bluuebunny/crossref_metadata_2025 huggingface dataset:
Revealing the atomic and electronic structure of a SrTiO3/LaNiO3/SrTiO3 heterostructure interface
Authors: Zhang Zaoli , Soltan S. , Schmid H. , Habermeier H.-U. , Keimer B. , Kaiser U.
Published: March 2014

The atomic structures of SrTiO3 (STO)/LaNiO3 (LNO)/STO heterostructure interfaces were investigated by spherical aberration-corrected (CS) (scanning) transmission electron microscopy. Atomic displacement and lattice distortion measurements and electron energy loss spectroscopy (EELS) were used to quantitatively analyze the distortion of the interfacial octahedra and the bond length at the interfaces. Combined with high-resolution transmission electron microscopy (HRTEM) and scanning transmission electron microscopy analyses, two distinct interfacial atomic terminating layers are unambiguously determined. Ensuing quantitative HRTEM measurements revealed that the Ni-O bond length in the interfacial octahedral is elongated at the bottom interface (–NiO2-SrO–). Atomic displacement shows structural relaxation effects when crossing the interfaces and lattice distortions across the interface is more pronounced in LNO than in STO. The Ti/O atomic ratio, La and Ti relative atomic ratio as derived by EELS quantification indicate non-stoichiometric composition at the interfaces. Distinct fine structures of Ti-L2,3 edge and O-K edge at the bottom and top interfaces are observed. By comparison, we are able to estimate Ti valency at both interfaces. Combining the structural distortions and Ti valency, the polar discontinuity and charge transfer at the interfaces are discussed.
Real-time reflectance-difference spectroscopy of GaAs molecular beam epitaxy homoepitaxial growth
Authors: Lastras-Martínez A. , Ortega-Gallegos J. , Guevara-Macías L. E. , Nuñez-Olvera O. , Balderas-Navarro R. E. , Lastras-Martínez L. F. , Lastras-Montaño L. A. , Lastras-Montaño M. A.
Published: March 2014

We report on real time-resolved Reflectance-difference (RD) spectroscopy of GaAs(001) grown by molecular beam epitaxy, with a time-resolution of 500 ms per spectrum within the 2.3–4.0 eV photon energy range. Through the analysis of transient RD spectra we demonstrated that RD line shapes are comprised of two components with different physical origins and determined their evolution during growth. Such components were ascribed to the subsurface strain induced by surface reconstruction and to surface stoichiometry. Results reported in this paper render RD spectroscopy as a powerful tool for the study of fundamental processes during the epitaxial growth of zincblende semiconductors.
High power semiconductor disk laser with a semiconductor-dielectric-metal compound mirror
Authors: Rantamäki A. , Saarinen E. J. , Lyytikäinen J. , Lahtonen K. , Valden M. , Okhotnikov O. G.
Published: March 2014

We present optically pumped semiconductor disk lasers with a thin dielectric layer placed between the semiconductor distributed Bragg reflector and the metallization interface. The approach is shown to enhance the reflectivity of the semiconductor mirror while introducing a negligible penalty to the thermal resistance of the device. The design has potential for improving the performance of semiconductor disk lasers by avoiding highly pump-absorbing metal layers and allowing thinner mirror structures. The advantages are expected to be especially prominent for material systems that employ thick thermally insulating semiconductor mirrors.
Hydrogen dynamics and metallic phase stabilization in VO2
Authors: Warnick Keith H. , Wang Bin , Pantelides Sokrates T.
Published: March 2014

Experimental doping of VO2 with hydrogen has been shown to trigger the semiconductor-to-metal phase transition below room temperature. Here, we report the results of density functional calculations showing that hydrogen-induced lattice distortion stabilizes the metallic phase. We also show that hydrogen diffuses preferentially along the rutile [001] direction whereby surface orientations can be tailored for optimal transport. Finally, we show that hydrogen doping is energetically favored, but there is a 1.6 eV barrier for dissociation of hydrogen molecules on a (100) monoclinic surface. These results give insight into the effect of hydrogen on the properties and phase transition of VO2.
Bandwidth-enhanced polarization-insensitive microwave metamaterial absorber and its equivalent circuit model
Authors: Ghosh Saptarshi , Bhattacharyya Somak , Kaiprath Yadunath , Vaibhav Srivastava Kumar
Published: March 2014

