bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria
Authors: Hall James P. J. , Brockhurst Michael A. , Harrison Ellie 
Published: October 2017

In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also ‘horizontally’ between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.
Pseudo Dollo models for the evolution of binary characters along a tree
Authors: Bouckaert Remco R. , Robbeets Martine 
Published: October 2017

AbstractThe stochastic Dollo model is a model for capturing evolution of features, for example cognate data in language evolution. However, it is rather sensitive to borrowing events, coding errors, semantic shift and other anomalies, so other models, in particular the covarion model, tends to have a better fit to the data. Here, we introduce the pseudo Dollo model, a model of character evolution along a tree that can be formulated as a three-state continuous time Markov chain (CTMC) model. The initial state represent absence of a feature, then a birth event allows the feature to be present. A death event can follow so that the feature becomes absent again. However, no new birth events are allowed after a death event has taken place.We examine the model in a fully Bayesian setting, and demonstrate it can have a better fit than some of the popular alternative models on some real world datasets. Some variations on the pseudo Dollo model are introduced as well, including the multi-state pseudo Dollo model and pseudo Dollo covarion model.The model is implemented in open source software Babel, a package to BEAST [2] licensed under LGPL. A user friendly way to set up an analysis is available through BEAUti, the graphical user interface of BEAST.
Delirium, frailty and mortality: interactions in a prospective study of hospitalized older people
Authors: Dani Melanie , Owen Lucy H , Jackson Thomas A , Rockwood Kenneth , Sampson Elizabeth L , Davis Daniel 
Published: October 2017

AbstractBackgroundIt is unknown if the association between delirium and mortality is consistent for individuals across the whole range of health states. A bimodal relationship has been proposed, where delirium is particularly adverse for those with underlying frailty, but may have a smaller effect (perhaps even protective) if it is an early indicator of acute illness in fitter people. We investigated the impact of delirium on mortality in a cohort simultaneously evaluated for frailty.MethodsWe undertook an exploratory analysis of a cohort of consecutive acute medical admissions aged ≥70. Delirium on admission was ascertained by psychiatrists. A Frailty Index (FI) was derived according to a standard approach. Deaths were notified from linked national mortality statistics. Cox regression was used to estimate associations between delirium, frailty and their interactions on mortality.ResultsThe sample consisted of 710 individuals. Both delirium and frailty were independently associated with increased mortality rates (delirium: HR 2.4, 95%CI 1.8-3.3, p<0.01; frailty (per SD): HR 3.5, 95%CI 1.2-9.9, p=0.02). Estimating the effect of delirium in tertiles of FI, mortality was greatest in the lowest tertile: tertile 1 HR 3.4 (95%CI 2.1-5.6); tertile 2 HR 2.7 (95%CI 1.5-4.6); tertile 3 HR 1.9 (95% CI 1.2-3.0).ConclusionWhile delirium and frailty contribute to mortality, the overall impact of delirium on admission appears to be greater at lower levels of frailty. In contrast to the hypothesis that there is a bimodal distribution for mortality, delirium appears to be particularly adverse when precipitated in fitter individuals.
HebbPlot: An intelligent tool for learning and visualizing chromatin mark signatures
Authors: Girgis Hani Z , Velasco Alfredo , Reyes Zachary E 
Published: October 2017

AbstractHistone modifications play important roles in gene regulation, heredity, imprinting, and many human diseases. The histone code is complex, consisting of about 100 marks. Biologists need computational tools for characterizing general signatures representing the distributions of tens of chromatin marks around thousands of regions. To this end, we developed a software tool called HebbPlot, which utilizes a Hebbian neural network to learn such signatures. HebbPlot presents a signature as a digitized image, which can be easily interpreted. We validated HebbPlot in six case studies. HebbPlot is applicable to a wide array of studies, facilitating the deciphering of the histone code.
Accelerated DNA methylation aging and increased resilience in veterans: the biological cost for soldiering on
Authors: Mehta Divya , Bruenig Dagmar , Lawford Bruce , Harvey Wendy , Carrillo-Roa Tania , Morris Charles P , Jovanovic Tanja , Young Ross McD , Binder Elisabeth B , Voisey Joanne 
Published: October 2017

