bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase of atmospheric secondary organic material affects its reactivity
Authors: Kuwata Mikinori , Martin Scot T. 
Published: October 2012

The interconversion of atmospheric organic particles among solid, semisolid, and liquid phases is of keen current scientific interest, especially for particles of secondary organic material (SOM). Herein, the influence of phase on ammonia uptake and subsequent particle-phase reactions was investigated for aerosol particles of adipic acid and α-pinene ozonolysis SOM. The nitrogen content of the particles was monitored by online mass spectrometry for increasing ammonia exposure. Solid and semisolid adipic acid particles were inert to the ammonia uptake for low RH (< 5%). For the solid particles, ammonia exposure at high relative humidity (RH; > 94%) induced a first-order deliquescence phase transition into aqueous particles. Solid particles exposed to supersaturated (RH > 100%) conditions and cycled back to high RH (> 94%), thereby becoming acidic metastable particles, underwent a gradual second-order transition upon ammonia exposure to form aqueous, partially neutralized particles. For α-pinene SOM, ammonia exposure at low RH increased the particle-phase ammonium content by a small amount. Mass spectrometric observations suggest a mechanism of neutralization and co-condensation of acidic gas-phase species, consistent with a highly viscous semisolid upon which adsorption occurs. At high RH the ammonium content increased greatly, indicative of rapid diffusion and absorption in a liquid environment. The mass spectra indicated the production of organonitrogen compounds, possibly by particle-phase reactive chemistry. The present results demonstrate that phase can be a key regulator of the reactivity of atmospheric SOM particles.
Magnetization studies of first-order magnetostructural phase transition in polycrystalline FeRh thin films
Authors: Lu Wei , Huang Ping , Chen Zhe , He Chenchong , Wang Yuxin , Yan Biao 
Published: October 2012

Abstract
The nucleation and growth of the transformed phase in the matrix of the original phase played an important role in the progress of magnetic transition. In spite of extensive investigations in B2 ordered FeRh alloy systems, until now few studies have been conducted for clarifying the nucleation and growth mechanism of the antiferromagnetic–ferromagnetic phase transition in FeRh alloys. In this work, B2 ordered polycrystalline FeRh thin films were fabricated on glass substrates by a sputtering technique and subsequent heat treatment. The as-deposited film shows a nonmagnetic property because of its face centred cubic structure. After annealing, the polycrystalline FeRh thin films show a clear first-order magnetostructural phase transition. The FeRh thin film shows an overall activation energy of about 228.6 kJ mol−1 for the entire first-order magnetostructural phase transition process. Results suggest that the first-order magnetostructural phase transition in ordered FeRh thin films follows the Johnson–Mehl–Avrami model with characteristic exponent n in the range 1–4, indicating that the phase transition process is a multi-step process characterized by different nucleation and growth mechanisms of the new ferromagnetic phase. The results obtained in this study will shed light on the underlying physics of the first-order magnetostructural phase transition of ordered FeRh alloys. The applicability of the concepts used in this study to the FeRh system shows universality and can be applied to other material systems where there is a first-order magnetostructural phase transition such as in manganites.
A novel missense-mutation-related feature extraction scheme for ‘driver’ mutation identification
Authors: Tan Hua , Bao Jiguang , Zhou Xiaobo 
Published: October 2012

Abstract
Motivation: It becomes widely accepted that human cancer is a disease involving dynamic changes in the genome and that the missense mutations constitute the bulk of human genetic variations. A multitude of computational algorithms, especially the machine learning-based ones, has consequently been proposed to distinguish missense changes that contribute to the cancer progression (‘driver’ mutation) from those that do not (‘passenger’ mutation). However, the existing methods have multifaceted shortcomings, in the sense that they either adopt incomplete feature space or depend on protein structural databases which are usually far from integrated.
Results: In this article, we investigated multiple aspects of a missense mutation and identified a novel feature space that well distinguishes cancer-associated driver mutations from passenger ones. An index (DX score) was proposed to evaluate the discriminating capability of each feature, and a subset of these features which ranks top was selected to build the SVM classifier. Cross-validation showed that the classifier trained on our selected features significantly outperforms the existing ones both in precision and robustness. We applied our method to several datasets of missense mutations culled from published database and literature and obtained more reasonable results than previous studies.
Availability: The software is available online at http://www.methodisthealth.com/software and https://sites.google.com/site/drivermutationidentification/.
Contact: xzhou@tmhs.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Gene set analysis for self-contained tests: complex null and specific alternative hypotheses
Authors: Rahmatallah Y. , Emmert-Streib F. , Glazko G. 
Published: October 2012

