bluuebunny/crossref_metadata_2025 huggingface dataset:
Which Kind of Causal Specificity Matters Biologically?
Authors: Weber Marcel
Published: March 2017

Paul Griffiths et al. have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.
Practice, Practice, Practice
Authors: Miller Kiri
Published: March 2017

This chapter analyzes dance games as transmission systems, assessing their capacity to notate, transmit, and archive embodied repertoires that are typically taught in face-to-face, body-to-body contexts. Dance games ask players to sight-read unfamiliar choreography in real time, mirroring the screen dancer as the routine unfolds. They imply that choreography can work like streaming audio or video—passing straight into a player’s proprioceptive system—and challenge players to cultivate techniques of anticipation to minimize “kinesthetic lag.” The games teach these techniques using hybrid notation systems, modular choreography tied to musical structure, and patterned repetition that integrates technical training into a repertoire of works. Close readings of Dance Central’s version of “Crank That” and Just Dance’s version of “Apache (Jump On It)” show how this technical pedagogy dovetails with the games’ remediation of existing song-and-dance repertoires to reinforce racialized models of dance authenticity.
Choreographic Labor, FTFO
Authors: Miller Kiri
Published: March 2017

This chapter focuses on choreographic labor, highlighting the perspectives of game choreographers. These creative workers function as cultural intermediaries between the game industry and various dance cultures; their embodied and affective labor position them as representatives of “real dance.” The technical constraints imposed by motion-capture and animation processes impact the nature of creative labor in dance game production. Choreographers have pushed against those constraints to assert their own creative agency and affirm particular dance values. This chapter also addresses issues of ownership—in terms of choreographic copyright, cultural heritage, and cultural appropriation—and shows how dance games reflect choreographers’ experiences as teachers, students, competitors, and producers of creative content in an era of precarious labor.
Sex and Salvation in the Vergilian Cento of the Fourth Century
Authors: Pollmann Karla
Published: March 2017

In a cento, a writer uses fragments from texts of canonical authors (Genette’s hypotext) taken out of their original context to create a new work (Genette’s hypertext), which one could call ‘literary patchwork’. This chapter argues innovatively to differentiate between the predominantly parodical aim of pagan centos and the predominantly exegetical aim of Christian centos, and illustrates the implications and consequences of this assumption by analysing the centos of the fourth-century writers Ausonius and Proba. While both poets are adhering to a classicism that sees Vergil as indispensable for conveying a culturally convincing message, they manage to exploit the authority and embedded polysemy of the hypotext for diametrically opposed messages. Thus the chapter programmatically demonstrates that the literary genre of the cento, instead of being wrongly accused of epigonality, is a highly original and complex literary form.
Entanglement spectroscopy and its application to the quantum Hall effects
Authors: Regnault Nicolas
Published: March 2017

Entanglement spectroscopy has stimulated an extensive range of studies. The entanglement spectrum is the spectrum of the reduced density matrix when the system is partitioned into two. For many quantum systems, when computed from the bulk ground-state wavefunction, it gives access to the physics of edge excitations. It is thus a valuable tool to diagnose topological ordering. These lecture notes provide an overview of entanglement spectroscopy, mostly in the context of the fractional quantum Hall effect. The basic concepts are introduced through the example of quantum spin chains. The connection with entanglement entropy and the matrix product state representation is discussed. The entanglement spectrum can be computed for non-interacting topological phases, revealing edge excitation from the ground state. Application to fractional quantum Hall phases shows how much information is encoded within the ground state and how different partitions probe different types of excitations. Application to fractional Chern insulators is discussed.
Transport of Dirac surface states
Authors: Carpentier D.
Published: March 2017

The occurrence of robust states at the surface of three-dimensional topological insulators is their most salient feature. Indeed, it is their existence in ARPES experiments that is used as a signature of the topological property of the bulk bands. These surface states turn out to be described by a relativistic two-dimensional Dirac equation at low energy. These lecture notes focus on the transport properties of these Dirac surface states. While transport may not be the ideal probe of the existence of Dirac-like electronic excitations, it remains a tool of choice in condensed matter. These notes survey some of the transport properties of Dirac excitations and the techniques appropriate to their studies. For the sake of pedagogy, the focus is on the simplest transport properties, neglecting in particular transport in hybrid structures with superconductors.
Spin textures in quantum Hall systems
Authors: Douçot Benoît
Published: March 2017

The subject of these lecture notes combines several different manifestations of topology in a condensed matter system. The most classical of these is through the notion of texture. By this is meant any non-singular and topologically non-trivial spatial configuration of some relevant order parameter. The goal of these notes is to provide a theory-oriented introduction to the physics of textures in quantum Hall ferromagnets. They do not attempt to provide a comprehensive review of this very rich subject, and many important aspects are not mentioned, but instead they focus on recent advances in this field.
Out-of-equilibrium behaviour in topologically ordered systems on a lattice: fractionalized excitations and kinematic constraints
Authors: Castelnovo Claudio
Published: March 2017

