bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational Properties of h-BN and h-BN-Graphene Heterostructures Probed by Inelastic Electron Tunneling Spectroscopy
Authors: Jung Suyong , Park Minkyu , Park Jaesung , Jeong Tae-Young , Kim Ho-Jong , Watanabe Kenji , Taniguchi Takashi , Ha Dong Han , Hwang Chanyong , Kim Yong-Sung 
Published: November 2015

AbstractInelastic electron tunneling spectroscopy is a powerful technique for investigating lattice dynamics of nanoscale systems including graphene and small molecules, but establishing a stable tunnel junction is considered as a major hurdle in expanding the scope of tunneling experiments. Hexagonal boron nitride is a pivotal component in two-dimensional Van der Waals heterostructures as a high-quality insulating material due to its large energy gap and chemical-mechanical stability. Here we present planar graphene/h-BN-heterostructure tunneling devices utilizing thin h-BN as a tunneling insulator. With much improved h-BN-tunneling-junction stability, we are able to probe all possible phonon modes of h-BN and graphite/graphene at Γ and K high symmetry points by inelastic tunneling spectroscopy. Additionally, we observe that low-frequency out-of-plane vibrations of h-BN and graphene lattices are significantly modified at heterostructure interfaces. Equipped with an external back gate, we can also detect high-order coupling phenomena between phonons and plasmons, demonstrating that h-BN-based tunneling device is a wonderful playground for investigating electron-phonon couplings in low-dimensional systems.
Dual-polarity metamaterial circular polarizer based on giant extrinsic chirality
Authors: Shi J. H. , Shi Q. C. , Li Y. X. , Nie G. Y. , Guan C. Y. , Cui T. J. 
Published: November 2015

AbstractChirality is ubiquitous in nature. The associated optical activity has received much attention due to important applications in spectroscopy, analytical chemistry, crystallography and optics, however, artificial chiral optical materials are complex and difficult to fabricate, especially in the optical range. Here, we propose an ultrathin dual-polarity metamaterial circular polarizer by exploiting the mechanism of giant extrinsic chirality. The polarity of the circular polarizer with large suppression of linear anisotropy can be switched by changing the sign of incident angle. The microwave experiments and optical simulations demonstrate that the large angle of incidence facilitates the high-efficiency circular polarizer, which can be realized in the whole spectra from microwave to visible frequencies. The ultrathin single-layer metamaterials with extrinsic chirality will be a promising candidate for circular polarization devices.
The balance between IL-17 and IL-22 produced by liver-infiltrating T-helper cells critically controls NASH development in mice
Authors: Rolla Simona , Alchera Elisa , Imarisio Chiara , Bardina Valentina , Valente Guido , Cappello Paola , Mombello Cristina , Follenzi Antonia , Novelli Francesco , Carini Rita 
Published: November 2015

The mechanisms responsible for the evolution of steatosis towards NASH (non-alcoholic steatohepatitis) and fibrosis are not completely defined. In the present study we evaluated the role of CD4+ T-helper (Th) cells in this process. We analysed the infiltration of different subsets of CD4+ Th cells in C57BL/6 mice fed on a MCD (methionine choline-deficient) diet, which is a model reproducing all phases of human NASH progression. There was an increase in Th17 cells at the beginning of NASH development and at the NASH–fibrosis transition, whereas levels of Th22 cells peaked between the first and the second expansion of Th17 cells. An increase in the production of IL (interleukin)-6, TNFα (tumour necrosis factor α), TGFβ (transforming growth factor β) and CCL20 (CC chemokine ligand 20) accompanied the changes in Th17/Th22 cells. Livers of IL-17−/− mice were protected from NASH development and characterized by an extensive infiltration of Th22 cells. In vitro, IL-17 exacerbated the JNK (c-Jun N-terminal kinase)-dependent mouse hepatocyte lipotoxicity induced by palmitate. IL-22 prevented lipotoxicity through PI3K (phosphoinositide 3-kinase)-mediated inhibition of JNK, but did not play a protective role in the presence of IL-17, which up-regulated the PI3K/Akt inhibitor PTEN (phosphatase and tensin homologue deleted on chromosome 10). Consistently, livers of IL-17−/− mice fed on the MCD diet displayed decreased activation of JNK, reduced expression of PTEN and increased phosphorylation of Akt compared with livers of wild-type mice. Hepatic infiltration of Th17 cells is critical for NASH initiation and development of fibrosis in mice, and reflects an infiltration of Th22 cells. Th22 cells are protective in NASH, but only in the absence of IL-17. These data strongly support the potentiality of clinical applications of IL-17 inhibitors that can prevent NASH by both abolishing the lipotoxic action of IL-17 and allowing IL-22-mediated protection.
Nanoscale CMOS battery cells for gate level on‐chip security designs
Authors: Muresan R. , Mayhew M. 
Published: November 2015