AbstractMotivation: The analysis of differentially expressed gene sets became a routine in the analyses of gene expression data. There is a multitude of tests available, ranging from aggregation tests that summarize gene-level statistics for a gene set to true multivariate tests, accounting for intergene correlations. Most of them detect complex departures from the null hypothesis but when the null hypothesis is rejected, the specific alternative leading to the rejection is not easily identifiable.Results: In this article we compare the power and Type I error rates of minimum-spanning tree (MST)-based non-parametric multivariate tests with several multivariate and aggregation tests, which are frequently used for pathway analyses. In our simulation study, we demonstrate that MST-based tests have power that is for many settings comparable with the power of conventional approaches, but outperform them in specific regions of the parameter space corresponding to biologically relevant configurations. Further, we find for simulated and for gene expression data that MST-based tests discriminate well against shift and scale alternatives. As a general result, we suggest a two-step practical analysis strategy that may increase the interpretability of experimental data: first, apply the most powerful multivariate test to find the subset of pathways for which the null hypothesis is rejected and second, apply MST-based tests to these pathways to select those that support specific alternative hypotheses.Contact: gvglazko@uams.edu or yrahmatallah@uams.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Pathway-based visualization of cross-platform microarray datasets
Authors: Wrzodek Clemens , Eichner Johannes , Zell Andreas 
Published: October 2012

Abstract
Motivation: Traditionally, microarrays were almost exclusively used for the genome-wide analysis of differential gene expression. But nowadays, their scope of application has been extended to various genomic features, such as microRNAs (miRNAs), proteins and DNA methylation (DNAm). Most available methods for the visualization of these datasets are focused on individual platforms and are not capable of integratively visualizing multiple microarray datasets from cross-platform studies. Above all, there is a demand for methods that can visualize genomic features that are not directly linked to protein-coding genes, such as regulatory RNAs (e.g. miRNAs) and epigenetic alterations (e.g. DNAm), in a pathway-centred manner.
Results: We present a novel pathway-based visualization method that is especially suitable for the visualization of high-throughput datasets from multiple different microarray platforms that were used for the analysis of diverse genomic features in the same set of biological samples. The proposed methodology includes concepts for linking DNAm and miRNA expression datasets to canonical signalling and metabolic pathways. We further point out strategies for displaying data from multiple proteins and protein modifications corresponding to the same gene. Ultimately, we show how data from four distinct platform types (messenger RNA, miRNA, protein and DNAm arrays) can be integratively visualized in the context of canonical pathways.
Availability: The described method is implemented as part of the InCroMAP application that is freely available at www.cogsys.cs.uni-tuebingen.de/software/InCroMAP.
Contact: clemens.wrzodek@uni-tuebingen.de or andreas.zell@uni-tuebingen.de
KGBassembler: a karyotype-based genome assembler for Brassicaceae species
Authors: Ma Chuang , Chen Hao , Xin Mingming , Yang Ruolin , Wang Xiangfeng 
Published: October 2012

Abstract
Motivation: The Brassicaceae family includes the most important plant model Arabidopsis thaliana and many cruciferous vegetable crops. A number of close relatives of Arabidopsis and economically important Brassica species are being sequenced with whole-genome shotgun sequencing technologies. However, de novo assembly of full chromosomes is difficult, since many non-model Brassicaceae species are lacking genetic and/or physical maps. As a unique feature for Brassicaceae, the genome of each member is composed of 24 conserved chromosomal blocks, and the arrangement of the 24 blocks can be obtained from karyotype analysis via comparative chromosome painting experiments. Taking this advantage, we developed a bioinformatic tool named KGBassembler to automatically finalize assembly of full chromosomes from contigs and/or scaffolds based on available karyotypes of Brassicaceae species.
Availability: KGBassembler was implemented in C++ with a graphical user interface. It is freely available to academic users at http://www.cmbb.arizona.edu/KGBassembler/.
Contact: xwang1@cals.arizona.edu
SemMedDB: a PubMed-scale repository of biomedical semantic predications
Authors: Kilicoglu Halil , Shin Dongwook , Fiszman Marcelo , Rosemblat Graciela , Rindflesch Thomas C. 
Published: October 2012

Abstract
Summary: Effective access to the vast biomedical knowledge present in the scientific literature is challenging. Semantic relations are increasingly used in knowledge management applications supporting biomedical research to help address this challenge. We describe SemMedDB, a repository of semantic predications (subject–predicate–object triples) extracted from the entire set of PubMed citations. We propose the repository as a knowledge resource that can assist in hypothesis generation and literature-based discovery in biomedicine as well as in clinical decision-making support.
Availability and implementation: The SemMedDB repository is available as a MySQL database for non-commercial use at http://skr3.nlm.nih.gov/SemMedDB. An UMLS Metathesaurus license is required.
Contact: kilicogluh@mail.nih.gov
De novo detection of copy number variation by co-assembly
Authors: Nijkamp Jurgen F. , van den Broek Marcel A. , Geertman Jan-Maarten A. , Reinders Marcel J. T. , Daran Jean-Marc G. , de Ridder Dick 
Published: October 2012