These lecture notes deal with aspects of out-of-equilibrium behaviour in topologically ordered systems, broadly interpreted as systems that do not develop a local order parameter at low temperature (e.g. symmetry breaking) and yet exhibit non-trivial global properties. The specific cases of classical spin ice and the quantum toric code are discussed. Within classical systems, it is found that substantial progress can be made in understanding the dynamics through effective modelling of the vacuum and its emergent excitations. However, at the quantum level, modelling is limited to that of leading energy barriers and asymptotic behavior, although it turns out that an intriguing parallel can be drawn between the toric code Hamiltonian and a class of lattice systems known as kinetically constrained models.
Local Transformation
Authors: Beck Ulrik
Published: March 2017

This chapter documents the local transformation of rural Vietnamese communes in twelve different provinces from 2006 to 2014. Two key areas are considered, namely occupational and agricultural choice and provision of public goods. While many areas showed improvements and steady structural transformation into other activities supporting agriculture, the level and the speed of transformation process varied between different geographical regions and, on some indicators, it appears that some communes are not currently reaping the benefits of the high levels of economic growth. While communes report fewer problems in 2014 than in 2006, there has been a marked increase in the number of communes who feel climate change is a problem. Commune administrators expect this to increase even more going forward.
Labour and Migration
Authors: Narciso Gaia
Published: March 2017

This chapter provides an overview of the characteristics of households with a migrant away, and analyses the effects of migration in Viet Nam, on the basis of the VARHS conducted in 2012 and 2014. The data reveal significant movements of household members, both intra- and inter-province. Differences are uncovered between sending and non-sending households: households with a migrant are wealthier than non-sending households, as measured by food expenditure. The analysis shows that migration acts as a shock-coping mechanism, especially in the presence of natural shocks. Remittance-recipient households seem to react better to natural shocks, as the remittance flows counterbalance the need for borrowing.
Social and Political Capital
Authors: Markussen Thomas
Published: March 2017

This chapter exploits five waves of VARHS to investigate issues of social and political capital in rural Viet Nam. The chapter analyses membership of the Communist Party, ‘mass organizations’ (MOs) (Farmers’ Union, Women’s Union, etc.) and other voluntary organizations (such as sports clubs, cultural groups, etc.), trust, and the significance of family ties in economic transactions (e.g. the share of land tenants who are relatives of their landlord). The chapter also presents fixed effects regressions, exploring the effects of social and political capital on household income. The results indicate positive returns to Communist Party membership, trust, and access to informal insurance.
SynergyFinder: a web application for analyzing drug combination dose–response matrix data
Authors: Ianevski Aleksandr , He Liye , Aittokallio Tero , Tang Jing
Published: March 2017

Summary: Rational design of drug combinations has become a promising strategy to tackle the drug sensitivity and resistance problem in cancer treatment. To systematically evaluate the pre-clinical significance of pairwise drug combinations, functional screening assays that probe combination effects in a dose–response matrix assay are commonly used. To facilitate the analysis of such drug combination experiments, we implemented a web application that uses key functions of R-package SynergyFinder, and provides not only the flexibility of using multiple synergy scoring models, but also a user-friendly interface for visualizing the drug combination landscapes in an interactive manner.

Availability and Implementation: The SynergyFinder web application is freely accessible at https://synergyfinder.fimm.fi; The R-package and its source-code are freely available at http://bioconductor.org/packages/release/bioc/html/synergyfinder.html.
Creating a Culture of Collaboration: A Brief History of Academic Neurosurgery in Washington, DC
Authors: Siu Alan , Neal Christopher J , Syed Hasan R , Felbaum Daniel R , Nair M Nathan , McGrail Kevin M , Caputy Anthony J , Shields Donald C
Published: March 2017

Clinical neurosurgery has been practiced in the US capital for just over 100 years. As former residents and fellows of Drs. Harvey Cushing and Walter Dandy moved to the region, hospitals at Georgetown and George Washington Universities became early adopters of this new surgical discipline. Later academic neurosurgery programs were established at the National Institutes of Health, Walter Reed Medical Center, and Children's National Medical Center. Neurosurgical pioneers at these institutions developed new technologies and diagnostic procedures which continue to inform our current practice. In addition, continued collaboration between the multiple training sites in Washington, DC has uniquely enriched our residents’ training experience.
Genetic Analysis and QTL Mapping of Resistance to Gummy Stem Blight inCucumis sativusSeedling Stage
Authors: Liu Shulin , Shi Yanxia , Miao Han , Wang Min , Li Baoju , Gu Xingfang , Zhang Shengping
Published: March 2017

Gummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum), is an important disease of cucumber (Cucumis sativus L.) worldwide. To better understand the resistance to GSB in cucumber seedlings, a set of 160 F9recombinant inbred lines (RILs) and a total of 405 pairs of SSR primers were employed to detect quantitative trait loci (QTLs) conferring the resistance. Genetic analysis indicated that the resistance to GSB in PI 183967 seedlings was quantitative and mainly governed by two pairs of major QTLs and multiple minor QTLs. Six QTLs, gsb3.1, gsb3.2, gsb3.3, gsb4.1, gsb5.1, and gsb6.1, for resistance to GSB in cucumber seedlings were detected. The stable locus gsb5.1 on Chr.5 was repeatedly detected in three seasons. Locus gsb5.1 accounted for the highest phenotypic variation, 17.9%, and was flanked by SSR15321 and SSR07711 within the genetic distance of 0.5 cM. There were 102 candidate genes predicted in the region harboring the stable QTL gsb5.1, of which seven genes were related to disease resistance. These results can provide a good base for further study and molecular markers for fine-mapping the major QTL conferring GSB resistance in cucumber.
GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data
Authors: Beagrie Robert A. , Schueler Markus
Published: March 2017

Genome Architecture Mapping (GAM) is a recently developed method for mapping chromatin interactions genome-wide. GAM is based on sequencing genomic DNA extracted from thin cryosections of cell nuclei. As a new approach, GAM datasets require specialized analytical tools and approaches. Here we present GAMtools, a pipeline for analysing GAM datasets. GAMtools covers the automated mapping of raw next-generation sequencing data generated by GAM, detection of genomic regions present in each nuclear slice, calculation of quality control metrics, generation of inferred proximity matrices, plotting of heatmaps and detection of genomic features for which chromatin interactions are enriched/depleted.
RegCyanoDB: a database of regulatory interactions in cyanobacteria
Authors: Nair Ajay , Chetty Madhu , Vinh Nguyen Xuan
Published: March 2017

Background

Cyanobacteria are photoautotrophic organisms with environmental, evolutionary, and industrial importance. Knowledge of its regulatory interactions are important to predict, optimise, and engineer their characteristics. However, at present, very few of their regulatory interactions are known. The regulatory interactions are known only for a few model organisms such asEscherichia colidue to technical and economical constraints, which are unlikely to change soon. Thus, mapping of regulatory interactions from well-studied organisms to less-studied organisms by using computational techniques is widely used. Reverse Best Hit (RBH), with appropriate algorithm parameters, is a simple and efficient method for detecting functional homologs.

Description

We predict the regulatory interactions in 30 strains of cyanobacteria using the known regulatory interactions from the best-studied organism,E. coli.RBH method with appropriate parameters is used to identify the functional homologs. An interaction is mapped to a cyanobacterial strain if functional homologs exist for a known transcription factor and its target gene. The confidence of the detected homologs and interactions are also provided. Since RBH is a conservative method, homolog-grouping is performed to recover lost putative interactions. A database of the predicted interactions from all the 30 strains of cyanobacteria is constructed.

Conclusion

RegcyanoDB contains 20,280 interactions with confidence levels for 30 cyanobacterial strains. The predicted regulatory interactions exhibit a scale free network topology as observed in model organisms. The interacting genes inE. coliand cyanobacteria are mostly found to have the same gene annotation. This database can be used for posing novel hypotheses and validation studies in wet-lab and computational domains.

The database is available athttp://www.che.iitb.ac.in/grn/RegCyanoDB/
Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously
Authors: Taroni Jaclyn N , Greene Casey S
Published: March 2017

Motivation: Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. The majority of available RNA assays are run on microarray, while RNA-seq is becoming the platform of choice for new experiments. The data structure and distributions between the platforms differ, making it challenging to combine them. We performed supervised and unsupervised machine learning evaluations, as well as differential expression analyses, to assess which normalization methods are best suited for combining microarray and RNA-seq data. Results: We find that quantile and Training Distribution Matching normalization allow for supervised and unsupervised model training on microarray and RNA-seq data simultaneously. Nonparanormal normalization and z-scores are also appropriate for some applications, including differential expression analysis. Availability and Implementation: These analyses were performed in R and are available at https://www.github.com/greenelab/RNAseq_titration_results under a BSD-3 clause license.
Amending published articles: time to rethink retractions and corrections?
Authors: Barbour Virginia , Bloom Theo , Lin Jennifer , Moylan Elizabeth
Published: March 2017

