bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defect based real‐time diagnostics of ferroelectric domain wall motion
Authors: Dierolf V. , Sandmann C. , Capek P. 
Published: March 2007

AbstractWe investigated the static and dynamic interaction of defect dipoles and ferroelectric domain walls in lithium niobate. Using a home‐built confocal microscope with high spatial and temporal resolution we are able to image both the static domain wall region and the domain wall regions associated with a moving domain wall by monitoring the emission from rare earth ions. We find that the extent of perturbation induced by the presence of a domain wall is increasing with the speed of the domain wall motion. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A narrow band, green‐red colour centre laser in LiF fabricated by femtosecond laser pulses
Authors: Kurobori T. , Sakai T. , Aoshima S. 
Published: March 2007

AbstractRecent advances in high‐intensity femtosecond (fs) laser pulses have made it possible to encode non‐erasable functional micro‐structures inside almost any type of photo‐insensitive transparent materials. We focus our attention on bulk lithium fluoride (LiF) because of its broad emission band from the green‐to‐red spectral range under excitation of a single absorption band at about 450 nm. Here a room temperature, visible laser action in LiF from a distributed‐feedback laser with embedded fine‐pitched gratings written by fs pulses and from a laser‐active colour centre laser with multilayer dielectric mirrors has been demonstrated. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Energy transfer and charge carrier capture processes in wide‐band‐gap scintillators
Authors: Nikl M. , Laguta V. V. , Vedda A. 
Published: March 2007

AbstractElectron and hole trapping phenomena below room temperature were studied by simultaneous use of electron paramagnetic resonance (EPR) and thermostimulated luminescence (TSL) experiments in Ce‐doped YAlO3, Y3Al5O12 and Lu3Al5O12 single crystals. Charge‐carrier trapping associated with O– centers and antisite Y(Lu)Al defects in perovskite and garnet structures, respectively, was evidenced by EPR and associated with the dominant TSL peaks. Existence of F+ centers was proved by EPR in YAlO3. A Ce3+ ion at the Al site and spatially correlated CeLu and LuAl centers were evidenced in Lu3Al5O12 by the same method. Spatial correlation of the latter two centers is further supported by the associated tunneling‐driven radiative recombination process evidenced by phosphorescence decay. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization of deep levels at GaAs/GaAs and GaAs/InAs interfaces grown by MBE‐interrupted growth technique
Authors: Kaniewska M. , Engström O. , Pacholak‐Cybulska M. , Sadeghi M. 
Published: March 2007

AbstractIn order to find the origin of crystalline defects occurring in the preparation of InAs/GaAs quantum dots (QDs), their appearance was tracked through three different sample types designed as Schottky diodes. Specimens with a GaAs cap layer on a GaAs buffer layer as well as with an InAs wetting layer without QDs were grown by molecular beam epitaxy (MBE) using the interrupted growth technique. Deep level transient spectroscopy (DLTS) was used for comparison with structures containing InAs QDs. It was found that two main levels with thermal activation energies of 0.14–0.16 eV and 0.46–0.52 eV from the conduction band edge, respectively, are grown‐in defects, which are characteristic of the growth interrupted interface occuring under an excess of As. Both these levels together with an additional level at 0.10–0.12 eV found in the InAs wetting layer structures were also present in those with QDs, probably resulting from strain or In penetration. All three defects were agglomerated close to the interface created by the interrupted growth. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Feature Article: Recent developments in micromachining of fused silica and quartz using excimer lasers
Authors: Tseng Ampere A. 
Published: March 2007

