bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Significant Computational Building Blocks through Comprehensive Investigation of NGS Secondary Analysis Methods
Authors: Vasimuddin Md , Misra Sanchit , Aluru Srinivas 
Published: April 2018

AbstractRapid advances in next-generation sequencing technologies are improving the throughput and cost of sequencing at a rate significantly faster than the Moore’s law. This necessitates equivalent rate of acceleration of NGS secondary analysis that assembles reads into full genomes and identifies variants between genomes. Conventional improvement in hardware can at best help accelerate this according to the Moore’s law. Moreover, a majority of the software tools used for secondary analysis do not use the hardware efficiently. Therefore, we need hardware that is designed taking into account the computational requirements of secondary analysis, along with software tools that use it efficiently. Here, we take the first step towards these goals by identifying the computational requirements of secondary analysis. We surveyed dozens of software tools from all the three major problems in secondary analysis – sequence mapping, De novo assembly, and variant calling – to select seven popular tools and a workflow for an in-depth analysis. We performed runtime profiling of the tools using multiple real datasets to find that the majority of the runtime is dominated by just four building blocks – Smith-Waterman alignment, FM-index based sequence search, Debruijn graph construction and traversal, and pairwise hidden markov model algorithm – covering 80.5%-98.2%, 63.9%-99.4% and 72%-93% of the runtime, respectively, for sequence mapping, De novo assembly, and variant calling. The key outcome of this result is that by just targeting software and hardware optimizations to these building blocks, major performance improvements for NGS secondary analysis can be achieved.
Stress relaxation in epithelial monolayers is controlled by actomyosin
Authors: Khalilgharibi Nargess , Fouchard Jonathan , Asadipour Nina , Yonis Amina , Harris Andrew , Mosaffa Payman , Fujita Yasuyuki , Kabla Alexandre , Baum Buzz , Muñoz José J , Miodownik Mark , Charras Guillaume 
Published: April 2018

AbstractEpithelial monolayers are one-cell thick tissue sheets that separate internal and external environments. As part of their function, they withstand extrinsic mechanical stresses applied at high strain rate. However, little is known about how monolayers respond to mechanical deformations. In stress relaxation tests, monolayers respond in a biphasic manner and stress dissipation is accompanied by an increase in monolayer resting length, pointing to active remodelling of cell architecture during relaxation. Consistent with this, actomyosin remodels at a rate commensurate with mechanical relaxation and governs the rate of monolayer stress relaxation – as in single cells. By contrast, junctional complexes and intermediate filaments form stable connections between cells, enabling monolayers to behave rheologically as single cells. Together, these data show actomyosin cytoskeletal dynamics govern the rheological properties of monolayers by enabling active, ATP-dependent changes in the resting length. These findings have far-reaching consequences for our understanding of developmental morphogenesis and tissue response to mechanical stress.
Identification of Key Proteins Involved in Axon Guidance Related Disorders: A Systems Biology Approach
Authors: Ahammad Ishtiaque 
Published: April 2018

AbstractAxon guidance is a crucial process for growth of the central and peripheral nervous systems. In this study, 3 axon guidance related disorders, namely-Duane Retraction Syndrome (DRS), Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) and Congenital fibrosis of the extraocular muscles type 3 (CFEOM3) were studied using various Systems Biology tools to identify the genes and proteins involved with them to get a better idea about the underlying molecular mechanisms including the regulatory mechanisms. Based on the analyses carried out, 7 significant modules have been identified from the PPI network. Five pathways/processes have been found to be significantly associated with DRS, HGPPS and CFEOM3 associated genes. From the PPI network, 3 have been identified as hub proteins-DRD2, UBC and CUL3.
Corrosion inhibition of curcuma and saffron on A106 Gr B carbon steel in 3% NaCl medium
Authors: Dob Karima , Zouaoui Emna , Zouied Daoiya 
Published: April 2018

Purpose
Electrochemical measurements were used to characterize the inhibiting effectiveness of Curcuma and saffron, considered as green inhibitors in a corrosive environment 3% NaCl on A106 Gr B carbon steel.

Design/methodology/approach
This study/paper aims to polarization and potentiodynamic impedance spectroscopy techniques were performed on A106 Gr B carbon steel in the 3% NaCl environment only and containing various concentrations of Curcuma and Saffron (0.005, 0.01, 0.02, 0.04, g/L) after 30 min of immersion; these measures were taken at a temperature of (298 ± 1)K. A voltlab PGZ 301 assembled by A 106 Gr B carbon steel working electrode, a platinum counter electrode (CE) and a saturated calomel electrode as the reference electrode were used in the experiment. In this research, potentiodynamic polarization and electrochemical impedance spectroscopy were used.