Academic publishing is evolving and our current system of correcting research post-publication is failing, both ideologically and practically. It does not encourage researchers to engage in consistent post-publication changes. Worse yet, post-publication ‘updates’ are misconstrued as punishments or admissions of guilt. We propose a different model that publishers of research can apply to the content they publish, ensuring that any post-publication amendments are seamless, transparent and propagated to all the countless places online where descriptions of research appear. At the center, the neutral term “amendment” describes all forms of post-publication change to an article. We lay out a straightforward and consistent process that applies to each of the three types of amendments: insubstantial, substantial, and complete. This proposed system supports the dynamic nature of the research process itself as researchers continue to refine or extend the work, removing the emotive climate particularly associated with retractions and corrections to published work. It allows researchers to cite and share the correct versions of articles with certainty, and for decision makers to have access to the most up to date information.
A porcine ex vivo model of pigmentary glaucoma
Authors: Dang Yalong , Waxman Susannah , Wang Chao , Loewen Ralista T. , Sun Ming , Loewen Nils A.
Published: March 2017

Pigment dispersion syndrome can lead to pigmentary glaucoma (PG), a poorly understood condition of younger, myopic eyes with fluctuating, high intraocular pressure (IOP). The absence of a model similar in size and behavior to human eyes has made it difficult to investigate its pathogenesis. Here, we present a porcine ex vivo model that recreates the features of PG including intraocular hypertension, pigment accumulation in the trabecular meshwork and relative failure of phagocytosis. Inin vitromonolayer cultures as well as inex vivoeye perfusion cultures, we found that the trabecular meshwork (TM) cells that regulate outflow, form actin stress fibers and have a decreased phagocytosis. Gene expression microarray and pathway analysis indicated key roles of RhoA in regulating the TM cytoskeleton, motility, and phagocytosis thereby providing new targets for PG therapy.
Mercury and water level fluctuations in lakes of northern Minnesota
Authors: Larson James H. , Maki Ryan P. , Christensen Victoria G. , Sandheinrich Mark B. , LeDuc Jaime F. , Kissane Claire , Knights Brent C.
Published: March 2017

Large lake ecosystems support a variety of ecosystem services in surrounding communities, including recreational and commercial fishing. However, many northern temperate fisheries are contaminated by mercury. Annual variation in mercury accumulation in fish has previously been linked to water level (WL) fluctuations, opening the possibility of regulating water levels in a manner that minimizes or reduces mercury contamination in fisheries. Here, we compiled a long-term dataset (1997–2015) of mercury content in young-of-year Yellow Perch (Perca flavescens) from six lakes on the border between the U.S. and Canada and examined whether mercury content appeared to be related to several metrics of WL fluctuation (e.g., spring WL rise, annual maximum WL, and year-to-year change in maximum WL). Using simple correlation analysis, several WL metrics appear to be strongly correlated to Yellow Perch mercury content, although the strength of these correlations varies by lake. We also used many WL metrics, water quality measurements, temperature and annual deposition data to build predictive models using partial least squared regression (PLSR) analysis for each lake. These PLSR models showed some variation among lakes, but also supported strong associations between WL fluctuations and annual variation in Yellow Perch mercury content. The study lakes underwent a modest change in WL management in 2000, when winter WL minimums were increased by about 1 m in five of the six study lakes. Using the PLSR models, we estimated how this change in WL management would have affected Yellow Perch mercury content. For four of the study lakes, the change in WL management that occurred in 2000 likely reduced Yellow Perch mercury content, relative to the previous WL management regime.
Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II
Authors: Zhang Miao , Bommer Martin , Chatterjee Ruchira , Hussein Rana , Yano Junko , Dau Holger , Kern Jan , Dobbek Holger , Zouni Athina
Published: March 2017

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn4CaO5-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII fromThermosynechococcus elongatuswithout the Mn4CaO5-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn4CaO5-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn4CaO5-cluster agree with a specific bi-manganese cluster, likely a di-μ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.
Discoveringin vivocytokine eQTL interactions from a lupus clinical trial
Authors: Davenport Emma E. , Amariuta Tiffany , Gutierrez-Arcelus Maria , Slowikowski Kamil , Westra Harm-Jan , Luo Yang , Shen Ciyue , Rao Deepak A. , Zhang Ying , Pearson Stephen , von Schack David , Beebe Jean S. , Bing Nan , John Sally , Vincent Michael S. , Zhang Baohong , Raychaudhuri Soumya
Published: March 2017

Background

Cytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by cytokines is central to defining drug and disease mechanisms. One promising strategy is to use interactions between expression quantitative trait loci (eQTLs) and cytokine levels to define target genes and mechanisms.