AbstractThis issue's Feature Article reports on the current achievements of structuring fused silica and crystal quartz materials on the micrometer scale by excimer laser ablation techniques [1]. It discusses the characteristics of direct ablation as well as the more specialized methods of laser‐induced backside wet etching and laser‐induced plasma‐assisted ablation. As an example of such high‐precision, high‐quality structures, the cover picture shows a set of scanning electron microscopy images of the morphologies of different patterns ablated on quartz substrates by an ArF excimer laser. These micro‐structures were ablated using the 193 nm line of an excimer laser at a fluence of 3.4 J/cm2 with 100 pulse shots. The cover picture was contributed by Ying‐Tung Chen, Chung Cheng Institute of Technology (Taiwan).The Feature Article is authored by Ampere A. Tseng, who is a professor at the Department of Mechanical and Aerospace Engineering of Arizona State University. His main research interests lie with micro‐ and nanofabrication of various devices and systems.The issue also includes an Editor's Choice article presenting experimental results on laser‐assisted debonding of GaN high electron mobility transistors [2]. The authors show how the laser‐assisted debonding process can be accomplished without compromising the electrical device characteristics or the material defect density.
Preparation of Ferrocene Nanocrystals by the Ultrasonic‐Solvent‐Substitution Method and Their Electrochemical Properties
Authors: Chen Ping , Wu Qing‐Sheng , Ding Ya‐Ping 
Published: March 2007

AbstractFerrocene nanocrystals are successfully prepared by the ultrasonic‐solvent‐substitution method. Transmission electron microscopy images show that the average diameter of the nanocrystals is about (40±5)nm and X‐ray diffraction analysis indicated that the products obtained have a high purity. The optical properties of the products are studied by IR and UV/Vis spectroscopy. UV/Vis spectra indicate that, compared with ferrocene bulk material, the nanospheres show an obvious blue shift. Cyclic voltammetry is used to test the electrocatalytic oxidation properties of the ferrocene nanospheres towards ascorbic acid on the glassy carbon electrode. The results show that the ferrocene‐nanosphere‐modified glassy carbon electrode exhibits a better electrocatalytic effect than that modified by the ferrocene bulk material in phosphate buffer (pH 5.00). The important factors in the preparation of and a possible mechanism for the formation of ferrocene nanospheres is also discussed. The method could potentially be applied to the preparation of nanomaterials of other organometallic compounds.
Laboratory fretting tests with thin wire specimens
Authors: Urchegui M.A. , Hartelt M. , Klaffke D. , Gómez X. 
Published: March 2007

AbstractWire ropes, due to their construction and application, are prone to fretting damages. In order to know the wear behaviour of individual wires under fretting conditions, laboratory tests are required. The present work describes the preliminary fretting tests accomplished with thin steel wires to optimise the testing procedure. The tests were carried out with ‘crossed‐cylinders’ configuration varying the stroke and normal load. Afterwards, the fretted surfaces were characterised by means of an optical and scanning electron microscope, and a diamond stylus. No significant influence of selected parameters was detected and a good correlation was proved for on‐line measured parameters and off‐line obtained values. Copyright © 2007 John Wiley & Sons, Ltd.
Validation-study conclusions from dietary reports by fourth-grade children observed eating school meals are generalisable to dietary reports by comparable children not observed
Authors: Smith Albert F , Baxter Suzanne Domel , Hardin James W , Guinn Caroline H , Royer Julie A , Litaker Mark S 
Published: March 2007

AbstractObjectiveTo investigate the effect of observing school meals on children's dietary reports.Subjects and settingOne hundred and twenty children randomly selected, but with half girls, from usual school-meal eaters among 312 volunteers (from all 443 fourth-grade children in six schools in one district).DesignChildren were assigned randomly to one of 12 conditions yielded by crossing observation status (observed; not observed), target period (previous day; prior 24 hours), and interview time (morning; afternoon; evening).ResultsResponse variables included interview length, number of meals and snacks reported for the target period, and, for two school meals, number of meal components reported, importance-weighted number of items reported and kilocalories reported. These variables were transformed to principal components; two were retained (1, the school meal variables; 2, interview length and number of meals and snacks). Analyses of variance on principal component scores tested effects of observation status, target period, interview time and all interactions. Observation status did not affect scores on either retained principal component. Scores on Component 2 showed that more intake was reported in prior-24-hours interviews than in previous-day interviews.ConclusionsThe effect of target period on reported intake indicates that the response variables were sufficiently reliable to detect manipulations. This, together with the finding that response variables did not depend on observation status, suggests that observation of school meals does not affect fourth-grade children's dietary reports, and that conclusions about dietary reports by fourth-grade children observed eating school meals in validation studies may be generalised to dietary reports by comparable children not observed.
Glycaemic index, glycaemic load and ovarian cancer risk: a prospective cohort study
Authors: Silvera Stephanie AN , Jain Meera , Howe Geoffrey R , Miller Anthony B , Rohan Thomas E 
Published: March 2007

