bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface morphology of homoepitaxial GaN grown on non‐ and semipolar GaN substrates
Authors: Wernicke Tim , Ploch Simon , Hoffmann Veit , Knauer Arne , Weyers Markus , Kneissl Michael 
Published: January 2011

AbstractGaN layers on bulk m‐plane, $(11{\bar {2}}2)$, $(10{\bar {1}}2)$ and $(10{\bar {1}}1)$ GaN substrates were grown by metal organic vapor phase epitaxy. XRD rocking curves have a FWHM of less than 150″, indicating excellent crystalline quality. However in many cases surface morphology exhibits hillocks with a height of 1–2 µm and a lateral extension of 50–200 µm whereas a smooth surface would be desirable for optoelectronic devices. The influence of growth parameters on the surface morphology was studied. The goal was, to constrain the material redistribution, that is necessary to form large hillocks. This was achieved by lowering the adatom diffusion length by a reduction of temperature and an increased reactor pressure. In the case of the $(10{\bar {1}}1)$ and $(10{\bar {1}}2)$ semipolar planes a reduction of the adatom diffusion length leads to a reduction of hillock density, hillock size and a smoother surface between hillocks. However, the m‐plane surface does not react to a reduction of adatom mobility. Even at 890°C and 400 mbar rectangular pyramids cover the surface. In contrast to the other planes, the $(11{\bar {2}}2)$ becomes instable, when the adatom diffusion length is reduced.
Reducing noise associated with the Monte Carlo Independent Column Approximation for weather forecasting models
Authors: Hill P. G. , Manners J. , Petch J. C. 
Published: January 2011

AbstractThe Monte Carlo Independent Column Approximation (McICA) is a flexible method for representing subgrid‐scale cloud inhomogeneity in radiative transfer schemes. It does, however, introduce conditional random errors but these have been shown to have little effect on climate simulations, where spatial and temporal scales of interest are large enough for effects of noise to be averaged out. This article considers the effect of McICA noise on a numerical weather prediction (NWP) model, where the time and spatial scales of interest are much closer to those at which the errors manifest themselves; this, as we show, means that noise is more significant. We suggest methods for efficiently reducing the magnitude of McICA noise and test these methods in a global NWP version of the UK Met Office Unified Model (MetUM). The resultant errors are put into context by comparison with errors due to the widely used assumption of maximum‐random‐overlap of plane‐parallel homogeneous cloud. For a simple implementation of the McICA scheme, forecasts of near‐surface temperature are found to be worse than those obtained using the plane‐parallel, maximum‐random‐overlap representation of clouds. However, by applying the methods suggested in this article, we can reduce noise enough to give forecasts of near‐surface temperature that are an improvement on the plane‐parallel maximum‐random‐overlap forecasts. We conclude that the McICA scheme can be used to improve the representation of clouds in NWP models, with the provision that the associated noise is sufficiently small. © Crown Copyright 2011. Published by John Wiley & Sons, Ltd.
Morphology and tensile properties of crosslinked nanocomposite foams of low‐density polyethylene and poly(ethylene‐co‐vinyl acetate) blends
Authors: Riahinezhad M. , Ghasemi I. , Karrabi M. , Azizi H. 
Published: January 2011

AbstractThis paper studies the morphology and tensile properties of nanocomposite foams of blends of low‐density polyethylene (LDPE) and poly(ethylene‐co‐vinyl acetate) (EVA). Preparations of LDPE/EVA nanocomposites were conducted in an internal mixer, and then samples were foamed via a batch foaming method. Morphology of the nanocomposite blends and nanocomposite foams was studied by X‐ray diffraction, transmission electron microscopy, and scanning electron microscopy. Morphological observations showed that nanoparticle dispersion in the polymeric matrix was affected by the blend ratio in a way such that EVA‐rich samples had a better dispersion of nanoclay than LDPE‐rich ones. In addition, the tensile properties of the nanocomposite foams were related to different variables such as blend ratio, clay content, and foam density. J. VINYL ADDIT. TECHNOL., 2010. © 2010 Society of Plastics Engineers
Efficient preparation of polymer‐based hollow spheres for the photocatalytic degradation of methylene blue
Authors: Khalil A.M. , Hamed El‐Nazer H.A. , Badr M.M. , Nada A.A. 
Published: January 2011

AbstractTitanium dioxide hollow spheres were synthesized by utilizing polystyrene‐co‐methacrylic acid latex particles coated with titanium isopropoxide. Hollow spheres prepared with different ruthenium salt concentrations showed considerable levels of organic pollutant degradation upon UV irradiation. In the present study, methylene blue (MB) was selected as a model for these pollutants. Thus its degradation indicated the activity of the hollow spheres as photocatalysts for decomposing the pollutants. The efficiencies of these photocatalysts were determined in terms of chemical oxygen demand removal. During these experiments, several conditions were monitored such as the effects of pH, ruthenium salt concentration, and initial MB load concentration. The prepared particles were characterized by using transmission electron microscopy and scanning electron microscopy. J. VINYL ADDIT. TECHNOL., 2010. © 2010 Society of Plastics Engineers
SIM‐RIXS: a program to simulate resonant inelastic X‐ray scattering
Authors: Hayashi Hisashi 
Published: January 2011