AbstractAccelerated epigenetic aging, the difference between the DNA methylation-predicted age (DNAm age) and the chronological age, is associated with a myriad of diseases. This study investigates the relationship between epigenetic aging and risk and protective factors of PTSD. Genome-wide DNA methylation analysis was performed in 211 individuals including combat-exposed Australian veterans (discovery cohort, n = 96 males) and trauma-exposed civilian males from the Grady Trauma Project (replication cohort, n = 115 males). Primary measures included the Clinician Administered PTSD Scale for DSM-5 and the Connor-Davidson Resilience Scale (CDRISC). DNAm age prediction was performed using the validated epigenetic clock calculator. Veterans with PTSD had increased PTSD symptom severity (P-value = 3.75 x 10-34) and lower CDRISC scores (P-value = 7.5 x 10-8) than veterans without PTSD. DNAm age was significantly correlated with the chronological age (P-value = 3.3 x 10-6), but DNAm age acceleration was not different between the PTSD and non-PTSD groups (P-value = 0.24). Evaluating potential protective factors, we found that DNAm age acceleration was significantly associated with CDRISC resilience scores in veterans with PTSD, these results remained significant after multiple testing correction (P-value = 0.023; r = 0.32). This finding was also replicated in an independent trauma-exposed civilian cohort (P-value = 0.02; r = 0.23). Post-hoc factor analyses revealed that this association was driven by “self-efficacy” items within the CDRISC (P-value = 0.015). These results suggest that among individuals already suffering from PTSD, some aspects of increased resilience might come at a biological cost.
Geometry of antiparallel microtubule bundles regulates relative sliding and stalling by PRC1 and Kif4A
Authors: Wijeratne Sithara S. , Subramanian Radhika 
Published: October 2017

AbstractMotor and non-motor crosslinking proteins play critical roles in determining the size and stability of microtubule-based architectures. Currently, we have a limited understanding of how geometrical properties of microtubule arrays, in turn, regulate the output of crosslinking proteins. Here we investigate this problem in the context of microtubule sliding by two interacting proteins: the non-motor crosslinker PRC1 and the kinesin Kif4A. The collective activity of PRC1 and Kif4A also results in their accumulation at microtubule plus-ends (‘end-tag’). Sliding stalls when the end-tags on antiparallel microtubules collide, forming a stable overlap. Interestingly, we find that structural properties of the initial array regulate PRC1-Kif4A mediated microtubule organization. First, sliding velocity scales with initial microtubule-overlap length. Second, the width of the final overlap scales with microtubule lengths. Our analyses reveal how micron-scale geometrical features of antiparallel microtubules can regulate the activity of nanometersized proteins to define the structure and mechanics of microtubule-based architectures.
ascend: R package for analysis of single cell RNA-seq data
Authors: Senabouth Anne , Lukowski Samuel W , Alquicira Hernandez Jose , Andersen Stacey , Mei Xin , Nguyen Quan H , Powell Joseph E 
Published: October 2017

AbstractSummaryascend is an R package comprised of fast, streamlined analysis functions optimized to address the statistical challenges of single cell RNA-seq. The package incorporates novel and established methods to provide a flexible framework to perform filtering, quality control, normalization, dimension reduction, clustering, differential expression and a wide-range of plotting. ascend is designed to work with scRNA-seq data generated by any high-throughput platform, and includes functions to convert data objects between software packages.AvailabilityThe R package and associated vignettes are freely available at https://github.com/IMB-Computational-Genomics-Lab/ascend.Contactjoseph.powell@uq.edu.auSupplementary informationAn example dataset is available at ArrayExpress, accession number E-MTAB-6108
A reliable and unbiased human protein network with the disparity filter
Authors: Alanis-Lobato Gregorio , Andrade-Navarro Miguel A. 
Published: October 2017

AbstractThe living cell operates thanks to an intricate network of protein interactions. Proteins activate, transport, degrade, stabilise and participate in the production of other proteins. As a result, a reliable and systematically generated protein wiring diagram is crucial for a deeper understanding of cellular functions. Unfortunately, current human protein networks are noisy and incomplete. Also, they suffer from both study and technical biases: heavily studied proteins (e.g. those of pharmaceutical interest) are known to be involved in more interactions than proteins described in only a few publications. Here, we use the experimental evidence supporting the interaction between proteins, in conjunction with the so-called disparity filter, to construct a reliable and unbiased proteome-scale human interactome. The application of a global filter, i.e. only considering interactions with multiple pieces of evidence, would result in an excessively pruned network. In contrast, the disparity filter preserves interactions supported by a statistically significant number of studies and does not overlook small-scale protein associations. The resulting disparity-filtered protein network covers 67% of the human proteome and retains most of the network’s weight and connectivity properties.
Lineage and stage-specific expressedCYCD7;1coordinates the single symmetric division that creates stomatal guard cells
Authors: Weimer Annika K. , Matos Juliana L. , Dewitte Walter , Murray James A.H. , Bergmann Dominique C. 
Published: October 2017

