bluuebunny/crossref_metadata_2025 huggingface dataset:
TiO2-based MIM capacitors featuring suppressed leakage current by embedding Ge nanocrystals
Authors: Yu Meng-Ting , Chen Kuen-Yi , Chen Yu-Hsun , Lin Chia-Chun , Wu Yung-Hsien
Published: January 2015

Leakage current suppression of TiO2-based MIM capacitors is achieved by using plasma treatment and embedding Ge nanocrystals.
π-stacking intercalation and reductant assisted stabilization of osmium organosol for catalysis and SERS applications
Authors: Anantharaj S. , Nithiyanantham U. , Ede Sivasankara Rao , Ayyappan E. , Kundu Subrata
Published: January 2015

Size-selective, mono-dispersed osmium organosol have been synthesized in toluene which is stabilized by π-stacking intercalation and electrostatic interactions for application in catalysis and SERS studies.
Regio- and stereo-selective oxidation of β-boswellic acids transformed by filamentous fungi
Authors: Wang Chao , Dong Peipei , Zhang Liyuan , Huo Xiaokui , Zhang Baojing , Wang Changyuan , Huang Shanshan , Wang Xiaobo , Yao Jihong , Liu Kexin , Ma Xiaochi
Published: January 2015

Biotransformation of 11-keto-β-boswellic acid (KBA) and acetyl-11-keto-β-boswellic acid (AKBA) catalyzed by two fungal strains (Cunninghamella elegans AS 3.1207 and Penicillium janthinellum AS 3.510) was performed in the present investigation.
Conformational preferences of Ac-Gly-NHMe in solution
Authors: Cormanich R. A. , Rittner R. , Bühl M.
Published: January 2015

The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF3-C(O)-Gly-NHMe] andN-methyl[Ac-Gly-N(Me)2] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.
Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration
Authors: Yang Yongliang , Li Guohui , Zhao Dongyu , Yu Haoyang , Zheng Xiliang , Peng Xiangda , Zhang Xiaoe , Fu Ting , Hu Xiaoqing , Niu Mingshan , Ji Xuefei , Zou Libo , Wang Jin
Published: January 2015

Pazopanib, a tyrosine kinase inhibitor marketed for cancer treatment, abrogates the course of neurodegeneration.
Inherently chiral electrodes: the tool for chiral voltammetry
Authors: Arnaboldi Serena , Benincori Tiziana , Cirilli Roberto , Kutner Włodzimierz , Magni Mirko , Mussini Patrizia Romana , Noworyta Krzysztof , Sannicolò Francesco
Published: January 2015

Artificial inherently chiral electrode surfaces perform clear enantiodiscrimination and enantiomeric ratio quantification, opening the way to chiral voltammetry.
Real-space evidence of the equilibrium ordered bicontinuous double diamond structure of a diblock copolymer
Authors: Chu C. Y. , Jiang X. , Jinnai H. , Pei R. Y. , Lin W. F. , Tsai J. C. , Chen H. L.
Published: January 2015

A thermally stable ordered bicontinuous double diamond (OBDD) structure in a stereoregular diblock copolymer has been revealed by electron tomography. The structure underwent a thermally reversible transition to double gyroid upon heating, accompanied by a reduction of domain spacing.
Purification of phenol-contaminated water by adsorption with quaternized poly(dimethylaminopropyl methacrylamide)-grafted PVBC microspheres
Authors: Yuan Shaojun , Gu Juntao , Zheng Yu , Jiang Wei , Liang Bin , Pehkonen Simo Olavi
Published: January 2015

Cross-linked PVBC microspheres were tethered with quaternized PDMAPMA brushes via surface-initiated ATRP as effective anionic sorbents for phenol removal.
Structural evolution and carrier scattering of Si nanowires as a function of oxidation time
Authors: Bae Jung min , Lee Woo-Jung , Ma Jin won , Kim Jung hun , Oh Seung hoon , Cho Mann-Ho , Chul Kang , Jung Seonghoon , Park Jaehun
Published: January 2015

We investigated the morphological characteristics of the cross-sectional shape of Si-core nanowires (NWs) as a function of oxidation time.
Raman scattering and photoluminescence investigation of YBO3:Eu3+ under high temperature and high pressure
Authors: Song W. S. , Huang G. X. Y. , Dai R. C. , Wang Z. P. , Zhang Z. M.
Published: January 2015

The effect of temperature and pressure on structure of YBO3:Eu was characterized by Raman scattering and on optical properties was analyzed by luminescent dynamic method.
Generation of orange and green emissions in Ca2GdZr2(AlO4)3:Ce3+, Mn2+, Tb3+ garnets via energy transfer with Mn2+ and Tb3+ as acceptors
Authors: Lü Wei , Lv Wenzhen , Zhao Qi , Jiao Mengmeng , Shao Baiqi , You Hongpeng
Published: January 2015

Utilizing Mn2+ and Tb3+ ions as energy-transfer acceptors, we report a series of emission color-tunable Ca2GdZr2(AlO4)3:Ce3+, Mn2+, Tb3+ aluminate garnets.
High density array of multiferroic nanoislands in a large area
Authors: Hyun Seung , Seo Hosung , Yang Il-Kyu , Kim Youngsuk , Jeon Gumhye , Lee Bom-yi , Jeong Yoon Hee , Kim Yunseok , Kim Jin Kon
Published: January 2015

