bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries
Authors: Ávila-Arcos María C. , Sandoval-Velasco Marcela , Schroeder Hannes , Carpenter Meredith L. , Malaspinas Anna-Sapfo , Wales Nathan , Peñaloza Fernando , Bustamante Carlos D. , Gilbert M. Thomas P.
Published: July 2014

The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing.

We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments.

Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries.

Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
Authors: Ha Gavin , Roth Andrew , Khattra Jaswinder , Ho Julie , Yap Damian , Prentice Leah M. , Melnyk Nataliya , McPherson Andrew , Bashashati Ali , Laks Emma , Biele Justina , Ding Jiarui , Le Alan , Rosner Jamie , Shumansky Karey , Marra Marco A. , Gilks C. Blake , Huntsman David G. , McAlpine Jessica N. , Aparicio Samuel , Shah Sohrab P.
Published: July 2014

The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN.
Auxin and Strigolactone Signaling Are Required for Modulation of Arabidopsis Shoot Branching by Nitrogen Supply
Authors: de Jong Maaike , George Gilu , Ongaro Veronica , Williamson Lisa , Willetts Barbara , Ljung Karin , McCulloch Hayley , Leyser Ottoline
Published: July 2014

The degree of shoot branching is strongly affected by environmental conditions, such as nutrient availability. Here we demonstrate that nitrate limitation reduces shoot branching in Arabidopsis (Arabidopsis thaliana) both by delaying axillary bud activation and by attenuating the basipetal sequence of bud activation that is triggered following floral transition. Ammonium supply has similar effects, suggesting that they are caused by plant nitrogen (N) status, rather than direct nitrate signaling. We identify increased auxin export from active shoot apices, resulting in increased auxin in the polar auxin transport stream of the main stem, as a likely cause for the suppression of basal branches. Consistent with this idea, in the auxin response mutant axr1 and the strigolactone biosynthesis mutant more axillary growth1, increased retention of basal branches on low N is associated with a failure to increase auxin in the main stem. The complex interactions between the hormones that regulate branching make it difficult to rule out other mechanisms of N action, such as up-regulation of strigolactone synthesis. However, the proposed increase in auxin export from active buds can also explain how reduced shoot branching is achieved without compromising root growth, leading to the characteristic shift in relative biomass allocation to the root when N is limiting.
Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem
Authors: Lakshmanan Venkatachalam , Selvaraj Gopinath , Bais Harsh P.
Published: July 2014

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.
Crystal structures and catalytic mechanism of theC-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway
Authors: Dai Ya-Nan , Zhou Kang , Cao Dong-Dong , Jiang Yong-Liang , Meng Fei , Chi Chang-Biao , Ren Yan-Min , Chen Yuxing , Zhou Cong-Zhao
Published: July 2014

Saccharomyces cerevisiaeCoq5 is anS-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the onlyC-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2 Å resolution and in the SAM-bound form (Coq5-SAM) at 2.4 Å resolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule.
Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting
Authors: Farley Christopher , Burks Geoffry , Siegert Thomas , Juers Douglas H.
Published: July 2014

In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection.
High-resolution structures of mutants of residues that affect access to the ligand-binding cavity of human lipocalin-type prostaglandin D synthase
Authors: Perduca Massimiliano , Bovi Michele , Bertinelli Mattia , Bertini Edoardo , Destefanis Laura , Carrizo Maria E. , Capaldi Stefano , Monaco Hugo L.
Published: July 2014