Results

In a clinical trial for anti-IL-6 in patients with systemic lupus erythematosus we measured interferon (IFN) status, anti-IL-6 drug exposure and genome-wide gene expression at three time points (379 samples from 157 individuals). First, we show that repeat transcriptomic measurements increases the number ofciseQTLs identified compared to using a single time point by 64%. Then, after identifying 4,818 cis-eQTLs, we observed a statistically significant enrichment ofin vivoeQTL interactions with IFN status (p<0.001 by permutation) and anti-IL-6 drug exposure (p<0.001). We observed 210 and 72 interactions for IFN and anti-IL-6 respectively (FDR<20%). Anti-IL-6 interactions have not yet been described while 99 of the IFN interactions are novel. Finally, we found transcription factor binding motifs interrupted by eQTL interaction SNPs, pointing to key regulatory mediators of these environmental stimuli and therefore potential therapeutic targets for autoimmune diseases. In particular, genes with IFN interactions are enriched for ISRE binding site motifs, while those with anti-IL-6 interactions are enriched for IRF4 motifs.

Conclusion

This study highlights the potential to exploit clinical trial data to discoverin vivoeQTL interactions with therapeutically relevant environmental variables.
Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes
Authors: Kang Hyun Min , Subramaniam Meena , Targ Sasha , Nguyen Michelle , Maliskova Lenka , Wan Eunice , Wong Simon , Byrnes Lauren , Lanata Cristina , Gate Rachel , Mostafavi Sara , Marson Alexander , Zaitlen Noah , Criswell Lindsey A , Ye Jimmie
Published: March 2017

Droplet-based single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes from tens of thousands of cells. Multiplexing samples for single cell capture and library preparation in dscRNA-seq would enable cost-effective designs of differential expression and genetic studies while avoiding technical batch effects, but its implementation remains challenging. Here, we introduce an in-silico algorithm demuxlet that harnesses natural genetic variation to discover the sample identity of each cell and identify droplets containing two cells. These capabilities enable multiplexed dscRNA-seq experiments where cells from unrelated individuals are pooled and captured at higher throughput than standard workflows. To demonstrate the performance of demuxlet, we sequenced 3 pools of peripheral blood mononuclear cells (PBMCs) from 8 lupus patients. Given genotyping data for each individual, demuxlet correctly recovered the sample identity of > 99% of singlets, and identified doublets at rates consistent with previous estimates. In PBMCs, we demonstrate the utility of multiplexed dscRNA-seq in two applications: characterizing cell type specificity and inter-individual variability of cytokine response from 8 lupus patients and mapping genetic variants associated with cell type specific gene expression from 23 donors. Demuxlet is fast, accurate, scalable and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes.
Influence of the electrical circuit configurations of a DVR coupling transformer with a magnetic bypass
Authors: Majchrzak Virginie , Parent Guillaume , Brudny Jean-François , Costan Valentin , Guuinic Philippe
Published: March 2017

Purpose

For the proposed coupling transformer, a magnetic bypass based on the virtual air gap principle is realized by inserting auxiliary windings in a return leg added to a standard transformer. With such a setup, it is able to act as a voltage regulator as well as protect the power electronics of the dynamic voltage restorer from electrical grid fault currents. This paper focuses on the electrical design part of the coupling transformer. It aims to explain how the behavior of the auxiliary windings electrical circuit of the magnetic bypass impacts the performances of the device.

Design/methodology/approach

The influence of the electrical auxiliary windings circuit configurations on the operation of the coupling transformer is studied by finite element analyses with nonlinear and isotropic magnetic materials.

Findings

A configuration for the realization of the electrical circuit of the auxiliary windings is determined according to the finite element simulation results to achieve the design of the coupling transformer whose magnetic core was previously designed.

Originality/value

By studying the operation of a special coupling transformer with nonlinear saturation phenomenon by finite element analyses, a to-do list of the electrical circuit parameters is described to design this device well.
Minimization of a SynRel’s oscillating torque by calculation of the appropriate skew angle
Authors: Martinez Javier , Krischan Klaus , Muetze Annette
Published: March 2017

Purpose

Synchronous Reluctance (SynRel) motors are known to suffer from excessive torque ripples. The classical way to avoid this drawback of the motor is skewing the slots. This paper aims to provide an analytic estimation of the best skew angle to minimize the ripples in such SynRel motors with tooth windings. The approach used in this paper consists of the minimization of the spectral components of the magnetic energy that cause these oscillation torques. The method was validated by means of a multi-slice finite element model (FEM).

Design/methodology/approach

An analytic model, based on permeance theory, is derived to analyse the electromagnetic phenomena taking place inside of the motor. This model allows the identification of the causes underlying the torque ripple production. Based on this understanding, the most suitable skew angle can be determined. The analytic method, together with the best skew angle, is validated by means of an FEM of a SynRel machine.