To extend the existing AAO mask assisted pulsed laser deposition (PLD) method, which is limited to fabricating a nanoisland array in a small area, we introduced a novel method to fabricate a high density array of multiferroic BFO nanoislands in a large area (wafer scale) by utilizing a nanoporous polymer template.
Mechano-induced luminescent and chiroptical switching in chiral cyclometalated platinum(ii) complexes
Authors: Zhang Xiao-Peng , Mei Jin-Feng , Lai Jian-Cheng , Li Cheng-Hui , You Xiao-Zeng
Published: January 2015

Chiral cyclometalated platinum(ii) complexes exhibited interesting mechano-induced luminescent and chiroptical switching properties. The mechanochromic performance can be tuned by changing the counteranions.
Sizing and siting static synchronous compensator devices in the Portuguese transmission system for improving system security
Authors: Barbeiro Pedro Nuno Pereira , Moreira Carlos , Keko Hrvoje , Teixeira Henrique , Rosado Nuno , Moreira João , Rodrigues Reis
Published: January 2015

This study presents a methodology for siting and sizing static synchronous compensator (STATCOM) devices in the Portuguese transmission system in order to improve system security following severe grid faults. Security issues arise since the Portuguese transmission system incorporates significant levels of wind generation without fault ride through and reactive current injection capabilities during grid faults. As the transmission system operator (TSO) is responsible for assuring system security, the goal of the study is to take advantage of the proved STATCOM ability for injecting reactive current in order to mitigate the disconnection of large amounts of wind farms in case of severe grid faults. The proposed methodology was developed and tested in coordination with the Portuguese TSO and it is based on the formulation of an optimisation problem in order to minimise the installed STATCOM power while ensuring its compliance with the current grid code requirements, namely in what concerns to the system stability and security. Given the discrete and complex nature of the problem, a hybrid approach, combining both a heuristic method and an evolutionary particle swarm optimisation (EPSO) algorithm was developed. Results show the effectiveness of the proposed methodology as well as its robustness regarding the validity of the obtained solutions while facing the most severe operational scenarios.
Further investigation on water antennas
Authors: Xing Lei , Huang Yi , Shen Yaochun , Al Ja'afreh Saqer , Xu Qian , Alrawashdeh Rula
Published: January 2015

Water antennas are a special type of antennas and have attracted limited attention so far. In this study, a monopole water antenna with a dielectric layer is chosen as an example to study some less obvious characteristics of the water antenna. The resonant frequency, radiation efficiency and fractional bandwidth are of particular interest. Firstly, the effects of the dielectric layer between the water and the ground plane are studied. The results show that this layer has a crucial effect on the antenna resonant frequency and radiation efficiency. Secondly, the water with different conductivity is investigated. With different conductivity, the antenna may be regarded as a dielectric resonant antenna, a conducting antenna or their combination. Thirdly, a water antenna with a supporting structure is fabricated for validation. Measurements are conducted in an anechoic chamber and a reverberation chamber to evaluate its performance as a function of various parameters. Finally, the water temperature electromagnetic characteristics are investigated. Good agreements are achieved between the simulation and measurement results. It is shown that this type of antenna shows better performance than the conventional antenna in aspects such as broadband, cost, reconfigurability, transparency and it can be a promising candidate for a range of applications.
Low profile dual‐band antenna loaded with artificial magnetic conductor for indoor radar systems
Authors: Yan Sen , Soh Ping Jack , Mercuri Marco , Schreurs Dominique M.M.‐P. , Vandenbosch Guy A.E.
Published: January 2015

A dual‐band antenna is designed for a fall‐detection radar and telemetry system. The radar is designed based on the stepped frequency continuous wave (SFCW) concept, which requires Ultra Wideband (UWB) operation, low inter‐element coupling and a directive radiation pattern with low backlobe. The telemetry system uses the 2.45 GHz band to enable signal transmission/reception in an indoor environment and the 6–7.5 GHz band for radar sensing part. A main dual‐band radiator with a slotted patch is used as the basis for the antenna design: the patch resonates at 2.45 GHz whereas the antenna slot enables a wide band operation for the radar system. To enable a low‐profile, an artificial magnetic conductor (AMC) structure is integrated into the antenna. It works as a perfect magnetic conductor (PMC) plane from 6 to 7.5 GHz and can be located close to the slot antenna functioning as a reflector. Both numerical and experimental results indicate a satisfactory antenna performance in terms of reflection coefficient and radiation pattern. The antenna was also integrated into the radar system and tested in a real environment on three subjects at fixed distances. A fall‐detection up to 6 meters was achieved.
Vortices at the magnetic equator generated by hybrid Alfvén resonant waves
Authors: Hiraki Yasutaka
Published: January 2015

