bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interfacial and electrical properties of HfO2 gate dielectrics grown on GaAs by atomic layer deposition using different oxidants
Authors: Byun Young-Chul , Mahata Chandreswar , An Chee-Hong , Oh Jungwoo , Choi Rino , Kim Hyoungsub 
Published: October 2012

Abstract
In this paper, we examined the effects of two different oxidants (H2O and O3) used during the atomic layer deposition (ALD) of HfO2 films on GaAs, particularly focusing on its interfacial and electrical properties. In comparison with the H2O-based ALD process, the O3-based process produced a large amount of elemental As and Ga–O related bonds near the HfO2/GaAs interface due to its stronger oxidizing power. High interface state and border trap densities of the O3-based sample degraded the low-field electrical stability, which was confirmed by the capacitance and leakage current measurements under various voltage-stressing conditions. However, in terms of high-field stability, the O3-based sample showed a much stronger resistance to stress-induced trap generation than the H2O-based sample.
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data
Authors: Zhu Zhengwei , Niu Beifang , Chen Jing , Wu Sitao , Sun Shulei , Li Weizhong 
Published: October 2012

Abstract
Summary: Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are not suitable for alignment data in metagenomics, which are often interspecies alignments. We have developed a web browser-based desktop application for interactively visualizing alignment data of metagenomic sequences. This viewer is easy to use on all computer systems with modern web browsers and requires no software installation.
Availability: http://weizhongli-lab.org/mgaviewer
Contact: liwz@sdsc.edu
‘Location, Location, Location’: a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate
Authors: Fier Heide , Won Sungho , Prokopenko Dmitry , AlChawa Taofik , Ludwig Kerstin U. , Fimmers Rolf , Silverman Edwin K. , Pagano Marcello , Mangold Elisabeth , Lange Christoph 
Published: October 2012

Abstract
Motivation: For the analysis of rare variants in sequence data, numerous approaches have been suggested. Fixed and flexible threshold approaches collapse the rare variant information of a genomic region into a test statistic with reduced dimensionality. Alternatively, the rare variant information can be combined in statistical frameworks that are based on suitable regression models, machine learning, etc. Although the existing approaches provide powerful tests that can incorporate information on allele frequencies and prior biological knowledge, differences in the spatial clustering of rare variants between cases and controls cannot be incorporated. Based on the assumption that deleterious variants and protective variants cluster or occur in different parts of the genomic region of interest, we propose a testing strategy for rare variants that builds on spatial cluster methodology and that guides the identification of the biological relevant segments of the region. Our approach does not require any assumption about the directions of the genetic effects.
Results: In simulation studies, we assess the power of the clustering approach and compare it with existing methodology. Our simulation results suggest that the clustering approach for rare variants is well powered, even in situations that are ideal for standard methods. The efficiency of our spatial clustering approach is not affected by the presence of rare variants that have opposite effect size directions. An application to a sequencing study for non-syndromic cleft lip with or without cleft palate (NSCL/P) demonstrates its practical relevance. The proposed testing strategy is applied to a genomic region on chromosome 15q13.3 that was implicated in NSCL/P etiology in a previous genome-wide association study, and its results are compared with standard approaches.
Availability: Source code and documentation for the implementation in R will be provided online. Currently, the R-implementation only supports genotype data. We currently are working on an extension for VCF files.
Contact: heide.fier@googlemail.com
Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes
Authors: Gascoigne Dennis K. , Cheetham Seth W. , Cattenoz Pierre B. , Clark Michael B. , Amaral Paulo P. , Taft Ryan J. , Wilhelm Dagmar , Dinger Marcel E. , Mattick John S. 
Published: October 2012