In this paper, a bandwidth-enhanced polarization-insensitive ultra-thin metamaterial absorber has been presented. A simple equivalent circuit model has been proposed describing the absorption phenomenon to estimate the frequency of absorption of the proposed microwave absorber. The basic structure consists of concentric rings embedded one inside another to enhance bandwidth by incorporating the scalability property of the metamaterials. Simulation results show that the structure has enhanced bandwidth response with full width at half maxima (FWHM) of 1.15 GHz (9.40–10.55 GHz) with two absorption peaks at 9.66 and 10.26 GHz (96% and 92.5% absorptivity, respectively). The structure is symmetric in design giving rise to polarization-insensitivity and can achieve high absorption for oblique incidence up to 40°. The proposed absorber has been fabricated and measured in anechoic chamber, showing that experimental results agree well with the simulated responses.
A methodology to identify and quantify mobility-reducing defects in 4H-silicon carbide power metal-oxide-semiconductor field-effect transistors
Authors: Ettisserry D. P. , Goldsman N. , Lelis A.
Published: March 2014

In this paper, we present a methodology for the identification and quantification of defects responsible for low channel mobility in 4H-Silicon Carbide (SiC) power metal-oxide-semiconductor field-effect transistors (MOSFETs). To achieve this, we use an algorithm based on 2D-device simulations of a power MOSFET, density functional simulations, and measurement data. Using physical modeling of carrier mobility and interface traps, we reproduce the experimental I-V characteristics of a 4H-SiC doubly implanted MOSFET through drift-diffusion simulation. We extract the position of Fermi level and the occupied trap density as a function of applied bias and temperature. Using these inputs, our algorithm estimates the number of possible trap types, their energy levels, and concentrations at 4H-SiC/SiO2 interface. Subsequently, we use density functional theory (DFT)-based ab initio simulations to identify the atomic make-up of defects causing these trap levels. We study silicon vacancy and carbon di-interstitial defects in the SiC side of the interface. Our algorithm indicates that the Dit spectrum near the conduction band edge (3.25 eV) is composed of three trap types located at 2.8–2.85 eV, 3.05 eV, and 3.1–3.2 eV, and also calculates their densities. Based on DFT simulations, this work attributes the trap levels very close to the conduction band edge to the C di-interstitial defect.
Ballistic thermal conductance by phonons through superlattice quantum-waveguides
Authors: Xie Zhong-Xiang , Zhang Yong , Yu Xia , Li Ke-Min , Chen Qiao
Published: March 2014

Ballistic thermal conductances (BTCs) by phonons through superlattice quantum-waveguides are investigated by using the scattering-matrix method and the elastic continuum theory. A comparison for the cylindrical model (CM) and the rectangular model (RM) is addressed. We find that for these two models, the quantum thermal conductance can be observed even when the superlattices exist in quantum-waveguides. At low temperature, BTCs for the CM and the RM present almost the same behaviors regardless of the periodic length of superlattices. However, at higher temperature, BTCs for the RM are larger than those for the CM stemming from lower cutoff frequencies of high order modes for the RM. We also find that BTCs undergo a noticeable transformation from the monotonic decrease to constant with increasing the periodic number of superlattices. A brief analysis of these results is given.
Numerical analysis of dominant loss parameters of ferrite thin films for conduction noise absorption in microstrip lines
Authors: Yoo Gi-Bong , Kim Sung-Soo
Published: March 2014

The dominant power loss mechanism from conduction noise in a microstrip line was verified by investigating the effects of electrical conductivity and magnetic loss on noise reflection and transmission, and of power absorption in thin film absorbers (Ni-Zn ferrite thin film with high electrical resistivity, and electrically conductive ITO and Fe3O4 films). Using a simulation model of a microstrip line attached by thin films, the S parameters and power absorption were calculated for the frequency range from 0.05 to 3 GHz. Even if the film has a large value of magnetic loss due to ferromagnetic resonance, it is predicted that power dissipation by magnetic loss would be quite small, as was predicted for the Ni-Zn ferrite films. For the conductive and magnetic Fe3O4 thin film with similar magnetic loss dispersion, the contribution of magnetic loss to total power loss is also quite small. The values of S11, S21, and power absorption were almost the same as that for conductive ITO thin film of which the electrical resistivity was on the same order as that of the Fe3O4 thin film. The simulation of power absorption by the hybrid structure of ITO/Ni-Zn ferrite and ITO/Fe3O4 also supports this conclusion.
Templated fabrication and characterization of SiO2 nanotube covered Fe nanowires
Authors: Dastagir Tawab , Yu Hongbin
Published: March 2014