We performed three-dimensional magnetohydrodynamic simulations of shear Alfvén waves in a full field line system with magnetosphere-ionosphere coupling and plasma non-uniformities. Feedback instability of the Alfvén resonant modes showed various nonlinear features under the field line cavities: (i) a secondary flow shear instability occurs at the magnetic equator, (ii) trapping of the ionospheric Alfvén resonant modes facilitates deformation of field-aligned current structures, and (iii) hybrid Alfvén resonant modes grow to cause vortices and magnetic oscillations around the magnetic equator. Essential features in the initial brightening of auroral arc at substorm onsets could be explained by the dynamics of Alfvén resonant modes, which are the nature of the field line system responding to a background rapid change.
3D printed microfluidic devices with integrated valves
Authors: Rogers Chad I. , Qaderi Kamran , Woolley Adam T. , Nordin Gregory P.
Published: January 2015

We report the successful fabrication and testing of 3D printed microfluidic devices with integrated membrane-based valves. Fabrication is performed with a low-cost commercially available stereolithographic 3D printer. Horizontal microfluidic channels with designed rectangular cross sectional dimensions as small as 350 μm wide and 250 μm tall are printed with 100% yield, as are cylindrical vertical microfluidic channels with 350 μm designed (210 μm actual) diameters. Based on our previous work [Rogers et al., Anal. Chem. 83, 6418 (2011)], we use a custom resin formulation tailored for low non-specific protein adsorption. Valves are fabricated with a membrane consisting of a single build layer. The fluid pressure required to open a closed valve is the same as the control pressure holding the valve closed. 3D printed valves are successfully demonstrated for up to 800 actuations.
Nonprice incentives and energy conservation
Authors: Asensio Omar I. , Delmas Magali A.
Published: January 2015

Significance

We investigate the effectiveness of nonprice incentives to motivate conservation behavior. We test whether tailored information about environmental and health damages produces behavior change in the residential electricity sector. In a randomized controlled trial with real-time appliance-level energy metering over 8 mo, we find that environment and health-based information strategies outperform monetary savings information to drive energy conservation. Environment and health-based messages, which communicate the environmental and public health externalities of electricity production—such as pounds of pollutants, childhood asthma, and cancer—motivated 8% energy savings versus control. This strategy was particularly effective on families with children, who achieved 19% energy savings. However, we do not study the persistence of these behavioral changes after the conclusion of the study.
Timely sleep facilitates declarative memory consolidation in infants
Authors: Seehagen Sabine , Konrad Carolin , Herbert Jane S. , Schneider Silvia
Published: January 2015

Significance

The potential benefits of infant sleep for memory processing are largely unexplored. Here we show evidence that having an extended nap (≥30 min) within 4 h of learning helps 6- and 12-month-old infants to retain their memories for new behaviors across a 4- and 24-h delay. These results suggest that infants rely on frequent naps for the formation of long-term memories.
The effects of bilingualism on the white matter structure of the brain
Authors: Pliatsikas Christos , Moschopoulou Elisavet , Saddy James Douglas
Published: January 2015

Significance

This article fills an important gap in the literature on structural changes in the brain that are induced by speaking two languages. It has been suggested that early lifelong bilingualism affects the structure of white matter (WM) of the brain and preserves its integrity in older age. Here we show that similar WM effects are also found in bilingual individuals who learn their second language (L2) later in life and are active users of both languages. This finding presents a strong argument for the general benefits of additional language learning and the importance of language learning and use in a naturalistic environment.
Multiprotein complex between the GPI-anchored CyRPA with PfRH5 and PfRipr is crucial for
Plasmodium falciparum
erythrocyte invasion
Authors: Reddy K. Sony , Amlabu Emmanuel , Pandey Alok K. , Mitra Pallabi , Chauhan Virander S. , Gaur Deepak
Published: January 2015

Significance

Plasmodium falciparum
reticulocyte binding-like homologous protein 5 (PfRH5) is a leading blood-stage malaria vaccine candidate that elicits potent strain-transcending invasion inhibitory antibodies. However, it lacks both transmembrane domains and a GPI-anchor and is thus anchored to the merozoite surface through an unknown mechanism. We have demonstrated that PfRH5 and its known partner, PfRH5-interacting protein (PfRipr), associates with a conserved GPI-anchored protein, Cysteine-rich protective antigen (CyRPA), to form a complex on the merozoite surface. CyRPA was shown to be GPI-linked, refractory to knockout, and like PfRH5, elicited potent strain-transcending invasion inhibitory antibodies. This discovery elucidates the formation of a previously unidentified PfRH5/PfRipr/CyRPA protein complex on the merozoite surface, which facilitates the PfRH5–Basigin interaction and offers another highly conserved, potent target (CyRPA) for novel antimalarial strategies that could abrogate formation of this crucial complex.
Benthic perspective on Earth’s oldest evidence for oxygenic photosynthesis
Authors: Lalonde Stefan V. , Konhauser Kurt O.
Published: January 2015

Significance

The history of oxygen at Earth’s surface is intimately tied to its production by oxygenic photosynthesis, whereby plants, algae, and cyanobacteria release O
2
as a waste product. Despite this metabolism’s profound importance, its evolutionary timing is poorly understood. Studies have increasingly revealed a temporal disconnect between evidence for the presence of O
2
during weathering as early as 3.0 billion years ago and its atmospheric accumulation 500 million years later. We review this problem and numerically demonstrate that local O
2
production and immediate consumption in surface-bound (benthic) microbial ecosystems at profound disequilibrium conditions is the most parsimonious explanation for this delay. Thus, emergence of continental landmass was likely a crucial factor in the earliest oxygenation of Earth’s surface environment.
Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes
Authors: Gibbons John G. , Branco Alan T. , Godinho Susana A. , Yu Shoukai , Lemos Bernardo
Published: January 2015