Abstract
Motivation: Comparing transcriptomic data with proteomic data to identify protein-coding sequences is a long-standing challenge in molecular biology, one that is exacerbated by the increasing size of high-throughput datasets. To address this challenge, and thereby to improve the quality of genome annotation and understanding of genome biology, we have developed an integrated suite of programs, called Pinstripe. We demonstrate its application, utility and discovery power using transcriptomic and proteomic data from publicly available datasets.
Results: To demonstrate the efficacy of Pinstripe for large-scale analysis, we applied Pinstripe’s reverse peptide mapping pipeline to a transcript library including de novo assembled transcriptomes from the human Illumina Body Atlas (IBA2) and GENCODE v10 gene annotations, and the EBI Proteomics Identifications Database (PRIDE) peptide database. This analysis identified 736 canonical open reading frames (ORFs) supported by three or more PRIDE peptide fragments that are positioned outside any known coding DNA sequence (CDS). Because of the unfiltered nature of the PRIDE database and high probability of false discovery, we further refined this list using independent evidence for translation, including the presence of a Kozak sequence or functional domains, synonymous/non-synonymous substitution ratios and ORF length. Using this integrative approach, we observed evidence of translation from a previously unknown let7e primary transcript, the archetypical lncRNA H19, and a homolog of RD3. Reciprocally, by exclusion of transcripts with mapped peptides or significant ORFs (&gt;80 codon), we identify 32 187 loci with RNAs longer than 2000 nt that are unlikely to encode proteins.
Availability and implementation: Pinstripe (pinstripe.matticklab.com) is freely available as source code or a Mono binary. Pinstripe is written in C# and runs under the Mono framework on Linux or Mac OS X, and both under Mono and .Net under Windows.
Contact: m.dinger@garvan.org.au or j.mattick@garvan.org.au
Supplementary information: Supplementary data are available at Bioinformatics online.
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays
Authors: McCall Matthew N. , Jaffee Harris A. , Irizarry Rafael A. 
Published: October 2012

Abstract
Summary: Frozen robust multiarray analysis (fRMA) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. Here, we extend the fRMA algorithm to two new microarray platforms—Affymetrix Human Exon and Gene 1.0 ST—by modifying the fRMA probe-level model and extending the frma package to work with oligo ExonFeatureSet and GeneFeatureSet objects.
Availability and implementation: All packages are implemented in R. Source code and binaries are freely available through the Bioconductor project. Convenient links to all software and data packages can be found at http://mnmccall.com/software
Contact: mccallm@gmail.com
miR-EdiTar: a database of predicted A-to-I edited miRNA target sites
Authors: Laganà Alessandro , Paone Alessio , Veneziano Dario , Cascione Luciano , Gasparini Pierluigi , Carasi Stefania , Russo Francesco , Nigita Giovanni , Macca Valentina , Giugno Rosalba , Pulvirenti Alfredo , Shasha Dennis , Ferro Alfredo , Croce Carlo M. 
Published: October 2012

Abstract
Motivation: A-to-I RNA editing is an important mechanism that consists of the conversion of specific adenosines into inosines in RNA molecules. Its dysregulation has been associated to several human diseases including cancer. Recent work has demonstrated a role for A-to-I editing in microRNA (miRNA)-mediated gene expression regulation. In fact, edited forms of mature miRNAs can target sets of genes that differ from the targets of their unedited forms. The specific deamination of mRNAs can generate novel binding sites in addition to potentially altering existing ones.
Results: This work presents miR-EdiTar, a database of predicted A-to-I edited miRNA binding sites. The database contains predicted miRNA binding sites that could be affected by A-to-I editing and sites that could become miRNA binding sites as a result of A-to-I editing.
Availability: miR-EdiTar is freely available online at http://microrna.osumc.edu/mireditar.
Contact: alessandro.lagana@osumc.edu or carlo.croce@osumc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
EXTENSIVE CHOROIDAL INFILTRATES IN CHOROIDAL BIOPSY PROVEN OCULAR SARCOIDOSIS
Authors: Chen Ling , Xu Gezhi 
Published: October 2012

Purpose:
To report a rare manifestation of ocular sarcoidosis.

Methods:
Case report.

Results:
A 50-year-old man was misdiagnosed and treated as acute retinal necrosis and was referred to our clinic. Fundus examination revealed bilateral, extensive, confluent, subretinal yellowish white infiltrates throughout the fundus. Choroidal biopsy was performed and revealed noncaseating granuloma.

Conclusion:
This case presents a rare manifestation of ocular sarcoidosis as extensive confluent choroidal infiltrates throughout the fundus. The lack of the evidence for systemic sarcoidosis and unusual ocular presentation necessitate choroidal biopsy to confirm the diagnosis.
MACULAR HOLE OVERLYING PIGMENT EPITHELIAL DETACHMENT AFTER INTRAVITREAL INJECTION WITH RANIBIZUMAB
Authors: Raiji Veena R. , Eliott Dean , Sadda Srinivas R. 
Published: October 2012

Purpose:
To describe a previously unrecognized complication of intravitreal injection in a patient with exudative macular degeneration and vitreomacular adhesion.

Methods:
Case report of a 69-year-old woman.

Results:
One month after intravitreal injection with ranibizumab for exudative macular degeneration, our patient developed a full-thickness macular hole with visual acuity of 20/100. After pars plana vitrectomy with membrane peeling and fluid-gas exchange, the macular hole was closed and the visual acuity improved to 20/60.