AbstractPlants, with cells fixed in place by rigid walls, often utilize spatial and temporally distinct cell division programs to organize and maintain organs. This leads to the question of how developmental regulators interact with the cell cycle machinery to link cell division events with particular developmental trajectories. InArabidopsisleaves, the development of stomata, two-celled epidermal valves that mediate plant-atmosphere gas exchange, relies on a series of oriented stem-cell-like asymmetric divisions followed by a single symmetric division. The stomatal lineage is embedded in a tissue whose cells transition from proliferation to post-mitotic differentiation earlier, necessitating stomatal lineage-specific factors to prolong competence to divide. We show that the D-type cyclin, CYCD7;1 is specifically expressed just prior to the symmetric guard-cell forming division, and that it is limiting for this division. Further, we find that CYCD7;1 is capable of promoting divisions in multiple contexts, likely through RBR-dependent promotion of the G1/S transition, but that CYCD7;1 is regulated at the transcriptional level by cell-type specific transcription factors that confine its expression to the appropriate developmental window.
Demographic challenges for the future business leader: evidence from a Greek survey
Authors: Galanaki Eleanna , Papalexandris Nancy 
Published: October 2017

PurposeThe purpose of this paper is to identify the challenges posed to business leaders from major global demographic changes expected in the workforce composition, such as higher participation of women and more active involvement of elder and more experienced people in the future workforce.Design/methodology/approachThe authors ran a survey among 733 middle managers, focusing on their ideal leadership behavior. The Global Leadership and Organizational Behavior project methodology was applied for data collection and analyses.FindingsSeveral significant differences were established in leadership ideals according to gender, age and managerial experience. The differences based on gender had higher practical significance than the ones based on age and experience of the respondents.Research limitations/implicationsThe paper adds up to the pertinent in the implicit leadership approach dialogue over the existence of stable, global and unchanging aspects of leadership.Practical implicationsLeader behaviors traditionally deemed as positive, such as the participative and charismatic/value-based leadership, are shown to be critical for the future business leader. Leadership development in organizations should focus on these two aspects.Social implicationsLeaders who can meet the expectations of diverse groups of people will be able to achieve inclusion of least privileged groups at the business level, leading to higher inclusion at the social, aggregate level.Originality/valueThe paper is the first to explore how documented demographic trends could affect the way that leadership will evolve in the near future.
Enterprise social media impact on human resource practices
Authors: Offong Godwin Oscar , Costello Joyce 
Published: October 2017

Purpose
The purpose of this paper is to investigate how individual attitudes toward using enterprise social media (ESM) impact trust, explicit and tacit knowledge sharing as well as work performance in emerging economies.

Design/methodology/approach
The authors use data from a survey of 293 employed individuals in Lagos, Nigeria, who work at organizations that have ESM systems.

Findings
The authors find that ESM usage is significantly associated with trust. However, ESM usage does not impact explicit or tacit knowledge transfer.

Practical implications
This paper provides empirical evidence that individuals who perceive high levels of performance expectancy will engage in ESM usage which in turn increases trust amongst colleagues. Human resource managers can argue that by adopting ESM, they can facilitate improved trust and collaboration through online engagement amongst employees. This is important for multi-national organizations wanting to expand into emerging economies where the organization and local workforce need to foster trust in knowledge sharing.

Originality/value
There has been little evidence regarding HRM use of ESM in emerging economies. By understanding individual attitudes toward ESM and how the use impacts knowledge sharing, the academic discussions concerning use of technology to enhance knowledge sharing can continue to evolve.
Pay is not everything
Authors: Peluso Alessandro M. , Innocenti Laura , Pilati Massimo 
Published: October 2017

PurposeMonetary and non-monetary rewards have rarely been considered together under the HRM perspective. Despite the vast literature on HRM, there is still a lack of studies that explicitly discuss the link between the adoption of a total reward system (TRS) and employee-related outcomes. The purpose of this paper is to investigate this important issue in order to provide insights that can help organisations devise compensation strategies that are effective in sustaining employees’ positive attitudes and behaviours.Design/methodology/approachUsing a survey of 1,092 employees, the authors examine the effect of the overall TRS on three outcome variables (i.e. job satisfaction, affective commitment, and innovative behaviour at work). Furthermore, the authors examine the impact that each component of the TRS (i.e. base pay, training and development opportunities, and positive work environment) has on the dependent variables.FindingsThe results confirm that the adoption of a TRS exerts a positive influence on the aforementioned outcomes. However, interesting differences emerged when looking at the individual components in the overall sample.Originality/valueThis paper provides original insights into the complex relationship between TRS and the employee-related outcomes of job satisfaction, affective commitment, and innovative behaviour at work.
Perceptions of adaptation, resilience and climate knowledge in the Pacific
Authors: Walshe Rory A. , Chang Seng Denis , Bumpus Adam , Auffray Joelle 
Published: October 2017