Lipocalin-type prostaglandin D synthase (L-PGDS) catalyzes the isomerization of the 9,11-endoperoxide group of PGH2(prostaglandin H2) to produce PGD2(prostaglandin D2) with 9-hydroxy and 11-keto groups. The product of the reaction, PGD2, is the precursor of several metabolites involved in many regulatory events. L-PGDS, the first member of the important lipocalin family to be recognized as an enzyme, is also able to bind and transport small hydrophobic molecules and was formerly known as β-trace protein, the second most abundant protein in human cerebrospinal fluid. Previous structural work on the mouse and human proteins has focused on the identification of the amino acids responsible and the proposal of a mechanism for catalysis. In this paper, the X-ray structures of the apo and holo forms (bound to PEG) of the C65A mutant of human L-PGDS at 1.40 Å resolution and of the double mutant C65A/K59A at 1.60 Å resolution are reported. The apo forms of the double mutants C65A/W54F and C65A/W112F and the triple mutant C65A/W54F/W112F have also been studied. Mutation of the lysine residue does not seem to affect the binding of PEG to the ligand-binding cavity, and mutation of a single or both tryptophans appears to have the same effect on the position of these two aromatic residues at the entrance to the cavity. A solvent molecule has also been identified in an invariant position in the cavity of virtually all of the molecules present in the nine asymmetric units of the crystals that have been examined. Taken together, these observations indicate that the residues that have been mutated indeed appear to play a role in the entrance–exit process of the substrate and/or other ligands into/out of the binding cavity of the lipocalin.
Structure of the virulence-associated protein VapD from the intracellular pathogenRhodococcus equi
Authors: Whittingham Jean L. , Blagova Elena V. , Finn Ciaran E. , Luo Haixia , Miranda-CasoLuengo Raúl , Turkenburg Johan P. , Leech Andrew P. , Walton Paul H. , Murzin Alexey G. , Meijer Wim G. , Wilkinson Anthony J.
Published: July 2014

Rhodococcus equiis a multi-host pathogen that infects a range of animals as well as immune-compromised humans. Equine and porcine isolates harbour a virulence plasmid encoding a homologous family of virulence-associated proteins associated with the capacity ofR. equito divert the normal processes of endosomal maturation, enabling bacterial survival and proliferation in alveolar macrophages. To provide a basis for probing the function of the Vap proteins in virulence, the crystal structure of VapD was determined. VapD is a monomer as determined by multi-angle laser light scattering. The structure reveals an elliptical, compact eight-stranded β-barrel with a novel strand topology and pseudo-twofold symmetry, suggesting evolution from an ancestral dimer. Surface-associated octyl-β-D-glucoside molecules may provide clues to function. Circular-dichroism spectroscopic analysis suggests that the β-barrel structure is preceded by a natively disordered region at the N-terminus. Sequence comparisons indicate that the core folds of the other plasmid-encoded virulence-associated proteins fromR. equistrains are similar to that of VapD. It is further shown that sequences encoding putativeR. equiVap-like proteins occur in diverse bacterial species. Finally, the functional implications of the structure are discussed in the light of the unique structural features of VapD and its partial structural similarity to other β-barrel proteins.
Structure of the type VI secretion phospholipase effector Tle1 provides insight into its hydrolysis and membrane targeting
Authors: Hu Haidai , Zhang Heng , Gao Zengqiang , Wang Dongqi , Liu Guangfeng , Xu Jianhua , Lan Ke , Dong Yuhui
Published: July 2014

A diverse superfamily of phospholipases consisting of the type VI lipase effectors Tle1–Tle5 secreted by the bacterial type VI secretion system (T6SS) have recently been identified as antibacterial effectors that hydrolyze membrane phospholipids. These effectors show no significant homology to known lipases, and their mechanism of membrane targeting and hydrolysis of phospholipids remains unknown. Here, the crystal structure of Tle1 (∼96.5 kDa) fromPseudomonas aeruginosarefined to 2.0 Å resolution is reported, representing the first structure of this superfamily. Its overall structure can be divided into two distinct parts, the phospholipase catalytic module and the putative membrane-anchoring module; this arrangement has not previously been observed in known lipase structures. The phospholipase catalytic module has a canonical α/β-hydrolase fold and mutation of any residue in the Ser-Asp-His catalytic triad abolishes its toxicity. The putative membrane-anchoring module adopts an open conformation composed of three amphipathic domains, and its partial folds are similar to those of several periplasmic or membrane proteins. A cell-toxicity assay revealed that the putative membrane-anchoring module is critical to Tle1 antibacterial activity. A molecular-dynamics (MD) simulation system in which the putative membrane-anchoring module embedded into a bilayer was stable over 50 ns. These structure–function studies provide insight into the hydrolysis and membrane-targeting process of the unique phospholipase Tle1.
Mapping the conformational space accessible to catechol-O-methyltransferase
Authors: Ehler Andreas , Benz Jörg , Schlatter Daniel , Rudolph Markus G.
Published: July 2014