AbstractWe have developed a program for simulating resonant inelastic X‐ray scattering (RIXS), SIM‐RIXS that can be run on personal computers with a Microsoft Windows XP/Vista operating system. RIXS primarily reflects lifetime‐broadening‐suppressed (LBS) or lifetime‐broadening‐suppressed state‐selective (LBSS) X‐ray absorption fine structure (XAFS). SIM‐RIXS can convert theoretical LBS/LBSS–XAFS profiles to RIXS spectra, and it can derive an optimal LBS/LBSS–XAFS profile to reproduce experimental RIXS spectra. SIM‐RIXS has three basic modules, and each user‐friendly graphical user interface enables even novices, who are unfamiliar with RIXS analysis, to use this software. In this software, the first module sets conditions using conventional XAFS data; the second module does the same for conventional X‐ray fluorescence data; and the third module is used for RIXS simulation based on the Tulkki–Åberg equation. An example of its application to the EuLγ4RIXS of Eu2O3is presented. SIM‐RIXS can readily provide a basic description of the excitation and emission energy dependence of EuLγ4RIXS, elucidating the existence of the ‘hidden’ peak at 8056 eV in the Eu(III) L1‐XAFS. This demonstrates the usefulness of SIM‐RIXS in RIXS analyses. Copyright © 2011 John Wiley & Sons, Ltd.
Levels and growth of specific and general norms for nonviolence among middle school students
Authors: Dymnicki Allison B. , Antônio Tiago , Henry David B. 
Published: January 2011

ABSTRACTThis study examined the levels and growth of specific and general normative beliefs about nonviolence (called norms for nonviolence). The sample consisted of 1254 middle school students from four metropolitan areas who participated in the control condition of the Multisite Violence Prevention Project. We predicted that the association and endorsement of specific and general norms for nonviolence would strengthen over time, levels and growth of norms for nonviolence would be moderated by gender and ethnicity, and norms for nonviolence would be related to youths’ behaviors. Linear mixed models found that levels and direction of growth in specific and general norms varied as a function of gender, age, and ethnicity, providing partial support for our hypotheses. Specific and general norms for nonviolence were also consistently positively related to students’ social skills and negatively related to students’ aggressive behavior. Implications for understanding adolescent development are discussed.
Frequency of chronic pain descriptors: Implications for assessment of pain quality
Authors: Linl Chen‐Ping , Kupperl Amy E. , Gammaitonil Arnold R. , Galerl Bradley S. , Jensenl Mark P. 
Published: January 2011

AbstractThe current study interviewed patients with chronic pain to: (1) identify the most common words used by patients in the samples to describe the “quality” of their pain (i.e. sharp, dull) and (2) evaluate the validity of existing pain quality measures. Two‐hundred and thirteen individuals with pain associated with spinal cord injury (SCI) or multiple sclerosis (MS) were asked to describe their pain. Consistent with previous research that has shown that patients with different types of pain problems describe their pain using different pain quality descriptors, there was variability in the frequency of pain descriptors used by the study participants. For example, patients with SCI and below injury level pain used “burning” more often than patients with SCI and shoulder, arm, or neck pain or patients with MS. Regarding the validity of existing pain measures, only one pain quality measure assessed all 14 of the most common pain descriptors volunteered by the sample. Also, although a number of pain quality measures have been developed to discriminate neuropathic from nociceptive pain, there was surprisingly little overlap in descriptors between these measures. The results of the current study and other studies using similar procedures would be useful for evaluating and developing existing and future pain quality measures.
Nitecapone reduces development and symptoms of neuropathic pain after spinal nerve ligation in rats1
Authors: Kamburl Oleg , Männistöl Pekka T. , Pusal Anne M. , Käenmäkil Mikko , Kalsol Eija A. , Kontinenl Vesa K. 
Published: January 2011

