bluuebunny/crossref_metadata_2025_split huggingface dataset:
gmos: Rapid detection of genome mosaicism over short evolutionary distances
Authors: Domazet-Lošo Mirjana , Domazet-Lošo Tomislav 
Published: May 2016

AbstractProkaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenicEnterococcus faeciumstrain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).
We live in a VUCA World: the importance of responsible leadership
Authors: Sarkar Anita 
Published: May 2016

Purpose
This paper aims to describe the role of responsible leadership in a VUCA (volatile, uncertain, complex and ambiguous) world.

Design/methodology/approach
This paper explains how responsible leadership is aligned with the critical success factors necessary to thrive in a VUCA world.

Findings
Critical success factors in the VUCA world are: sound business principles, a firm’s agility to respond speedily, strong collaborative networks, innovation and ethical practices. These are aligned with a responsible leadership style, which is a combination of transformational, servant and authentic leadership.

Socialimplications
This paper argues that responsible leadership embraces the broader societal issues and concerns based on ethical judgment.

Originality/value
This paper provides insights on how responsible leaders can meet the requirements of VUCA world.
Motivating language theory: antecedent variables – critical to both the success of leaders and organizations
Authors: Holmes William T. 
Published: May 2016

Purpose
The purpose of this conceptual paper is twofold, i.e. first, to elevate an assumption of Motivating Language Theory (MLT) – walk and talk congruence – to the level of antecedent variable serving as a prerequisite to the implementation of Motivating Language (ML) and second, to explore the components of walk and talk congruence (Behavioral Integrity and Credibility) to understand how they are vital in the establishment of trust at the organizational level which is the key lever for ML to be strategically implemented.

Design/methodology/approach
The approach is cross-disciplinary, as it utilized MLT from the field of business; applied in the field of education with research from educational researchers; and for the purpose of utilization by organizations, leaders, and scholars from all fields.

Findings
The findings are leadership communication matters and is how leadership gets done, ML makes a difference to employees and organizations, trust is a critical factor in organizational success, Credibility is all that stands between a leader’s believability or not, and Behavioral Intergrity is the key determiner in walk and talk alignment.

Researchlimitations/implications
The implications for researchers are new research opportunities in the ML field.

Practicalimplications
The implications for practitioners are clear in terms of how to maximize leader effectiveness and organizational trust/citizenship, increase employee and organizational outcomes and drive leadership development.

Originality/value
The value of this paper is to both the practitioner and scholar in terms of application and deepening of the field.
A comparative study of fractional step method in its quasi-implicit, semi-implicit and fully-explicit forms for incompressible flows
Authors: Bevan Rhodri LT , Boileau Etienne , van Loon Raoul , Lewis R.W. , Nithiarasu P 
Published: May 2016

Purpose
– The purpose of this paper is to describe and analyse a class of finite element fractional step methods for solving the incompressible Navier-Stokes equations. The objective is not to reproduce the extensive contributions on the subject, but to report on long-term experience with and provide a unified overview of a particular approach: the characteristic-based split method. Three procedures, the semi-implicit, quasi-implicit and fully explicit, are studied and compared.

Design/methodology/approach
– This work provides a thorough assessment of the accuracy and efficiency of these schemes, both for a first and second order pressure split.

Findings
– In transient problems, the quasi-implicit form significantly outperforms the fully explicit approach. The second order (pressure) fractional step method displays significant convergence and accuracy benefits when the quasi-implicit projection method is employed. The fully explicit method, utilising artificial compressibility and a pseudo time stepping procedure, requires no second order fractional split to achieve second order or higher accuracy. While the fully explicit form is efficient for steady state problems, due to its ability to handle local time stepping, the quasi-implicit is the best choice for transient flow calculations with time independent boundary conditions. The semi-implicit form, with its stability restrictions, is the least favoured of all the three forms for incompressible flow calculations.

Originality/value
– A comprehensive comparison between three versions of the CBS method is provided for the first time.
The effect of an embedded solid block on the onset of convection in a porous cavity
Authors: Rees D.  Andrew S. , Nield Donald A. 
Published: May 2016

Purpose
– The purpose of this paper is to determine how the presence of an embedded, centrally placed, solid but heat-conducting block affects the onset and development of Darcy-Bénard convection.

Design/methodology/approach
– Steady solutions are obtained using finite difference methods with SOR as the smoother. A detailed presentation is given of how the interface conditions are modelled, and how a continuity of pressure argument is used to determine the value of the streamfunction on the solid block.

Findings
– The presence of the block affects strongly both the onset of convection and the nonlinear properties such as the mean Nusselt number and the strength of the fluid circulation. The smallest possible critical Darcy-Rayleigh is found to be 22.0152, which is smaller than 4π2, the value when the block is absent.