PurposeWhile the South Pacific is often cited as highly vulnerable to the impacts of climate change, there is comparatively little known about how different groups perceive climate change. Understanding the gaps and differences between risk and perceived risk is a prerequisite to designing effective and sustainable adaptation strategies.Design/methodology/approachThis research examined three key groups in Samoa, Fiji and Vanuatu: secondary school teachers, media personnel, and rural subsistence livelihood-based communities that live near or in conservation areas. This study deployed a dual methodology of participatory focus groups, paired with a national mobile phone based survey to gauge perceptions of climate change. This was the first time mobile technology had been used to gather perceptual data regarding the environment in the South Pacific.FindingsThe research findings highlighted a number of important differences and similarities in ways that these groups perceive climate change issues, solutions, personal vulnerability and comprehension of science among other factors.Practical implicationsThese differences and similarities are neglected in large-scale top-down climate change adaptation strategies and have key implications for the design of disaster risk reduction and climate change adaptation and therefore sustainable development in the region.Originality/valueThe research was innovative in terms of its methods, as well as its distillation of the perceptions of climate change from teachers, media and rural communities.
Data envelopment analysis of efficiency of real estate investment trusts in Singapore
Authors: Ahmed Aminath Amany , Mohamad Azhar 
Published: October 2017

PurposeIn this study, the authors use data envelopment analysis to assess the technical efficiency and performance of real estate investment trusts (REITs) in Singapore, for the years 2009 through 2013.Design/methodology/approachThe authors apply the Malmquist Productivity Index to express the productivity change of the REITs over time.FindingsThe authors find that while most REITs have experienced efficiency improvements, there has been little productivity growth at the frontier during the study period.Originality/valueThe finding indicates that it is possible to improve the performance of the REITs by further improving technological efficiency because technological regress has been the main reason for the poor productivity growth of the REITs in Singapore.
Promoting brand engagement behaviors and loyalty through perceived service value and innovativeness
Authors: Leckie Civilai , Nyadzayo Munyaradzi W. , Johnson Lester W. 
Published: October 2017

Purpose
The purpose of this study is to investigate the role of perceived value and innovativeness (service concept newness and relative advantage) in promoting customer brand engagement behaviors (CBEBs) and brand loyalty.

Design/methodology/approach
The conceptual model was empirically tested using nationwide survey data from 430 customers of Uber in Australia. The data were analyzed using structural equation modeling.

Findings
The results of this study show that collecting brand information is positively influenced by perceived value, service concept newness and relative advantage. Participating in brand marketing activities is positively influenced by service concept newness and relative advantage. Interacting with others is positively influenced by perceived value and service concept newness. Subsequently, brand loyalty is positively influenced by participating in brand marketing activities and interacting with others. The direct impacts of perceived value and relative advantage on brand loyalty are also established.

Research limitations/implications
This study only collected data from Uber customers. Another limitation of this study is the use of cross-sectional data.

Practical implications
To promote brand loyalty, service innovation needs to have both the right characteristics (i.e. perceived value, service concept newness and relative advantage) and practices that foster customer brand engagement behaviors.

Originality/value
Although service-dominant logic (SDL) is a theoretical lens used by research in the areas of service innovation and customer engagement, empirical studies that integrate the two areas remain limited. The findings of this study suggest a new mechanism in which service innovation can increase loyalty through increased CBEBs.
Influence of empathy on hotel guests’ emotional service experience
Authors: Umasuthan Hamsanandini , Park Oun-Joung , Ryu Jong-Hyun 
Published: October 2017

PurposeThe purpose of this study is to assess the comparative influence of two empathy dimensions (cognitive and emotional attributes) on emotional service experience and behavioral intention among business and leisure hotel guests. Studies relevant to empathy dimensions are relatively scarce in tourism and hospitality.Design/methodology/approachThe current study reviewed the concepts of empathy, and empirically compared perceptions of empathy attributes between the two groups. The survey was intended to examine how well the hotel employees emotionally handle hotel guests’ incidents or inquiries related to any discomforts through personalized attention. The data were collected from 330 hotel guests who had actually complained about service failures while staying at the hotel during the record-breaking summer of 2013 in terms of number of visitors to Jeju. An active empathetic listening (AEL) tool has been taken to measure the hotel guest’s cognitive views and behavioral intentions, as well as emotional empathy measures under the empathic concern and emotional contagion.FindingsThe results revealed that empathetic dimensions strongly influenced the service experiences of hotel guests. While the emotional service experience of business guests was almost completely determined by the cognitive empathy, the emotional service experience of the leisure guests was mainly governed by the emotional empathy.Practical implicationsThese outcomes suggest that the empathetic services through a “purpose of visit”-oriented manner might enhance the guest’s overall emotion positively.Originality/valueAccording to the prior literatures and empirical findings in hospitality and tourism, empathy can be seen as subscale in SERVQUAL instrument. This paper focus on insights of empathy dimensions, and it was revealed that the interaction of both the cognitive and emotional dimensions of empathy conjointly determines the overall emotional service experience and intention of hotel guests.