Methylation catalysed by catechol-O-methyltransferase (COMT) is the main pathway of catechol neurotransmitter deactivation in the prefrontal cortex. Low levels of this class of neurotransmitters are held to be causative of diseases such as schizophrenia, depression and Parkinson's disease. Inhibition of COMT may increase neurotransmitter levels, thus offering a route for treatment. Structure-based drug design hitherto seems to be based on the closed enzyme conformation. Here, a set of apo, semi-holo, holo and Michaelis form crystal structures are described that define the conformational space available to COMT and that include likely intermediates along the catalytic pathway. Domain swaps and sizeable loop movements around the active site testify to the flexibility of this enzyme, rendering COMT a difficult drug target. The low affinity of the co-substrateS-adenosylmethionine and the large conformational changes involved during catalysis highlight significant energetic investment to achieve the closed conformation. Since each conformation of COMT is abona fidetarget for inhibitors, other states than the closed conformation may be promising to address. Crystallographic data for an alternative avenue of COMT inhibition,i.e.locking of the apo state by an inhibitor, are presented. The set of COMT structures may prove to be useful for the development of novel classes of inhibitors.
Pushing the limits of sulfur SAD phasing:de novostructure solution of the N-terminal domain of the ectodomain of HCV E1
Authors: El Omari Kamel , Iourin Oleg , Kadlec Jan , Fearn Richard , Hall David R. , Harlos Karl , Grimes Jonathan M. , Stuart David I.
Published: July 2014

Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.
Processing of X-ray snapshots from crystals in random orientations
Authors: Kabsch Wolfgang
Published: July 2014

A functional expression is introduced that relates scattered X-ray intensities from a still or a rotation snapshot to the corresponding structure-factor amplitudes. The new approach was implemented in the programnXDSfor processing monochromatic diffraction images recorded by a multi-segment detector where each exposure could come from a different crystal. For images containing indexable spots, the intensities of the expected reflections and their variances are obtained by profile fitting after mapping the contributing pixel contents to the Ewald sphere. The varying intensity decline owing to the angular distance of the reflection from the surface of the Ewald sphere is estimated using a Gaussian rocking curve. This decline is dubbed `Ewald offset correction', which is well defined even for still images. Together with an image-scaling factor and other corrections, an explicit expression is defined that predicts each recorded intensity from its corresponding structure-factor amplitude. All diffraction parameters, scaling and correction factors are improved by post-refinement. The ambiguous case of a lower point group than the lattice symmetry is resolved by a method reminiscent of the technique of `selective breeding'. It selects the indexing alternative for each image that yields, on average, the highest correlation with intensities from all other images. Processing a test set of rotation images byXDSand treating the same images bynXDSas snapshots of crystals in random orientations yields data of comparable quality, clearly indicating an anomalous signal from Se atoms.
Identifying, studying and making good use of macromolecular crystals
Authors: Calero Guillermo , Cohen Aina E. , Luft Joseph R. , Newman Janet , Snell Edward H.
Published: July 2014

Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.
The new paradigm of collection management in university libraries: from crisis to revolution
Authors: San Jose Montano Blanca
Published: July 2014

Purpose

– This paper aims to argue regarding the evolution of the collection management as a gradual process where internal and external factors interact to transform the collection and its management activities. In this progress, cooperation is used as a necessary strategy for assuming its roles and to fit the new goals, mission and context of the library. Libraries are living organisms in continuous change to adapt to the context where they exist and which is the cause of their progress. It is formed by “vital elements” such as the collection – which is its basic element and the nucleus of its activity.

Design/methodology/approach

– This argumentative paper establishes a logical reasoning of the evolution process of the “collection management”, with the application of Kuhn’s structure of scientific revolutions.