Abstract
Motivation: Comparing genomes of individual organisms using next-generation sequencing data is, until now, mostly performed using a reference genome. This is challenging when the reference is distant and introduces bias towards the exact sequence present in the reference. Recent improvements in both sequencing read length and efficiency of assembly algorithms have brought direct comparison of individual genomes by de novo assembly, rather than through a reference genome, within reach.
Results: Here, we develop and test an algorithm, named Magnolya, that uses a Poisson mixture model for copy number estimation of contigs assembled from sequencing data. We combine this with co-assembly to allow de novo detection of copy number variation (CNV) between two individual genomes, without mapping reads to a reference genome. In co-assembly, multiple sequencing samples are combined, generating a single contig graph with different traversal counts for the nodes and edges between the samples. In the resulting ‘coloured’ graph, the contigs have integer copy numbers; this negates the need to segment genomic regions based on depth of coverage, as required for mapping-based detection methods. Magnolya is then used to assign integer copy numbers to contigs, after which CNV probabilities are easily inferred. The copy number estimator and CNV detector perform well on simulated data. Application of the algorithms to hybrid yeast genomes showed allotriploid content from different origin in the wine yeast Y12, and extensive CNV in aneuploid brewing yeast genomes. Integer CNV was also accurately detected in a short-term laboratory-evolved yeast strain.
Availability: Magnolya is implemented in Python and available at: http://bioinformatics.tudelft.nl/
Contact: d.deridder@tudelft.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Wages and Human Capital in the U.S. Finance Industry: 1909–2006*
Authors: Philippon Thomas , Reshef Ariell 
Published: October 2012

AbstractWe study the allocation and compensation of human capital in the U.S. finance industry over the past century. Across time, space, and subsectors, we find that financial deregulation is associated with skill intensity, job complexity, and high wages for finance employees. All three measures are high before 1940 and after 1985, but not in the interim period. Workers in finance earn the same education-adjusted wages as other workers until 1990, but by 2006 the premium is 50% on average. Top executive compensation in finance follows the same pattern and timing, where the premium reaches 250%. Similar results hold for other top earners in finance. Changes in earnings risk can explain about one half of the increase in the average premium; changes in the size distribution of firms can explain about one fifth of the premium for executives.
Striking Natural Diversity in Glandular Trichome Acylsugar Composition Is Shaped by Variation at the Acyltransferase2 Locus in the Wild Tomato Solanum habrochaites
Authors: Kim Jeongwoon , Kang Kiyoon , Gonzales-Vigil Eliana , Shi Feng , Jones A. Daniel , Barry Cornelius S. , Last Robert L. 
Published: October 2012

Abstract
Acylsugars are polyesters of short- to medium-length acyl chains on sucrose or glucose backbones that are produced in secretory glandular trichomes of many solanaceous plants, including cultivated tomato (Solanum lycopersicum). Despite their roles in biotic stress adaptation and their wide taxonomic distribution, there is relatively little information about the diversity of these compounds and the genes responsible for their biosynthesis. In this study, acylsugar diversity was assessed for 80 accessions of the wild tomato species Solanum habrochaites from throughout the Andes Mountains. Trichome metabolites were analyzed by liquid chromatography-time of flight-mass spectrometry, revealing the presence of at least 34 structurally diverse acylsucroses and two acylglucoses. Distinct phenotypic classes were discovered that varied based on the presence of glucose or sucrose, the numbers and lengths of acyl chains, and the relative total amounts of acylsugars. The presence or absence of an acetyl chain on the acylsucrose hexose ring caused clustering of the accessions into two main groups. Analysis of the Acyltransferase2 gene (the apparent ortholog of Solyc01g105580) revealed differences in enzyme activity and gene expression correlated with polymorphism in S. habrochaites accessions that varied in acylsucrose acetylation. These results are consistent with the hypothesis that glandular trichome acylsugar acetylation is under selective pressure in some populations of S. habrochaites and that the gene mutates to inactivity in the absence of selection.
Service receivers' negative emotions in airline and hospital service settings
Authors: Petzer Daniel J. , De Meyer Christine F. , Svari Sander , Svensson Göran 
Published: October 2012