In this study, Fe nanowires coated with SiO2 nanotubes have been synthesized by electrodeposition method using anodic alumina oxide template. Before growing Fe nanowires, 6–8 nm thick SiO2 nanotubes are grown inside the template using a “surface sol-gel” technique. The nanotube structures were characterized by field emission scanning electron microscopy and energy dispersive x-ray spectroscopy. Magnetic properties of the SiO2 insulated Fe nanowires inside the membrane are characterized by superconducting quantum interference device. Coercivities of around 120 Oe with field parallel to the nanowire axis and 240 Oe with field perpendicular the nanowire axis are observed at room temperature. These values are comparable to Fe nanowires without insulating layer in membrane. The magnetic hysteresis loop suggests that the SiO2 insulated nanowires have uniaxial magnetic anisotropy with the easy axis magnetization direction along the nanowire arrays due to their large shape anisotropy.
Acoustic focusing of sub-wavelength scale achieved by multiple Fabry-Perot resonance effect
Authors: Lin Zhou , Guo Xiasheng , Tu Juan , Cheng Jianchun , Wu Junru , Zhang Dong
Published: March 2014

It is demonstrated that a novel design of a multi-branch structure can converge plane acoustic waves to a focal region of sub-wavelength scale. The structure consists of multiple sub-wavelength apertures; each has length equal to the integer times that of the shortest aperture. The periodicity length of the inlet array is selected equal to the length of the structure, inducing a cooperation between the surface resonances and the Fabry-Perot (FP) resonances in apertures. The design allows FP resonances to exhibit in all apertures simultaneously, hence a multiple FP resonance is achieved. The generated evanescent waves are amplified effectively, and the acoustic focusing of sub-wavelength scale is realized within a wide frequency range, with an approximate maximum transmission gain of 7 dB.
Magneto-photoluminescence of InAs/InGaAs/InAlAs quantum well structures
Authors: Terent'ev Ya. V. , Danilov S. N. , Loher J. , Schuh D. , Bougeard D. , Weiss D. , Durnev M. V. , Tarasenko S. A. , Mukhin M. S. , Ivanov S. V. , Ganichev S. D.
Published: March 2014

Photoluminescence (PL) and highly circularly polarized magneto-PL (up to 50% at 6 T) from two-step bandgap InAs/InGaAs/InAlAs quantum wells (QWs) are studied. Bright PL is observed up to room temperature, indicating a high quantum efficiency of the radiative recombination in these QWs. The sign of the circular polarization indicates that it stems from the spin polarization of heavy holes caused by the Zeeman effect. Although in magnetic field the PL lines are strongly circularly polarized, no energy shift between the counter-polarized PL lines was observed. The results suggest the electron and the hole g-factor to be of the same sign and close magnitudes.
Stimulated emission and optical gain in AlGaN heterostructures grown on bulk AlN substrates
Authors: Guo Wei , Bryan Zachary , Xie Jinqiao , Kirste Ronny , Mita Seiji , Bryan Isaac , Hussey Lindsay , Bobea Milena , Haidet Brian , Gerhold Michael , Collazo Ramón , Sitar Zlatko
Published: March 2014

Optical gain spectra for ∼250 nm stimulated emission were compared in three different AlGaN-based structures grown on single crystalline AlN substrates: a single AlGaN film, a double heterostructure (DH), and a Multiple Quantum Well (MQW) structure; respective threshold pumping power densities of 700, 250, and 150 kW/cm2 were observed. Above threshold, the emission was transverse-electric polarized and as narrow as 1.8 nm without a cavity. The DH and MQW structures showed gain values of 50–60 cm−1 when pumped at 1 MW/cm2. The results demonstrated the excellent optical quality of the AlGaN-based heterostructures grown on AlN substrates and their potential for realizing electrically pumped sub-280 nm laser diodes.
Spin transistor operation driven by the Rashba spin-orbit coupling in the gated nanowire
Authors: Wójcik P. , Adamowski J. , Spisak B. J. , Wołoszyn M.
Published: March 2014