An efficient power analysis attack countermeasure at the transistor gate level using novel nanoscale CMOS battery cells in a decoupling‐based technique is presented. The proposed CMOS battery cells are used as decoupling elements between the gates implementing a sensitive operation inside a cryptographic module and the power supply rail of the integrated circuit. As a result, the battery cells form an intermediate on‐chip power storage element, providing a masked power supply point for gates that are on a critical security path. The circuitry of the battery cells and the gates are designed using 65 nm TSMC CMOS technology. A test system was simulated with an 8 bit XOR serving as a target operation for a correlation power analysis attack. A total of 16 battery cells, two per gate for complementary cycles, were created with 1.74 µm2 P‐type MOS transistors serving as energy storage devices. Results showed that the test system offered protection at 10 000 traces.
Epitaxial growth of graphene thin film by pulsed laser deposition
Authors: Wang Jin , Xiong Zhengwei , Yu Jian , Yin Hongbu , Wang Xuemin , Peng Liping , Wang Yuying , Wang Xinmin , Jiang Tao , Cao Linhong , Wu Weidong , Wang Chuanbin , Zhang Lianmeng 
Published: November 2015

Epitaxial graphene films have been prepared by pulsed laser deposition. X‐ray photoelectron spectroscopy analysis shows that the carbon binding energy is 284.7 eV, corresponding to sp2‐C. Raman spectroscopy indicates that there exists 2D and D peaks and thus graphene structures have been formed. Meanwhile, according to high‐resolution transmission electron microscopy analysis, suitable depositing temperature for graphene films is found to be 873 K and the single oriented crystal domains of graphene are observed only with the condition of 100 pulses laser.
Identification of differentially methylated loci using wavelet-based functional mixed models
Authors: Lee Wonyul , Morris Jeffrey S. 
Published: November 2015

Abstract
Motivation: DNA methylation is a key epigenetic modification that can modulate gene expression. Over the past decade, a lot of studies have focused on profiling DNA methylation and investigating its alterations in complex diseases such as cancer. While early studies were mostly restricted to CpG islands or promoter regions, recent findings indicate that many of important DNA methylation changes can occur in other regions and DNA methylation needs to be examined on a genome-wide scale. In this article, we apply the wavelet-based functional mixed model methodology to analyze the high-throughput methylation data for identifying differentially methylated loci across the genome. Contrary to many commonly-used methods that model probes independently, this framework accommodates spatial correlations across the genome through basis function modeling as well as correlations between samples through functional random effects, which allows it to be applied to many different settings and potentially leads to more power in detection of differential methylation.
Results: We applied this framework to three different high-dimensional methylation data sets (CpG Shore data, THREE data and NIH Roadmap Epigenomics data), studied previously in other works. A simulation study based on CpG Shore data suggested that in terms of detection of differentially methylated loci, this modeling approach using wavelets outperforms analogous approaches modeling the loci as independent. For the THREE data, the method suggests newly detected regions of differential methylation, which were not reported in the original study.
Availability and implementation: Automated software called WFMM is available at https://biostatistics.mdanderson.org/SoftwareDownload. CpG Shore data is available at http://rafalab.dfci.harvard.edu. NIH Roadmap Epigenomics data is available at http://compbio.mit.edu/roadmap.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: jefmorris@mdanderson.org
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
Authors: Misirli Goksel , Cavaliere Matteo , Waites William , Pocock Matthew , Madsen Curtis , Gilfellon Owen , Honorato-Zimmer Ricardo , Zuliani Paolo , Danos Vincent , Wipat Anil 
Published: November 2015

Abstract
Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model.
Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general.
Availability and implementation: The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo. The krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf.
Contact: anil.wipat@newcastle.ac.uk or vdanos@inf.ed.ac.uk
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Authors: Hoff Katharina J. , Lange Simone , Lomsadze Alexandre , Borodovsky Mark , Stanke Mario 
Published: November 2015