Findings

– The library collection has had great changes, such as its origin, composition, ownership, volume and diversity, different life cycle from paper to digital formats and evaluation process. These changes have affected the principles and practices of collection management in three key areas: expansion and change of traditional activities in collection management; enlargement and modification of agents involved; and fundamental mission of giving access to all information resources needed by actual or potential remote users. The “cooperation” becomes an essential element and the main engine of great part of the collection management.

Originality/value

– In this paper, Kuhn’s structure of scientific revolutions theory is used to establish the evolution of the collection management, to become a revolution, with a new paradigm “cooperative collection management”.
Andy Warhol: documentaries and biographical films
Authors: Joan Kelly Elizabeth
Published: July 2014

Purpose

– This paper aims to compile an annotated list of films about or pertaining to the artist Andy Warhol.

Design/methodology/approach

– Films were located using library catalogs, databases and online searches. Selections were evaluated through inspection and both academic and popular film reviews. Inclusion was predicated not only on subject matter and merit but also on availability either on home media or online.

Findings

– Warhol’s many artistic creations can be introduced and evaluated using a combination of visual and auditory representation. Movies and television (TV) depicting Warhol through dramatization, primary source film, biographical documentary and his art in the context of other artists and movements are readily available through a variety of media.

Originality/value

– The selected titles provide a comprehensive introduction to the scholarly analysis of Warhol’s art and work through a format that allows the most extensive representation of Warhol’s artistic output.
A two-step model to optimise transcutaneous electrical stimulation of the human upper arm
Authors: Goffredo Michela , Schmid Maurizio , Conforto Silvia , Bilotti Filiberto , Palma Claudio , Vegni Lucio , D’Alessio Tommaso
Published: July 2014

Purpose

– A novel model of the upper arm under transcutaneous electrical stimulation with multi-pad electrodes is presented and experimentally validated. The model aims at simulating and analysing the effects of surface electrical stimulation on biceps brachii. The paper aims to discuss these issues.

Design/methodology/approach

– Both the passive properties of tissues surrounding nerve bundles and the active characteristics of the nervous system are included. The output of the proposed model is nerve recruitment and muscle contraction.

Findings

– Simulations and experimental tests on six healthy young adults have been conducted and results show that the proposed model gives information on electrically elicited muscle contraction in accordance with in-vivo tests and literature on motor unit recruitment order. Tests with different electrodes configurations show that the spatial distribution of active electrodes is a critical factor in electrically elicited muscle contractions, and that multi-pad electrodes can optimise the stimulation effectiveness and patient comfort with sequences of biphasic pulses of 350 μs at 30 pulses/s and threshold values of 2 mA.

Originality/value

– Results encourage the use of the proposed model of the upper arm as a valid and viable solution for predicting the behaviour of the neuromuscular system when surface electrical stimulation is applied, thus optimising the design of neuroprosthetics.
A multi-valve controlled saturable reactor and its harmonic optimization
Authors: Wang Yifan , Chen Guozhu
Published: July 2014

Purpose

– As arc suppression coils (ASCs), magnetically controlled reactors (MCRs) are usually operated in the single-phase mode. Due to the lack of a third order harmonic compensation circuit, the current harmonics are high. The purpose of this paper is to propose a novel structure of MCR and a genetic algorithm (GA) to determine the parameters which will result in minimum total harmonics.

Design/methodology/approach

– This paper proposes the structure and the working principle of the multi-valve controlled saturable reactor (MCSR). There are several sorts of magnetic valves in the iron cores of the MCSR. The saturation degree of each magnetic valve is different when the same direct component of the magnetic flux is generated in the iron core, therefore current harmonics of different phases emerging, i.e. the total harmonics can be reduced. The magnetization characteristics and the mathematical model of the current harmonics of the MCSR are presented by introducing three parameters. The optimal values of the parameters that result in the smallest total harmonic distortion in the output current are calculated by a GA.

Findings

– The simulation and experimental results are coincident with the theoretical analyses, which prove the effectiveness of the proposed method on harmonic suppression.

Practical implications

– The method proposed in this paper can successfully reduce the current harmonics of the conventional MCR, including but not limited to the ASC. A prototype MCSR (540 kVA/10 kV) has been designed and constructed.

