable outputs simultaneously, and for promoting sustainable development in construction by identifying competitiveness factors.
Science-industry R&D cooperation effects on firm’s appropriation strategy
Authors: Milesi Dario , Verre Vladimiro , Petelski Natalia 
Published: June 2017

Purpose
The purpose of this paper is to show how science-industry R&D cooperation (SIRC) generates effects on the strategy developed by firms to appropriate the benefits of innovations. Given the plurality of cooperation patterns between firms and public R&D institutions and the variety of appropriation mechanisms used by firms to protect generated knowledge or to strengthen their market position, this paper investigates to what extent different forms of cooperation are associated with different effects on appropriation strategy.

Design/methodology/approach
As evidence of this, the authors carry out a multiple case study, covering nine biopharmaceutical Argentine firms whose innovation projects are developed in cooperation with public R&D institutions. Using critical dimensions identified by public-private R&D cooperation literature, the paper analyzes the characteristics of cooperation in the cases studied, looking for different patterns. Given the existence of various appropriation mechanisms identified by appropriability literature, the paper analyzes how firms use (or not) those mechanisms within the specific context of jointly generated innovation.

Findings
The paper shows that SIRC generates opposing effects on the various appropriation mechanisms used by firms, both challenging and strengthening them. Likewise, the identification of three cooperation patterns in Argentine biopharmaceutical sector, namely, contract R&D, internalization and coordination, allows appreciating how each pattern affects differently the appropriation mechanisms used by firms, being the coordination one, the most functional to the appropriation strategy of firms analyzed.

Research limitations/implications
The arguments presented here are necessarily limited to the biopharmaceutical Argentine sector, which is strategic to the country, for accumulated capabilities in scientific and business aspects. The analysis could be enriched by extending it to other industries with similar innovation characteristics and to other countries, where patents have a similar weight (emerging countries) or a different one (developed countries).

Practical implications
Innovation and public-private collaboration policies may benefit from the analysis presented here, which helps to assess advantages and challenges of different SIRC logics on firms’ appropriation issues and to considerate which aspects allow cooperation and appropriation combining in a more virtuous form.

Originality/value
There is no paper that explicitly examines the effects generated by different SIRC patterns on the appropriation strategy of firms, conceived as a combination of different mechanisms which may include patents but is not limited to them.
Innovation performance of Italian manufacturing firms
Authors: Paula Fabio de Oliveira , Silva Jorge Ferreira da 
Published: June 2017

Purpose
The purpose of this paper is to explain how internal and external sources of knowledge influence the innovation performance (IP) in Italian manufacturing firms and how different these relationships are for low-technology (LT) and high-technology (HT) firms.

Design/methodology/approach
The study proposed a model relating external knowledge, internal knowledge and IP that was tested using Bayesian structural equation modeling with a sample of Italian manufacturing firms of Community Innovation Survey 2010. It was run separately for high-tech firms (including HT and medium-HT aggregations of manufacturing industries of NACE Rev. 2) and low-tech firms (including LT and medium-LT aggregations).

Findings
The results showed a difference between high-tech and low-tech manufacturing firms in Italy. The investments to leverage internal knowledge sources are important for high-techs and not significant for low-techs. On the other hand, the level of external KS improves significantly the IP of low-techs and has a negative effect for high-techs. The level of absorptive capacity is central to improve the positive effect of the external knowledge on the IP for all firms, but it is still underdeveloped.

Originality/value
The effects of 2008 economic crisis hit the Italian manufacturing industry specifically hard and are still felt. Innovation is a solution for firms’ growth and Italy is considered a below-average innovator country in Europe. The study could identify important gaps in Italian manufacturing firms that hinder their innovative performance improvement.
Intervention research and its influence on nonintervention research in human resource development
Authors: Park Sunyoung , Chae Chungil 
Published: June 2017

PurposeThe purpose of this paper is to identify how intervention research weighed in nonintervention research in the field of human resource development (HRD) by examining the number, citation frequency and use of experimental studies in HRD academic journals.Design/methodology/approachA total of 2,700 articles published between 1990 and 2014 fromAdvances in Developing Human Resources(ADHR),European Journal of Training and Development(EJTD),Human Resource Development International(HRDI) andHuman Resource Development Quarterly(HRDQ) were reviewed and analyzed to identify 91 experimental studies in the field.FindingsThe total citation frequency of the 91 articles was 1,100 (14 fromADHR, 222 fromEJTD, 56 fromHRDIand 808 fromHRDQ). The authors reviewed the 1,100 subsequent studies that cited 91 experimental research studies and coded them to identify the research methods that each article adopted and to determine whether the studies used the citation to make causal statements. As a result, the authors found 459 causal statements from 1,100 citations. In particular, they identified the citation frequency of the causal statements used in nonintervention research to examine how often nonintervention studies used causal statements from intervention studies.Research limitations/implicationsThe results of the citation frequency could be different according to the search engines and timeframes. Books, technical reports, non-English studies, non-academic articles and inaccessible articles were not considered in this study. Theoretically, this study aimed to illuminate the magnitude of HRD experimental research conducted over 25 years and to what extent it influenced non-experimental studies. In addition, this study emphasized the importance of using the causal statements from experimental research to improve empirical validation in other studies.Practical implicationsWhen HRD practitioners need to identify alternative interventions to replace previous ones or to justify the use of specific interventions, they could consider causal statements from empirical studies as valid evidence. Further, HRD practitioners might collaborate with researchers to receive more direct and relevant information from experimental research.Originality/valueSignificantly, this study provides an integrative review of experimental research conducted in the field of HRD in terms of the number, citation frequency and proportion of using experimental research. An additional contribution is that it summarizes the research methods used in HRD studies over 25 years.
Women’s leadership development in sport settings
Authors: Megheirkouni Majd , Roomi Muhammad Azam 
Published: June 2017

PurposeThis study explores the positive and negative factors influencing transformational learning experiences of female leaders in women’s leadership development programmes in sports and examines the differences in learning/change factors cited by those who successfully addressed them and those who failed.

