bluuebunny/crossref_metadata_2025 huggingface dataset:
The catalytically inactive tyrosine phosphatase HD-PTP/PTPN23 is a novel regulator of SMN complex localization
Authors: Husedzinovic Alma , Neumann Beate , Reymann Jürgen , Draeger-Meurer Stefanie , Chari Ashwin , Erfle Holger , Fischer Utz , Gruss Oliver J.
Published: November 2014

The survival motor neuron (SMN) complex fulfils essential functions in the assembly of snRNPs, which are key components in the splicing of pre-mRNAs. Little is known about the regulation of SMN complex activity by posttranslational modification despite its complicated phosphorylation pattern. Several phosphatases had been implicated in the regulation of SMN, including the nuclear phosphatases PPM1G and PP1γ. Here we systematically screened all human phosphatase gene products for a regulatory role in the SMN complex. We used the accumulation of SMN in Cajal bodies of intact proliferating cells, which actively assemble snRNPs, as a readout for unperturbed SMN complex function. Knockdown of 29 protein phosphatases interfered with SMN accumulation in Cajal bodies, suggesting impaired SMN complex function, among those the catalytically inactive, non–receptor-type tyrosine phosphatase PTPN23/HD-PTP. Knockdown of PTPN23 also led to changes in the phosphorylation pattern of SMN without affecting the assembly of the SMN complex. We further show interaction between SMN and PTPN23 and document that PTPN23, like SMN, shuttles between nucleus and cytoplasm. Our data provide the first comprehensive screen for SMN complex regulators and establish a novel regulatory function of PTPN23 in maintaining a highly phosphorylated state of SMN, which is important for its proper function in snRNP assembly.
Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data
Authors: Li Wenyuan , Gong Ke , Li Qingjiao , Alber Frank , Zhou Xianghong Jasmine
Published: November 2014

Summary: Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability—the software is capable of normalizing Hi-C data of any size in reasonable times; (ii) memory efficiency—the sequential version can run on any single computer with very limited memory, no matter how little; (iii) fast speed—the parallel version can run very fast on multiple computing nodes with limited local memory.

Availability and implementation: The sequential version is implemented in ANSI C and can be easily compiled on any system; the parallel version is implemented in ANSI C with the MPI library (a standardized and portable parallel environment designed for solving large-scale scientific problems). The package is freely available at http://zhoulab.usc.edu/Hi-Corrector/.

Contact:  alber@usc.edu or xjzhou@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
pFPL Vectors for High-Throughput Protein Localization in Fungi: Detecting Cytoplasmic Accumulation of Putative Effector Proteins
Authors: Gong Xiaoyan , Hurtado Oscar , Wang Baohua , Wu Congqing , Yi Mihwa , Giraldo Martha , Valent Barbara , Goodin Michael , Farman Mark
Published: November 2014

As part of a large-scale project whose goal was to identify candidate effector proteins in Magnaporthe oryzae, we developed a suite of vectors that facilitate high-throughput protein localization experiments in fungi. These vectors utilize Gateway recombinational cloning to place a gene's promoter and coding sequences upstream and in frame with enhanced cyan fluorescent protein, green fluorescent protein (GFP), monomeric red fluorescence protein (mRFP), and yellow fluorescent protein or a nucleus-targeted mCHERRY variant. The respective Gateway cassettes were incorporated into Agrobacterium-based plasmids to allow efficient fungal transformation using hygromycin or geneticin resistance selection. mRFP proved to be more sensitive than the GFP spectral variants for monitoring proteins secreted in planta; and extensive testing showed that Gateway-derived fusion proteins produced localization patterns identical to their “directly fused” counterparts. Use of plasmid for fungal protein localization (pFPL) vectors with two different selectable markers provided a convenient way to label fungal cells with different fluorescent proteins. We demonstrate the utility of the pFPL vectors for identifying candidate effector proteins and we highlight a number of important factors that must be taken into consideration when screening for proteins that are translocated across the host plasma membrane.
Coordinated Regulation of Arbuscular Mycorrhizal Fungi and Soybean MAPK Pathway Genes Improved Mycorrhizal Soybean Drought Tolerance
Authors: Liu Zhilei , Li Yuanjing , Ma Lina , Wei Haichao , Zhang Jianfeng , He Xingyuan , Tian Chunjie
Published: November 2014