AbstractBackgroundThere is some evidence that plasma insulin levels might influence ovarian cancer risk. Glyacemic index (GI) and glycaemic load (GL) are measures that allow the carbohydrate content of individual foods to be classified according to their postprandial glycaemic effects and hence their effects on circulating insulin levels. Therefore, we examined ovarian cancer risk in association with GI and GL, and intake of dietary carbohydrate and sugar.MethodsThe study was conducted in a prospective cohort of 49 613 Canadian women enrolled in the National Breast Screening Study (NBSS) who completed a self-administered food-frequency questionnaire (FFQ) between 1980 and 1985. Linkages to national mortality and cancer databases yielded data on deaths and cancer incidence, with follow-up ending between 1998 and 2000. Data from the FFQ were used to estimate overall GI and GL, and Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between energy-adjusted quartile levels of GL, overall GI, total carbohydrates, total sugar and ovarian cancer risk.ResultsDuring a mean 16.4 years of follow-up, we observed 264 incident ovarian cancer cases. GI and total carbohydrate and sugar intakes were not associated with ovarian cancer risk in the total cohort. GL was positively associated with a 72% increase in risk of ovarian cancer (HR = 1.72, 95% CI = 1.13–2.62,Ptrend = 0.01) and the magnitude of the association was slightly greater among postmenopausal (HR = 1.89, 95% CI = 0.98–3.65,Ptrend = 0.03) than among premenopausal women (HR = 1.64, 95% CI = 0.95–2.88,Ptrend = 0.07).ConclusionsOur data suggest that consumption of diets with high GL values may be associated with increased risk of ovarian cancer.
The role of parents' educational background in healthy lifestyle practices and attitudes of their 6-year-old children
Authors: Stenhammar Christina , Sarkadi Anna , Edlund Birgitta 
Published: March 2007

AbstractObjectiveThe aim of the present study was to examine parents' reported and desired frequencies (practices vs. attitudes) of their 6-year-old children's meals, nutritional intake and lifestyle components, as well as possible obstacles and desired support with respect to higher or lower educational backgrounds.DesignCross-sectional questionnaire study.SettingFive elementary schools in Uppsala, Sweden.SubjectsParents of 176 6-year-old pupils attending the first grade. The total response rate was 89.7%.ResultsParents with a college degree reported that their 6-year-olds had a higher frequency of milk, fruit and vegetable intake, more physical activity and fewer hours watching television compared with parents with a secondary school degree. Congruent to these differences in reported practices, more parents with a college degree desired a higher frequency of milk, fruit and vegetable intake, more physical exercise and less television viewing for their children. Regarding parents' desired meal frequencies during the week, no differences between the groups with higher and lower levels of education were found. Despite similar attitudes, however, parents with a college degree reported that their children ate mostly all meals significantly more often during the week. Both parent groups stated lack of time as the most common obstacle in providing their children with desired lifestyle practices, although parents with a secondary school education added lack of money as a contributing factor.ConclusionsAs attitudes are not always reflected in reported practices, it seems a fruitful approach to assess both, as well as obstacles perceived by parents, before planning interventions to enhance healthy lifestyle habits in children.
PhyloGena—a user-friendly system for automated phylogenetic annotation of unknown sequences
Authors: Hanekamp Kristian , Bohnebeck Uta , Beszteri Bánk , Valentin Klaus 
Published: March 2007