Research limitations/implications
– The Darcy-Rayleigh number is restricted to values at or below 200, which is five times the critical value without a solid block, but the size and conductivity of the block vary between all admissible values.

Originality/value
– This is the first investigation of the effect of internal obstacles on Darcy-Bénard convection.
On the accuracy of some explicit and implicit methods for the inviscid GRLW equation subject to initial Gaussian conditions
Authors: Ramos J I 
Published: May 2016

Purpose
– The purpose of this paper is to both determine the effects of the nonlinearity on the wave dynamics and assess the temporal and spatial accuracy of five finite difference methods for the solution of the inviscid generalized regularized long-wave (GRLW) equation subject to initial Gaussian conditions.

Design/methodology/approach
– Two implicit second- and fourth-order accurate finite difference methods and three Runge-Kutta procedures are introduced. The methods employ a new dependent variable which contains the wave amplitude and its second-order spatial derivative. Numerical experiments are reported for several temporal and spatial step sizes in order to assess their accuracy and the preservation of the first two invariants of the inviscid GRLW equation as functions of the spatial and temporal orders of accuracy, and thus determine the conditions under which grid-independent results are obtained.

Findings
– It has been found that the steepening of the wave increase as the nonlinearity exponent is increased and that the accuracy of the fourth-order Runge-Kutta method is comparable to that of a second-order implicit procedure for time steps smaller than 100th, and that only the fourth-order compact method is almost grid-independent if the time step is on the order of 1,000th and more than 5,000 grid points are used, because of the initial steepening of the initial profile, wave breakup and solitary wave propagation.

Originality/value
– This is the first study where an accuracy assessment of wave breakup of the inviscid GRLW equation subject to initial Gaussian conditions is reported.
Computations of anomalous phase change
Authors: Voller V R 
Published: May 2016

Purpose
– The purpose of this paper is to demonstrate how anomalous diffusion behaviors can be manifest in physically realizable phase change systems.

Design/methodology/approach
– In the presence of heterogeneity the exponent in the diffusion time scale can become anomalous, exhibiting values that differ from the expected value of 1/2. Here the author investigates, through directed numerical simulation, the two-dimensional melting of a phase change material (PCM) contained in a pattern of cavities separated by a non-PCM matrix. Under normal circumstances we would expect that the progress of melting F(t) would exhibit the normal diffusion time exponent, i.e., F∼t1/2. The author’s intention is to investigate what features of the PCM cavity pattern might induce anomalous phase change, where the progress of melting has a time exponent different from n=1/2.

Findings
– When the PCM cavity pattern has an internal length scale, i.e., when there is a sub-domain pattern which, when reproduced, gives us the full domain pattern, the direct simulation recovers the normal ∼t1/2 phase change behavior. When, however, there is no internal length scale, e.g., the pattern is a truncated fractal, an anomalous super diffusive behavior results with melting going as t
n; n
>
1/2. By studying a range of related fractal patterns, the author is able to relate the observed sub-diffusive exponent to the cavity pattern’s fractal dimension. The author also shows, how the observed behavior can be modeled with a non-local fractional diffusion treatment and how sub-diffusion phase change behavior (F∼t
n; n
<
1/2) results when the phase change nature of the materials in the cavity and matrix are inverted.

Research limitations/implications
– Although the results clearly demonstrate under what circumstances anomalous phase change behavior can be practically produced, the question of an exact theoretical relationship between the cavity pattern geometry and the observed anomalous time exponent is not known.

Practical implications
– The clear role of the influence of heterogeneity on heat flow behavior is illustrated. Suggesting that modeling heat and fluid flow in heterogeneous systems requires careful consideration.

Originality/value
– The novel direct simulation of melting in a two-dimensional PCM cavity pattern provides a clear illustration of anomalous behavior in a classic heat and fluid flow system and by extension provides motivation to continue the numerical investigation of anomalous and non-local behaviors and fractional calculus tools.
Analytical characterization of gaseous slip flow and heat transport through a parallel-plate microchannel with a centered porous substrate
Authors: Wang Keyong , Vafai Kambiz , Wang Dazhong 
Published: May 2016

Purpose
– The purpose of this paper is to analytically perform gaseous slip flow and heat transfer analysis within a parallel-plate microchannel partially filled with a centered porous medium under local thermal non-equilibrium (LTNE) condition. Heat transfer of gaseous flow in a porous microchannel is analytically studied. Energy communication at the porous-fluid interface is considered by two approaches: the gas rarefaction negatively impacts the heat transfer performance, and the optimum ratio of porous thickness is found to be around 0.8.

