bluuebunny/crossref_metadata_2025_split huggingface dataset:
Luminescence centers and spectrum characteristics of a novel Eu2+‐activated hexa‐aluminate CaZrBAl9O18
Authors: Yu Ruijin , Li Hongjuan , Ma Hailong , Wang Caifeng , Wang Huan 
Published: December 2013

A new blue‐emitting phosphor of Eu2+‐activated hexa‐aluminate CaZrBAl9O18 was synthesized by a conventional solid‐state reaction method. The crystalline phase formation was confirmed by X‐ray powder diffraction (XRD) measurements. The photoluminescence excitation and emission spectra, the luminescence decay curves and the time‐resolved spectra of CaZrBAl9O18:Eu2+ were taken to investigate the luminescence characteristics. The dependence of CaZrBAl9O18:Eu2+ luminescence intensity on the Eu2+ doping concentrations was investigated. This phosphor can be efficiently excited by UV light and presents blue luminescence. There is one kind of Eu2+ luminescence center in the lattices, which was confirmed by the time‐resolved luminescence spectra. The temperature‐dependent luminescence intensity was measured and the activation energy (ΔE) for thermal quenching was reported. The phosphor shows high luminescence intensity and an excellent thermal stability on temperature quenching. Eu2+‐doped hexa‐aluminate CaZrBAl9O18 presents bright blue‐emitting luminescence with high thermal quenching; only one Eu2+ center was confirmed in this hexa‐aluminate lattices.
Electronic structure and band gap of oxygen bearing c‐Zr3N4 and of c‐Hf3N4 by soft X‐ray spectroscopy
Authors: Yablonskikh Mikhail , Dzivenko Dmytro , Bourguille Judith , Riedel Ralf , Magnano Elena , Parmigiani Fulvio , Zerr Andreas 
Published: December 2013

Electronic band structures of two novel semiconducting nitrides of the group‐IV elements of Th3P4‐type crystal structure, c‐M3N4, where MZr or Hf, is investigated using an element specific soft X‐ray spectroscopy for the first time. From the pairs of N 1s X‐ray absorption and N 2p → 1s resonant X‐ray emission spectra partial densities of states (PDOS) of nitrogen, predicted to be strongly hybridized with those of the metals, are obtained for both compounds. From these data the electronic band gaps of oxygen bearing c‐Zr3N4 and of c‐Hf3N4, predicted before to be direct or nearly direct, are derived to be Eg = 1.6 eV and Eg = 1.8 eV, respectively. While the experimentally determined Eg for c‐Hf3N4 agrees with the theoretical one obtained using the local density approximation (LDA) method, the Eg measured for oxygen bearing c‐Zr3N4 is significantly higher than those calculated using both the LDA and the generalized gradient approximation method. The examined compounds, having high hardness, elastic moduli and oxidation resistance, appear to be multifunctional materials suitable also for applications as (opto)electronic materials. Band gap evolution in c‐M3N4 nitrides as a function of the cation type, Zr or Hf.
Metabolite identification studies on amiodarone in in vitro (rat liver microsomes, rat and human liver S9 fractions) and in vivo (rat feces, urine, plasma) matrices by using liquid chromatography with high‐resolution mass spectrometry and multiple‐stage mass spectrometry: Characterization of the diquinone metabolite supposedly responsible for the drug's hepatotoxicity
Authors: Varkhede Ninad Ramesh , Jhajra Shalu , Ahire Deepak Suresh , Singh Saranjit 
Published: December 2013

RATIONALESeveral mechanisms have been anticipated for the toxicity of amiodarone, such as oxidative stress, lipid peroxidation, phospholipidosis, free radical generation, etc. Amiodarone is structurally similar to benzbromarone, an uricosuric agent, which was withdrawn from European markets due to its idiosyncratic hepatotoxicity. A proposed reason behind the toxicity of benzbromarone was the production of a reactive ortho‐diquinone metabolite, which was found to form adducts with glutathione. Therefore, taking a clue that a similar diquinone metabolite of amiodarone may be the reason for its hepatotoxicity, metabolite identification studies were carried out on the drug using liquid chromatography/mass spectrometry (LC/MS) tools.METHODSThe studies involved in vitro (rat liver microsomes, rat liver S9 fraction, human liver S9 fraction) and in vivo (rat feces, urine, plasma) models, wherein the samples were analyzed by employing LC/HRMS, LC/MSn and HDE‐MS.RESULTS AND CONCLUSIONSA total of 26 metabolites of amiodarone were detected in the investigated in vitro and in vivo matrices. The suspected ortho‐diquinone metabolite was one of them. The formation of the same might be an added reason for the hepatotoxicity shown by the drug. Copyright © 2013 John Wiley & Sons, Ltd.
Lake Louise Water (USGS47): A new isotopic reference water for stable hydrogen and oxygen isotope measurements
Authors: Qi Haiping , Lorenz Jennifer M. , Coplen Tyler B. , Tarbox Lauren , Mayer Bernhard , Taylor Steve 
Published: December 2013