Design/methodology/approachThe study adopted a qualitative research method, using phone interviews with women leaders in a sports setting.

FindingsThe findings revealed that participants presented clear progress in terms of leadership skills, but they failed to report whether this progress can be achieved if the programme is running within a specific sports organisation, targeting a specific kind of sports leadership in the long term.

Research limitations/implicationsThere were a number of limitations for this study, e.g. selection of participants, sample size, exploratory methodology, which affected generalising the findings to other sports organisations or other countries.

Originality/valueThe study provides a starting point for the exploration of the effectiveness of women leadership development programmes and how designers can evaluate the outcome of such initiatives in the UK.
Taking stock of the waqf-based Islamic microfinance model
Authors: Abdullah Rose , Ismail Abdul Ghafar 
Published: June 2017

Purpose
The purpose of this paper is to explore two main aspects of waqf: the characteristics of waqf property and the management of waqf. This paper also discusses the governance of waqf management as a source of funds for Islamic microfinance institutions (MFIs).

Design/methodology/approach
This research uses content analysis method to examine various literatures that discuss the concept and management of waqf.

Findings
The characteristics of cash waqf such as permanence, irrevocability and perpetuity differentiate waqf from other type of donations. Therefore, cash waqf-based Islamic microfinance needs to be sustainable. Good corporate governance is vital to ensure the sustainability. As the donors of cash waqf do not aim to make financial profit, waqf-based Islamic MFIs will be able to provide low-cost capital to the poor entrepreneurs. Furthermore, to ensure the perpetuity of the waqf, it is suggested that only revenue from the waqf property should be used for microfinance fund.

Social implications
The cash waqf-based Islamic microfinance will help the micro entrepreneurs to get low-cost capital without collateral. At the same time, public can donate any amount they afford to contribute to cash waqf.

Originality/value
The creation of a cash waqf-based Islamic MFI must observe the issues of agency conflicts and the right of stakeholders to a transparent management. This paper emphasizes the importance of good governance in managing the waqf property as a source of fund for Islamic MFIs.
Multidimensional poverty status of rural households in Nigeria
Authors: Adepoju Abimbola Oluyemisi , Akinluyi Oluwatofunmi Ibukun 
Published: June 2017

Purpose
The purpose of this paper is to examine the factors influencing the use of family planning and its link with multidimensional poverty in rural Nigeria.

Design/methodology/approach
The Alkire and Foster measure of poverty as well as the Logistic and Probit models were used to identify the factors influencing the use of family planning and its effect on the multidimensional poverty status of rural households in Nigeria.

Findings
The results indicate that 31.1 percent of rural households were poor with deprivations in health and education contributing the most to multidimensional poverty. The low use of contraception was closely linked to low level of literacy, lack of awareness of the different methods and high levels of poverty. The use of contraception reduced the level of poverty in the household.

Social implications
The intensity of poverty should be considered in the design of policies and programs. The wide and proper use of family planning is a sine qua non for any significant reduction in poverty. Potent and assertive family planning programs by government could be achieved through public-private sector partnership and assistance of international development partners.

Originality/value
This paper attempts to bridge the knowledge gap in the empirical literature on the link between multidimensional poverty and family planning. In particular`, its application to the rural context, often characterized by high rate of poverty and unmet needs for family planning employing nationally representative data is of immense value for social policy.
How Chinese executives view economic challenges and global opportunities
Authors: Davidson Steven , Ding Wei , Marshall Anthony 
Published: June 2017

Purpose
To better understand the challenges and opportunities facing China, the IBM Institute for Business Value in cooperation with Oxford Economics surveyed 1,150 executives from across China. Survey respondents represented a variety of industries and included executives from Chinese corporations, start-up enterprises, the government sector and educational institutions.

Design/methodology/approach
This report shares the executives’ vision for the Chinese economy, and proposes actions to help spark growth and positive change.

Findings
The Chinese executives surveyed see the current economic environment in China as encompassing five main challenges – immature services sector, declining domestic consumption growth, lending decisions creating over investment in some sectors, declining export growth and environmental issues impacting economic development.

Practical implications
The article identifies the six most important ways to accelerate China’s growth according to the executives:

Originality/value
Despite challenges, Chinese executives are optimistic about the country’s economic growth prospects. In fact, 93 percent of executives believe China will maintain stable to high growth of more than 5 percent over the next five years. And almost a quarter of them believe China will be able to return to its recent very high growth rates in excess of 8 percent.
Do Parent Units Benefit from Reverse Knowledge Transfer?
Authors: Nair Smitha R. , Demirbag Mehmet , Mellahi Kamel , Pillai Kishore Gopalakrishna 
Published: June 2017

AbstractEmerging market multinationals resort to knowledge acquisitions from their overseas subsidiaries to springboard and realize their global ambitions. Drawing from the knowledge‐based view and social capital perspective, this study explores the effects of organizational collaboration and tacitness on multiple dimensions of reverse knowledge transfer (RKT). Data were collected through a survey, from senior and middle level managers of parent Indian multinationals, pertaining to RKT from their overseas subsidiaries. The hypotheses are analysed using partial least squares modelling. The results demonstrate positive effects between the extent and benefits of RKT. Collaboration was found to have a positive influence on both dimensions of RKT. Tacitness also has a positive impact on the benefits from RKT. The implications of the findings and the limitations of the study are discussed along with suggestions for future research.