bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magic pools: parallel assessment of transposon delivery vectors in bacteria
Authors: Liu Hualan , Price Morgan N. , Waters Robert Jordan , Ray Jayashree , Carlson Hans K. , Lamson Jacob S. , Chakraborty Romy , Arkin Adam P. , Deutschbauer Adam M. 
Published: July 2017

AbstractTransposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a parts-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term “magic pools”. Within a magic pool, each transposon vector has a different combination of promoters and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. To identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use the best vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylumBacteroidetes.
The pomegranate (Punica granatumL.) genome provides insights into fruit quality and ovule developmental biology
Authors: Yuan Zhaohe , Fang Yanming , Zhang Taikui , Fei Zhangjun , Han Fengming , Liu Cuiyu , Liu Min , Xiao Wei , Zhang Wenjing , Zhang Mengwei , Ju Youhui , Xu Huili , Dai He , Liu Yujun , Chen Yanhui , Wang Lili , Zhou Jianqing , Guan Dian , Yan Ming , Xia Yanhua , Huang Xianbin , Liu Dongyuan , Wei Hongmin , Zheng Hongkun 
Published: July 2017

AbstractPomegranate(Punica granatumL.) with an uncertain taxonomic status has an ancient cultivation history, and has become an emerging fruit due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the absence of genomic resources has restricted further elucidating genetics and evolution of these interesting traits. Here we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336 Mb genome, consists of 2,177 scaffolds with an N50 size of 1.7 Mb, and contains 30,903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate andEucalyptus grandisshares the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the color formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence represents the first reference in Lythraceae, providing an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.
Reward learning over weeks versus minutes increases the neural representation of value in the human brain
Authors: Wimmer G. Elliott , Li Jamie K. , Gorgolewski Krzysztof J. , Poldrack Russell A. 
Published: July 2017

AbstractOver the past few decades, neuroscience research has illuminated the neural mechanisms supporting learning from reward feedback. Learning paradigms are increasingly being extended to study mood and psychiatric disorders as well as addiction. However, one potentially critical characteristic that this research ignores is the effect of time on learning: human feedback learning paradigms are usually conducted in a single rapidly paced session, while learning experiences in ecologically relevant circumstances and in animal research are almost always separated by longer periods of time. In our experiments, we examined reward learning in short condensed sessions distributed across weeks vs. learning completed in a single “massed” session in male and female participants. As expected, we found that after equal amounts of training, accuracy was matched between the spaced and massed conditions. However, in a 3-week follow-up, we found that participants exhibited significantly greater memory for the value of spaced-trained stimuli. Supporting a role for short-term memory in massed learning, we found a significant positive correlation between initial learning and working memory capacity. Neurally, we found that patterns of activity in the medial temporal lobe and prefrontal cortex showed stronger discrimination of spaced-vs. massed-trained reward values. Further, patterns in the striatum discriminated between spaced-and massed-trained stimuli overall. Our results indicate that single-session learning tasks engage partially distinct learning mechanisms from spaced sessions of training. Our studies begin to address a large gap in our knowledge of human learning from reinforcement, with potential implications for our understanding of mood disorders and addiction.Significance statementHumans and animals learn to associate predictive value with stimuli and actions, and these values then guide future behavior. Such reinforcement-based learning often happens over long time periods, in contrast to most studies of reward-based learning in humans. In experiments that tested the effect of spacing on learning, we found that associations learned in a single massed session were correlated with short-term memory and significantly decayed over time, while associations learned in short massed sessions over weeks were well-maintained. Additionally, patterns of activity in the medial temporal lobe and prefrontal cortex discriminated the values of stimuli learned over weeks but not minutes. These results highlight the importance of studying learning over time, with potential applications to drug addiction and psychiatry.
Widespread intronic polyadenylation diversifies immune cell transcriptomes
Authors: Singh Irtisha , Lee Shih-Han , Samur Mehmet K , Tai Yu-Tzu , Samur Mehmet K , Tai Yu-Tzu , Munshi Nikhil C , Mayr Christine , Leslie Christina S. 
Published: July 2017