Design/methodology/approach
– Both Models A and B are utilized to consider the heat flux splitting for the fluid and solid phases at the porous-fluid interface.

Findings
– Analytical solutions for the fluid and solid phase temperature distributions and the Nusselt number are derived. In the no-slip flow limit, the present analytical solutions are validated by the partially and fully filled cases available in the literature.

Research limitations/implications
– The continuum flow (no-slip flow) is only a special case of the slip flow. Meanwhile, the effects of pertinent parameters on the heat transfer are also discussed.

Practical implications
– A survey of available literature mentioned above indicates a shortage of information for slip flow and heat transfer in partially filled porous systems. The main objective of the present study is to investigate the slip flow and heat transfer characteristics for forced convection through a microchannel partially filled with a porous medium under LTNE condition. The porous substrate is placed at the center of the microchannel. Analytical solutions for the temperature distributions of the fluid and solid phases and the Nusselt number at the microchannel wall are obtained.

Originality/value
– Heat transfer of gaseous flow in a porous microchannel is analytically studied. Energy communication at the porous-fluid interface is considered by two approaches: the gas rarefaction negatively impacts the heat transfer performance, and the optimum ratio of porous thickness is found to be around 0.8. Gaseous slip flow and heat transfer analysis is analytically performed within a parallel-plate microchannel partially filled with a centered porous medium under LTNE condition. Analytical solutions for the fluid and solid phase temperature distributions and the Nusselt number are derived for the first time. The effects of pertinent parameters on the heat transfer are also discussed. Compared with the results obtained for the continuum flow regime, the gas rarefaction negatively impacts the heat transfer efficiency and has little influence on the optimal porous thickness.
A short remark on Chien’s variational principle of maximum power losses for viscous fluids
Authors: Liu H.Y. , Si Na , He Ji-Huan 
Published: May 2016

Purpose
– The purpose of this paper is to point out a paradox in variational theory for viscous flows. Chien (1984) claimed that a variational principle of maximum power loses for viscous fluids was established, however, it violated the well-known Helmholtz’s principle.

Design/methodology/approach
– Restricted variables are introduced in the derivation, the first order and the second order of variation of the restricted variables are zero.

Findings
– An approximate variational principle of minimum power loses is established, which agrees with the Helmholtz’s principle, and the paradox is solved.

Research limitations/implications
– This paper focusses on incompressible viscose flows, and the theory can be extended to compressible one and other viscose flows. It is still difficult to obtain a variational formulation for Navier-Stokes equations.

Practical implications
– The variational principle of minimum power loses can be directly used for numerical methods and analytical analysis.

Originality/value
– It is proved that Chien’s variational principle is a minimum principle.
Constrained large-eddy simulation of turbulent flow and heat transfer in a stationary ribbed duct
Authors: Jiang Zhou , Xiao Zuoli , Shi Yipeng , Chen Shiyi 
Published: May 2016

Purpose– The knowledge about the heat transfer and flow field in the ribbed internal passage is particularly important in industrial and engineering applications. The purpose of this paper is to identify and analyze the performance of the constrained large-eddy simulation (CLES) method in predicting the fully developed turbulent flow and heat transfer in a stationary periodic square duct with two-side ribbed walls.Design/methodology/approach– The rib height-to-duct hydraulic diameter ratio is 0.1 and the rib pitch-to-height ratio is 9. The bulk Reynolds number is set to 30,000, and the bulk Mach number of the flow is chosen as 0.1 in order to keep the flow almost incompressible. The CLES calculated results are thoroughly assessed in comparison with the detached-eddy simulation (DES) and traditional large-eddy simulation (LES) methods in the light of the experimentally measured data.Findings– It is manifested that the CLES approach can predict both aerodynamic and thermodynamic quantities more accurately than the DES and traditional LES methods.Originality/value– This is the first time for the CLES method to be applied to simulation of heat and fluid flow in this widely used geometry.
Effects of cambers on gliding and hovering performance of corrugated dragonfly airfoils
Authors: Shi Xing , Huang Xianwen , Zheng Yao , Zhao Susu 
Published: May 2016

