bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zebra diel migrations reduce encounter risk with lions over selection for safe habitats
Authors: Courbin Nicolas , Loveridge Andrew J. , Fritz Hervé , Macdonald David W. , Patin Rémi , Valeix Marion , Chamaillé-Jammes Simon 
Published: July 2017

AbstractDiel migrations (DMs) undertaken by prey to avoid visual predators during the day have been demonstrated in many taxa in aquatic ecosystems. We reveal that zebras in Hwange National Park (Zimbabwe) employ a similar anti-predator strategy. Zebras forage near waterholes during the day but move away from them at sunset. We demonstrate that this DM, occurring over a few km, dramatically reduces their night-time risk of encountering lions, which generally remain close to waterholes. By contrast, zebra changes in night-time selection for vegetation types marginally reduced their risk of encountering lions. This may arise from a trade-off between encounter risk and vulnerability across vegetation types, with zebras favouring low vulnerability once DM has reduced encounter risk. In summary, here we (1) quantify the effect of a predator-induced DM in a terrestrial system on the likelihood of encountering a predator, (2) distinguish the effects of the DM from those related to day/night changes in selection for vegetation types. We discuss how revealing how prey partition their risk between predator encounter risk and habitat-driven vulnerability is likely critical to understand the emergence of anti-predator behavioural strategies.
Integrated Human-Virus Metabolic Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses
Authors: Aller Sean , Scott Andrew E. , Sarkar-Tyson Mitali , Soyer Orkun S. 
Published: July 2017

ABSTRACTCurrent and reoccurring viral epidemic outbreaks such as those caused by Zika virus illustrate the need for rapid development of antivirals. Such development would be immensely facilitated by computational approaches that can provide experimentally testable predictions for possible antiviral strategies. A key factor that has not been considered fully to date in the study of antiviral targets is the high dependence of viruses to their host metabolism for reproduction. Here, we focus on this dependence and develop a stoichiometric, genome-scale metabolic model that integrates human macrophage cell metabolism with the biochemical demands arising from virus production. Focusing this approach to currently epidemic viruses Chikungunya, Dengue and Zika, we find that each virus causes specific alterations in the host metabolic flux towards fulfilling their individual biochemical demands as predicted by their genome and capsid structure. Subsequent analysis of this integrated model allows us to predict a set of host reactions, which when constrained can inhibit virus production. We show that this prediction recovers most of the known targets of existing antiviral drugs, while highlighting a set of hitherto unexplored reactions with either broad or virus specific antiviral potential. Thus, this computational approach allows rapid generation of experimentally testable hypotheses for novel antiviral targets within a host.SIGNIFICANCE STATEMENTA key challenge in combatting any new and emerging virus outbreaks is rapid drug development. In particular, generation of experimentally testable hypotheses through computational approaches is mostly lacking. Here, we address this gap by developing host-virus metabolic models for three viruses that cause current (or previously) epidemic viral outbreaks. We develop viral biomass functions using information from their genomes and physical structure, and incorporate these within a genome-scale metabolic model of human macrophage cells. The resulting integrated model allows us to predict host reactions, which when blocked, stop the system from attaining optimal viral production. These predictions recover currently known antiviral targets within human cells, and highlight a set of new reactions that are hitherto not explored for antiviral capacity.
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs inDrosophila melanogaster
Authors: Meers Michael P. , Adelman Karen , Duronio Robert J. , Strahl Brian D. , McKay Daniel J. , Matera A. Gregory 
Published: July 2017

AbstractBackgroundHigh-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis.ResultsThe data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for “enhancer RNAs” (eRNAs) in defining transcriptional programs that are important for animal development.ConclusionsHigh-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development.
Optimal Point Process Filtering for Birth-Death Model Estimation
Authors: Parag Kris V , Pybus Oliver G 
Published: July 2017