AbstractAlternative cleavage and polyadenylation (ApA) can generate mRNA isoforms with differences in 3’UTR length without changing the coding region (CDR). However, ApA can also recognize intronic polyadenylation (IpA) signals to generate transcripts that lose part or all of the CDR. We analyzed 46 3’-seq and RNA-seq profiles from normal human tissues, primary immune cells, and multiple myeloma (MM) samples and created an atlas of 4,927 high confidence IpA events. Up to 16% of expressed genes in immune cells generate IpA isoforms, a majority of which are differentially used during B cell development or in different cellular environments, while MM cells display a striking loss of IpA isoforms expressed in plasma cells, their cell type of origin. IpA events can lead to truncated proteins lacking C-terminal functional domains. This can mimic ectodomain shedding through loss of transmembrane domains or alter the binding specificity of proteins with DNA-binding or protein-protein interaction domains, thus contributing to diversification of the transcriptome.
Column subset selection for single-cell RNA-Seq clustering
Authors: McCurdy Shannon R. , Ntranos Vasilis , Pachter Lior 
Published: July 2017

SUMMARYThe first step in the analysis of single-cell RNA sequencing (scRNA-Seq) is dimensionality reduction, which reduces noise and simplifies data visualization. However, techniques such as principal components analysis (PCA) fail to preserve non-negativity and sparsity structures present in the original matrices, and the coordinates of projected cells are not easily interpretable. Commonly used thresholding methods avoid those pitfalls, but ignore collinearity and covariance in the original matrix. We show that a deterministic column subset selection (DCSS) method possesses many of the favorable properties of PCA and common thresholding methods, while avoiding pitfalls from both. We derive new spectral bounds for DCSS. We apply DCSS to two measures of gene expression from two scRNA-Seq experiments with different clustering workflows, and compare to three thresholding methods. In each case study, the clusters based on the small subset of the complete gene expression profile selected by DCSS are similar to clusters produced from the full set. The resulting clusters are informative for cell type.
Small subsets of highly connected taxa predict compositional change in microbial communities
Authors: Herren Cristina M. , McMahon Katherine D. 
Published: July 2017

AbstractFor decades, ecological theory has predicted that the complexity of communities should be related to their stability. However, this prediction has rarely been tested empirically, because of both the difficulty of finding suitable systems where the question is tractable and the trouble of defining “stability” in real systems. Microbial communities provide the opportunity to investigate a related question: how does community connectivity relate to the rate of compositional turnover? We used a newly developed metric called community “cohesion” to test how microbial community connectivity relates to Bray-Curtis dissimilarity through time. In three long-term datasets, we found that stronger connectivity corresponded to lower rates of compositional turnover. Using two case studies of disturbed and reference communities, we found that the predictive power of community connectivity was diminished by external disturbance. Finally, we tested whether the highly connected taxa were disproportionately important in explaining compositional turnover. We found that subsets of highly connected “keystone” taxa, generally comprising 1-5% of community richness, explained community turnover better than using all taxa. Our results suggest that stronger biotic interactions within microbial community dynamics are stabilizing to community composition, and that highly connected taxa are good indicators of pending community shifts.
Guest editorial: leadership and organizational development in Africa
Authors: Sanda Mohammed-Aminu 
Published: July 2017

Purpose
The purpose of this paper is to preview contributions on leadership and organizational development in the African context, covered in this special issue of the African Journal of Business and Economic Studies.

Design/methodology/approach
Summaries of the underlying theoretical/conceptual and/or empirical frameworks, as well as key findings for each paper, were outlined in order to provide insights of each paper’s thematic contribution.

Findings
Paper 1 identified four basic modes of understanding organizational culture which provides a unique and expanded view on pursuing research in the field. Paper 2 found that managers use authentic and transactional leadership skills to cultivate and nurture the creativities of employees toward increased performances. Paper 3 found the interaction between authentic leaders and followers as inducing high levels of moral and ethical behaviors in followers. Paper 4 found that employee engagement and affective commitment minimize employees’ attrition, irrespective of leadership styles. Paper 5 found that, managers can enhance organizational development by creating an atmosphere for innovation development, and being involved in its implementation. Paper 6 found that leaders who are emotionally intelligent positively evoke subordinates’ citizenship behaviors. Paper 7 identified three distinct and interrelated archetypes of managerial role preferences (i.e. change agents, affective leaders, and result-oriented realists) needed by leaders in their administrative practices.