AbstractMotivation: Phylogenomic approaches towards functional and evolutionary annotation of unknown sequences have been suggested to be superior to those based only on pairwise local alignments. User-friendly software tools making the advantages of phylogenetic annotation available for the ever widening range of bioinformatically uninitiated biologists involved in genome/EST annotation projects are, however, not available. We were particularly confronted with this issue in the annotation of sequences from different groups of complex algae originating from secondary endosymbioses, where the identification of the phylogenetic origin of genes is often more problematic than in taxa well represented in the databases (e.g. animals, plants or fungi).Results: We present a flexible pipeline with a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a basic local alignment search tool (BLAST) search of query sequences, selects a representative subset of them, then creates a multiple alignment from the selected sequences, and finally computes a phylogenetic tree. The pipeline, named PhyloGena, uses public domain software for all standard bioinformatics tasks (similarity search, multiple alignment, and phylogenetic reconstruction). As the major technological innovation, selection of a meaningful subset of BLAST hits was implemented using logic programing, mimicing the selection procedure (BLAST tables, multiple alignments and phylogenetic trees) are displayed graphically, allowing the user to interact with the pipeline and deduce the function and phylogenetic origin of the query. PhyloGena thus makes phylogenomic annotation available also for those biologists without access to large computing facilities and with little informatics background. Although phylogenetic annotation is particularly useful when working with composite genomes (e.g. from complex algae), PhyloGena can be helpful in expressed sequence tag and genome annotation also in other organisms.Availability: PhyloGena (executables for LINUX and Windows 2000/XP as well as source code) is available by anonymous ftp from http://www.awi.de/en/phylogenaContact: kvalentin@awi-bremerhaven.de
Improving metabolic flux estimation via evolutionary optimization for convex solution space
Authors: Chen Jiusheng , Zheng Haoran , Liu Haiyan , Niu Junqing , Liu Jianping , Shen Tie , Rui Bin , Shi Yunyu 
Published: March 2007

AbstractMotivation: Flux estimation by using 13 C-labeling pattern information of metabolites is currently the only method that can give accurate, detailed quantification of all intracellular fluxes in the central metabolism of a microorganism. In essence, it corresponds to a constrained optimization problem which minimizes a weighted distance between measured and simulated results. Characteristics, such as existence of multiple local minima, non-linear and non-differentiable make this problem a special difficulty.Results: In the present work, we propose an evolutionary-based global optimization algorithm taking advantage of the convex feature of the problem's solution space. Based on the characteristics of convex spaces, specialized initial population and evolutionary operators are designed to solve 13C-based metabolic flux estimation problem robustly and efficiently. The algorithm was applied to estimate the central metabolic fluxes in Escherichia coli and compared with conventional optimization technique. Experimental results illustrated that our algorithm is capable of achieving fast convergence to good near-optima and maintaining the robust nature of evolutionary algorithms at the same time.Availability: Available from the authors upon request.Contact: hrzheng@ustc.edu.cnSupplementary information: Colour versions of the figure are available online as a part of the Supplementary data.
Phylogenetic exploration of bacterial genomic rearrangements
Authors: Fremez Romain , Faraut Thomas , Fichant Gwennaele , Gouzy Jérôme , Quentin Yves 
Published: March 2007

AbstractSummary: We present a graphical tool dedicated to the exploration of bacterial genome rearrangements. The principle of this exploration relies on the reconstruction of ancestral genomes at each internal node of a gene-order-based phylogenetic tree. This tool allows the selection of internal nodes to visualize the rearrangements between the inferred chromosome of this node and its direct descendant on the tree.Availability: PEGR is available at the Genopole Toulouse Bioinformatics platform.Supplementary information: Online supplementary data are available at PEGR web site: http://bioinfo.genopole-toulouse.prd.fr/pegr.
Culture ofDrosophila: The Laboratory Setup
Authors: Ashburner Michael , Roote John 
Published: March 2007

INTRODUCTIONSince its introduction to experimental biology more than 90 years ago,Drosophila melanogasterhas proved to be an easily cultured and robust laboratory animal. Although culture techniques and the ways in which flies are handled have changed over the years, if he were to enter a fly room today, T.H. Morgan would clearly recognize what is being done, and why. This article provides the basic methods for the laboratory culture ofD. melanogaster. The intelligent culture ofDrosophilarequires a basic understanding of the life cycle of this fly. For this reason, we begin by describing the life cycle ofDrosophilaand then present information for setting up a fly laboratory.
Protein Arrays: Preparation of Microscope Slides
Authors: MacBeath Gavin 
Published: March 2007