Findings

A method to determine the optimum skew angle for a SynRel machine is presented. It depends on the wave-number of the magnetic waves producing the torque ripple. It is twice the one typically chosen for induction machines.

Practical/implications

The proposed approach allows improving on the design methodology for the production of smoothly running SynRel machines.

Originality/value

The methodology utilized in this paper is based on the relationship between the mechanical torque and the magnetic energy stored in the motor (virtual work law). From this, the best skew angle to eliminate the magnetic energy causing torque ripple can be determined. It, therefore, proposes an effective alternative to the common use of inductance models to determine such angles.
Parallelized numerical modeling of the interaction of a solid object with immiscible incompressible two-phase fluid flow
Authors: Ghasemi Amirmahdi , Nikbakhti R. , Ghasemi Amirreza , Hedayati Faraz , Malvandi Amir
Published: March 2017

Purpose

A numerical method is developed to capture the interaction of solid object with two-phase flow with high density ratios. The current computational tool would be the first step of accurate modeling of wave energy converters in which the immense energy of the ocean can be extracted at low cost.

Design/methodology/approach

The full two-dimensional Navier–Stokes equations are discretized on a regular structured grid, and the two-step projection method along with multi-processing (OpenMP) is used to efficiently solve the flow equations. The level set and the immersed boundary methods are used to capture the free surface of a fluid and a solid object, respectively. The full two-dimensional Navier–Stokes equations are solved on a regular structured grid to resolve the flow field. Level set and immersed boundary methods are used to capture the free surface of liquid and solid object, respectively. A proper contact angle between the solid object and the fluid is used to enhance the accuracy of the advection of the mass and momentum of the fluids in three-phase cells.

Findings

The computational tool is verified based on numerical and experimental data with two scenarios: a cylinder falling into a rectangular domain due to gravity and a dam breaking in the presence of a fixed obstacle. In the former validation simulation, the accuracy of the immersed boundary method is verified. However, the accuracy of the level set method while the computational tool can model the high-density ratio is confirmed in the dam-breaking simulation. The results obtained from the current method are in good agreement with experimental data and other numerical studies.

Practical/implications

The computational tool is capable of being parallelized to reduce the computational cost; therefore, an OpenMP is used to solve the flow equations. Its application is seen in the following: wind energy conversion, interaction of solid object such as wind turbine with water waves, etc.

Originality/value

A high efficient CFD approach method is introduced to capture the interaction of solid object with a two-phase flow where they have high-density ratio. The current method has the ability to efficiently be parallelized.
A comparative study of wall jet flow containing carbon nanotubes with convective heat transfer and MHD
Authors: Ali Zaidi Syed Zulfiqar , Mohyud-din Syed Tauseef , Bin-Mohsen Bandar
Published: March 2017

Purpose

The purpose of this study is to conduct a comparative investigation for incompressible electrically conducting nanofluid fluid through wall jet. Single-walled carbon nanotubes (SWCNTs) and multiple-walled carbon nanotubes (MWCNTs) are considered as the nanoparticles. To record the effect of Lorentz forces, a magnetic field is applied normally with the assumption that the induced magnetic field is negligible.

Design/methodology/approach

Boundary layer approximation is used to convert governing equations into ordinary differential equations along with appropriate boundary conditions. To obtain the results, used homotopy analysis method (HAM) has been used as an analytical technique and to validate the obtained results a famous numerical Runge–Kutta–Fehlberg method is also exploited. It has been observed that the results obtained through both of the methods are in excellent agreement with exact solution.

Findings

The Hartmann number is used as controlling parameter for velocity and temperature profile. That can be recorded as its extended values help to normalize the velocity, whereas it controls the rapid increase in temperature. The temperature profile is boosted by increasing the value of the Biot number, a physical parameter. Similarly, it also increases for an increased percentage of volume fraction of particles (SWCNTs/MWCNTs). The Hartmann number plays an important role in decreasing local skin friction coefficient. The influence of the Biot number and volume fraction of nanoparticles caused similar increasing effects on the local Nusselt number. Nanoparticles of the form SWCNT provide better heat transfer as compared to MWCNTs. Influence of the Biot number and volume fraction of nanoparticles caused similar increasing effects on the local Nusselt number. Nanoparticles of the form SWCNT provide better heat transfer as compared to MWCNTs.

Originality/value

To gain insight into the problem, the effects of various emerging parameters and physical quantities such as Biot number, Nusselt number and skin friction coefficient, have been explored.
Simulation of partial differential equations models in Java
Authors: Cano María José , Chacon-Vera Eliseo , Esquembre Francisco
Published: March 2017

Purpose

Computer simulations improve the knowledge of physical models and are widely used in teaching and research. Key aspects are to understand their solutions and to make interactive changes to the models, observing their effects in real-time. The drawback of creating interactive simulations of physical models is the high level of programming expertise required. The purpose of this study is to facilitate this task.