Mitogen-activated protein kinase (MAPK) cascades play important roles in the stress response in both plants and microorganisms. The mycorrhizal symbiosis established between arbuscular mycorrhizal fungi (AMF) and plants can enhance plant drought tolerance, which might be closely related to the fungal MAPK response and the molecular dialogue between fungal and soybean MAPK cascades. To verify the above hypothesis, germinal Glomus intraradices (syn. Rhizophagus irregularis) spores and potted experiments were conducted. The results showed that AMF GiMAPKs with high homology with MAPKs from Saccharomyces cerevisiae had different gene expression patterns under different conditions (nitrogen starvation, abscisic acid treatment, and drought). Drought stress upregulated the levels of fungi and soybean MAPK transcripts in mycorrhizal soybean roots, indicating the possibility of a molecular dialogue between the two symbiotic sides of symbiosis and suggesting that they might cooperate to regulate the mycorrhizal soybean drought-stress response. Meanwhile, the changes in hydrogen peroxide, soluble sugar, and proline levels in mycorrhizal soybean as well as in the accelerated exchange of carbon and nitrogen in the symbionts were contributable to drought adaptation of the host plants. Thus, it can be preliminarily inferred that the interactions of MAPK signals on both sides, symbiotic fungus and plant, might regulate the response of symbiosis and, thus, improve the resistance of mycorrhizal soybean to drought stress.
First Report of Fig mosaic virus Infecting Common Fig (Ficus carica) in China
Authors: Mijit M. , Li S. F. , Zhang S. , Zhang Z. X.
Published: November 2014

The common fig (Ficus carica) is one of the earliest plants domesticated by humans. It has been cultivated in China ever since the early seventh century. Fig fruit is an important traditional Chinese medicine and a fine health food, featuring a unique flavor and rich nutrients. In addition to its great medicinal values, its abundant availability in the Xinjiang province of China has made the fig one of the most popular fruits in the country. One of the major diseases that affect figs is the fig mosaic disease (FMD) (1,4), which was reported in China in 1935 (3). A causal agent of this disease is associated with the Fig mosaic virus (FMV), a negative-strand RNA virus with six RNA segments (2). In 2013, and later during a survey in 2014, fig plants in several orchards in Xinjiang displayed symptoms of a virus-like disease, which was characterized as FMD. These symptoms included chlorotic clearing as well as banding of leaf veins along with various patterns of discoloration, severely distorted leaves, and deformed fruits. Total RNA extracts (TRIzol reagent, Ambion) from 18 symptomatic and four asymptomatic leaf samples were subjected to reverse reaction (RT) assays using M-MLV reverse transcriptase (Promega, Fitchburg, WI) with primer FMV-GP-R (TATTACCTGGATCAACGCAG). PCR analysis of the synthesized cDNA was performed using FMV-specific primers FMV-GP-F (ACTTGCAAAGGCAGATGATA) and FMV-GP-R. Amplicons of 706 bp produced by RT-PCR assays were obtained from most (15 out of 18) of the symptomatic samples; however, none was obtained from the four asymptomatic leaves. The purified amplicons were cloned and sequenced. BLAST analysis of these sequences revealed more than 94% nucleotide identity with glycoprotein precursor (GP) genes of an FMV-Serbia isolate (SB1). One sequence was deposited in NCBI databases, and one sequence was submitted to GenBank (Accession No. KM034915). RNA segments 2 to 6 of FMV were also amplified by RT-PCR and sequenced. These sequences showed 94 to 96% identity with FMV sequences deposited in the NCBI databases. The collected samples were further detected by Northern-blot hybridization with a digoxigenin-labeled RNA probe, which targets the RNA1 genome of the FMV. The result was in line with RT-PCR detection. To our knowledge, this is the first report of FMV in fig trees in China. Considering the economic importance of fig plants and the noxious nature of FMV, this virus poses a great threat to the economy of the fig industry of Xinjiang. Thus, it is important to develop immediate effective quarantine and management of this virus to reduce any further predictable loss.

References: (1) T. Elbeaino et al. J. Gen. Virol. 90:1281, 2009. (2) K. Ishikawa et al. J. Gen. Virol. 93:1612, 2012. (3) H. A. Pittman. J. West Aust. Dept. Agric. 12:196, 1935. (4) J. J. Walia et al. Plant Dis. 93:4, 2009.
Nabumetone and 6-MNA Pharmacokinetics, Assessment of Intrasubject Variability and Gender Effect
Authors: Světlík Svatopluk , Štícha Martin , Matoušková Olga , Nespěšná Lenka , Sklenář Zbyněk , Bartůněk Aleš , Perlík František , Slanař Ondřej
Published: November 2014

In this open-label, laboratory-blinded, 2-way single dose study in 24 volunteers of both sexes we found that (1) nabumetone reaches mean Cmax ± SD of 0.56 ± 0.20 mg·L−1 at mean tmax of 8.63 ± 7.05 hours, and mean area under the curve (AUC)last of 18.07 ± 7.19 h·mg·L−1; (2) there are no statistically significant differences between both sexes in pharmacokinetics of nabumetone; (3) 6-methoxy-2-naphthylacetic acid (6-MNA) reaches higher AUClast in men compared with women (mean ± SD, 721.23 ± 185.53 h·mg·L−1 and 545.27 ± 97.69 h·mg·L−1, respectively; P = 0.013); (4) there is lower 6-MNA clearance in men (0.65 ± 0.22 L·h−1) in comparison with women (0.88 ± 0.18 L·h−1, P = 0.019), (5) intersubject variability of nabumetone and 6-MNA is between 35%–45% and 10%–30% for all assessed pharmacokinetics parameters (AUClast, Cmax, partial AUC values); (6) intrasubject variability (ISCV) for AUClast is low, 15.59% and 6.40% for nabumetone and 6-MNA, respectively, (7) ISCV for Cmax is 13.66% and 5.42% for nabumetone and 6-MNA, respectively. Nabumetone thus belongs to compounds with low to moderate ISCV and therefore this product is expected to produce consistent effects in clinical practice.
A novel Bcr-Abl–mTOR–eIF4A axis regulates IRES-mediated translation of LEF-1
Authors: Tsai Becky Pinjou , Jimenez Judith , Lim Sharon , Fitzgerald Kerry D. , Zhang Min , Chuah Charles T. H. , Axelrod Haley , Nelson Luke , Ong S. Tiong , Semler Bert L. , Waterman Marian L.
Published: November 2014