Originality/value

– In this paper, a MCSR is proposed. The mathematical model of the MCSR for harmonic analysis is developed. The optimal parameters that result in the smallest THD in the output current are calculated. The mathematical model can be also used for the harmonic analysis of conventional MCRs.
Through silicon vias: from a physical point of view to a compact models initiation
Authors: Sun Fengyuan , Lorival Jean-Etienne , Calmon Francis , Gontrand Christian
Published: July 2014

Purpose

– The substrate coupling and loss in integrated circuits are analyzed. Then, the authors extract impedances between any numbers of embedded contacts. The paper aims to discuss these issues.

Design/methodology/approach

– The paper proposes a new substrate network 3D extraction technique, adapted from a transmission line method or Green kernels, but in the whole volume.

Findings

– Extracting impedances between any numbers of embedded contacts with variable shapes or/and through silicon via. This 3D method is much faster comparing with FEM

Originality/value

– Previous works consider TSVs alone, contacts onto the substrate. The authors do study entanglement between the substrate and the interconnections.
A novel and fast voltage estimation scheme for assessment of power system component outages
Authors: Masoud Fatemi Seyed , Abedi Mehrdad , Vahidi Behrooz , Abedi Sajjad , Rastegar Hassan
Published: July 2014

Purpose

– The purpose of this paper is to pursue two following main goals: first, theorizing a new concept named as equivalent bus load in order to make a promising simplification over power system analysis. Second, proposing an outstanding fast and simple approach based on introduced concept for voltage estimation after multiple component outages while satisfying required accuracy.

Design/methodology/approach

– Equivalent load bus theory introduces three transfer matrices that describe power system topology. Mentioned matrices could be calculated simply after system reconfiguration without matrix inversion. Using transfer matrices a large-scale power system can be modeled by a simple two-bus power system from the viewpoint of any desired bus so that load flow calculation leads to same value. The analysis of simplified power system yields to extract a new incremental model based on equivalent bus load theory that will be distinguished as an outstanding fast method for voltage estimation aim.

Findings

– A deep study for fast voltage estimation aim is dedicated to evaluate proposed method from the accuracy and quickness point of view and the outcomes are compared to a well-known method as Distribution Factors (DF). Results and computational times unveil that presented approach is more accurate and much faster.

Originality/value

– A novel and new fast voltage estimation method for assessment of power system component outages is introduced.
Iso-geometric shape optimization of magnetic density separators
Authors: Dang Manh Nguyen , Evgrafov Anton , Gravesen Jens , Lahaye Domenico
Published: July 2014

Purpose

– The waste recycling industry increasingly relies on magnetic density separators. These devices generate an upward magnetic force in ferro-fluids allowing to separate the immersed particles according to their mass density. Recently, a new separator design has been proposed that significantly reduces the required amount of permanent magnet material. The purpose of this paper is to alleviate the undesired end-effects in this design by altering the shape of the ferromagnetic covers of the individual poles.

Design/methodology/approach

– The paper represents the shape of the ferromagnetic pole covers with B-splines and defines a cost functional that measures the non-uniformity of the magnetic field in an area above the poles. The authors apply an iso-geometric shape optimization procedure, which allows us to accurately represent, analyze and optimize the geometry using only a few design variables. The design problem is regularized by imposing constraints that enforce the convexity of the pole cover shapes and is solved by a non-linear optimization procedure. The paper validates the implementation of the algorithm using a simplified variant of the design problem with a known analytical solution. The algorithm is subsequently applied to the problem posed.

Findings

– The shape optimization attains its target and yields pole cover shapes that give rise to a magnetic field that is uniform over a larger domain.

Research limitations/implications

– This increased magnetic field uniformity is obtained at the cost of a pole cover shape that differs per pole. This limitation has negligible impact on the manufacturing of the separator. The new pole cover shapes therefore lead to improved performance of the density separation.

Practical implications

– Due to the larger uniformity the generated field, these shapes should enable larger amounts of waste to be processed than the previous design.