Design/methodology/approach

Java is the perfect language for this task; it yields high-quality graphics and is widely spread in the scientific community. Because many important physical models are described by means of partial differential equations (PDEs), the combination of Java with FreeFem++, a C++ PDE solver based on the finite element method, is considered.

Findings

In this study, a Java library is introduced to numerically solve PDE equations via a run-time connection with FreeFem++. The solution is encapsulated into Java objects that are ready to be used in different programming tasks. The library also includes new Java visualization elements for solutions and meshes in the context of the Open Source Physics project library. Together, the connection features and the visualization elements facilitate the creation of Java simulations by programming researchers. For those with less programming capabilities, this work has been included into Easy Java Simulations, a tool to further ease the creation of interactive simulations.

Originality/value

The present study approach allows simulating models given PDEs. The equations are solved either in local or in remote mode (e.g. by a network accessible to a high-performance computer) and visualized locally, providing a high degree of interactivity to the end user.
MHD squeezing flow between two parallel disks with suction or injection via Legendre wavelet-quasilinearization technique
Authors: Mohyud-din Syed Tauseef , Iqbal Muhammad Asad , Khan Umar , Yang Xiao-Jun
Published: March 2017

Purpose

This paper aims to propose a method by merging Legendre wavelets method and quasilinearization technique to tackle with the nonlinearity and to get better and more accurate results.

Design/methodology/approach

To test the significance of the proposed scheme, the authors applied the method on the model representing magneto-hydrodynamic squeezing flow of a viscous fluid between two parallel infinite disks, where one disk is impermeable and the other is porous with either suction or injection of the fluid. For the sake of comparison, numerical solution by using RK-4 is also computed. From the graphs and tables, it is evident that the proposed method shows an excellent accordance with the numerical solution.

Findings

The solution converges to the numerical solution when the degree of Legendre polynomials m is increased. For m = 20 in all the three cases, for different values of S, M and A, the graphs of solutions obtained by Legendre wavelet quasilinearization technique show an excellent agreement with numerical solution. Also, it is evident from figures that suction and injection affects the velocity profile in opposite way. For suction, maximum velocity is seen to be at the center of the channel. Magnetic field can be used to regularize the flow and it stabilizes the flow behavior.

Originality/value

Magnetic field can be used to regularize the flow and it stabilizes the flow behavior.
International construction joint ventures between Singapore and developing countries
Authors: Hwang Bon-Gang , Zhao Xianbo , Chin Eileen Wei Yan
Published: March 2017

Purpose

The purposes of this paper is twofold: first, to assess the risks associated with the international construction joint ventures (ICJVs) between Singapore and developing countries and second, to investigate the risk allocation preferences in these ICJVs.

Design/methodology/approach

A questionnaire survey was conducted and responses were received from 38 firms that had participated in ICJVs with developing countries. A risk criticality (RC) index was adopted to evaluate the criticality of each risk.

Findings

The survey results reported “political instability” as the most critical risk and market-level risks were less critical than country and project-level risks. Additionally, the results showed agreement on the risk ranking between building and infrastructure ICJVs, despite significant differences in the criticalities of five risks. Furthermore, five risks were preferably allocated to host and foreign partners, respectively, while 13 risks could be shared among partners.

Research limitations/implications

First, due to the sample size, one should be cautious when interpreting and generalizing the results. Second, the RC index proposed in this study was subjective as it was influenced by the individual experience and risk attitude of the respondents. Also, the RC values were calculated without considering the weights of the respondents. Lastly, the questionnaire survey, which has been widely used in identifying risk allocation preferences, may not identify the insights of practitioners into the risk allocation practices.

Practical implications

This study provides a clear understanding of the risks associated with forming ICJVs with developing countries and the preferred risk allocation. Although, this study is focused on the risks faced by the Singapore-developing country ICJVs, the identification of the potential risks allows companies from other countries to customize their risk profile and assess the risks before they form ICJVs with developing countries.

Originality/value

As few studies have explored the risk allocation preferences in ICJVs, this study expands the literature and provides practitioners with important information for preparing joint venture contracts or agreements. Thus, this study can contribute to the literature relating to ICJVs.
Participatory design, wicked problems, choosing by advantages
Authors: Kpamma Zoya Evans , Adjei-Kumi Theophilus , Ayarkwa Joshua , Adinyira Emmanuel
Published: March 2017

Purpose

The phenomenon of wicked problems is inextricably associated with a design process, especially participatory design. The management of wicked problems in participatory design, however, remains largely unexplored. The purpose of this paper is to explore the use of the choosing by advantages (CBA) decision system to manage wicked problems in participatory design.