Internal ribosome entry sites (IRESs) in cellular mRNAs direct expression of growth-promoting factors through an alternative translation mechanism that has yet to be fully defined. Lymphoid enhancer factor-1 (LEF-1), a Wnt-mediating transcription factor important for cell survival and metastasis in cancer, is produced via IRES-directed translation, and its mRNA is frequently upregulated in malignancies, including chronic myeloid leukaemia (CML). In this study, we determined that
LEF1
expression is regulated by Bcr-Abl, the oncogenic protein that drives haematopoietic cell transformation to CML. We have previously shown that the
LEF1
5′ untranslated region recruits a complex of proteins to its IRES, including the translation initiation factor eIF4A. In this report, we use two small molecule inhibitors, PP242 (dual mTOR (mammalian target of rapamycin) kinase inhibitor) and hippuristanol (eIF4A inhibitor), to define IRES regulation via a Bcr-Abl–mTOR–eIF4A axis in CML cell lines and primary patient leukaemias. We found that
LEF1
and other IRESs are uniquely sensitive to the activities of Bcr-Abl/mTOR. Most notably, we discovered that eIF4A, an RNA helicase, elicits potent non-canonical effects on the
LEF1
IRES. Hippuristanol inhibition of eIF4A stalls translation of IRES mRNA and triggers dissociation from polyribosomes. We propose that a combination drug strategy which targets mTOR and IRES-driven translation disrupts key factors that contribute to growth and proliferation in CML.
Proposal to rename Carnobacterium inhibens as Carnobacterium inhibens subsp. inhibens subsp. nov. and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a psychrotolerant bacterium isolated from Siberian permafrost
Authors: Nicholson Wayne L. , Zhalnina Kateryna , de Oliveira Rafael R. , Triplett Eric W.
Published: November 2014

A novel, psychrotolerant facultative anaerobe, strain WN1359T, was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive-staining, non-motile, rod-shaped cells were observed with sizes of 1–2 µm long and 0.4–0.5 µm wide. Growth occurred in the range of pH 5.8–9.0 with optimal growth at pH 7.8–8.6 (pH optimum 8.2). The novel isolate grew at temperatures from 0–37 °C and optimal growth occurred at 25 °C. The novel isolate does not require NaCl; growth was observed between 0 and 8.8 % (1.5 M) NaCl with optimal growth at 0.5 % (w/v) NaCl. The isolate was a catalase-negative, facultatively anaerobic chemo-organoheterotroph that used sugars but not several single amino acids or dipeptides as substrates. The major metabolic end-product was lactic acid in the ratio of 86 % l-lactate : 14 % d-lactate. Strain WN1359T was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin and vancomycin, and resistant to nalidixic acid and aztreonam. The fatty acid content was predominantly unsaturated (70.2 %), branched-chain unsaturated (11.7 %) and saturated (12.5 %). The DNA G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7 % sequence identity between strain WN1359T and

Carnobacterium inhibens

. Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359T belonging to the species

C. inhibens

. On the basis of these results, the permafrost isolate WN1359T represents a novel subspecies of

C. inhibens

, for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed. The type strain is WN1359T ( = ATCC BAA-2557T = DSM 27470T). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is created automatically. An emended description of

C. inhibens

is also provided.
Wide field-of-view, multi-region two-photon imaging of neuronal activityin vivo
Authors: Stirman Jeffrey N. , Smith Ikuko T. , Kudenov Michael W. , Smith Spencer L.
Published: November 2014

We demonstrate a two-photon imaging system with corrected optics including a custom objective that provides cellular resolution across a 3.5 mm field of view (9.6 mm2). Temporally multiplexed excitation pathways can be independently repositioned in XY and Z to simultaneously image regions within the expanded field of view. We used this new imaging system to measure activity correlations between neurons in different cortical areas in awake mice.
TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
Authors: Sammons Morgan A. , Zhu Jiajun , Drake Adam M. , Berger Shelley L.
Published: November 2014

Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide data sets, we examined the relationship between TP53 binding and the dynamics of the local chromatin environment. Our analysis revealed three distinct categories of TP53 binding events that differ based on the dynamics of the local chromatin environment. The first class of TP53 binding events occurs near transcriptional start sites (TSS) and is defined by previously characterized promoter-associated chromatin modifications. The second class comprises a large cohort of preestablished, promoter-distal enhancer elements that demonstrates dynamic histone acetylation and transcription upon TP53 binding. The third class of TP53 binding sites is devoid of classic chromatin modifications and, remarkably, fall within regions of inaccessible chromatin, suggesting that TP53 has intrinsic pioneer factor activity and binds within structurally inaccessible regions of chromatin. Intriguingly, these inaccessible TP53 binding sites feature several enhancer-like properties in cell types within the epithelial lineage, indicating that TP53 binding events include a group of “proto-enhancers” that become active enhancers given the appropriate cellular context. These data indicate that TP53, along with TP63, may act as pioneer factors to specify epithelial enhancers. Further, these findings suggest that rather than following a global cell-type invariant stress response program, TP53 may tune its response based on the lineage-specific epigenomic landscape.
Crystallization and preliminary X-ray characterization of the full-length bacteriophytochrome from the plant pathogenXanthomonas campestrispv.campestris
Authors: Klinke Sebastián , Otero Lisandro H. , Rinaldi Jimena , Sosa Santiago , Guimarães Beatriz G. , Shepard William E. , Goldbaum Fernando A. , Bonomi Hernán R.
Published: November 2014

Phytochromes give rise to the largest photosensor family known to date. However, they are underrepresented in the Protein Data Bank. Plant, cyanobacterial, fungal and bacterial phytochromes share a canonical architecture consisting of an N-terminal photosensory module (PAS2–GAF–PHY domains) and a C-terminal variable output module. The bacteriumXanthomonas campestrispv.campestris, a worldwide agricultural pathogen, codes for a single bacteriophytochrome (XccBphP) that has this canonical architecture, bearing a C-terminal PAS9 domain as the output module. Full-length XccBphP was cloned, expressed and purified to homogeneity by nickel–NTA affinity and size-exclusion chromatography and was then crystallized at room temperature bound to its cofactor biliverdin. A complete native X-ray diffraction data set was collected to a maximum resolution of 3.25 Å. The crystals belonged to space groupP43212, with unit-cell parametersa=b= 103.94,c= 344.57 Å and a dimer in the asymmetric unit. Refinement is underway after solving the structure by molecular replacement.
Crystallization and preliminary X-ray diffraction analysis of UspE fromEscherichia coli
Authors: Xu Yongbin , Quan Chun-Shan , Jin Xuanzhen , Jin Xiaoling , Zhao Jing , Li Xihui , Zheng Wei , Jin Liming , Liu Dedi , Fan Shengdi , Ha Nam-Chul
Published: November 2014

Universal stress proteins (Usps) are among the most highly induced genes when bacteria are subjected to several stress conditions such as heat shock, nutrient starvation or the presence of oxidants or other stress agents.Escherichia colihas five small Usps and one tandem-type Usp. UspE (or YdaA) is the tandem-type Usp and consists of two Usp domains arranged in tandem. To date, the structure of UspE remains to be elucidated. To contribute to the molecular understanding of the function of the tandem-type UspE, UspE fromE. coliwas overexpressed and the recombinant protein was purified using Ni–NTA affinity, Q anion-exchange and gel-filtration chromatography. Crystals of UspE were obtained by sitting-drop vapour diffusion. A diffraction data set was collected to a resolution of 3.2 Å from flash-cooled crystals. The crystals belonged to the tetragonal space groupI4122 orI4322, with unit-cell parametersa=b= 121.1,c = 241.7 Å.
Purification, crystallization and preliminary X-ray crystallographic studies of KstR2 (ketosteroid regulatory protein) fromMycobacterium tuberculosis
Authors: Dawes Stephanie S. , Kendall Sharon L. , Baker Edward N. , Lott J. Shaun
Published: November 2014

KstR2 (Rv3557c) is one of two TetR-family transcriptional repressors of cholesterol metabolism inMycobacterium tuberculosis. The ability to degrade cholesterol fully is important for pathogenesis, and therefore this repressor was expressed, purified and crystallized. Crystals of KstR2 diffracted to better than 1.9 Å resolution and belonged to space groupC2, with unit-cell parametersa = 72.3,b= 90.3,c= 49.7 Å, α = γ = 90, β = 128.2°.
Crystallization and preliminary crystallographic analysis of human aquaporin 1 at a resolution of 3.28 Å
Authors: Ruiz Carrillo David , To Yiu Ying Janet , Darwis Dina , Soon Cin Huang , Cornvik Tobias , Torres Jaume , Lescar Julien
Published: November 2014