Findings
The inhibition efficiencies increased with increase in the concentrations of the inhibitor but decreased with rise in temperature. The obtained results show an optimal efficiency with 0.04 g/L which are ordered of 78 and 96 per cent successively for the two inhibitors. Curcuma and saffron acts as a mixed type inhibitor. Adsorption of the inhibitor molecules corresponds to Langmuir adsorption isotherm. Mechanism of inhibition was also investigated by calculating the thermodynamic and activation parameters like (ΔG), (Ea), (ΔHa) and (ΔSa). The inhibitor molecules followed physical adsorption on the surface of carbon steel.

Originality/value
The present trend in research on environmental friendly corrosion inhibitors is concentrating on products of natural origin due principally to non-toxicity and eco-friendliness. Among these natural products are curcuma and saffron.
The mediating effect of dividend payout on the relationship between internal governance and free cash flow
Authors: Guizani Moncef 
Published: April 2018

PurposeThis paper aims to examine the mediating effect of dividend payout on the relationship between internal governance mechanisms (board of directors and ownership structure) and the free cash flow level.Design/methodology/approachLinear regression models are used to investigate such relationships applying data from a sample of 207 non-financial firms listed on the Gulf Cooperation Council countries’ stock markets between 2009 and 2016. To test the significance of mediating effect, the author uses the Sobel test.FindingsThe author finds a partial mediation effect of dividend on the relationship between both board independence and managerial ownership and the level of free cash flow. The results confirm the major role of outside directors in corporate governance. This governance mechanism contributes to the protection of shareholders’ interests through a generous dividend policy. However, the author finds that large managerial shareholdings increase the level of free cash flow through lower dividend payouts. This result suggests that powerful managers follow their preference of retaining excess cash to their own interests.Practical implicationsThis paper offers insights to policy-makers of emerging economies interested in the development of the corporate governance. This study provides guidance for firms in the construction and implementation of their own corporate governance policies.Originality/valueThe main contribution of the present paper is to examine the dividend payout as a potential mediating variable between internal governance mechanisms and free cash flow. Moreover, it highlights the issue of efficient management of substantial funds inSharia-compliant and non-Sharia-compliant firms.
A new numerical model for simulating top surface soil moisture and runoff
Authors: Chen Jiongfeng , Zhang Wan-chang 
Published: April 2018

PurposeThis paper aims to construct a simplified distributed hydrological model based on the surveyed watershed soil properties database.Design/methodology/approachThe new established model requires fewer parameters to be adjusted than needed by former hydrological models. However, the achieved stream-flow simulation results are similar and comparable to the classic hydrological models, such as the Xinanjiang model and the TOPMODEL.FindingsGood results show that the discharge and the top surface soil moisture can be simultaneously simulated, and that is the exclusive character of this new model. The stream-flow simulation results from two moderate hydrological watershed models show that the daily stream-flow simulation achieved the classic hydrological results shown in the TOPMODEL and Xinanjiang model. The soil moisture validation results show that the modeled watershed scale surface soil moisture has general agreement with the obtained measurements, with a root-mean-square error (RMSE) value of 0.04 (m3/m3) for one of the one-measurement sites and an averaged RMSE of 0.08 (m3/m3) over all measurements.Originality/valueIn this paper, a new simplified distributed hydrological model was constructed.
A numerical algorithm for computational modelling of coupled advection-diffusion-reaction systems
Authors: Jiwari Ram , Tomasiello Stefania , Tornabene Francesco 
Published: April 2018

Purpose
This paper aims to capture the effective behaviour of nonlinear coupled advection-diffusion-reaction systems and develop a new computational scheme based on differential quadrature method.

Design/methodology/approach
The developed scheme converts the coupled system into a system of ordinary differential equations. Finally, the obtained system is solved by a four-stage RK4 scheme.

Findings
The developed scheme helped to capture the different types of patterns of nonlinear time-dependent coupled advection-diffusion-reaction systems such as Brusselator model, Chemo-taxis model and linear model which are similar to the existing patterns of the models.