AbstractNeuropathic pain is caused by damage or malfunctioning of the nervous system. It is fairly common and more resistant to treatment than other types of pain. Since nitecapone, an inhibitor of catechol‐O‐methyl‐transferase (COMT), has decreased neuropathic symptoms in diabetic rats, we studied its effects in another model of neuropathic pain, the spinal nerve ligation (SNL) model. Spinal nerves L5–6 were ligated in male Wistar rats under anaesthesia to produce the SNL model of neuropathic pain. Nitecapone (30 mg/kg,i.p.) or vehicle was administered once daily starting either 1 h before or 2 days after surgery and continued for 14–19 days. Threshold for mechanical allodynia was measured with the digital von Frey test and responses to cold stimuli with the acetone test, before surgery and every other day after it 1 h before drug administration.Mechanical and cold allodynia developed in all study groups. Both nitecapone treatments significantly reduced mechanical allodynia and withdrawal thresholds were 80–95% higher compared with the control group. In the acetone test, both nitecapone groups also showed less signs of cold allodynia than the control groups. In nitecapone‐naïve animals a single dose of nitecapone also reduced mechanical allodynia on the 14th day after the surgery. Nitecapone reduced the symptoms of neuropathic pain after the SNL, which is in line with the earlier study. Our results suggest that nitecapone and other COMT inhibitors should be studied further in the treatment of neuropathic pain.
Integrating microbial community data with ecological theory
Authors: Allison Steven 
Published: January 2011

Abstract
Background/Question/Methods
Molecular and bioinformatics techniques are revealing the rich diversity of microbial communities. These approaches generate valuable data that ecologists could use to develop and test theories that apply to a large fraction of living organisms. However, the complexity of microbial community data is a challenge to achieving this integration. A fundamental question in microbial ecology is how to aggregate microbial communities so that their taxa may be represented in theoretical models. Recently, models based on microbial traits have been developed to tackle this question. Such models may represent microbial taxa as functional groups or stochastic assemblages with a distribution of trait values. Here, I define these two model types and show how they can be used to make predictions about the function of complex microbial communities. I focus on organic matter decomposition and nutrient mineralization because this function is typically driven by complex microbial communities.

Results/Conclusions
When applying ecological theory to predict rates of organic matter turnover, complex communities can be aggregated based on relevant traits, such as the ability to produce extracellular enzymes. Ecological and evolutionary theories provide a framework for predicting the distribution of these traits across time and space. For example, theories on ecological succession may predict the temporal progression of enzyme traits that occur in association with a decomposing substrate. Dispersal parameters from island biogeography theory may determine the movement of enzyme traits across the microbial landscape. Evolutionary theory can be used to predict the appearance and loss of enzyme traits due to selective pressures in microbial ecosystems. All of these theories then determine the abundance of particular functional groups, or the means and variances of trait distributions that directly affect ecological function. Functional group models may be useful in simple systems, but stochastic models based on distributions may be more relevant for complex communities with a diversity of continuous traits and many unidentified members.*The audio track for talks in this symposium may be obtained at the following web address:**https://sites.google.com/site/esa2010symposium13audiocontent/esa2010-symposium13-audio-content*
Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).
Authors: Almeida Jonas , Deus Helena , Maass Wolfgang 
Published: January 2011

AbstractUse of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed, cloud based, integrative bioinformatics infrastructure. This presentation derives from recent publication:Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315].These PowerPoint slides were presented at Semantic Web Applications and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am.
Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
Authors: Chen Dong-Hua , Baker Matthew L. , Hryc Corey F. , DiMaio Frank , Jakana Joanita , Wu Weimin , Dougherty Matthew , Haase-Pettingell Cameron , Schmid Michael F. , Jiang Wen , Baker David , King Jonathan A. , Chiu Wah 
Published: January 2011

Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This process, conserved among dsDNA viruses such as herpes viruses and bacteriophages, is key to forming infectious virions. Bacteriophage P22 has served as a model system for this study in the past several decades. However, how capsid assembly is initiated, where and how scaffolding proteins bind to coat proteins in the procapsid, and the conformational changes upon capsid maturation still remain elusive. Here, we report Cα backbone models for the P22 procapsid and infectious virion derived from electron cryomicroscopy density maps determined at 3.8- and 4.0-Å resolution, respectively, and the first procapsid structure at subnanometer resolution without imposing symmetry. The procapsid structures show the scaffolding protein interacting electrostatically with the N terminus (N arm) of the coat protein through its C-terminal helix-loop-helix motif, as well as unexpected interactions between 10 scaffolding proteins and the 12-fold portal located at a unique vertex. These suggest a critical role for the scaffolding proteins both in initiating the capsid assembly at the portal vertex and propagating its growth on a
T
= 7 icosahedral lattice. Comparison of the procapsid and the virion backbone models reveals coordinated and complex conformational changes. These structural observations allow us to propose a more detailed molecular mechanism for the scaffolding-mediated capsid assembly initiation including portal incorporation, release of scaffolding proteins upon DNA packaging, and maturation into infectious virions.
R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines
Authors: Huang B. Emma , George Andrew W. 
Published: January 2011