Aquaporin water channels (AQPs) are found in almost every organism from humans to bacteria. In humans, 13 classes of AQPs control water and glycerol homeostasis. Knockout studies have suggested that modulating the activity of AQPs could be beneficial for the treatment of several pathologies. In particular, aquaporin 1 is a key factor in cell migration and angiogenesis, and constitutes a possible target for anticancer compounds and also for the treatment of glaucoma. Here, a preliminary crystallographic analysis at 3.28 Å resolution of crystals of human aquaporin 1 (hAQP1) obtained from protein expressed in Sf9 insect cells is reported. The crystals belonged to the tetragonal space groupI422, with unit-cell parametersa=b= 89.28,c= 174.9 Å, and contained one monomer per asymmetric unit. The hAQP1 biological tetramer is generatedviathe crystallographic fourfold axis. This work extends previous electron crystallographic studies that used material extracted from human red blood cells, in which the resolution was limited to approximately 3.8 Å. It will inform efforts to improve lattice contacts and the diffraction limit for the future structure-based discovery of specific hAQP1 inhibitors.
The effect of epoxy‐polyester sealing of sprayed metal coatings for additional corrosion protection
Authors: Akinci A. , Yilmaz F.
Published: November 2014

Purpose

The purpose of this paper is to report salt spray testing of epoxy‐polyester top‐coating applied on Zn‐sprayed, Al‐sprayed and 85Zn‐15Al‐sprayed steel samples.

Design/methodology/approach

In these tests, steel substrates sprayed with Zn, Al and 85Zn‐15Al coatings of different average thicknesses ranging from 120 to 210 μm were top‐coated with an epoxy‐polyester sealing layer. The corrosion test was performed with salt solution for over 2,000‐h. The degree of damage to the samples was evaluated quantitatively in terms of ratio of scribed to unscribed area of coating.

Findings

It was evident that the corrosion resistance of Al‐sprayed top‐coated surfaces was better than coated Zn‐spray or coated 85Zn‐15Al‐spray systems. As a result, when Al‐coated surfaces were top‐coated with polymeric layer, it was found that their surfaces were remarkably unaffected by the salt spray environment.

Originality/value

The salt spray measurements indicated that the Al‐spray epoxy‐polyester polymer double system was more durable than the other two systems (polymeric top‐coated Zn‐spay, and polymeric top‐coated 85Zn‐15Al‐spray), so far as protection from the chloride salt spray environment was concerned.
A hierarchical approach for shape optimization
Authors: Beux F. , Dervieux A.
Published: November 2014

We consider the gradient method applied to the optimal control of a
system for which each simulation is expensive. A method for increasing the
number of unknowns, and relying on multilevel ideas is tested for the
academic problem of shape optimization of a nozzle in a subsonic or transonic
Euler flow.
New ALE applications in non‐linear fast‐transient solid
dynamics
Authors: Huerta A. , Casadei F.
Published: November 2014

The arbitrary Lagrangian—Eulerian (ALE)
formulation, which is already well established in the hydrodynamics and
fluid‐structure interaction fields, is extended to materials with
memory, namely, non‐ linear path‐dependent materials. Previous
attempts to treat non‐ linear solid mechanics with the ALE
description have, in common, the implicit interpolation technique employed.
Obviously, this implies a numerical burden which may be uneconomical and may
induce to give up this formulation, particularly in fast‐transient
dynamics where explicit algorithms are usually employed. Here, several
applications are presented to show that if adequate stress updating
techniques are implemented, the ALE formulation could be much more
competitive than classical Lagrangian computations when large deformations
are present. Moreover, if the ALE technique is interpreted as a simple
interpolation enrichment, adequate—in opposition to distorted or
locally coarse—meshes are employed. Notice also that impossible
computations (or at least very involved numerically) with a
Lagrangian code are easily implementable in an ALE analysis. Finally,
it is important to observe that the numerical examples shown range from a
purely academic test to real engineering simulations. They show the
effective applicability of this formulation to non‐linear solid
mechanics and, in particular, to impact, coining or forming
analysis.
Derivative recovery techniques for C° plate problems
Authors: Lee Sang‐Ho , Blacker Ted , Belytschko Ted
Published: November 2014

An enhanced L2 projection method for recovering accurate
derivatives such as moments, or shears, from finite element solutions for
C° plates is presented. In the enhanced global and local projections, the
square of the residuals in the equilibrium equations is included. Results are
compared with those of standard global and local projection methods.
Numerical examples show that in the global projection, the enhanced technique
improves the accuracy of projected solution significantly. In the local
projection, the enhanced projection technique circumvents the numerical
ill‐conditioning which occurs in some meshes, and usually recovers
derivatives with better accuracy. These techniques are effective for both
thin and thick plate problems, and can provide more reliable error estimates
for mesh adaptivity.
An anisotropic elastoplastic model based on an isotropic
formulation
Authors: Oller S. , Botello S. , Miquel J. , Oñate E.
Published: November 2014

This paper shows a generalization of the classic isotropic plasticity
theory to be applied to orthotropic or anisotropic materials. This approach
assumes the existence of a real anisotropic space, and other fictitious
isotropic space where a mapped fictitious problem is solved. Both spaces are
related by means of a linear transformation using a fourth order
transformation tensor that contains all the information concerning the real
anisotropic material. The paper describes the basis of the spaces
transformation proposed and the expressions of the resulting secant and
tangent constitutive equations. Also details of the numerical integration of
the constitutive equation are provided. Examples of application showing the
good performance of the model for analysis of orthotropic materials and
fibre‐reinforced composites are given.
Application of porous media mechanics to the numerical simulation of the rolling of sugar cane
Authors: Owen D.R.J. , Zhao S.Y. , Loughran J.G.
Published: November 2014