Significance

Ribosomes are essential intracellular machines composed of proteins and RNA molecules. The DNA sequences [i.e., ribosomal DNA (rDNA)] encoding rRNAs are tandemly repeated and give rise to the nucleolus. The rRNAs are transcribed from two array kinds (the 5S and the 45S arrays). Here we show that variation in the 5S and 45S rDNA arrays is tightly coupled, despite their location on different chromosomes. Our observations suggest that natural selection contributes to maintain balanced rDNA dosage across unlinked rDNA arrays. Finally, we show that bisphenol A can induce parallel loss of rDNA units in 5S and 45S arrays. These observations raise the prospect that human diseases might be traced to disrupted rDNA dosage balance in the genome.
Translation initiation mediated by RNA looping
Authors: Paek Ki Young , Hong Ka Young , Ryu Incheol , Park Sung Mi , Keum Sun Ju , Kwon Oh Sung , Jang Sung Key
Published: January 2015

Significance

“Ribosomal scanning” is the generally accepted hypothesis for explaining how eukaryotic 40S ribosomal subunits find initiation codons. Some recently described phenomena cannot be explained by the ribosomal scanning hypothesis, however. Here we show that 43S ribosomal complexes recruited to locations downstream of a reporter gene can direct translation of the reporter independent of the 5′ end, suggesting that 43S ribosomal complex recognizes the initiation codon by “RNA looping” of the intervening mRNA segment between the ribosome recruiting site and the initiation codon. Moreover, we provide a mathematical model for the RNA looping hypothesis. The RNA looping hypothesis provides a logical explanation for translational augmentation by translation-enhancing elements located upstream and/or downstream of a protein-coding region.
STEP61is a substrate of the E3 ligase parkin and is upregulated in Parkinson’s disease
Authors: Kurup Pradeep K. , Xu Jian , Videira Rita Alexandra , Ononenyi Chimezie , Baltazar Graça , Lombroso Paul J. , Nairn Angus C.
Published: January 2015

Significance

In neurons, STEP61(striatal-enriched protein tyrosine phosphatase) protein levels are tightly regulated, and the protein’s up-regulation is implicated in several neuropsychiatric disorders. Here, we demonstrate that parkin is a major E3 ligase regulating STEP61levels through the ubiquitin proteasome system. In Parkinson’s disease, in which parkin function is compromised, STEP61levels increase, which is associated with down-regulation of synaptic proteins required for neuronal plasticity.
Low-dose exposure to bisphenol A and replacement bisphenol S induces precocious hypothalamic neurogenesis in embryonic zebrafish
Authors: Kinch Cassandra D. , Ibhazehiebo Kingsley , Jeong Joo-Hyun , Habibi Hamid R. , Kurrasch Deborah M.
Published: January 2015

Significance

Here we demonstrate that bisphenol A (BPA) exposure during a time point analogous to the second trimester in humans has real and measurable effects on brain development and behavior. Furthermore, our study is the first, to our knowledge, to show that bisphenol S, a replacement used in BPA-free products, equally affects neurodevelopment. These findings suggest that BPA-free products are not necessarily safe and support a societal push to remove all structurally similar bisphenol analogues and other compounds with endocrine-disruptive activity from consumer goods. Our data here, combined with over a dozen physiological and behavioral human studies that begin to point to the prenatal period as a BPA window of vulnerability, suggest that pregnant mothers limit exposure to plastics and receipts.
Colorimetric Method of Loop-Mediated Isothermal Amplification with the Pre-Addition of Calcein for Detecting Flavobacterium columnare and its Assessment in Tilapia Farms
Authors: Suebsing Rungkarn , Kampeera Jantana , Sirithammajak Sarawut , Withyachumnarnkul Boonsirm , Turner Warren , Kiatpathomchai Wansika
Published: January 2015

Flavobacterium columnare, the causative agent of columnaris disease in fish, affects many economically important freshwater fish species. A colorimetric method of loop-mediated isothermal amplification with the pre-addition of calcein (LAMP–calcein) was developed and used to detect the presence of F. columnare in farmed tilapia (Nile Tilapia Oreochromis niloticus and red tilapia [Nile Tilapia × Mozambique Tilapia O. mossambicus]) and rearing water. The detection method, based on a change in color from orange to green, could be performed within 45 min at 63°C. The method was highly specific, as it had no cross-detections with 14 other bacterial species, including other fish pathogens and two Flavobacterium species. The method has a minimum detection limit of 2.2 × 102  F. columnare CFU; thus, it is about 10 times more sensitive than conventional PCR. With this method, F. columnare was detected in gonad, gill, and blood samples from apparently healthy tilapia broodstock as well as in samples of fertilized eggs, newly hatched fry, and rearing water. The bacteria isolated from the blood were further characterized biochemically and found to be phenotypically identical to F. columnare. The amplified products from the LAMP–calcein method had 97% homology with the DNA sequence of F. columnare.