RATIONALEBecause of the paucity of isotopic reference waters for daily use, a new secondary isotopic reference material has been prepared from Lake Louise water from Alberta, Canada, for international distribution.METHODSThis water was filtered, homogenized, loaded into glass ampoules, sealed with a torch, autoclaved to eliminate biological activity, and measured by dual‐inlet isotope‐ratio mass spectrometry. This isotopic reference water is available by the case of 144 glass ampoules containing 5 mL of water in each ampoule.RESULTSThe δ2H and δ18O values of this reference water are −150.2 ± 0.5 ‰ and −19.80 ± 0.02 ‰, respectively, relative to VSMOW, on scales normalized such that the δ2H and δ18O values of SLAP reference water are, respectively, –428 and −55.5 ‰. Each uncertainty is an estimated expanded uncertainty (U = 2uc) about the reference value that provides an interval that has about a 95 % probability of encompassing the true value.CONCLUSIONSThis isotopic reference material, designated as USGS47, is intended as one of two isotopic reference waters for daily normalization of stable hydrogen and stable oxygen isotopic analysis of water with a mass spectrometer or a laser absorption spectrometer. Published in 2013. This article is a U.S. Government work and is in the public domain in the USA.
Identification of unusual butanetriol dialkyl glycerol tetraether and pentanetriol dialkyl glycerol tetraether lipids in marine sediments
Authors: Zhu Chun , Meador Travis B. , Dummann Wolf , Hinrichs Kai‐Uwe 
Published: December 2013

RATIONALEGlycerol serves as the principal backbone moiety bound to various acyl/alkyl chains for membrane lipids of Eukarya, Bacteria, and Archaea. In this study, we report a suite of unusual tetraether lipids in which one of the two conventional glycerol backbones is substituted by butanetriol or pentanetriol.METHODSIdentification of these lipids was achieved via diagnostic fragments and their expected acetylation products using liquid chromatography/mass spectrometry (LC/MS), and their diagnostic ether cleavage products using gas chromatography/mass spectrometry (GC/MS).RESULTSWe observed structural variations in the polyol backbones and alkyl chains and term these core lipid derivatives: isoprenoidal butanetriol dialkyl glycerol tetraethers (iso‐BDGTs), isoprenoidal pentanetriol dialkyl glycerol tetraethers (iso‐PDGTs), and hybrid isoprenoidal/branched BDGTs and PDGTs (ib‐BDGTs, ib‐PDGTs). Of these, iso‐BDGTs were the most abundant with a methylation at either the sn‐1 or sn‐3 position of glycerol and were also found as part of intact polar lipids, adjoined to mono‐ or diglycosidic headgroups. Iso‐BDGTs and iso‐PDGTs are likely produced by Archaea, as indicated by the presence of the characteristic biphytanyl moieties.CONCLUSIONSButanetriol‐ and pentanetriol‐based tetraether lipids occur in modern estuarine and deeply buried subseafloor sediments, suggesting the presence of alternative backbones in archaeal lipids. Copyright © 2013 John Wiley & Sons, Ltd.
A mixed cluster ion beam to enhance the ionization efficiency in molecular secondary ion mass spectrometry
Authors: Wucher Andreas , Tian Hua , Winograd Nicholas 
Published: December 2013

RATIONALEChemical modification of a rare gas cluster ion beam (GCIB) to increase the intensity of desorbed molecular ions in secondary ion mass spectrometry experiments relative to the pure Ar cluster.METHODSDoping of the GCIB by mixing small concentration levels (1–3% relative partial pressure) of CH4 into the Ar gas driving the cluster ion source.RESULTSMass spectra measured on a trehalose film using the doped GCIB exhibit enhanced molecular ion signals. From depth profiling experiments, the results are shown to arise from an increase in the ionization efficiency of the sputtered molecules rather than a change in the sputtering yield of neutral species.CONCLUSIONSTuning of the chemistry of mixed clusters is suggested as a general approach to enhancing the ionization probability of sputtered molecules. Copyright © 2013 John Wiley & Sons, Ltd.
Stability and stabilization of piecewise‐affine slab systems subject to Wiener process noise
Authors: Raouf Jamila , Rodrigues Luis 
Published: December 2013