AbstractThe discrete space, continuous time birth-death model is a key process for describing phylogenies in the absence of coalescent approximations. Extensively used in macroevolution for analysing diversification, and in epidemiology for estimating viral dynamics, the birth-death process (BDP) is an important null model for inferring the parameters of reconstructed phylogenies. In this paper we show how optimal, point process (Snyder) filtering techniques can be used for parametric inference on BDPs. Specifically, we introduce the Bayesian Snyder filter (SF) to estimate birth and death rate parameters, given a reconstructed phylogeny. Our estimation procedure makes use of the equivalent Markov birth process description for a reconstructed birth-death phylogeny (Neeet al, 1994). We first analyse the popular constant rate BDP and show that our method gives results consistent with previous work. Among these results is an analytic solution to the special case of the Yule-Furry model. We also find an equivalence between the SF Poisson likelihood and two standard conditioned birth-death model likelihoods. We then generalise our estimation problem to BDPs with time varying rates and numerically solve the SF for two illustrative cases. Our results compare well with a recent Markov chain Monte Carlo method by Hohnaet al(2016) and we numericaly show that both methods are solving the same likelihood functions. Lastly we apply the SF to a model selection problem on empirical data. We use the Australian Agamid dataset and predict the same relative model fit as that of the original maximum likelihood technique developed and used by Rabosky (2006) for this dataset. While several capable parametric and non-parametric birth-death estimators already exist, ours is the first to take the Neeet alapproach, and directly computes the posterior distribution of the parameters. The SF makes no approximations, beyond those required for parameter space discretisation and numerical integration, and is mean square error optimal. It is deterministic, easily implementable and flexible. We think SFs present a promising alternative parametric BDP inference engine.
Structure of the deactive state of mammalian respiratory complex I
Authors: Blaza James N. , Vinothkumar Kutti R. , Hirst Judy 
Published: July 2017

AbstractComplex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, ‘active’ complex I gradually enters a pronounced resting or ‘deactive’ state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly-active preparation ofBos tauruscomplex I into the biochemically-defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. The deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding templates their reordering. Our structure both rationalizes biochemical data on the deactive state, and offers new insights into its physiological and cellular roles.
Experimental evaluation of numerical errors for multi-physics coupling methods using disparate meshes
Authors: Jüttner Matthias , Pflug Andreas , Wick Markus , Rucker Wolfgang M. 
Published: July 2017

Purpose
Multiphysics problems are solved either with monolithic or segregated approaches. For accomplishing contrary discretisation requirements of the physics, disparate meshes are essential. This paper is comparing experimental results of different interpolation methods for a segregated coupling with monolithic approaches, implemented using a global and a local nearest neighbour method. The results show the significant influence of discretisation for multiphysics simulation.

Design/methodology/approach
Applying disparate meshes to the monolithic as well as the segregated calculation of finite element problems and evaluating the related numerical error is content of the contribution. This is done by an experimental evaluation of a source and a material coupling applied to a multiphysics problem. After an introduction to the topic, the evaluated multiphysics model is described based on two bidirectional coupled problems and its finite element representation. Afterwards, the considered methods for approximating the coupling are introduced. Then, the evaluated methods are described and the experimental results are discussed. A summary concludes this work.

Findings
An experimental evaluation of the numerical errors for different multiphysics coupling methods using disparate meshes is presented based on a bidirectional electro-thermal simulation. Different methods approximating the coupling values are introduced and challenges of applying these methods are given. It is also shown, that the approximation of the coupling integrals is expensive. Arguments for applying the different methods to the monolithic and the segregated solution strategies are given and applied on the example. The significant influence of the mesh density within the coupled meshes is shown. Since the projection and the interpolation methods do influence the result, a careful decision is advised.

Originality/value
In this contribution, existing coupling methods are described, applied and compared on their application for coupling disparate meshes within a multiphysics simulation. Knowing their performance is relevant when deciding for a monolithic or a segregated calculation approach with respect to physics dependent contrary discretisation requirements. To the authors’ knowledge, it is the first time these methods are compared with a focus on an application in multiphysics simulations and experimental results are discussed.
Analysis and design of electrical machines with material uncertainties in iron and permanent magnet
Authors: Li Min , Mohammadi Mohammad Hossain , Rahman Tanvir , Lowther David 
Published: July 2017

Purpose
Manufacturing processes, such as laminations, may introduce uncertainties in the magnetic properties of materials used in electrical machines. This issue, together with magnetization errors, can cause serious deterioration in the performance of the machines. Hence, stochastic material models are required for the study of the influences of the material uncertainties. The purpose of this paper is to present a methodology to study the impact of magnetization pattern uncertainties in permanent magnet electric machines.