Received May 21, 2014; accepted August 10, 2014
Tubulin transport by IFT is upregulated during ciliary growth by a cilium-autonomous mechanism
Authors: Craft Julie M. , Harris J. Aaron , Hyman Sebastian , Kner Peter , Lechtreck Karl F.
Published: January 2015

The assembly of the axoneme, the structural scaffold of cilia and flagella, requires translocation of a vast quantity of tubulin into the growing cilium, but the mechanisms that regulate the targeting, quantity, and timing of tubulin transport are largely unknown. In Chlamydomonas, GFP-tagged α-tubulin enters cilia as an intraflagellar transport (IFT) cargo and by diffusion. IFT-based transport of GFP-tubulin is elevated in growing cilia and IFT trains carry more tubulin. Cells possessing both nongrowing and growing cilia selectively target GFP-tubulin into the latter. The preferential delivery of tubulin boosts the concentration of soluble tubulin in the matrix of growing versus steady-state cilia. Cilia length mutants show abnormal kinetics of tubulin transport. We propose that cells regulate the extent of occupancy of IFT trains by tubulin cargoes. During ciliary growth, IFT concentrates soluble tubulin in cilia and thereby promotes elongation of the axonemal microtubules.
Blocking follistatin-like 1 attenuates bleomycin-induced pulmonary fibrosis in mice
Authors: Dong Yingying , Geng Yan , Li Lian , Li Xiaohe , Yan Xiaohua , Fang Yinshan , Li Xinxin , Dong Siyuan , Liu Xue , Li Xue , Yang Xiuhong , Zheng Xiaohong , Xie Ting , Liang Jiurong , Dai Huaping , Liu Xinqi , Yin Zhinan , Noble Paul W. , Jiang Dianhua , Ning Wen
Published: January 2015

Progressive tissue fibrosis is a cause of major morbidity and mortality. Pulmonary fibrosis is an epithelial-mesenchymal disorder in which TGF-β1 plays a central role in pathogenesis. Here we show that follistatin-like 1 (FSTL1) differentially regulates TGF-β and bone morphogenetic protein signaling, leading to epithelial injury and fibroblast activation. Haplodeletion of Fstl1 in mice or blockage of FSTL1 with a neutralizing antibody in mice reduced bleomycin-induced fibrosis in vivo. Fstl1 is induced in response to lung injury and promotes the accumulation of myofibroblasts and subsequent fibrosis. These data suggest that Fstl1 may serve as a novel therapeutic target for treatment of progressive lung fibrosis.
CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations
Authors: Chikina Maria , Zaslavsky Elena , Sealfon Stuart C.
Published: January 2015

Motivation: Identifying alterations in gene expression associated with different clinical states is important for the study of human biology. However, clinical samples used in gene expression studies are often derived from heterogeneous mixtures with variable cell-type composition, complicating statistical analysis. Considerable effort has been devoted to modeling sample heterogeneity, and presently, there are many methods that can estimate cell proportions or pure cell-type expression from mixture data. However, there is no method that comprehensively addresses mixture analysis in the context of differential expression without relying on additional proportion information, which can be inaccurate and is frequently unavailable.

Results: In this study, we consider a clinically relevant situation where neither accurate proportion estimates nor pure cell expression is of direct interest, but where we are rather interested in detecting and interpreting relevant differential expression in mixture samples. We develop a method, Cell-type COmputational Differential Estimation (CellCODE), that addresses the specific statistical question directly, without requiring a physical model for mixture components. Our approach is based on latent variable analysis and is computationally transparent; it requires no additional experimental data, yet outperforms existing methods that use independent proportion measurements. CellCODE has few parameters that are robust and easy to interpret. The method can be used to track changes in proportion, improve power to detect differential expression and assign the differentially expressed genes to the correct cell type.

Availability and implementation: The CellCODE R package can be downloaded at http://www.pitt.edu/∼mchikina/CellCODE/ or installed from the GitHub repository ‘mchikina/CellCODE’.

Contact:  mchikina@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets
Authors: Ikebata Hisaki , Yoshida Ryo
Published: January 2015

Motivation

The motif discovery problem consists of finding recurring patterns of short strings in a set of nucleotide sequences. This classical problem is receiving renewed attention as most early motif discovery methods lack the ability to handle large data of recent genome-wide ChIP studies. New ChIP-tailored methods focus on reducing computation time and pay little regard to the accuracy of motif detection. Unlike such methods, our method focuses on increasing the detection accuracy while maintaining the computation efficiency at an acceptable level. The major advantage of our method is that it can mine diverse multiple motifs undetectable by current methods.

Results

The repulsive parallel Markov chain Monte Carlo (RPMCMC) algorithm that we propose is a parallel version of the widely used Gibbs motif sampler. RPMCMC is run on parallel interacting motif samplers. A repulsive force is generated when different motifs produced by different samplers near each other. Thus, different samplers explore different motifs. In this way, we can detect much more diverse motifs than conventional methods can. Through application to 228 transcription factor ChIP-seq datasets of the ENCODE project, we show that the RPMCMC algorithm can find many reliable cofactor interacting motifs that existing methods are unable to discover.

Availability and implementation

A C++ implementation of RPMCMC and discovered cofactor motifs for the 228 ENCODE ChIP-seq datasets are available from http://daweb.ism.ac.jp/yoshidalab/motif.