A finite element solution to the rolling of two‐phase materials is presented and applied to the rolling of prepared sugar cane. The generalized Biot theory is extended and modified to suit the present problem and the velocity of the solid skeleton and the pore pressure are taken as the primary unknowns. The finite element approach is applied to the governing equations for spatial discretization, followed by time domain discretization by standard difference methods. A constitutive relation evaluated from a finite element simulation of experiments performed on a constrained compression test cell is employed. The computational model of the rolling of prepared cane with two rolls is presented. The material parameters of prepared cane are described and their variation during the rolling process are derived and discussed. Numerical results are presented to illustrate the performance and capability of the model and solution procedures.
Automated structural design based on knowledge engineering and fuzzy
control
Authors: Yoshimura S. , Mochizuki Y. , Yagawa G.
Published: November 2014

This paper describes an automated design system for nuclear structural
components under complicated loading conditions. As a basic strategy of
designing structures considering various loading conditions, the
“generate and test” strategy is adopted because of simplicity and
broad applicability. The object‐oriented knowledge representation
technique is adopted to store knowledge modules related to design problems,
while the data‐flow processing technique is utilized as an inference
mechanism among the knowledge modules. As efficient design modification
mechanisms, the present system utilizes two approaches, (a) an
empirical approach based on experts’ empirical knowledge and the fuzzy
control, and (b) a mathematical approach based on numerical
sensitivity analysis. Using the present system, one can also obtain a
“design window” which designates a satisfaction area for all
design criteria in a design variable space. The fundamental performances of
this system are clearly demonstrated through the design of a
two‐dimensional model of the fusion first wall with a circular cooling
channel.
Filling through holes and blind microvias with copper using reverse pulse plating and insoluble anodes
Authors: Roelfs Bernd , Dambrowsky Nina , Erben Christof , Kenny Stephen
Published: November 2014

Purpose

The purpose of this paper is to present a summary of development work made in technical centres and on the subsequent customer qualification of copper filled through holes and blind microvias.

Design/methodology/approach

Various copper deposition parameters were investigated in a small‐scale production line which was then extended to full‐scale production qualification in a horizontal conveyorised system. Samples of substrates with copper filled through holes were qualified at end‐user facilities.

Findings

The copper plating process may be used to replace an existing production process for printed circuit boards. The proposed system can give a more reliable result in terms of filling and technical capability for the produced substrate. Overall production cost savings are possible.

Research limitations/implications

The technology is based on a copper plating electrolyte using a redox pair for copper replenishment. The results achieved depend on use of this system and on production equipment which can control the redox system and copper concentration within a tight range.

Originality/value

The paper shows how the use of a horizontal production system with redox copper replenishment can achieve filling of though holes and blind microvias with reduced surface plated copper thickness. Reduction in the use of copper saves both resources and also reduces production costs. The process is proposed as an alternative to existing paste plugging processes, which are both cost and labour intensive.
Flaw detection on FPC solder surface
Authors: Ye Feng , Li Di , Huang Jie‐xian , Dong Zhi‐jie
Published: November 2014

Purpose

The purpose of this paper is to study the application of advanced computer image processing techniques for flaw detection on flexible printed circuit (FPC) solder.

Design/methodology/approach

Texture directionality feature is obtained based on texture gradient, contour's position is extracted and directionality information obtained through analyzing the distribution of directionality. Contour similarity function is established to filter out false contour and keep proper contour, and the solder's location work is accomplished based on reversed contour. After that, a combination of grey and texture gradient's value deviation from reference value is utilized to reflect and describe texture on the solder's surface. Flaw can be distinguished from homogeneous texture background.

Findings

The method has been applied to the inspecting system and achieved a higher accuracy and a lower false defect rate. It demonstrates that the method can detect flaws efficiently and effectively.

Research limitations/implications

Although the work on FPC solder's location and flaw detection is presented, defective classification is not involved that is also very important content for inspection.

Originality/value

The paper provides a new way to locate solder based on directionality. The method not only extracts contour feature but also gains directional parameters to help realize accurate location, especially for some solders that are deformed to some extent. Entropy statistic based on distribution of grey and texture gradient is proposed to describe and measure solder's surface texture. The new algorithm performs stably and efficiently and is fit for practical application.
Using a tubular electrode for radiofrequency ablation
Authors: Antunes Carlos L. , Almeida Tony Richard O. , Raposeiro Nélia , Gonçalves Belarmino , Almeida Paulo
Published: November 2014

Purpose

Due to its good mechanical and biocompatibility characteristics, nitinol SEMS is a popular endoprothesis used for relieving stricture problems in hollow organs due to carcinomas. Besides its mechanical application, SEMS can be regarded as well as potential electrode for performing RF ablation therapy on the tumor. The purpose of this work is to perform numerical and experimental analyses in order to characterize the lesion volume induced in biological tissue using this kind of tubular electrode.