Abstract
Motivation: Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.
Results: We present BRAKER1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-Seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step.
Availability and implementation: BRAKER1 is available for download at http://bioinf.uni-greifswald.de/bioinf/braker/ and http://exon.gatech.edu/GeneMark/.
Contact: katharina.hoff@uni-greifswald.de or borodovsky@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
WormExp: a web-based application for a Caenorhabditis elegans-specific gene expression enrichment analysis
Authors: Yang Wentao , Dierking Katja , Schulenburg Hinrich 
Published: November 2015

Abstract
Motivation: A particular challenge of the current omics age is to make sense of the inferred differential expression of genes and proteins. The most common approach is to perform a gene ontology (GO) enrichment analysis, thereby relying on a database that has been extracted from a variety of organisms and that can therefore only yield reliable information on evolutionary conserved functions.
Results: We here present a web-based application for a taxon-specific gene set exploration and enrichment analysis, which is expected to yield novel functional insights into newly determined gene sets. The approach is based on the complete collection of curated high-throughput gene expression data sets for the model nematode Caenorhabditis elegans, including 1786 gene sets from more than 350 studies.
Availability and implementation: WormExp is available at http://wormexp.zoologie.uni-kiel.de.
Contacts: hschulenburg@zoologie.uni-kiel.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Favourable outcome of combined medical surgical treatment of cerebral aspergillosis of pulmonary origin
Authors: Ruiz-Santana Sergio , Cabrera-Arrocha Jesús , Hernández-Socorro Carmen-Rosa , Paz-Cruz Inmaculada , Campos-Herrero María-Isolina , León-Gil Cristóbal 
Published: November 2015

Introduction:
Cerebral aspergillosis is a highly fatal infection. Its origin is most likely blood-borne from the lungs and most patients are immunosuppressed. Mortality is over 90 % and the treatment chosen is key for survival.

Case presentation:
We report a 32-year-old female with a history of acute myeloid leukaemia (M3) who was admitted to the hospital due to a nodular infiltrate in the right superior lobe. A lung computed tomography (CT) scan displayed a right upper lobe cavitated nodule. A brain CT scan showed a right hemisphere deep abscess. Pulmonary aspergillosis was diagnosed after bronchoalveolar lavage. Three weeks later, while on antifungal treatment with voriconazole and liposomal amphotericin B, she suffered left motor focal deficits, and brain abscess puncture and aspiration by neuronavigation were performed for diagnosis and decompression. A PCR assay was positive for Aspergillus fumigatus. One week later, she developed an intraventricular brain haemorrhage requiring external ventricular drainage and intrathecal fibrinolysis with recombinant tissue plasminogen activator. She eventually achieved a good neurological outcome. A control brain CT showed an important reduction in mass size.

Conclusion:
Antifungal treatment is the mainstay for brain abscess treatment, and its combination with stereotactic needle aspiration is a better option compared with open surgery, particularly in abscesses located in deep motor areas.
Evolutionary responses to conditionality in species interactions across environmental gradients
Authors: O’Brien Anna M. , Sawers Ruairidh J.H. , Ross-Ibarra Jeffrey , Strauss Sharon Y. 
Published: November 2015

AbstractThe outcomes of many species interactions are conditional on the environments in which they occur. A common pattern is that outcomes grade from being more positive under stressful conditions to more antagonistic or neutral under benign conditions. The evolutionary implications of conditionality in interactions have received much less attention than the documentation of conditionality itself, with a few notable exceptions. Here, we predict patterns of adaptation and co-adaptation between partners along abiotic gradients, positing that when interactions become more positive in stressful environments, fitness outcomes for mutations affecting interactions align across partners and selection should favor greater mutualistic adap-tation and co-adaptation between interacting species. As a corollary, in benign environments, if interactions are strongly antagonistic, we predict antagonistic co-adaptation resulting in Red Queen or arms-race dynamics, or reduction of antagonism through character displacement and niche partitioning. We predict no adaptation if interactions are more neutral. We call this the CoCoA hypothesis: (Co)-adaptation and Conditionality across Abiotic gradients. We describe experimental designs and statistical models that allow testing predictions of CoCoA, with a focus on positive interactions. While only one study has included all the elements to test CoCoA, we briefly review the literature and summarize study findings relevant to CoCoA and highlight opportunities to test CoCoA further.
Adding value to value stocks in Indian stock market: an empirical analysis
Authors: Singh Jaspal , Kaur Kiranpreet 
Published: November 2015