Originality/value

– This paper treats the shapes optimization of magnetic density separators systematically and presents new shapes for the ferromagnetic poles covers.
Broadband surface impedance boundary conditions for higher order time domain discontinuous Galerkin method
Authors: Woyna Irene , Gjonaj Erion , Weiland Thomas
Published: July 2014

Purpose

– The purpose of this paper is to present a time domain discontinuous Galerkin (DG) approach for modeling wideband frequency dependent surface impedance boundary conditions.

Design/methodology/approach

– The paper solves the Maxwellian initial value problem in a computational domain, which is spatially discretized by the higher order DG method. On the boundary of the computational domain the paper applies a suitable impedance boundary condition (IBC). The frequency dependency of the impedance function is modeled by auxiliary differential equations (ADE).

Findings

– The authors will study the resonance frequency and the Q factor of different types of cavity resonators including lossy materials. The lossy materials are modeled by means of IBCs. The authors will compare the results with analytical results, as well as numerical results obtained by direct calculations where lossy materials are included explicitly into the numerical model. Several convergence studies are performed which demonstrate the accuracy of the approach.

Originality/value

– Modeling of frequency dependent boundary conditions in time domain with finite difference time domain method (FDTD) method is considered in numerous papers, as well as in frequency domain finite element method (FEM), and in a few papers also time domain FEM. However, FDTD method is only first order accurate and fails in modeling of complicated surfaces. FEM allows for high order accuracy, but time domain modeling is numerically extremely expensive. In frequency domain, broadband modeling of frequency dependent boundary conditions requires several simulations as opposed to the time domain, where a single simulation is needed. The time domain DG method proposed in this paper allows to overcome the difficulties. The authors introduce a broadband surface impedance formulation based on the ADE approach for the higher order DG method.
Heat generation in silicon nanometric semiconductor devices
Authors: Muscato Orazio , Wagner Wolfgang , Di Stefano Vincenza
Published: July 2014

Purpose

– The purpose of this paper is to deal with the self-heating of semiconductor nano-devices.

Design/methodology/approach

– Transport in silicon semiconductor devices can be described using the Drift-Diffusion model, and Direct Simulation Monte Carlo (MC) of the Boltzmann Transport Equation.

Findings

– A new estimator of the heat generation rate to be used in MC simulations has been found.

Originality/value

– The new estimator for the heat generation rate has better approximation properties due to reduced statistical fluctuations.
Polynomial fitting of nonlinear sources with correlating inputs
Authors: P. Aikio Janne , Rahkonen Timo , Karanko Ville
Published: July 2014

Purpose

– The purpose of this paper is to propose methods to improve the least square error polynomial fitting of multi-input nonlinear sources that suffer from strong correlating inputs.

Design/methodology/approach

– The polynomial fitting is improved by amplitude normalization, reducing the order of the model, utilizing Chebychev polynomials and finally perturbing the correlating controlling voltage spectra. The fitting process is estimated by the reliability figure and the condition number.

Findings

– It is shown in the paper that perturbing one of the controlling voltages reduces the correlation to a large extend especially in the cross-terms of the multi-input polynomials. Chebychev polynomials reduce the correlation between the higher-order spectra derived from the same input signal, but cannot break the correlation between correlating input and output voltages.

Research limitations/implications

– Optimal perturbations are sought in a separate optimization loop, which slows down the fitting process. This is due to the fact that each nonlinear source that suffers from the correlation needs a different perturbation.

Originality/value

– The perturbation, harmonic balance run and refitting of an individual nonlinear source inside a device model is new and original way to characterize and fit polynomial models.
Extended Brauer model for ferromagnetic materials: analysis and computation
Authors: Hülsmann Timo , Bartel Andreas , Schöps Sebastian , De Gersem Herbert
Published: July 2014

Purpose

– The purpose of this paper is to develop a fast and accurate analytic model function for the single-valued H-B curve of ferromagnetic materials, where hysteresis can be disregarded (normal magnetization curve). Nonlinear magnetoquasistatic simulations demand smooth monotone material models to ensure physical correctness and good convergence in Newton's method.