Design/methodology/approach

Data concerning electrical conductivity and dimension of the damaged tissue after RF ablation procedure were obtained from ex vivo samples. Next, numerical models using 3D finite element method were obtained reassembling the conditions considered at experimentation setup and results were compared.

Findings

Numerical and experimental results show that a regular volume of damaged tissue can be obtained considering this type of electrode. Also, results obtained from numerical simulation are close to those obtained by experimentation.

Originality/value

SEMSs, commonly used as devices to minimize obstruction problems due to the growth of tumors, may still be considered as an active electrode for RF ablation procedures. A method considering this observation is presented in this paper. Also, numerical simulation can be regarded in this case as a tool for determining the lesion volume.
Evaluation of induced AC voltages in underground metallic pipeline
Authors: Micu Dan D. , Czumbil Levente , Christoforidis Georgios C. , Ceclan Andrei , Şteţ Denisa
Published: November 2014

Purpose

The purpose of this paper is to make a study of electromagnetic interference between electrical power lines and nearby underground metallic pipelines.

Design/methodology/approach

The equivalent electrical circuit of the studied electromagnetic interference problem between electrical power lines and nearby metallic pipelines is created and solved using a loop currents technique based on a hybrid method. The used circuit solving technique was implemented in a software application developed by the authors.

Findings

The authors have identified the influence of phase sequence on induced voltage level in an underground pipeline for a double circuit electrical power line. Also the effect of different normal operation and phase to earth fault currents have been revealed.

Practical implications

The study has been made through a research project with the Romanian gas transportation company, in order to find the proper protection techniques for underground metallic pipelines.

Originality/value

The paper reveals the influence of some electrical and geometrical parameters that have not been studied in detail previously.
An innovative microwave system for wooden art object disinfestation
Authors: Pia Pastore Anna , Bisceglia Bruno , De Leo Roberto , Diaferia Nicola
Published: November 2014

Purpose

Many objects made up of wood, as well as paper and carpets with artistic or cultural value, are seriously damaged by various infesting microorganisms and often such damage is irreversible. The purpose of this paper is to describe an equipment which has been realized, able to induce, inside the object to be treated, having any shape, and in particular in the infesting agents, a uniform distribution of temperature.

Design/methodology/approach

The equipment consists of a metallic shielding chamber where the objects to be disinfested are placed. Here, through appropriate openings in the walls, electromagnetic energy at the frequency of the microwaves is introduced. The electromagnetic waves provoke a heating effect in the infesting biological forms with no significant thermal effects in the materials of the artistic object due to the different dielectric characteristics and to the very little percentages of water in them.

Findings

The uniform distribution of temperature guarantees that the organisms or the microorganisms are heated up over their lethal temperature while the temperature reached by the object and its spatial variations do not provoke deformations.

Practical implications

The current technologies employed in disinfestation of works of art present big limits as regards excessive treatment times, risks of pollution both for the operator and for the environment and possible damage to the treated objects.

Originality/value

This new system described in the paper gives complete effectiveness of disinfestation, with a rapid treatment, without damage to the objects, with total protection for the operators and the possibility of re‐using the object immediately after the disinfestation process.
Damping of subsynchronous resonance using self‐tuning PID and wavelet neural network
Authors: Ganjefar Soheil , Farahani Mohsen
Published: November 2014

Purpose

Subsynchronous resonance (SSR) problem is often created in generator rotor systems with long shafts (non‐rigid shaft) and large inertias constituting a weakly damped mechanical system. When the electrical network resonance frequency (in which the transmission line is compensated by series capacitors) approaches shaft natural frequencies, the electrical system increases torsional torques amplitude on the shaft. The purpose of this paper is to propose a self‐tuning proportional, integral, derivative (PID) controller to damp the SSR oscillations in the power system with series compensated transmission lines.

Design/methodology/approach

To accommodate the PID controller in all power system loading conditions, the gradient descent (GD) method and a wavelet neural network (WNN) are used to update the PID gains on‐line. All parameters of the WNN are trained by the gradient descent method using adaptive learning rates (ALRs). The ALRs are derived from discrete Lyapunov stability theorem, which are applied to guarantee the convergence of the proposed control system. Also, the suggested controller is designed based on a non‐linear model.

Findings

The proposed self‐tuning PID controller is applied to a power system non‐linear model. Simulation results are used to demonstrate the effectiveness and performance of the proposed controller. It has been shown that self‐tuning PID is able to damp the SSR under any circumstances, because the WNN ensures the robustness of the controller. Simplicity and practicality of the proposed controller with its excellent performance make it ideal to be implemented in real excitation systems.