INTRODUCTIONThis protocol describes the preparation of glass microscope slides with two particularly useful substrates: aldehyde and BSA-NHS. On aldehyde slides, amines on the proteins form a Schiff base with the aldehydes on the slide. BSA-NHS (bovine serum albumin-N-hydroxysuccinimide) slides contain a layer of BSA molecules that are chemically activated for covalent attachment of proteins to the slide. In this case, amines on the proteins of interest form amide or urea bonds with the activated carboxylates or activated amines of the BSA, respectively.
Protein Arrays: Sandwich Approach for Analyzing Complex Solutions
Authors: MacBeath Gavin 
Published: March 2007

INTRODUCTIONProtein arrays can be used to quantitate the abundance and modification states of proteins in complex mixtures. For this application, it is necessary to array-capture reagents, such as antibodies, on the slides and then use these molecules to specifically capture their cognate antigens from solution. The investigator has a choice in either labeling the proteins that are under study or detecting the captured proteins by an indirect labeling method. In the latter case, which is detailed in this protocol, each protein is captured by one antibody (or other capture reagent) and then detected in a second step with a second reagent. The second reagent, which in this case is also an antibody, recognizes the protein at a site that does not overlap with the recognition site of the capture reagent. In this sandwich approach, the second reagent is labeled and so provides the signal. The advantage of this approach is that it does not require labeling the proteins themselves. Moreover, additional specificity is gained by using two different reagents for each protein. The disadvantage, however, is that it is more difficult to assemble matched pairs of antibodies for each protein of interest.
General Method for MALDI-MS Analysis of Proteins and Peptides
Authors: Frecklington David 
Published: March 2007

INTRODUCTIONFor MALDI-TOF-MS analysis of proteins and peptides, samples are cocrystallized with an excess of organic matrix that absorbs at a specific wavelength (usually, UV337nm). Typically, sinapinic acid (SA) is the matrix of choice for large proteins, whereas α-cyano-4-hydroxy-cinnamic acid (HCCA) is the preferred matrix for peptide mapping. Following a short laser pulse, analytes are protonated and desorbed into the gas phase, and their m/z values are determined in a TOF mass analyzer. Mass accuracy determinations vary from ±0.01% to 0.1% depending on the sample preparation technique and the method used for mass calibration.
Cleavage of Asn-Gly Bonds by Hydroxylamine: Figure 1.
Authors: Simpson Richard J. 
Published: March 2007

INTRODUCTIONSelective cleavage of Asn-Gly bonds in proteins by hydroxylamine generates a relatively small number of large peptide fragments. This protocol describes a procedure for performing Asn-Gly bond cleavage in solution.
Performic Acid Oxidation of Proteins
Authors: Simpson Richard J. 
Published: March 2007

INTRODUCTIONDisulfide bond cleavage is a prerequisite to many peptide-mapping strategies. It facilitates protein unfolding and thus optimizes proteolytic digestion. It also simplifies the interpretation of peptide maps by removing possible peptide fragment(s) in the mixture that are held together by disulfide bonds. This protocol describes the performic acid oxidation method for cleaving disulfide bonds. It is convenient for determining the combined cysteine and cystine content and the total methionine content of a protein.
Maintaining a Population of Drosophila
Authors: Sisson John Charles 
Published: March 2007

INTRODUCTIONThe Drosophila embryo is a superb source of proteins for studies aimed at characterizing a variety of cellular functions, including replication, transcription, translation, signal transduction, and the functions of the extracellular matrix and the cytoskeleton. The success of these studies requires the efficient production of gram quantities of embryos by large populations of adult flies. This protocol outlines a simple and efficient method for maintaining a population of Drosophila.
In Vitro Transcription Using Drosophila Nuclear Extracts
Authors: Pazin Michael J. 
Published: March 2007

INTRODUCTIONDrosophila nuclear extracts are often used in gene expression studies. This protocol describes RNA polymerase II transcription in vitro using a Drosophila embryonic nuclear extract called soluble nuclear fraction (SNF). Transcription and RNA purification are followed by detection of the transcripts by primer extension with reverse transcriptase and a labeled oligonucleotide.