Supplementary information

Supplementary data are available from Bioinformatics online.
Changes in the lease and permanent sale quota markets of a rock lobster fishery in response to stock abundance
Authors: León Rafael , Gardner Caleb , van Putten Ingrid , Hartmann Klaas
Published: January 2015

Effective individual transferable quotas (ITQ) systems rebuild stocks and allow transfer of quotas to more efficient operators. This process requires functional markets for both quota sales and temporary quota leases. These markets are expected to respond to changes in economic rent from the fishery, which is influenced by stock abundance and the international rock lobster price. This research used multistate Markov modelling and Granger causality test to examine changes in the permanent and temporary quota trade in the Tasmanian rock lobster fishery quota market, during periods of both increasing and decreasing stock abundance. The permanent quota trade market was more active during the period of stock growth, while the quota lease market was active in both periods of stock growth and decline. In contrast to theoretical trends in ITQ fisheries, trades in both markets were not linked to the technical efficiency (i.e. catching capability) of operators, but were more driven by the quota owners' financial capacity (i.e. number of owned quotas). Prolonged and unexpected stock decline affected the quota market so that it deviated from the theoretical pattern of ITQ fisheries. Operators previously active in the market reduced their activity, while smaller operators and firms that previously had not traded became more active, so the fleet expanded with smaller operators entering.
Enhanced Effects of Isoflurane on the Long QT Syndrome 1–associated A341V Mutant
Authors: Mikuni Ikuomi , Torres Carlos G. , Bakshi Tania , Tampo Akihito , Carlson Brian E. , Bienengraeber Martin W. , Kwok Wai-Meng
Published: January 2015

AbstractAbstract

The long QT syndrome–associated A341V mutation rendered the slowly activating delayed rectifier potassium (IKs) channel more sensitive to the inhibitory effects of isoflurane compared to wild-type IKs in transfected cell lines.

Background:

The impact of volatile anesthetics on patients with inherited long QT syndrome (LQTS) is not well understood. This is further complicated by the different genotypes underlying LQTS. No studies have reported on the direct effects of volatile anesthetics on specific LQTS-associated mutations. We investigated the effects of isoflurane on a common LQTS type 1 mutation, A341V, with an unusually severe phenotype.

Methods:

Whole cell potassium currents (IKs) were recorded from HEK293 and HL-1 cells transiently expressing/coexpressing wild-type KCNQ1 (α-subunit), mutant KCNQ1, wild-type KCNE1 (β-subunit), and fusion KCNQ1 + KCNE1. Current was monitored in the absence and presence of clinically relevant concentration of isoflurane (0.54 ± 0.05 mM, 1.14 vol %). Computer simulations determined the resulting impact on the cardiac action potential.

Results:

Isoflurane had significantly greater inhibitory effect on A341V + KCNE1 (62.2 ± 3.4%, n = 8) than on wild-type KCNQ1 + KCNE1 (40.7 ± 4.5%; n = 9) in transfected HEK293 cells. Under heterozygous conditions, isoflurane inhibited A341V + KCNQ1 + KCNE1 by 65.2 ± 3.0% (n = 13) and wild-type KCNQ1 + KCNE1 (2:1 ratio) by 32.0 ± 4.5% (n = 11). A341V exerted a dominant negative effect on IKs. Similar differential effects of isoflurane were also observed in experiments using the cardiac HL-1 cells. Mutations of the neighboring F340 residue significantly attenuated the effects of isoflurane, and fusion proteins revealed the modulatory effect of KCNE1. Action potential simulations revealed a stimulation frequency–dependent effect of A341V.

Conclusions:

The LQTS-associated A341V mutation rendered the IKs channel more sensitive to the inhibitory effects of isoflurane compared to wild-type IKs in transfected cell lines; F340 is a key residue for anesthetic action.
Application of damage detection methods using passive reconstruction of impulse response functions
Authors: Tippmann J. D. , Zhu X. , Lanza di Scalea F.
Published: January 2015

In structural health monitoring (SHM), using only the existing noise has long been an attractive goal. The advances in understanding cross-correlations in ambient noise in the past decade, as well as new understanding in damage indication and other advanced signal processing methods, have continued to drive new research into passive SHM systems. Because passive systems take advantage of the existing noise mechanisms in a structure, offshore wind turbines are a particularly attractive application due to the noise created from the various aerodynamic and wave loading conditions. Two damage detection methods using a passively reconstructed impulse response function, or Green's function, are presented. Damage detection is first studied using the reciprocity of the impulse response functions, where damage introduces new nonlinearities that break down the similarity in the causal and anticausal wave components. Damage detection and localization are then studied using a matched-field processing technique that aims to spatially locate sources that identify a change in the structure. Results from experiments conducted on an aluminium plate and wind turbine blade with simulated damage are also presented.
Aspects of structural health and condition monitoring of offshore wind turbines
Authors: Antoniadou I. , Dervilis N. , Papatheou E. , Maguire A. E. , Worden K.
Published: January 2015