Design/methodology/approach
The impacts of material uncertainties on the performances of an interior permanent magnet (IPM) machine were analyzed using two different robustness metrics (worst-case analysis and statistical study). In addition, two different robust design formulations were applied to robust multi-objective machine design problems.

Findings
The computational analyses show that material uncertainties may result in deviations of the machine performances and cause nominal solutions to become non-robust.

Originality/value
In this paper, the authors present stochastic models for the quantification of uncertainties in both ferromagnetic and permanent magnet materials. A robust multi-objective evolutionary algorithm is demonstrated and successfully applied to the robust design optimization of an IPM machine considering manufacturing errors and operational condition changes.
Proximal predictors of breath alcohol level at venues primarily serving sexual minority patrons
Authors: Croff Julie M. , Currin Joseph M. , Hubach Randolph D. , Frederick Amanda F. , Jacobs Sue C. , Crethar Hugh C. 
Published: July 2017

Purpose
The purpose of this paper is to assess the proximal predictors of breath alcohol content (BrAC) at exit of a venue that primarily served sexual minority patrons. Contrary to prior research that relies on self-report of alcohol consumption, participants’ BrAC level was measured prior to entering the venue and again at exit.

Design/methodology/approach
A portal method was used to assess individuals before and after attending a sexual minority bar. Participants (n=96) were randomly selected for participation on weekends from four bars.

Findings
A multivariate path model was conducted to predict BrAC at exit from the bar. Individuals who drank before coming to the bar had a mean BrAC of 0.093 (SD=0.065) at exit from the bar and those who did not drink before attending the bar had a mean BrAC 0.030 (SD=0.050) at exit (t=5.47 (99), p<0.001). Drinking before bar attendance, BrAC at entrance, planning to drive, and drinking intentions were significant predictors of BrAC at exit from the bar. There were no significant variations in BrAC by sexual identity.

Research limitations/implications
BrAC levels at exit were mainly influenced by the BrAC levels at entrance and were not significantly changed while at the venue.

Originality/value
While previous research has demonstrated a higher incidence of problematic drinking behaviors in nonheterosexual populations, the current study suggests that bars and clubs who serve sexual minority patrons might not be adding to these problematic behaviors, and instead serve as a place of community for LGB individuals.
The effect of diagnostic and interactive uses of management control systems and managerial coaching on reflection in teams
Authors: Matsuo Makoto , Matsuo Takami 
Published: July 2017

Purpose
The purpose of this study was to investigate the effects of managerial coaching, as well as interactive and diagnostic uses of management control systems (MCS), on reflection and critical reflection, which are important for team learning.

Design/methodology/approach
Data were collected using a questionnaire survey. Hierarchical regression analyses were performed to test hypotheses using data from 235 employees in 50 teams from a Japanese automotive supplier.

Findings
The results indicated that: MCS used interactively have a positive influence on critical reflection in teams; MCS used diagnostically have no significant effect on reflection or critical reflection in teams; and managerial coaching has a positive influence on team reflection.

Research limitations/implications
These findings suggest that the interactive use of MCS should be combined with managerial coaching in promoting reflection and critical reflection within teams. Because this study used data from employees of a Japanese automotive supplier, the results may have been influenced by the Japanese management style.

Practical implications
Organizations need to implement interactive MCS at the team level, while coaching programs should be provided for managers to enhance team learning.

Originality/value
This study extends the existing literature by examining the effect of MCS at the team level, and identifying that managerial coaching plays a complementary role, supporting the interactive use of MCS in promoting reflection within a team.
Comprehensive performance measurement and management – innovativeness and performance through reflective practice
Authors: Ukko Juhani , Hildén Sanna , Saunila Minna , Tikkamäki Kati 
Published: July 2017

Purpose
The purpose of the study is to investigate how organizations can exploit performance management through reflective practice to foster innovativeness and performance.

Design/methodology/approach
A conceptual framework has been designed to link the studied concepts and to explicitly indicate current research gaps in the area. Moreover, the authors have conducted interventionist case studies to understand the interconnections between theory and practice.

Findings
This study showed that there are many possibilities with which to exploit performance management through reflective practice to foster innovativeness and performance. The study has three main implications. First, reflective practice can be learned and developed. Second, reflective practice is connected to innovativeness and performance. Third, performance management through performance measurement systems can assist in targeting the reflective practice.