Originality/value
The papers provide new insights, in terms of thematic learning and knowledge, which add to the understanding of the contemporary Afrocentric perspective on leadership and organizational development, especially, the dialogue of management activities that promote the relational, critical and constructionist perspectives on leadership and organizational development.
Administrative leadership
Authors: Mitiku Adare Assefa , Hondeghem Annie , Troupin Steve 
Published: July 2017

Purpose
The purpose of this paper is to examine the leadership roles the Ethiopian civil service managers preferably embody in their setting. As such, contextually preferred roles were identified and briefly contrasted with the leadership literature. It also outlined the directions for the future research agenda.

Design/methodology/approach
Q-methodology, an approach reasonably like “grounded-theory” was used. It is suited to embrace life as lived by the actors themselves. In this specific case, Q-methodology allows the managers to conceptualize their definitions or preferences of leadership roles. The data were obtained from 51 managers working in the federal civil service organizations covering a broad range of public policy and service fields.

Findings
Based on the Q-sorts of 51 managers, the authors found three distinct yet interrelated archetypes of role preferences, which the authors labeled as the change agents, affective leaders and result-oriented realists. The study, however, demonstrates that although the ostensible echoes of each of these perspectives were professed, there were overlooked functions that are needed to be performed for full practice of each.

Practical implications
Understanding the contextually preferred leadership roles, if considered in designing the management training and development programs, could prove productive. It also informs the staff recruitment and promotion activities of the civil service organizations.

Originality/value
Conceptualizations of public leadership roles are abound in the literature. As they mostly emerged in a Western context, their applicability to other settings is questionable. Studying the subject in the context of Ethiopia, this paper contributes to the growing body of African literature on administrative leadership and informs the practice as well as the scholarship in this area.
Determinants of employee turnover intention
Authors: Kim Soojin , Tam Lisa , Kim Jeong-Nam , Rhee Yunna 
Published: July 2017

PurposeThe purpose of this paper is to identify associations amongst organizational justice, supervisory justice, authoritarian culture, organization-employee relationship quality and employee turnover intention.Design/methodology/approachAn online survey (n=300) was conducted in South Korea.FindingsOrganizational justice and supervisory justice are positively associated with organization-employee relationship quality, while authoritarian organizational culture is negatively associated with it. In addition, there is a positive association between authoritarian organizational culture and turnover intention. Organizational justice and organization-employee relationship quality are negatively associated with turnover intention.Originality/valueThis study contributes to the lack of research on organization-employee relationship quality as a predictor of employee turnover intention and a mediator between authoritarian organizational culture and turnover intention.
Examining the use of sales force management practices
Authors: Reid David A. , Plank Richard E. , Peterson Robert M. , Rich Gregory A. 
Published: July 2017

Purpose
The purpose of this paper is to understand what sales management practices (SMPs) are being used by managers in the current market place, changes over time, insights that can be gained and future research needs.

Design/methodology/approach
Data for this paper were collected via a cross-sectional internet-based survey using a sampling frame provided by a professional sales publication. ANOVA was used to analyze 159 sales manager respondents.

Findings
Empirical results indicate that several differences are evident across the 68 SMPs items gathered, especially in terms of the size of the sales force and establish some data on using technology in sales management. However, in spite of significant changes in the sales environment, many SMPs have had limited change.

Research limitations/implications
The limitations of this paper include a sample frame drawn from a single source and via the internet and, thus, may have excluded some possible respondents from participation and somewhat limit generalizability.

Practical implications
The results of this paper raise a number of important issues for sales managers to consider. First, which SMPs should they be using? Managers need to give serious thought as to which practices they choose to use. Second, why are so many of them not making more extensive use of sales force technology? Third, is it wise for sales managers to be relying on executive opinion as their most extensively used forecasting method or should they be emphasizing another approach? A fourth issue is the continued heavy emphasis on generating sales volume as opposed to profits.

Originality/value
The data provide a rare and updated understanding of the use of SMPs by sales managers.
Cultural variations and ethical business decision making: a study of individualistic and collective cultures
Authors: Oumlil A. Ben , Balloun Joseph L. 
Published: July 2017