Conclusions:
Macular hole formation after intravitreal injection with ranibizumab is a potential complication that should be considered before treatment, especially in those patients with large subfoveal pigment epithelial detachments and vitreomacular adhesion. Although successful closure may be attained after pars plana vitrectomy, this potential morbidity should be considered when treating these patients. In addition to the already well-described tractional forces of the vitreous overlying the fovea, and the potential contractile nature of a choroidal neovascular complex in response to ranibizumab, a posterior pushing or stretching mechanism of a large pigment epithelial detachment may also contribute to macular hole formation.
A new method of calculating interplanar spacing: the position-factor method
Authors: Fan Quncheng 
Published: October 2012

When the formulae for calculating the interplanar spacingd′hklfor the seven primary lattices among the 14 Bravais lattices are used for crystal structures containing an additional atom,d′hklmust be corrected by multiplying by a correction coefficient. Based on a simple principle of analytical geometry, a new position-factor method has been developed to calculate these correction coefficients. The position factorP[whereP=hx+ky+lz=s+m/q, the scalar product of the position (x, y, z) of an additional atom in a unit cell and any plane (hkl) passing through the additional atom] indicates the following characteristics of the (hkl) plane: whether there is an additional plane (m≠ 0) or not (m= 0), what the correction coefficient (m/q) is for the interplanar spacing ifm≠ 0, and what the distance [(s+m/q)d′hkl] is from the plane to the origin. In order to provide two examples of calculations usingP, six possible interplanar spacings were obtained for a hexagonal close-packed crystal, and four possible interplanar spacings and the structure factor were obtained for a diamond crystal. In addition, the 12 undetermined plane indices in X-ray diffraction card 1-1249 (PDF-2, ICDD, Newtown Square, PA, USA) for diamond were determined using the new calculation.
Are we there yet? An analysis of e‐book equivalent coverage in highly‐circulated titles at The College of New Jersey Library
Authors: Link Forrest E. 
Published: October 2012

PurposeThis paper seeks to determine the extent of e‐book availability and how existing e‐books might meet library needs as defined by monograph circulation.Design/methodology/approachThis study identified highly circulated print titles and searched for e‐book versions available from aggregators or publishers.FindingsThe results indicate inadequate coverage levels to allow for a discontinuance of print purchasing, but offer clues as to where e‐books might have the greatest impact in this library's collection plans.Originality/valueThe paper introduces a method whereby libraries may determine where e‐book collections best meets user needs.
Renovation and roadblocks while protecting the collection
Authors: Mix Vickie 
Published: October 2012

PurposeThe purpose of this paper is to offer a reflective analysis of a recent renovation project and a disaster recovery effort affecting multiple collections in a mid‐sized university library.Design/methodology/approachThis paper provides a case study.FindingsThis paper examines planning for a re‐carpeting project, particularly the unexpected challenges associated with renovation activities.Originality/valueThe paper contributes to the discussion of collection disposition during renovation and disaster recovery projects.
Evaluating digital piracy intentions on behaviors
Authors: Taylor Steven A. 
Published: October 2012

PurposeThe purpose of this paper is to assess how well digital piracy self‐report intentions predict actual digital piracy behaviors in service marketing research.Design/methodology/approachStudy 1 collects 321 surveys to investigate potential measurement issues related to digital piracy intention formation. Study 2 replicates Study 1 based on a separate sample of 267 respondents, and additionally links digital piracy intentions to directly observed digital piracy behaviors across a peer‐to‐peer network.FindingsThe results first validate a strong predictive relationship between self‐report intentions and observed digital piracy behaviors (R2=0.36). Second, common method bias and measurement error do not appear to threaten the veracity of reported results. Third, a social psychological model of how digital piracy behaviors emerge is validated based upon the folk theory of the mind. Finally, a two‐dimensional conceptualization of frequency of past behaviors is identified based upon exploratory factor analysis using structural equation modeling.Research limitations/implicationsThe research reported here relies on experimental methods of measuring peer‐to‐peer network activity. Future research might consider the motivational and attitudinal antecedents to digital piracy intention formation.Practical implicationsThe results afford service marketers assurance that self‐report measures of digital piracy behavioral intentions can serve as predictive measures of future behaviors. This helps make the collection of data in this context both achievable and practical. Also, a methodological framework is identified to strengthen measurement models associated with this type of research.Originality/valueThe research provides a first effort to empirically relate behavioral intention data to unobtrusively observed digital piracy behaviors across peer‐to‐peer networks.
The impact of short‐term food regulations in New Zealand schools
Authors: Cushman Penni 
Published: October 2012