SummaryThe main contribution of this paper is to propose a convex formulation of sufficient conditions for both stability analysis and synthesis of stabilizing controllers for stochastic piecewise affine (PWA) systems with multiplicative noise. One of the main difficulties in PWA systems is the fact that the affine terms in the dynamics make it extremely difficult to formulate the synthesis problem as a convex optimization or even convex feasibility program. The presence of multiplicative noise modeled as a Wiener process adds an additional level of difficulty to the analysis and synthesis procedures. Sufficient conditions for stability of stochastic PWA slab systems in the mean square sense are developed first using a stochastic globally quadratic Lyapunov function. Second, PWA state feedback controllers are designed such that the closed‐loop system is stochastically exponentially mean square stable. The conditions for both stability and stabilization are formulated as LMIs, which can then be solved efficiently using currently available software packages. A numerical example shows the effectiveness of the approach. Copyright © 2013 John Wiley & Sons, Ltd.
Fundamental Investigations on the Corrosion of ZrO2–CRefractories during Interaction with a Casting Mould Meniscus Slag
Authors: Kumar Anup , Khanna Rita , Spink John , Sahajwalla Veena 
Published: December 2013

AbstractThe degradation behavior of Zirconia – 20% carbon refractory was investigated during high temperature (1550 °C) contact with a casting mould meniscus slag containing 50% MnO, 25% SiO2, and 25% Al2O3. Using the sessile drop approach, the transient progress of corrosion reactions was investigated as a function of time; in‐depth characterization and analysis of reacted assemblies was carried out using optical and scanning electron microscopy. Optical micrographs showed a significant penetration of slag within the refractory substrate, with very little slag remaining behind after 15 min of contact. In situ carbothermic reduction of zirconia and the presence of reducible oxides in the slag significantly depleted carbon from the substrate further aiding the penetration of slag. Interaction between slag and zirconia resulted in the depletion of phase‐stabilizing Y2O3from zirconia granules resulting in their fragmentation and subsequent diffusion in slag rich regions. An aggressive all‐round corrosion was observed with extensive refractory degradation over a period of time; a number of reaction products such as Mn5Si3were also observed. These experimental investigations were supplemented with thermodynamic investigations using FactSage.
Questioning Western Knowledge Transfer Methodologies: Toward a Reciprocal and Intercultural Transfer of Knowledge
Authors: Bengoa Dolores Sanchez , Kaufmann Hans Ruediger 
Published: December 2013

The rapid development of western European knowledge‐based societies has a drastic effect on the development of eastern European societies. Special attention should be paid to the past three years of economic crisis, where a shift of existing economic paradigms has occurred. In order to navigate through these turbulent times, many companies, as an option to survive or expand, have formed cross‐border alliances and cooperations. Due to these cross‐border initiatives, the geographic movement of employees and, implicitly, the flow of intellectual capital, play an important role. Paradoxically, however, the process of knowledge transfer has been affected by several shortcomings, for example, the knowledge receiver's lack of absorptive capacity or cognitive learning, a knowledge applicability gap, or the rise of knowledge sharing barriers.The reason for this situation lies in the flawed knowledge transfer process. This approach is characterized by a unidirectional flow of knowledge from the West, reflecting an ethnocentric approach; inappropriate attitudes on behalf of the knowledge transmitter and the knowledge receiver; by knowledge not being culturally embedded, which leads to an alienation of knowledge; and, finally, to a lack of cultural awareness and preparedness on behalf of the westerners.This article applies a phenomenological approach. By using grounded theory, it contributes to a better understanding of the complexity of the problems and its implications on management from a multidisciplinary perspective. It provides solutions to improve the knowledge transfer process between eastern and western European cooperations based on an intercultural and reciprocal methodology and a new conducive learning environment. © 2013 Wiley Periodicals, Inc.
Plasmon-Enhanced Fluorescence Biosensors: a Review
Authors: Bauch Martin , Toma Koji , Toma Mana , Zhang Qingwen , Dostalek Jakub 
Published: December 2013

Abstract
Surfaces of metallic films and metallic nanoparticles can strongly confine electromagnetic field through its coupling to propagating or localized surface plasmons. This interaction is associated with large enhancement of the field intensity and local optical density of states which provides means to increase excitation rate, raise quantum yield, and control far field angular distribution of fluorescence light emitted by organic dyes and quantum dots. Such emitters are commonly used as labels in assays for detection of chemical and biological species. Their interaction with surface plasmons allows amplifying fluorescence signal (brightness) that accompanies molecular binding events by several orders of magnitude. In conjunction with interfacial architectures for the specific capture of target analyte on a metallic surface, plasmon-enhanced fluorescence (PEF) that is also referred to as metal-enhanced fluorescence (MEF) represents an attractive method for shortening detection times and increasing sensitivity of various fluorescence-based analytical technologies. This review provides an introduction to fundamentals of PEF, illustrates current developments in design of metallic nanostructures for efficient fluorescence signal amplification that utilizes propagating and localized surface plasmons, and summarizes current implementations to biosensors for detection of trace amounts of biomarkers, toxins, and pathogens that are relevant to medical diagnostics and food control.
The long noncoding RNA
THRIL
regulates TNFα expression through its interaction with hnRNPL
Authors: Li Zhonghan , Chao Ti-Chun , Chang Kung-Yen , Lin Nianwei , Patil Veena S. , Shimizu Chisato , Head Steven R. , Burns Jane C. , Rana Tariq M. 
Published: December 2013