Purpose– The purpose of this study is to examine the relevance of an accounting-based fundamental strategy in adding value to value stocks in Indian stock market. The fundamentals-based investment strategy “F-score”, given by Joseph Piotroski, has been used on stocks having high book-to-market ratio to eliminate the firms with poor future prospects from the entire portfolio of value stocks.Design/methodology/approach– The market adjusted performance of all the firms in the sample is examined using one samplet-test. Further, F-score of all the firms in the sample is calculated and the independent samplet-test has been used to examine the significance of mean difference between high-score and low-score firms. Finally, the predictive ability of F-score in explaining the overall stock returns is examined using panel data regression analysis.Findings– Results reveal that the mean market-adjusted return of stocks, meeting all constructs of F-score is significantly larger than the entire portfolio of value stocks by 18.402 per cent annually across the period of study. The results of panel data regression made it evident that one-point improvement in aggregate F-score is associated with an about 4.93 per cent increase in one-year market-adjusted return.Practical implications– The significant mean return difference found between the high-F-score firms and the low-score firms suggests that an investor could constitute a hedge portfolio that generates positive return by selling expected losers stocks and buying expected winners.Originality/value– The present study is the first attempt made in emerging economy like India to enrich the literature on value investing strategies by examining the performance of F-score strategy to separate winners from losers in Indian stock market.
Retaining older workers – analysis of company surveys from 2005 and 2010
Authors: Hermansen Åsmund , Midtsundstad Tove 
Published: November 2015

Purpose– The purpose of this paper is to shed light on developments in Norwegian companies’ active-ageing policies, and hence offer insight into what characterises those Norwegian companies offering measures to retain their older workers.Design/methodology/approach– The research questions are investigated using data from two surveys carried out among a representative sample of Norwegian companies in 2005 and 2010. The two data sets are analysed both separately and jointly, being merged to obtain a pooled cross-section data set. Both multivariate logistic and linear regression are applied.Findings– The proportion of companies offering retention measures, as well as the extensiveness of their retention efforts (the number of different measures offered), has increased considerably from 2005 to 2010. What characterises these companies however is surprisingly similar in 2005 and 2010. The retention efforts of Norwegian companies seem to be part of a holistic approach to active ageing. Offering a number of different retention measures is more common among companies having initiated “measures to facilitate lifelong learning” and “measures to prevent health problems or reduced work capacity”. The financial incentives embedded in the contractual early retirement scheme seem also to have a significant impact on retention efforts.Originality/value– The employers’ perspective has received little attention in previous research and the authors are the first to report on developments in Norwegian companies’ retention efforts over time. Knowledge about what characterises employers offering such measures will be important for future efforts to increase employments rates among older workers, which is an aim for most European countries.
Minoritynationals
Authors: Mullen Cormac , Berrill Jenny 
Published: November 2015

Purpose
– This paper aims to conduct a longitudinal analysis of the patterns of internationalisation of multinational corporations and provide a measure of their degree of globalisation at the firm-level. There is much debate in the literature on the regional nature of the globalisation of multinational corporations (Rugman and Oh, 2013).

Design/methodology/approach
– The authors use firm-level sales data to analyse the location of sales and patterns of globalisation of 1,276 companies across ten countries and ten industries from 1998-2012.

Findings
– The results show that while international sales are rising and the proportion of home region-oriented firms is falling, the majority of sales of the companies in our data set continues to be in the Triad, with little growth in non-Triad regions. The authors find one common theme for the majority of countries, an increase in sales to Asia yet concentrated in just four industries, financials, basic materials, oil and gas and technology. Despite an increase in the percentage of host-region, bi-regional and global companies, 62.6 per cent of the firms have not changed multinational classification over the 15-year period, 43.1 per cent have not expanded out of their home region and 16.4 per cent have not expanded out of their home market. The authors find some evidence of liabilities of interregional foreignness at the industry and country level. The authors show regional sales are moving towards matching global economic activity for the 50 most globalised firms in our study but less so for the other firms in our sample. Overall, the results show that the majority of the growth in internationalisation comes from a small minority of firms.

Originality/value
– The authors make several advances across the literature on internationalisation, including a more in-depth longitudinal analysis of firm-level multinationality than exists to date and a novel method of measuring firm-level globalisation.