PurposeIn New Zealand, legislation was introduced to regulate the types of food sold and promoted in schools but 15 months later, part of the legislation was repealed. The purpose of this paper is to determine the extent to which a sample of schools implemented positive changes when the legislation was introduced and the extent to which they reversed the changes when the second clause was repealed.Design/methodology/approachAn anonymous survey containing qualitative and quantitative aspects was mailed to a randomly selected sample of 1,000 New Zealand primary and secondary schools. A respondent from each school was asked questions about health issues, including whether their school had implemented changes when the new legislation was introduced and whether they reversed or modified those changes when part of it was repealed 15 months later. Simple preliminary analyses are presented in this paper.FindingsResponses were received from 318 schools (32 percent): 66 percent of respondents made changes, 5 percent did not, and 11 percent reported that the changes had not been applicable to their school. A further 18 percent did not need to make changes, as they already complied with legislative requirements. Only three schools completely reversed their changes after repeal of part of the legislation and 29 other schools made minor changes.Originality/valueThe results of this small study suggest that even short‐lived regulations have the potential to make a significant and long‐term difference, especially when accompanied by substantial funding and comprehensive professional development.
Developing teenagers’ views on their health and the health of their future children
Authors: Grace Marcus , Woods‐Townsend Kathryn , Griffiths Janice , Godfrey Keith , Hanson Mark , Galloway Ian , Azaola Marta Cristina , Harman Kerry , Byrne Jenny , Inskip Hazel 
Published: October 2012

PurposeThe purpose of this paper is to report the outcome of a city‐wide survey of teenagers’ views on their health, and compare this with the outcomes of a science‐oriented health intervention called LifeLab, a hospital‐based classroom aimed at developing teenagers’ attitudes towards their health and that of their future children.Design/methodology/approachA questionnaire survey of 597 14‐year olds across the city of Southampton was conducted to gauge their views and behaviour in relation to their own health. The views of 37 students who took part in innovative, hospital‐based, hands‐on LifeLab activities were compared with those of their peers six months after the intervention to analyse long‐term impacts of the experience. Interviews were carried out with ten LifeLab students to gain further insights.FindingsThe intervention created a wider appreciation among students that food they eat now could affect their long‐term health and the health of their future children. Students became significantly more interested in studying science beyond compulsory schooling, and in considering science and healthcare career options.Research limitations/implicationsAlthough results were statistically significant, the intervention sample was quite small, and further data collection is ongoing. The city‐wide student response rate of 29 per cent was fairly low.Social implicationsThis study has shown that a carefully structured hospital‐based classroom visit, and associated science lessons can have a marked effect on student engagement with health‐related issues, and an impact on their consideration of their career choices.Originality/valueThe hospital‐based classroom is an innovative approach to improving teenagers’ knowledge and attitudes towards their health. The paper's findings should be of interest to a range of educational stakeholders including teachers, local education authorities and local politicians concerned with health education matters.
Managing the diversified team: challenges and strategies for improving performance
Authors: Agrawal Vidhi 
Published: October 2012

PurposeThe purpose of this paper is to highlight the important factors which need to be taken into consideration to manage a diversified team. It also aims to provide business managers and executives with a framework of how to best utilize and implement teams in the workplace so as to maximize both internal and external diversified skill sets and capabilities in team members.Design/methodology/approachAn extensive review of existing literature was done to form the views of the authors on the issue. A strengths, weaknesses, oppositions, threats (SWOT) analysis of diversified teams was done with the help of secondary research. The concept is based on the author's own practical experience. A combination of primary and secondary research was used to highlight and strengthen the author views and opinions. The original ideas and basic concepts are based on the author's own experiences.FindingsThe study found the maximum benefits of a diversified team. The findings show that effective teamwork requires members to recognize the team as a unit with common goals, values, and norms. The more that team members identify with each other, the more likely they are to believe they hold similar goals.Research limitations/implicationsThe paper is an attempt to express the real organizational scenario which is based on a sample of 20 corporate executives who dealt with a similar issue. The industries selected were in Delhi – NCR. There is reason to believe that if study had to be done in some other parts of the county, results may have been different. The sample taken was not very big, and was also non‐random. A large sample may have different results.Practical implicationsThe study includes an extensive analysis of the organizational diversity and its impact on the performance of the organizations. This may help business practitioners to encourage diversity in the workplace while improving teamwork, communication and cooperation among team members.Originality/valueThe paper highlights the different attributes of a diversified team. With the help of primary research and well‐supported secondary research, a good attempt is made to trace the four corners of leading a diversified team. It can help future managers to guide a diversified team for good team performance.