Wind power has expanded significantly over the past years, although reliability of wind turbine systems, especially of offshore wind turbines, has been many times unsatisfactory in the past. Wind turbine failures are equivalent to crucial financial losses. Therefore, creating and applying strategies that improve the reliability of their components is important for a successful implementation of such systems. Structural health monitoring (SHM) addresses these problems through the monitoring of parameters indicative of the state of the structure examined. Condition monitoring (CM), on the other hand, can be seen as a specialized area of the SHM community that aims at damage detection of, particularly, rotating machinery. The paper is divided into two parts: in the first part, advanced signal processing and machine learning methods are discussed for SHM and CM on wind turbine gearbox and blade damage detection examples. In the second part, an initial exploration of supervisor control and data acquisition systems data of an offshore wind farm is presented, and data-driven approaches are proposed for detecting abnormal behaviour of wind turbines. It is shown that the advanced signal processing methods discussed are effective and that it is important to adopt these SHM strategies in the wind energy sector.
An immersed-shell method for modelling fluid–structure interactions
Authors: Viré A. , Xiang J. , Pain C. C.
Published: January 2015

The paper presents a novel method for numerically modelling fluid–structure interactions. The method consists of solving the fluid-dynamics equations on an extended domain, where the computational mesh covers both fluid and solid structures. The fluid and solid velocities are relaxed to one another through a penalty force. The latter acts on a thin shell surrounding the solid structures. Additionally, the shell is represented on the extended domain by a non-zero shell-concentration field, which is obtained by conservatively mapping the shell mesh onto the extended mesh. The paper outlines the theory underpinning this novel method, referred to as the immersed-shell approach. It also shows how the coupling between a fluid- and a structural-dynamics solver is achieved. At this stage, results are shown for cases of fundamental interest.
Crystal structure ofN,N′-(1,2-phenylene)bis(2-chloroacetamide)
Authors: Tariq Javaria , Murtaza Shahzad , Tahir Muhammad Nawaz , Zaheer Muhammad
Published: January 2015

In the title compound, C10H10Cl2N2O2, the secondary amide groups are differently twisted relative to the benzene ring, with dihedral angles between the respective planes of 21.03 (2) and 81.22 (2)°. In the crystal, the molecules are connected by N—H...O and C—H...O hydrogen bonds, forming a two-dimensional polymeric network parallel to (001). One of the amide carbonyl O atoms accepts two H atoms in N—H...O and C—H...O interactions, forming anR22(6) ring motif.
Crystal structure of (E)-1-[4-({4-[(4-methoxybenzylidene)amino]phenyl}sulfanyl)phenyl]ethan-1-one
Authors: Hebbachi Rabihe , Djedouani Amel , Kadri Soumia , Mousser Hénia , Mousser Abdelhamid
Published: January 2015

The title Schiff base compound, C22H19NO2S, crystallized with two independent molecules (AandB) in the asymmetric unit. Both molecules have anEconformation about the C=N bond. The two molecules differ in the orientation of the aromatic rings with respect to each other. The outer 4-methoxybenzene ring is inclined to the central benzene ring and the outer 4-acetylbenzene ring by 1.80 (19) and 63.73 (19)°, respectively, in moleculeA, and by 6.72 (18) and 68.53 (19)°, respectively, in moleculeB. The two outer benzene rings are inclined to one another by 63.77 (18) and 63.19 (18)° in moleculesAandB, respectively. In the crystal, the individual molecules stack in columns along [010], and are linked by a number of C—H...π interactions, forming slabs lying parallel to (001).
The effect of message framing on pro-environmental behavior intentions
Authors: Chang Meng-Chen , Wu Chao-Chan
Published: January 2015

Purpose

– A considerable amount of research suggests that the way information is processed may influence a purchasing decision; however, this seems to be an issue rarely investigated in green marketing studies. Therefore, the purpose of this paper is to draw on the literature related to the Heuristic-Systematic Model of information processing to provide a deeper insight into the factors affecting pro-environmental behavior intention.

Design/methodology/approach

– The framework highlights the moderator role of environmental motivation and environmental knowledge in the relationships among message framing and pro-environmental behavior intention. The study used an internet survey to help reduce the social desirability bias associated with a face-to-face survey. In total, 497 questionnaires were collected, of which 68 were invalid and 429 were valid.

Findings

– The results indicate that it might be beneficial for green marketing proprietors to provide product-related information stressing the potential negative consequences of not buying organic food products. This effect, however, is moderated by the degree of the customer’s environmental motivation and environmental knowledge.

Originality/value

– This stands in marked contrast to the traditional information which emphasizes the positive consequences to motivate customers to purchase organic food products.
Measuring retail supply chain performance
Authors: Anand Neeraj , Grover Neha
Published: January 2015

Purpose

– A growing body of literature has begun in the direction of supply chain performance measurement. However, selecting the appropriate set of key performance indicators (KPIs) for measuring supply chain performance have always remained a challenge. The purpose of this paper is to identify the KPIs and categorize them specifically for measuring retail supply chain performance.

Design/methodology/approach

– A qualitative approach, based on literature has been adopted. Published literature from refereed journals on supply chain performance measurement has been considered and various approaches for developing KPIs have been studied to develop a theoretical framework for performance measurement in retail supply chain.

Findings

– The paper identifies key indicators for performance measurement and classifies them into four major categories: transport optimization, information technology optimization, inventory optimization and resource optimization. These key indicators are arranged precisely for retail industry. A theoretical framework is proposed to link the performance of these constructs on financial performance of the firm.