PurposeThe purpose of this paper is to examine service receivers' negative emotions in two different service settings, namely at an airport and in a hospital.Design/methodology/approachA descriptive, convenience sampling survey method was used to collect data in South Africa consisting of a sample of 294 respondents at an airport and 288 respondents in a hospital. Data analysis included an exploratory factor analysis, and the results reported in this paper are based on the critical incident technique.FindingsThe findings indicate both similarities and differences in service receivers' negative emotions between the two service settings. Furthermore, the results were found to be valid and reliable.Research limitations/implicationsThe results obtained pertaining to the negative emotions that service receivers experience in two service settings in South Africa may provide the foundation for further research and replication in other countries. Furthermore, the results can aid in refining and extending service providers' efforts of managing critical incidents in different service settings in airline and hospital service settings.Practical implicationsThree main aspects of negative incidences in service encounters should be considered in strategies to manage critical incidents, namely those that are caused by: the service receiver; the service provider; or the service encounter context.Originality/valueThis study complements and reinforces existing theory pertaining to the negative emotions service receivers' experience in negative service encounters.
The effects of exercise education intervention on the exercise behaviour, depression, and fatigue status of chronic kidney disease patients
Authors: Kao Yu‐Hsiu , Huang Yi‐Ching , Chen Pei‐Ying , Wang Kuo‐Ming 
Published: October 2012

PurposeThe purpose of this paper is to investigate the effects of an exercise education intervention on exercise behavior, depression and fatigue status of chronic kidney disease (CKD) patients.Design/methodology/approachThis was a pilot study using an exercise education program as an intervention for CKD patients. The authors used the transtheoretical model (TTM) to design the exercise education programs. A total of 94 subjects diagnosed with CKD at a medical center in Taiwan participated in this quasi‐experimental study. Subjects were randomly divided into the experimental group (n=45) and the control group (n=49). The education program included written materials and teaching activities designed to encourage participants to initiate and continue regular exercise. Both groups took the pre‐test and post‐test containing a depression inventory, a fatigue scale and an exercise behavior inventory.FindingsThe findings indicated that changes in the exercise behavior, depression and fatigue status of the experimental group were statistically significant after the exercise education intervention compared with the control group.Originality/valueThe paper demonstrates that exercise education intervention can be administered by nursing staff, or a health educator, to encourage patients to exercise in order to enhance their quality of care.
Healthy eating and physical activity in schools in Europe
Authors: Simovska Venka , Dadaczynski Kevin , Woynarowska Barbara 
Published: October 2012

PurposeThe purpose of this paper is to introduce the HEPS project (Healthy Eating and Physical Activity in Schools) and discuss initial steps of the project implementation within EU countries. On the basis of the Health Promoting School approach as a conceptual foundation for the project, HEPS aimed at developing and implementing an effective tool for supporting the development of national policies on healthy eating and physical activity in schools across Europe. For this purpose, a package of publications (HEPS Toolkit) was produced and disseminated within the Schools for Health in Europe (SHE) network.Design/methodology/approachAn initial implementation survey was carried out with national coordinators of the SHE network (n=24).FindingsResults indicate that more than half of the respondents were familiar with and disseminated the HEPS Toolkit to relevant stakeholders at national, regional and local levels. However a number of problems and barriers in the implementation were encountered, such as lack of support and resources, existence of competing programmes, and frequent education and health reforms.Practical implicationsThe findings are discussed against two models of implementation and a few recommendations are suggested for optimizing the further implementation of this, and other similar projects.Originality/valueTHE HEPS toolkit is the first attempt to support all EU member states in the development and implementation of a national policy on healthy eating and physical activity in schools. The involvement of the national coordinators of a well established European network of school health can be seen as an innovative way to implement and disseminate the project outcomes.
Health promotion in pre‐service teacher education
Authors: Byrne Jenny , Speller Viv , Dewhirst Sue , Roderick Paul , Almond Palo , Grace Marcus , Memon Anjum 
Published: October 2012

PurposeThe purpose of this paper is to discuss a curriculum change in the provision of health promotion in pre‐service teacher education in a one‐year postgraduate certificate in education (PGCE) secondary course in one Higher Education Institution (HEI) in England.Design/methodology/approachThe paper describes the iterative development process, from an initial survey and mapping of the existing pre‐service teacher training programme, which provided an evidence base for the piloting of a new health promotion component in the curriculum, and its subsequent evaluation. Changes to the health promotion element of the curriculum reflect the programme philosophy which balances the requirements of a competency based curriculum with a more liberal approach to education and training in which pre‐service teachers are expected to critically reflect on, and evaluate their practice. This work adopts a socio‐constructivist approach to teacher education, in which teachers develop their knowledge, skills and attitudes by interacting with others through dialogue, and learning from more knowledgeable others in a cooperative and scaffolded manner.FindingsThe paper presents the results of these changes and discusses implications for their sustainability. The changes made to the health promotion component of the programme and their implementation would not have been possible without the inter‐professional collaboration that took place over three years.Originality/valueTo the authors’ knowledge similar work involving a multi‐disciplinary collaborative approach to the development of a health education component of a pre‐service teacher education curriculum has not been employed or reported.