Design/methodology/approach

– The Brauer model has these beneficial properties, but is not sufficiently accurate for low and high fields in the normal magnetization curve. The paper extends the Brauer model to better fit material behavior in the Rayleigh region (low fields) and in full saturation. Procedures for obtaining optimal parameters from given measurement points are proposed and tested for two technical materials. The approach is compared with cubic spline and monotonicity preserving spline interpolation with respect to error and computational effort.

Findings

– The extended Brauer model is more accurate and even maintains the computational advantages of the classical Brauer model. The methods for obtaining optimal parameters yield good results if the measurement points have a distinctive Rayleigh region.

Originality/value

– The model function for ferromagnetic materials enhances the precision of the classical Brauer model without notable additional simulation cost.
Modeling of streamers in transformer oil using OpenFOAM
Authors: Lavesson Nils , Jogenfors Jonathan , Widlund Ola
Published: July 2014

Purpose

– A model for streamers based on charge transport has been developed by MIT and ABB. The purpose of this paper is to investigate the consequences of changing numerical method from the finite element method (FEM) to the finite volume method (FVM) for simulations using the streamer model. The new solver is also used to extend the simulations to 3D.

Design/methodology/approach

– The equations from the MIT-ABB streamer model are implemented in OpenFOAM which uses the FVM. Checks of the results are performed including verification of convergence. The solver is then applied to some of the key simulations from the FEM model and results presented.

Findings

– The results for second mode streamers are confirmed, whereas the results for third mode streamers differ significantly leading to questioning of one hypothesis proposed based on the FEM results. The 3D simulations give consistent results and show a way forward for future simulations.

Originality/value

– The FVM has not been applied to the model before and led to more confidence in second mode result and revising of third mode results. In addition the new simulation method makes it possible to extend the results to 3D.
Index-aware model order reduction: LTI DAEs in electric networks
Authors: Banagaaya N. , Schilders W.H.A. , Alì G. , Tischendorf C.
Published: July 2014

Purpose

– Model order reduction (MOR) has been widely used in the electric networks but little has been done to reduce higher index differential algebraic equations (DAEs). The paper aims to discuss these issues.

Design/methodology/approach

– Most methods first do an index reduction before reducing a higher DAE but this can lead to a loss of physical properties of the system.

Findings

– The paper presents a MOR method for DAEs called the index-aware MOR (IMOR) which can reduce a DAE while preserving its physical properties such as the index. The feasibility of this method is tested on real-life electric networks.

Originality/value

– MOR has been widely used to reduce large systems from electric networks but little has been done to reduce higher index DAEs. Most methods first do an index reduction before reducing a large system of DAEs but this can lead to a loss of physical properties of the system. The paper presents a MOR method for DAEs called the IMOR which can reduce a DAE while preserving its physical properties such as the index. The feasibility of this method is tested on real-life electric networks.
Convergence behaviour of coupled pressure and thermal networks
Authors: Blaszczyk Andreas , Flückiger Reto , Müller Thomas , Olsson Carl-Olof
Published: July 2014

Purpose

– The purpose of this paper is to present a method for thermal computations of power devices based on a coupling between thermal and pressure networks. The concept of the coupling as well as the solution procedure is explained. The included examples demonstrate that the new method can be efficiently used for design of transformers and other power devices.

Design/methodology/approach

– The bidirectional propagation of temperature signal is introduced to the pressure network, which enables control of the power flow and a close coupling to the thermal network. The solution method is based on automatic splitting of the network definition (netlist) into two separate networks and iteratively solving the model using the Newton-Raphson approach as well as the adaptive relaxation enhanced by the direction change control.

Findings

– The proposed approach offers reliable convergence behaviour even for models with unknown direction of the fluid flow (bidirectional flows). The accuracy is sufficient for engineering applications and comparable with the computational fluid dynamics method. The computation times in the range of milliseconds and seconds are attractive for using the method in engineering design tools.