A theoretical description has been proposed for the operation of the spin transistor in the gate-controlled InAs nanowire. The calculated current-voltage characteristics show that the electron current flowing from the source (spin injector) to the drain (spin detector) oscillates as a function of the gate voltage, which results from the precession of the electron spin caused by the Rashba spin-orbit interaction in the vicinity of the gate. We have studied the operation of the spin transistor under the following conditions: (A) the full spin polarization of electrons in the contacts, zero temperature, and the single conduction channel corresponding to the lowest-energy subband of the transverse motion and (B) the partial spin polarization of the electrons in the contacts, the room temperature, and the conduction via many transverse subbands taken into account. For case (A), the spin-polarized current can be switched on/off by the suitable tuning of the gate voltage, for case (B) the current also exhibits the pronounced oscillations but with no-zero minimal values. The computational results obtained for case (B) have been compared with the recent experimental data and a good agreement has been found.
Tackling soil diversity with the assembly of large, complex metagenomes
Authors: Howe Adina Chuang , Jansson Janet K. , Malfatti Stephanie A. , Tringe Susannah G. , Tiedje James M. , Brown C. Titus
Published: March 2014

Significance

Investigations of complex environments rely on large volumes of sequence data to adequately sample the genetic diversity of a microbial community. The assembly of short-read data into longer, more interpretable sequence currently is not possible for much of the research community because it requires specialized computational facilities. We present approaches that make de novo assembly of complex metagenomes more accessible. These approaches scale data size with community richness and subdivide the data into tractable subsets representing individual species. We applied these methods toward the assembly of two large soil metagenomes to identify important metagenomic references and show that considerably more data are needed to study the terrestrial microbiome comprehensively.
A Role and Reference Grammar parser  for German
Authors: Diedrichsen Elke
Published: March 2014

This paper describes the development of a sentence parser for German based on Role and Reference Grammar (RRG). German has a number of characteristics which are very challenging to a computational approach to syntactic processing that is semantically motivated. These include the German sentence structure, which is organised as a “bracket structure”, in which one component of the predicate, mostly the finite verb, is realised in an early position in the sentence and therefore forms the “left bracket”, whereas the more meaningful part of the predicate, mostly the infinite predicate, appears at the end of the sentence and forms the “right bracket”. Inside these brackets, the main information of the sentence is placed in an order that reflects information structure, i.e. the given information precedes the new information inside the bracket. The bracket structure has recurrent formal elements. It therefore provides a formal structuring principle for sentences that is particular for German and serves functions for sentence processing, information structure and turn taking. German has a three-way gender system for nouns. Gender is marked on the article. Tense is marked on the verb. There is an aspectual system in the realisation of perfect in that telic verbs select sein in the perfect, while atelic verbs select haben. The software is developed using Java and will accept an input sentence in German from the user through a Java Swing graphical user interface. The software parses an input sentence into its respective tokens using the Java native string processing capability. Each token is checked against the respective German lexicons (noun, verb, etc.) to determine its lexical category. The morphological markings of the tokens are unpacked for their feature sets. These features are recorded for each token. The lexical entry for the verb is determined and its logical structure is retrieved from the lexicon. The result of the parse displays the populated RRG logical structure and its operators, i.e. tense, aspect etc. A trace of the application of the linking system, in mapping from syntactic clause to semantic representation, is presented.
Extending a lexicalist functional grammar through speech acts, constructions and conversational software agents
Authors: Nolan Brian
Published: March 2014