Originality/value
The originality lies in the fact that the developed scheme is new for coupled advection-diffusion-reaction systems such as Brusselator model, Chemo-taxis model and linear models. Second, the captured pattern is similar to the existing patterns of the models.
Application of linear vibration modeling of cross-ply composite plates with viscoelastic core
Authors: Zhai Yanchun , Liang Sen 
Published: April 2018

PurposeThe purpose of this study is to facilitate the engineering technical personnel to easily choose the appropriate vibration analysis model in the design of symmetry composite sandwich structure with composite face layers and viscoelastic core. Therefore, the applicable condition of two linear vibration models was obtained by considering the vibration analysis of three-layered sandwich structures.Design/methodology/approachEquilibrium equations of three kinds of vibration models were deduced using Hamilton’s principle and were solved using the closed-form Navier solution. Then, numerical results were compared with those reported in the literature to verify the accuracy of the deduced calculating formulas.FindingsThe applicable conditions of two linear vibration models are obtained by examining the influence of the ratio of length to total thickness (q) and that of viscoelastic thickness to total thickness (c) on the solutions. Two cases are considered about the applicable conditions of two linear vibration models based on the error analysis.Originality/valueThe paper obtains the application conditions of two linear vibration models by using error analysis for the first time and provides the reference for engineering staff to easily choose a suitable vibration model to design a symmetry composite sandwich plate.
Moderated effect of value co-creation on project performance
Authors: Heredia Rojas Boris , Liu Li , Lu Duanfang 
Published: April 2018

Purpose
Value co-creation amongst project stakeholders is often necessary for situations where the expertises or resources required are beyond a single stakeholder. Certain project delivery models (PDMs) with strong emphasis on relationships and trust are especially suited to value co-creation approach by encouraging collaborations amongst stakeholders and innovations. However, anecdotal evidence suggests that value co-creation impacts positively on particular types of projects but not on others. The purpose of this paper is to investigate the effect of value co-creation on project performance (PP) and how the effect is moderated by requirements uncertainty (RU).

Design/methodology/approach
Based on the data from a cross-sectional survey of 120 Chilean construction project managers, the study validated a conceptual framework on the moderated effects of value co-creation process.

Findings
Value co-creation process underpinned through relational engagement, collaboration and innovativeness positively impacts on PP, and project’s RU moderates this relationship.

Practical implications
The findings empirically show that collaborative PDMs are best suited to projects where requirements are uncertain. Identifying the most suitable delivery model for a given context can reduce the project’s risk of failure and help maximise project value. When RU is low, the co-creating value is less critical to PP; whereas, when RU is high, choosing a collaborative PDM is fundamental to superior PP.

Originality/value
This study provides much-needed evidence on the effects of value co-creation process on PP. Additionally, it contributes to the literature by conceptualising and validating the moderated impact on PP by RU.
The importance of hard project management and team motivation for construction project performance
Authors: Larsson Johan , Eriksson Per Erik , Pesämaa Ossi 
Published: April 2018

Purpose
Hard project management practices, based on strict planning and control, are traditionally applied in construction projects, although research frequently promotes the importance of teams for various project outcomes. Thus, the purpose of this paper is to examine the importance of hard project management and team motivation for process performance in construction projects. A hypothesis tested is that hard project management can impair process performance if team motivation is not promoted.

Design/methodology/approach
The paper presents and empirically tests a structural equation model, with and without a mediating link between hard project management and process performance, based on data from a survey of 2,175 respondents, representing contractors and clients involved in 109 Swedish construction projects.

Findings
The results confirm that hard project management is best conveyed through teams to enhance process performance. “Path analysis,” using the model with the mediating link, confirms that neglecting team motivation can significantly impair process performance.

Research limitations/implications
The data set provides unusually high representation of views of contractors and clients involved in diverse Swedish construction projects. Thus, the results have likely relevance in other project-based industries and/or national settings, but this possibility requires further investigation.

Originality/value
The findings show that team motivation is a key process performance factor; hard project management may indeed be important, but its effects will be enhanced by (and partially mediated through) team motivation. Thus, the findings have important theoretical and practical implications for the development of project management practices.
Human factors and project challenges influencing employee engagement in a project-based organisation (PBO)
Authors: Matthews Judy , Stanley Tracy , Davidson Paul 
Published: April 2018

Purpose
The purpose of this paper is to provide insights into the project challenges, human factors and knowledge development that influence the nature of employee engagement in a project team within a global project-based organisation.