Originality/value

The proposed self‐tuning PID approach is interesting for the design of an intelligent control scheme based on non‐linear model to damp the torsional oscillations. In this suggested controller, the system conditions and requirements adjust on‐line the PID gains. On other words, to damp the SSR, PID gains are intelligently computed by the controlled system. The main contributions of this paper are: the overall control system is globally stable and hence, the SSR is controlled; the control error can be reduced to zero by appropriate chosen parameters and learning rates; and the self‐tuning PID can achieve favorable controlling performance.
Ownership effects of fractional reserve banking: an Islamic perspective
Authors: Kameel Mydin Meera Ahamed
Published: November 2014

Purpose

The purpose of this paper is to show that fractional reserve banking (FRB) has implications for the ownership structure of assets in the economy that violates the Islamic principles of ownership.

Design/methodology/approach

This is a theoretical paper that looks into the works of Islamic scholars on the issue of ownership that are based on Qur'an principles and the traditions of the Prophet, and evaluates the FRB from that perspective.

Findings

The conclusion of the paper is that money creation through FRB is creation of purchasing power out of nothing which brings about unjust ownership transfers of assets, from the economy to the bank effectively paid for by the whole economy through inflation. This transfer of ownership is not based on human effort by taking on legitimate risks and neither with the knowledge nor the consent of the initial owners. This violates the ownership principles in Islam and is tantamount to theft. It also has the elements of riba. Islamic governments should therefore not create fiat money since this is equivalent to taking assets of the people, rich and poor alike, forcefully without compensation.

Research limitations/implications

Empirical investigations into how bank loans along the years have changed the asset ownership structure in economies may shed further light.

Practical implications

It is, therefore, important that Shariah scholars render a fatwa on both the fiat money and the FRB system. Such a fatwa is urgent and pertinent before Islamic banking and finance, that operate under these systems, takes a course that may prove difficult to reverse later. The Islamic economics and finance cannot be founded upon a money system that is fundamentally equivalent to theft and riba.

Originality/value

The paper shows how the operations of Islamic banking and finance within the fiat money, FRB system are invalid from the Islamic perspective.
Corruption: measuring the unmeasurable
Authors: Zaman Asad , Faiz‐Ur‐Rahim
Published: November 2014

Purpose

The purpose of this paper is to argue that corruption is inherently unmeasurable. Measures of corruption produced by different sources are highly unsatisfactory. Useful measures may be possible for specific purposes in limited contexts. Reasons why highly unsatisfactory measures are in use have to do with politics and power, rather than utility of these measures.

Design/methodology/approach

The paper shows that different dimensions of corruption cannot be reduced to a single number without serious loss of information. For example the number and size of bribes cannot be reduced to a single index. The difference between perceptions of corruption and the reality also makes most popular indices useless.

Findings

The paper shows that commonly used measures of corruption are useless for their ostensible purposes. Evidence is presented that they are calculated and used for political purposes. In particular, they provide convenient excuses for the widespread failure of the structural adjustment programs of IMF and World Bank.

Originality/value

The paper's findings cast doubt on the vast amount of research which takes the corruption measures as objective and factual, and attempts to find causal factors for corruption, as well as effects of corruption on growth and other variables.
Judging books by their (lack of) covers
Authors: McMullen Anthony
Published: November 2014

Purpose

The purpose of this paper is to provide insights into issues encountered in maintaining library technologies and electronic collections on a limited budget and with limited personnel.

Design/methodology/approach

The paper uses real world experiences and data to report on collection development decisions as they relate to electronic resources in an era of shrinking budgets and changing user expectations.

Findings

On‐demand access to platform‐independent information has altered user expectations and shifted the balance of power from the content providers to the content consumers. Academic libraries have been slow to adapt and are suffering as a consequence.

Originality/value

This paper examines the colliding forces of progress and tradition as they relate to the provision of information resources in an academic library environment. The author employs real‐world circulation statistics to make a case for shifting the focus of collection development from printed books to ebooks.
Providing the ethical example
Authors: Crumpton Michael A.
Published: November 2014

Purpose

This paper aims to discuss the importance of maintaining an ethical point of view especially in times of economic uncertainty.

Design/methodology/approach

This paper presents some definitions of ethical behavior and reminds the reader of the consequences of not following an ethical course of action.

Findings

From current literature, ethical behaviors have been compromised in some industries, as libraries establish themselves in a new economy it is important to consider revisiting organizational training needs regarding ethics.

Originality/value

This paper is a reminder that regardless of economical situations, proper ethical behavior should be applied.
Assessment: what's in it for me?
Authors: Jackson Mildred L.
Published: November 2014

Purpose

Accreditation and other types of reports will continue to be required by libraries and other entities in higher education. However, the traditional means and methods of assessment for these reports can be limiting. The measures can be used as opportunities to think more creatively and broadly about what is being done and offered. This paper aims to addresses these issues.

Design/methodology/approach

The paper considers recent articles about transformation and new ways of thinking.

Findings

The paper recommends using traditional means of assessment in new ways and encouraging librarians to think outside the box and traditional boundaries of what the author has offered.

Originality/value

Considering various kinds of assessment and re‐thinking traditional means of assessment will be valuable for librarians and libraries.