Research limitations/implications

– Future research can be carried out to validate the relevance and applicability of identified indicators. The study can be further conducted to measure the interrelationships between the KPIs and their impact on financial performance of the firm.

Practical implications

– This study proposes a list of indicators for retail industry, which are presented in appropriate categories so that it can be used by the focussed teams for further improvement.

Originality/value

– To the best of authors’ knowledge, no other study has categorized the KPIs into groups, specifically for measuring retail supply chain performance. The researcher also intends to carry out further empirical study to test the proposed theoretical framework.
Antecedents of user satisfaction with ERP systems: mediation analyses
Authors: Al-Jabri Ibrahim M.
Published: January 2015

Purpose

– The purpose of this paper is to investigate the impact of four important influencing factors on user satisfaction with an in-house developed ERP module in a large oil and gas company in Saudi Arabia. It explores whether communication campaigns, training, benefits, ease of use (EoU) are key antecedents of user satisfaction, and examine the mediating effects of EoU and benefits on satisfaction.

Design/methodology/approach

– A questionnaire was developed and distributed to a sample of 104 ERP users who were actively engaged in the ERP system implementation process. The partial least square method was used to test the research model. Baron and Kenny’s approach was used to test the mediating effects.

Findings

– The proposed research model explained 62.7 percent of the variance in ERP user satisfaction. The results showed that EoU fully mediates the relationship between the training and communications and the benefits. Both EoU and benefits fully mediate the relationship between training and satisfaction and partially mediate the relationship between communications and satisfaction.

Practical implications

– The findings of this study imply that training programs and communication campaigns should be designed in such a way that foster the EoU and convey and convince the ERP stakeholders about the benefits and values of ERP systems.

Originality/value

– This study extends the understanding of salient factors affecting the ERP satisfaction in a different setting, namely in an oil & gas industry of a developing country. Although academic research of ERP satisfaction is abundant, this study contributes to the field by examining the mediating effects which rarely tackled in the extant research studies.
Implementing a nationwide quality improvement approach in health services
Authors: Sahel Amina , DeBrouwere Vincent , Dujardin Bruno , Kegels Guy , Belkaab Nejoua , Alaoui Belghiti Abdelali
Published: January 2015

Purpose

– The purpose of this paper is to present an innovative quality improvement intervention developed in Morocco and discuss its implementation. Until 2004, the Moroccan Ministry of Health (MoH) encouraged pilots of quality improvement approaches but none of them were revealed to be sustainable. Internal assessments pinpointed factors such as lack of recognition of the participating team’s efforts and lack of pressure on managers to become more accountable. In 2005, Morocco opted for an intervention called “Quality Contest” (QC) targeting health centres, hospitals and health district offices and combining quality measurement with structures ranking, performance disclosure and reward system.

Design/methodology/approach

– The QC is organized every 18 months. After the self-assessment and external audit step, the participating structures are ranked according to their scores. Their performances are then disseminated and the highest performing structures are rewarded.

Findings

– The results showed an improvement in performance among participating structures, constructive exchange of successful experiences between structures, as well as communication of constraints, needs and expectations between MoH managers at central and local levels; the use of peer-auditors was appreciated as it enabled an exchange of best practices between auditors and audited teams but this was mitigated by the difficulty of ensuring their neutrality; and the recognition of efforts was appreciated but seemed insufficient to ensure a sense of justice and maintain motivation.

Originality/value

– This intervention is an example of MoH leadership that has succeeded in introducing transparency and accountability mechanisms (ranking and performance disclosure) as leverage to change the management culture of the public health services; setting up a reward system to reinforce motivation and adapting continuously the intervention to enhance its sustainability and acceptability.
Conducting semi-structured interviews with the Vietnamese
Authors: Nguyen Thi Quynh Trang
Published: January 2015

Purpose

– The purpose of this paper is to discuss several cultural and psychological aspects that the author experienced in the interview fieldwork with Vietnamese and the strategies to deal with these methodological issues. It aims to assist non-Vietnamese researchers planning their qualitative fieldwork with Vietnamese participants.

Design/methodology/approach

– The results are drawn from using an autoethnographic approach, in which the author presents and analyses the experiences of conducting individual semi-structured interviews with 15 Vietnamese college teachers in the PhD qualitative study on the Vietnamese concept of face – thê diên.

Findings

– The author argues that in interviews with Vietnamese participants, an interviewer should be mindful of the interviewees’ unfamiliarity with the ethics approval procedure, their reliance on relationship and trust, their self-face concern and low level of elaboration. It is important that the interviewer be seen as an “insider” by the Vietnamese interviewees, not an “objective” outsider researcher. In addition, an interviewer needs to be sensitive to detect any subtle cues that may emerge, and be flexible enough to adjust the interview questions if necessary and employ suitable techniques to adapt to these changes.

Research limitations/implications

– The findings were limited to the scope of experiences within a PhD study with a small group of college teachers. Experiences with larger groups of Vietnamese participants from diverse backgrounds may be needed to confirm the findings of this paper.

Originality/value

– This paper addresses the gap in the discussion of conducting qualitative research with the Vietnamese. It also discusses several issues that have not been discussed before, such as the Vietnamese unfamiliarity with the paperwork required for ethics approval and their face concerns in interviews.