Abstract
Summary: Multiparent crosses of recombinant inbred lines provide opportunity to map markers and quantitative trait loci (QTL) with much greater resolution than is possible in biparental crosses. Realizing the full potential of these crosses requires computational tools capable of handling the increased statistical complexity of the analyses. R/mpMap provides a flexible and extensible environment, which interfaces easily with other packages to satisfy this demand. Functions in the package encompass simulation, marker map construction, haplotype reconstruction and QTL mapping. We demonstrate the easy-to-use features of mpMap through a simulated data example.
Availability: www.cmis.csiro.au/mpMap.
Contact: emma.huang@csiro.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Robust linear regression methods in association studies
Authors: Lourenço V. M. , Pires A. M. , Kirst M. 
Published: January 2011

Abstract
Motivation: It is well known that data deficiencies, such as coding/rounding errors, outliers or missing values, may lead to misleading results for many statistical methods. Robust statistical methods are designed to accommodate certain types of those deficiencies, allowing for reliable results under various conditions. We analyze the case of statistical tests to detect associations between genomic individual variations (SNP) and quantitative traits when deviations from the normality assumption are observed. We consider the classical analysis of variance tests for the parameters of the appropriate linear model and a robust version of those tests based on M-regression. We then compare their empirical power and level using simulated data with several degrees of contamination.
Results: Data normality is nothing but a mathematical convenience. In practice, experiments usually yield data with non-conforming observations. In the presence of this type of data, classical least squares statistical methods perform poorly, giving biased estimates, raising the number of spurious associations and often failing to detect true ones. We show through a simulation study and a real data example, that the robust methodology can be more powerful and thus more adequate for association studies than the classical approach.
Availability: The code of the robustified version of function lmekin() from the R package kinship is provided as Supplementary Material.
Contact: vmml@fct.unl.pt
Supplementary Information: Supplementary data are available at Bioinformatics online.
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Authors: Marçais Guillaume , Kingsford Carl 
Published: January 2011

Abstract
Motivation: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.
Results: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution.
Availability: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.
Contact: gmarcais@umd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Flavescence Dorée-Related Phytoplasma Affecting Grapevines in Croatia
Authors: Šeruga Musić M. , Škorić D. , Haluška I. , Križanac I. , Plavec J. , Mikec I. 
Published: January 2011

Flavescence dorée (FD) and Bois noir (BN) phytoplasmas are principal grapevine yellows (GY) agents in the wider Euro-Mediterranean Region. While BN phytoplasma belongs to the ribosomal subgroup 16SrXII-A, the FD agents belong either to the ribosomal subgroups 16SrV-C or -D. During the official GY survey in 2009, 40 symptomatic grapevines (Vitis vinifera L.) were sampled throughout grapevine-growing regions in Croatia. Typical GY symptoms of leaf yellowing or reddening were evident on white and red varieties, respectively. Leaf rolling as well as irregular lignification of the shoots and withering of clusters were also observed. Phloem tissue from cuttings and leaf veins from mature vines were sampled for total DNA extraction and amplification of phytoplasma 16S rRNA gene by using generic primers P1/P7 in a direct PCR assay followed by a nested PCR using primer pair R16F2n/R2 (2). Phytoplasma ribosomal group affiliation was determined by restriction fragment length polymorphism (RFLP) analysis of the nested PCR products with enzyme Tru1I (Fermentas, Vilnius, Lithuania). These initial findings were validated and augmented by a triplex real-time PCR assay targeting the nonribosomal map gene. This assay enables simultaneous detection of BN and FD (16SrV-C and -D) phytoplasmas in grapevine (3). Assay results revealed the majority of GY positive vines (19 of 40) contained BN phytoplasma which is widespread. For the first time in Croatia, two red variety samples, Pinot Noir and Plemenka Crvena, from the vicinity of Ozalj (Vivodina) and Zagreb (Brezje), respectively, were found to harbor FD-related phytoplasmas. Fragments amplified by P1/P7 primers from latter samples were cloned and sequenced. Sequence analyses using online interactive tool iPhyClassifier (4) revealed that the phytoplasma under study from Pinot Noir sample (GenBank Accession No. HQ712064) is a member of 16SrV-C subgroup and shares 99.87% similarity with 16S rDNA sequence of the reference strain (GenBank Accession No. AF176319). The sequence from the Plemenka Crvena sample (GenBank Accession No. HQ712065) shares 99.54% similarity with the reference strain and has the most similar virtual RFLP pattern to the one of the 16SrV-C subgroup (GenBank Accession No. AY197642). These findings are currently limited to vineyards in northwestern Croatia. Even so, the presence of FD principal cicadellid vector Scaphoideus titanus in the country and the occurrence and distribution of FD in neighboring countries (1,2) are factors indicating that the spread of FD in Croatia is highly probable. References: (1) L. Filippin et al. Plant Pathol. 58:826, 2009. (2) S. Kuzmanović et al. Vitis 47:105, 2008. (3) C. Pelletier et al. Vitis 48:87, 2009. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.