PurposeThis study aims to examine the ethical beliefs and moral philosophical typologies, the relative effect of religiosity on personal ethical beliefs and behavior of the collectivist and individualistic business executives.Design/methodology/approachThis research assesses the relative impact of significant cultural factors on the business ethical decision-making process in a Western and individualistic cultural context (the USA) in comparison to a non-Western and collective cultural context (Morocco). To understand how cultural variations influence business ethical practices, this study adopts Hofstede’s cultural framework for comparison of business executives’ ethical decisions within a cross-cultural context. Hypotheses are tested on survey data on 172 business executives.FindingsResults show that most collective business executives are “Situationists”. The findings reveal a strong, positive relationship between business managers’ religiosity and their idealism degrees. This study also reveals mixed findings in examining the correlation of religiosity with various components of ethical intentions.Research limitations/implicationsThe link between religiosity and ethical intentions needs to be viewed with caution. This calls for expanding the scope of this study into other cultures and religions.Practical implicationsDifferences of the findings in ethical typologies between collective and individualistic business executives may lead to different negotiation styles on ethical business decisions and issues. Managers from a collective culture are not as likely to exhibit much change in their initial ethical orientation(s). There is a strong positive relationship between a business manager’s religiosity and his/her degree of idealism. Thus, the more religious business managers are, the more Absolutist they are when making ethical and moral judgments.Originality/valueThis research works to fill the gap by examining the impact of culture on the business/marketing ethical decision-making processes within the contexts of a Western cultural and developed nation and a non-Western cultural, and developing/Mediterranean/North African nation. The findings clarify the influence of culture on business ethical decisions. Such an understanding can assist corporate managers in developing and successfully implementing business ethical codes that lead to enhanced moral conduct in their organizations.
Evaluation effects of bundle size and price presentation
Authors: Engeset Marit Gundersen , Opstad Birger 
Published: July 2017

Purpose
Marketers often combine products in bundles to increase demand. Research has shown that itemizing the prices of the individual products in the bundle raises evaluations in some situations. The purpose of this paper is to investigate how bundle size influences the effect itemizing prices have on bundle evaluation.

Design/methodology/approach
The authors conduct two experiments. In the first, they test the effects of price presentation formats (itemized vs consolidated) and bundle size on consumers’ evaluations of product bundles. In the second experiment, they test the proposed mechanism that itemizing the price leads to a more realistic price expectation which in turn enhances evaluation. The authors also test whether this effect is stronger for larger bundles.

Findings
In Study 1, the authors find that large, but not small, bundles are evaluated more positive when presented with itemized prices. In Study 2, mediated moderation analysis supports the prediction that price expectation mediates the effect of the price presentation × bundle size interaction on bundle evaluations. The findings show that itemizing prices results in more realistic price expectations and that this effect is stronger for larger bundles. In turn, more realistic price expectations lead to higher evaluation.

Research limitations/implications
The implication of this research is that by directing attention to individual items in the bundle, consumers are better able to assess bundle benefits. More research is needed to investigate other potential explanations for the findings in Study 1. Further research should also investigate whether the findings reported here holds in other settings, with other products and with other types and size of bundles.

Practical implications
Managers are recommended to itemize the prices of product bundles, particularly when bundles are large.

Originality/value
This paper extends our knowledge about the effect itemizing the prices of individual items in a bundle has on consumer evaluation by demonstrating the moderating effect of bundle size and showing that more realistic price expectation explains these effects.
Underdog effects: the role of consumption domain and retail crowding
Authors: Shirai Miyuri 
Published: July 2017

Purpose
When communicating with consumers, firms frequently highlight their underdog status to evoke a favorable attitude. Previous research has confirmed consumer preference for underdogs over top dogs in various domains. However, very little research has been conducted on the business types and decision contexts in which underdog effects produce the most impact. This paper aims to investigate some of the unexplored boundary conditions of underdog effects and addresses two issues: consumption domain and retail crowding.

Design/methodology/approach
Two experiments with a 2 (biography: underdog or top dog) × 2 (consumption domain: hedonic or utilitarian) × 2 (retail crowding: adequately crowded or uncrowded) factorial between-subjects design were conducted to test hypotheses. The two experiments differ in the consumption domains and the approaches used to depict crowding conditions. Furthermore, the first experiment targeted college students and the second experiment targeted online consumer panels across various age groups.

Findings
Underdog effects were more easily evoked when the consumption domain was more hedonic than utilitarian. In addition, retail crowding was an informational cue for judging acceptance of underdog businesses and enhanced the evaluation when the retail environment was adequately crowded rather than uncrowded. This role of crowding was also evident for top-dog businesses when consumers perceived high risk in the businesses.

Originality/value
This is the first study to distinguish between hedonic and utilitarian consumption domains with underdog effects and to demonstrate a positive effect of crowding as an informational cue, indicating acceptance by other consumers.