Design/methodology/approach

Two case studies, involving the application of CBA to make typical participatory design decisions, are evaluated to establish how responsively the CBA decision system operates in the midst of wicked problems in participatory design.

Findings

Findings point to the exploitability of some elements and attributes of the CBA process to manage wicked problems in participatory design, to some extent. The observed collaborative attributes of CBA is particularly helpful and play a key role in mitigating the adverse effects of wicked problems on collaboration in this regard.

Practical implications

The recommendation of the paper is the incorporation of CBA in the development of stakeholder involvement frameworks for a design process.

Originality/value

This paper contributes to knowledge on relying on elements and the attributes of a decision-making system, such as CBA, to manage stakeholder involvement in the design process, particularly focussing on wicked problems. The CBA decision system still remains emergent regarding its application and research in the AEC industry.
Mapping the knowledge flow in sustainable construction project teams using social network analysis
Authors: Schröpfer Veronika Lilly Meta , Tah Joe , Kurul Esra
Published: March 2017

Purpose

The purpose of this paper is to examine knowledge transfer (KT) practices in five construction projects delivering sustainable office buildings in Germany and the UK by using social network analysis (SNA).

Design/methodology/approach

Case studies were adopted as research strategy, with one construction project representing one case study. A combination of quantitative data, social network data and some qualitative data on perceptions of the sustainable construction process and its KT were collected through questionnaires. The data were analysed using a combination of descriptive statistics, cross-tabulations, content analysis and SNA. This resulted in a KT map of each sustainable construction project.

Findings

The findings resulted in a better understanding of how knowledge on sustainable construction is transferred and adopted. They show that large amounts of tacit knowledge were transferred through strong ties in sparse networks.

Research limitations/implications

The findings could offer a solution to secure a certain standard of sustainable building quality through improved KT. The findings indicate a need for further research and discussion on network density, tie strength and tacit KT.

Originality/value

This paper contributes to the literature on KT from a social network perspective. It provides a novel approach through combining concepts of network structure and relatedness in tie contents regarding specialised knowledge, i.e. sustainable construction knowledge. Thereby it provides a robust approach to mapping knowledge flows in office building projects that aim to achieve high levels of sustainability standards.
Analysis of delays in Tanzanian construction industry
Authors: Sambasivan Murali , Deepak T.J. , Salim Ali Nasoor , Ponniah Venishri
Published: March 2017

Purpose

The purpose of this paper is twofold: first, to develop theoretical underpinnings using TCE, and second, to run the analysis using an advanced tool such as structural equation modeling (SEM).

Design/methodology/approach

This study was conducted in the construction industry in Tanzania. A questionnaire-based survey method was used. A total of 308 respondents participated in the study. The relationships between the cause and effect factors were analyzed using SEM.

Findings

The important findings are as follows:cost overrun can be explained by consultant-related and material-related factors; disputes can be explained by cost overrun; arbitration can be explained by consultant-related, cost overrun, and dispute factors; litigation can be explained by client-related, disputes, and arbitration factors; and abandonment can be explained by consultant-related, external-related, disputes, arbitration, and litigation factors.

Originality/value

The main contributions of this study are theoretical development and comprehensive analyses of “cause” and “effect” factors of delays in the construction industry.
Managing housing needs of post conflict housing reconstruction: Sri Lankan perspective
Authors: Seneviratne Krisanthi , Amaratunga Dilanthi , Haigh Richard
Published: March 2017

Purpose

Post conflict housing reconstruction is crucial to development and peacekeeping. However, the success of it, is hindered by a number of problems related to a lack of addressing housing needs. The purpose of this paper is to explore how such housing needs can be effectively managed in post conflict housing reconstruction in Sri Lanka.

Design/methodology/approach

Using the grounded theory method as the research strategy, unstructured interviews were conducted with policy makers, practitioners, beneficiaries and academics in Sri Lanka. Data were analysed using open, axial and selective coding to develop the theoretical framework.

Findings

The study reveals the challenges, contributing factors and strategies in addressing housing needs of accessibility, habitability, affordability, location, facilities, cultural considerations and security of land tenure. It also identifies the gaps and recommendations. The paper establishes the links between these and presents a theoretical framework for managing housing needs effectively in post conflict housing reconstruction in Sri Lanka.

Practical implications

This research enhances the success of post conflict housing reconstruction through addressing housing needs effectively, which contributes to sustainable housing development after conflicts.

Originality/value

The study combines the literature from five main areas: conflicts, post conflict, post conflict reconstruction, post conflict housing reconstruction and housing needs and provides a better understanding on how the housing needs can be managed during post conflict housing reconstruction in developing countries based on empirical evidence.