Significance
Genome-wide identification of changes in the expression of large intergenic noncoding RNAs (lincRNAs) in a classical model of innate immune cell activation revealed a panel of 159 lincRNAs that were highly modulated in stimulated THP1 macrophages. One of the lincRNAs, named TNFα and heterogenous nuclear ribonucleoprotein L (hnRNPL) related immunoregulatory LincRNA (THRIL), was essential for induction of TNFα, functions through a ribonucleoprotein (RNP) complex with hnRNPL, and plays an important role as regulator of physiological and pathological inflammatory immune responses.
Application of the Predicted Heat Strain Model in Development of Localized, Threshold-based Heat Stress Management Guidelines for the Construction Industry
Authors: Rowlinson Steve , Jia Yunyan Andrea 
Published: December 2013

Abstract
Existing heat stress risk management guidelines recommended by international standards are not practical for the construction industry which needs site supervision staff to make instant managerial decisions to mitigate heat risks. The ability of the predicted heat strain (PHS) model [ISO 7933 (2004). Ergonomics of the thermal environment analytical determination and interpretation of heat stress using calculation of the predicted heat strain. Geneva: International Standard Organisation] to predict maximum allowable exposure time (D lim) has now enabled development of localized, action-triggering and threshold-based guidelines for implementation by lay frontline staff on construction sites. This article presents a protocol for development of two heat stress management tools by applying the PHS model to its full potential. One of the tools is developed to facilitate managerial decisions on an optimized work-rest regimen for paced work. The other tool is developed to enable workers’ self-regulation during self-paced work.
SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
Authors: Jaron Kamil S. , Moravec Jiří C. , Martínková Natália 
Published: December 2013

Abstract
Motivation: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.
Results: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.
Availability and implementation: Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research–data-analysis-tools–sighunt are implemented in C and R and are platform-independent.
Contact: 376090@mail.muni.cz or martinkova@ivb.cz
ALEA: a toolbox for allele-specific epigenomics analysis
Authors: Younesy Hamid , Möller Torsten , Heravi-Moussavi Alireza , Cheng Jeffrey B. , Costello Joseph F. , Lorincz Matthew C. , Karimi Mohammad M. , Jones Steven J. M. 
Published: December 2013

Abstract
The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data.
Availability: The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea.
Contact: mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data
Authors: Jorjani Hadi , Zavolan Mihaela 
Published: December 2013

Abstract
Motivation: Accurate identification of transcription start sites (TSSs) is an essential step in the analysis of transcription regulatory networks. In higher eukaryotes, the capped analysis of gene expression technology enabled comprehensive annotation of TSSs in genomes such as those of mice and humans. In bacteria, an equivalent approach, termed differential RNA sequencing (dRNA-seq), has recently been proposed, but the application of this approach to a large number of genomes is hindered by the paucity of computational analysis methods. With few exceptions, when the method has been used, annotation of TSSs has been largely done manually.
Results: In this work, we present a computational method called ‘TSSer’ that enables the automatic inference of TSSs from dRNA-seq data. The method rests on a probabilistic framework for identifying both genomic positions that are preferentially enriched in the dRNA-seq data as well as preferentially captured relative to neighboring genomic regions. Evaluating our approach for TSS calling on several publicly available datasets, we find that TSSer achieves high consistency with the curated lists of annotated TSSs, but identifies many additional TSSs. Therefore, TSSer can accelerate genome-wide identification of TSSs in bacterial genomes and can aid in further characterization of bacterial transcription regulatory networks.
Availability: TSSer is freely available under GPL license at http://www.clipz.unibas.ch/TSSer/index.php
Contact: mihaela.zavolan@unibas.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Authors: Niu Beifang , Ye Kai , Zhang Qunyuan , Lu Charles , Xie Mingchao , McLellan Michael D. , Wendl Michael C. , Ding Li 
Published: December 2013

AbstractMotivation: Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR–electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.Availability and implementation: https://github.com/ding-lab/msisensorContact: kye@genome.wustl.edu or lding@genome.wustl.eduSupplementary information: Supplementary data are available at Bioinformatics online.