Purpose– The purpose of this paper is to explore the effects of the camber on gliding and hovering performance of two-dimensional corrugated airfoils. While the flying mechanism of natural flyers remains a myth up to nowadays, the simulation serves as a minor step toward understanding the steady and unsteady aerodynamics of the dragonfly flight.Design/methodology/approach– The lattice Boltzmann method is used to simulate the flow past the cambered corrugated dragonfly airfoil at low Reynolds numbers. For gliding flight, the maximum camber, the distance of the location of maximum camber point from the leading edge and Reynolds number are regarded as control variables; for hovering flight, the maximum camber, the flapping amplitude and trajectory are considered as control variables. Then corresponding simulations are performed to evaluate the implications of these factors.Findings– Greater gliding ratio can be reached by increasing the maximum camber of the dragonfly wing section. When the location of the maximum camber moves backward along the wing chord, large scale flow separation can be delayed. These two effects result in better gliding performances. For hovering performances, it is found that for different flapping amplitudes along an inclined plane, the horizontal force exerted on the airfoils increases with the camber, and the drag growths first but then drops. It is also found that the elliptic flapping trajectory is most sensitive to the camber of the cambered corrugated dragonfly wing section.Originality/value– The effects of the camber on gliding and hovering performance of the cambered dragonfly wing section are explored in detail. The data obtained can be helpful when designing micro aerial vehicles.
The effects of shape on the performance of cathode catalyst agglomerates in polymer electrolyte fuel cells
Authors: Ismail Mohammed , Ingham Derek , Hughes Kevin J , Ma Lin , Pourkashanian Mohamed 
Published: May 2016

Purpose
– The purpose of this paper is to numerically investigate the effects of the shape on the performance of the cathode catalyst agglomerate used in polymer electrolyte fuel cells (PEFCs). The shapes investigated are slabs, cylinders and spheres.

Design/methodology/approach
– Three 1D models are developed to represent the slab like, cylindrical and spherical agglomerates, respectively. The models are solved for the concentration of the dissolved oxygen using a finite element software, COMSOL Multiphysics®. “1D” and “1D axisymmetric” schemes are used to model the slab like and cylindrical agglomerates, respectively. There is no one-dimensional scheme available in COMSOL Multiphysics® for spherical coordinate systems. To resolve this, the governing equation in “1D” scheme is mathematically modified to match that of the spherical coordinate system.

Findings
– For a given length of the diffusion path, the variation in the performances of the investigated agglomerates is dependent on the operational overpotential. Under low magnitudes of the overpotentials, where the performance is mainly limited by reaction, the slab-like agglomerate outperforms the spherical and cylindrical agglomerates. In contrast, under high magnitudes of the overpotentials where the agglomerate performance is mainly limited by diffusion, the spherical and cylindrical agglomerates outperform the slab-like agglomerate.

Practical implications
– The current advances in the nano-fabrication technology gives more flexibility in designing the catalyst layers in PEFCs to the desired structures. If the design of the agglomerate catalyst is to be assessed, the current micro-scale modelling offers an efficient and rapid way forward.

Originality/value
– The current micro-scale modelling is an efficient alternative to developing a full (or half) fuel cell model to evaluate the effects of the agglomerate structure.
New benchmark solutions for transient natural convection in partially porous annuli
Authors: Massarotti Nicola , Ciccolella Michela , Cortellessa Gino , Mauro Alessandro 
Published: May 2016

Purpose
– The purpose of this paper is to focus on the numerical analysis of transient free convection heat transfer in partially porous cylindrical domains. The authors analyze the dependence of velocity and temperature fields on the geometry, by analyzing transient flow behavior for different values of cavity aspect ratio and radii ratio; both inner and outer radius are assumed variable in order to not change the difference ro-ri. Moreover, several Darcy numbers have been considered.

Design/methodology/approach
– A dual time-stepping procedure based on the transient artificial compressibility version of the characteristic-based split algorithm has been adopted in order to solve the transient equations of the generalized model for heat and fluid flow through porous media. The present model has been validated against experimental data available in the scientific literature for two different problems, steady-state free convection in a porous annulus and transient natural convection in a porous cylinder, showing an excellent agreement.

Findings
– For vertically divided half porous cavities, with Rayleigh numbers equal to 3.4×106 for the 4:1 cavity and 3.4×105 for the 8:1 cavity, the numerical results show that transient oscillations tend to disappear in presence of cylindrical geometry, differently from what happens for rectangular one. The magnitude of this phenomenon increases with radii ratio; the porous layer also affects the stability of velocity and temperature fields, as oscillations tend to decrease in presence of a porous matrix with lower value of the Darcy number.

Research limitations/implications
– A proper analysis of partially porous annular cavities is fundamental for the correct estimation of Nusselt numbers, as the formulas provided for rectangular domains are not able to describe these problems.

Practical implications
– The proposed model represents a useful tool for the study of transient natural convection problems in porous and partially porous cylindrical and annular cavities, typical of many engineering applications. Moreover, a fully explicit scheme reduces the computational costs and ensures flexibility.

Originality/value
– This is the first time that a fully explicit finite element scheme is employed for the solution of transient natural convection in partially porous tall annular cavities.