Originality/value
New forms of performance measurement and management are receiving increasingly amount of attention, because the traditional forms of managing organizations do not fulfill the needs of rapidly changing environment. Prior studies maintain that a performance measurement and management supports the periodic execution of the same routines in organizations where changes are small or non-existent. In these forms, the role of reflection as an individual, collective or organizational practice is emphasized.
Impact of audit quality on the components of executive cash compensation
Authors: Fernando Guy D. , Thevaranjan Alex 
Published: July 2017

PurposeThis paper aims to study the impact of audit quality on the components of executive cash compensation. It is predicted that as audit quality improves, greater emphasis will be placed on the incentive components of cash compensation, and lower emphasis on the salary (fixed) component. Specifically, it is predicted that as audit quality enhances, greater emphasis will be placed on earnings and sales revenues in determining executive cash compensation. Using auditor specialization as a proxy for audit quality, empirical support is provided for all of our predictions.Design/methodology/approachThis paper provides empirical support with agency theoretic predictions.FindingsThis paper developed the following hypotheses:H1– in executive cash compensation, more weight is being placed on earnings-based measures as auditor specialization improves;H2– in executive cash compensation, more weight is also being placed on sales revenues as auditor specialization improves;H3– in executive cash compensation, salary levels decrease as auditor specialization improves; andH4– the impact of auditor specialization on the weight on earnings, sales and the salary levels is lower in the post-Sarbanes–Oxley Act (SOX) period compared to pre-SOX period.Research limitations/implicationsFirst, the article limits itself to cash compensation, while current executive compensation is largely made of equity. Second, the measure of audit quality used, ‘national level auditor specialization’, may not be as effective in the post-SOX era.Practical implicationsCompensation committees should pay attention to audit quality (in whatever way it may be proxied by) in determining executive compensation.Originality/valueThis is the first paper to show that audit quality not only improves the earnings response coefficient in firm valuation but also enhances the weight placed on earnings (and sales revenues) in executive compensation.
A technology-aided program for helping persons with Alzheimer’s disease perform daily activities
Authors: Lancioni Giulio , Singh Nirbhay , O’Reilly Mark , Sigafoos Jeff , D’Amico Fiora , Pinto Katia , De Vanna Floriana , Caffò Alessandro 
Published: July 2017

Purpose
Persons with mild and moderate Alzheimer’s disease experience increasing activity engagement failures, with consequent cognitive, social, and physical drawbacks. The purpose of this paper is to assess a technology-aided program to help these persons to independently start and carry out daily activities at the appropriate times.

Design/methodology/approach
The program was implemented with eight participants according to an adapted non-concurrent multiple baseline design across participants. The program provided each participant with: timely reminders about the activities to carry out, verbal instructions about the activity steps, and brief encouragements and praise.

Findings
All participants showed improvement during the program, that is, they managed to independently start the activities at the scheduled times and perform those activities with satisfactory levels of accuracy (i.e. with mean percentages of correct steps nearing or exceeding 90).

Originality/value
A technology-aided program, such as that used in this study, may help persons with mild and moderate Alzheimer disease engage in daily activities, with possible benefits for their cognitive functioning, social image, and physical condition.
Knowledge management, intellectual capital, structural holes, economic complexity and national prosperity
Authors: Roos Göran 
Published: July 2017

PurposeThe purpose of this paper is to tie together the insights from the body of research relating to economic complexity theory, structural holes, non-price based competition, and knowledge management. The insights relating to generating national prosperity are synthesised through an intellectual capital lens.Design/methodology/approachThe paper uses literature review combined with insights from an Australian project on state-based economic complexity.FindingsThe connectivist and autopoietic epistemological paradigms are found to be most aligned with the need to manage transformation between organisational and human resources that will achieve causal ambiguity and hence inimitability. This inimitability forms the basis for achieving non-price based competition and if there is a rich network of economic agents that, both individually and collectively through collaboration, have these characteristics a large share of the economy can operate on the basis of non-priced based competition. If all these agents have an export focus the economic complexity of the economy will be high, and likely increasing, which will enable both the creation and the appropriation of large amounts of value and hence result in increasing national prosperity.Research limitations/implicationsFindings are only relevant for OECD countries given the origins of the data used.Practical implicationsManagerial implications are outlined as are major implications for public policy.Originality/valueThis is the first time that these concepts are linked.