Originality/value

– The new method can be considered as a foundation for a consistent network modelling system of arbitrary thermodynamic problems including fluid flow. Such a modelling system can be used directly by device designers since the complexity of thermodynamic formulations is encapsulated in predefined network elements while the numerical solution is based on a standard network description and solvers (Spice).
Challenges facing Islamic Azad University academic leaders in managerial positions
Authors: Hamidifar Fatemeh
Published: July 2014

Purpose

– Over the past three decades, academic leaders at Islamic Azad University (IAU) have been facing different challenges for the success of the institutions. The purpose of this paper is to identify the challenges confronting IAU academic leaders in managerial positions.

Design/methodology/approach

– In this qualitative study, questionnaires containing open-ended questions were sent to academic leaders in managerial positions at IAU branches in Iran and the collected data were analyzed using qualitative content analysis.

Findings

– The results revealed that the main challenges were categorized into two themes: internal and external environmental factors. Internal challenges were sub-categorized into administration and managerial affairs, financial issues, organizational culture, and students’ affairs. External challenges were sub-categorized into political, economic, social, and technological factors, and international and national competitions.

Research limitations/implications

– This study is limited to Iran and IAU academic leaders who worked mainly in high-level and middle-level of managerial positions; therefore, the results cannot be generalized. The key implications are related to applying continuous professional growth through collaborative and qualified development programs. The implications could be appropriate for other higher education institutions in Iran.

Originality/value

– This is the first attempt to study the challenges confronting IAU academic leaders in Iran. The findings can help IAU academic leaders plan the most appropriate framework for professional academic leadership development programs.
Supply chain strategy, flexibility, and performance
Authors: Awais Ahmad Tipu Syed , A. Fantazy Kamel
Published: July 2014

Purpose

– The purpose of this paper is to compare the supply chain strategy, flexibility, and performance relationships in the context of SMEs in Canada and Pakistan.

Design/methodology/approach

– The research is based on a quantitative approach using a questionnaire survey from a total of 170 small and medium-sized Pakistani manufacturing companies. The current study draws upon the earlier work of Fantazy et al. (2009) for comparative purpose and employs path analysis technique.

Findings

– The results partially confirm the findings of previous study on Canadian SMEs with regard to the relationships among strategy, flexibility, and performance in the context of supply chain. The survey results revealed that SMEs in Pakistan adopt followers strategy in order to achieve financial and non-financial performance. Whereas in the previous study, Canadian SMEs adopted innovative strategy and customer-oriented strategy in order to enhance their performance.

Originality/value

– The literature did not reveal any study which attempted to compare supply chain strategy, flexibility, and performance of SMEs in developed and developing countries. The current study fills this important gap in the literature.
What gets suppliers to play and who gets the pay? On the antecedents and outcomes of collaboration in retailer-supplier dyads
Authors: Rossiter Hofer Adriana , Hofer Christian , A. Waller Matthew
Published: July 2014

Purpose

– The purpose of this paper is to adopt and contribute to the further development of the relational view by examining the drivers of retailer-supplier collaboration and its effect on the performance of both the retailer and the supplier.

Design/methodology/approach

– The paper draws its conclusions from a structural analysis of dyadic survey data collected from consumer packaged goods suppliers and retailers in Brazil. In addition, objective retailer performance measures (retailer in-stock performance) are included in the data set.

Findings

– The results indicate that a supplier's customer orientation is an important determinant of supplier relationship-specific investments and, ultimately, supply chain collaboration. The empirical results also indicate that retailers stand to benefit the most from a supplier's collaborative efforts. In addition, there is evidence that a supplier's customer orientation is positively related to its own performance.

Research limitations/implications

– The limited sample size – a result of the dyadic nature of the data – constitutes a limitation and, at the same time, presents opportunities for future, larger-scale studies. Nonetheless, this study highlights the value of customer orientation and collaboration in terms of driving performance outcomes for both suppliers and buyers, while invoking the notion that the benefits of supply chain collaboration accrue differentially over time from the retailers’ and suppliers’ perspectives.

Originality/value

– While many of the relationships set forth in this research have been implicitly assumed by proponents of the relational view, this study furthers the development of the relational view by explicitly modeling supplier relationship-specific investments and customer orientation as antecedents of collaboration. Moreover, the study contributes to the literature on buyer-supplier collaboration by simultaneously exploring to what extent both suppliers and retailers derive benefits from such collaboration.