Design/methodology/approach
A qualitative research design used semi-structured interviews, and observations in team meetings and the work environment to identify characteristics in the work environment which influenced employee engagement.

Findings
Workplace characteristics that influence employee engagement relate to the project challenges, the problem-solving nature of work, and achieving specified outcomes within time allocations. Human factors including the manager’s behaviours with feedback and recognition of effort, mentoring, and encouraging collaboration are important in team environment. The potential for learning and knowledge development from the project and with the team positively influence engagement.

Research limitations/implications
This study examines the characteristics of an established project team of 13 consultant engineers from eight nationalities, and forms a basis for future comparison with other project teams with different job types and demographic profiles.

Practical implications
This study contributes to project management (PM) research by broadening the focus from human factors influencing employee engagement to project challenges and knowledge development, with implications for managers in project-based organisations in terms of job design, development of team climate, team processes and their own behaviours.

Originality/value
This study contributes to human factors in PM literature through exploratory research into the antecedents of employee engagement.
Participative project management as a comprehensive response to postmodernism criticisms
Authors: Sarhadi Mehrdad , Yousefi Saied , Zamani Amin 
Published: April 2018

Purpose
The purpose of this paper is to understand the philosophical changes which underpin research and practices in project management. This study is an attempt to challenge previous studies that have tried to explain this change in order to provide a better explanation.

Design/methodology/approach
The authors adopt a critical review research method to challenge previous explanations of the paradigm change and definition of communication. For this purpose, philosophical and social theories and concepts have been used.

Findings
This paper proposed changing the paradigm from modernism to postmodernism and the paradigm shift, which happens from postmodernism to participation, as a better explanation for the paradigmatic change in project management. Furthermore, the important role of communication has been illustrated in the participation paradigm.

Originality/value
For the first time in project management, the authors attempt to clarify the role of power in this paradigmatic shift, especially because this concept is an axial concept in postmodern philosophy and a neglected concept in project management literature. In addition, communicative action theory has been used with the aim of pursuing the influence of informal power in the participation paradigm and paving the way for confronting its emerging challenges in future studies.
Process perspectives on entrepreneurship and projects
Authors: Kuura Arvi , Lundin Rolf A. 
Published: April 2018

Purpose
The purpose of this paper is to integrate research on entrepreneurship and projects by applying process perspectives on these two fields with the ambition to shed light on how this kind of alternative perspectives can be used to further the fields in research and practice.

Design/methodology/approach
This conceptual paper is based on previous research efforts in the two fields and on how they have been treated in the past. Business process research is introduced to enrich notions on how the two areas can be combined.

Findings
By rearranging thinking about projects, entrepreneurship and processes, and through introducing the notion of “chunks”, the authors illustrate how different types of business processes in different types of project contexts can be coordinated through orchestration and/or choreography.

Research limitations/implications
The research made for this conceptual paper has been thorough. However, the literature is huge, so the reservation must be made that the authors might have missed some important trends. Anyway, there are implications for how research and analyses of data can be used with the thinking described.

Originality/value
Combining various lines of research is not common as illustrated by the lack of studies combining entrepreneurship and projects; therefore, by adding process notions and “chunk” reasoning, this paper opens up for innovation and renewal in research. To the authors’ knowledge this approach is new.
Big data in spare parts supply chains
Authors: Andersson Joakim , Jonsson Patrik 
Published: April 2018

Purpose
The purpose of this paper is to explore and propose how product-in-use data can be used in, and improve the performance of, the demand planning process for automotive aftermarket services.

Design/methodology/approach
A literature review and a single case study investigate the underlying reasons for the demand for spare parts by conducting in-depth interviews, observing actual demand-generating activities, and studying the demand planning process.

Findings
This study identifies the relevant product-in-use data and divides them into five main categories. The authors have analysed how product-in-use data are best utilised in planning spare parts with different attributes, e.g. different life cycle phases and demand frequencies. Furthermore, the authors identify eight potentially relevant areas of application of product-in-use data in the demand planning process, and elaborate on their performance effects.

Research limitations/implications
This study details the understanding of what impact context has on the potential performance effects of using product-in-use data in aftermarket demand planning. Propositions generate several strands for future research.

Practical implications
This study shows the potential impact of using product-in-use data, using eight different types of interventions for spare parts, in the aftermarket demand planning.

Originality/value
The literature focusses on single applications of product-in-use data, but would benefit from considering the context of application. This study presents interventions and explores how these enable improved demand planning by analysing usage and effects.