This paper advances a model of conversational agents in a computational framework that builds on the notion of speech act performatives from discourse within a functional model of grammar. We describe the language specific elements of the intelligent conversational agents paradigm and how it can be usefully employed in the modelling of human language in software through use of agent-embedded speech acts. The linguistic model employed is Role and Reference Grammar (RRG). We propose a view in which a conversational agent has ‘internal’ and ‘external’ models to support the speech acts. The internal model of the agent is concerned with the internal state of the agent, based upon the intersection at any given time on the agent’s internal beliefs, desires, and intentions, known as BDI states. The external model of the agent is composed of an interaction model with its world (human and other agent). Importantly, the conversational agent also has a language model in software that is related to its interaction model to support bi-directional communication in human language through speech acts. For this, we employ the RRG model to motivate the design of the language model and use the RRG bi-directional linking system. We present a framework that connects the intelligent conversational agents paradigm to the RRG model of language. This has significance in that it has potential for use with linguistically oriented ontological semantics modelling and as a framework for testing of hypotheses on languages to support claims of adequacy within a functional approach. It also extends the breadth of computational work within RRG.
FunGramKB term extractor
Authors: Felices-Lago Ángel , Gómez-Moreno Pedro Ureña
Published: March 2014

Ontological engineering is a relatively young discipline that has nevertheless received considerable attention because of its great potential for application in a number of areas, including Machine Translation, Artificial Intelligence and the Semantic Web. A major field of research of the ontological endeavour concerns the building of specialised ontologies, i.e. concept hierarchies which formalise knowledge from expert areas of human activity such as medicine or law. This chapter focuses on the methodological aspects of the construction of specialised taxonomies in the framework of the FunGramKB knowledge base and in doing so it illustrates the FunGramKB Term Extractor, an innovative corpus-based tool for the semi-automatic extraction of terms.
A functional and constructional approach for specialized knowledge resources
Authors: Sánchez Cárdenas Beatriz , Faber Pamela
Published: March 2014

This paper describes how verbs are represented in EcoLexicon (ecolexicon.ugr.es), a specialized knowledge resource in environmental science. Based on the hypothesis that human cognition organizes concepts in semantic categories (Tranel et al. 2001; H. Damasio et al. 2004), verbs are conceptually structured in lexical domains (Mingorance 1985, 1900, 1995; Faber & Mairal 1999). These domains are based on the premises of the Lexical Grammar Model (Faber & Mairal 1999). Once the members of a lexical domain are specified, the conceptual structure of the domain is mapped out. Semantic categories are thus organized in a tangled hierarchy. The semantic relation of troponymy (Fellbaum 1990; Miller & Fellbaum 1991) determines the hierarchical structure of verbal lexical domains. The third step consists in the design of a lexical template based on the principles of the Lexical Constructional Model (Ruiz de Mendoza & Mairal 2008, Mairal & Ruiz de Mendoza 2009). Each lexical template consists of the following: (a) an Aktionsart module according to Role and Reference Grammar (Van Valin 1993, 2005, Van Valin & LaPolla 1997) in which the actantial structure of verbs is established; (b) a semantic module that specifies the thematic relations (Van Valin 2005), macroroles and types of noun selected by each verb. The French and English verbs of movement in the field of Volcanology are analyzed as an illustration of this method.
Applying the lexical constructional model to ontology building
Authors: Montiel-Ponsoda Elena , Aguado-de-Cea Guadalupe
Published: March 2014

Knowledge acquisition strategies based on lexico-syntactic patterns have shown to significantly contribute to the automatic identification of concepts and relations from texts, but have not investigated how to represent that information in ontologies. Since this is one of the most critical steps in ontology building, we propose to establish a correspondence between lexico-syntactic patterns, specifically verbal patterns representing taxonomic and meronymic relations, and their corresponding ontological structures represented by Ontology Design Patterns. In this way, the transformation of linguistic expressions into ontological structures could be automated and it would support domain experts in the development of ontologies. In order to reliably establish this correspondence, we need to dissect the meaning of predicates. For this aim, we rely on the Lexical Constructional Model, as a comprehensive theory of meaning construction. In this contribution we demonstrate how such a model permits to identify the ontological structure(s) that better capture the meaning of predicates in an ontological resource.
HookA is a novel dynein–early endosome linker critical for cargo movement in vivo
Authors: Zhang Jun , Qiu Rongde , Arst Herbert N. , Peñalva Miguel A. , Xiang Xin
Published: March 2014

Cytoplasmic dynein transports membranous cargoes along microtubules, but the mechanism of dynein–cargo interaction is unclear. From a genetic screen, we identified a homologue of human Hook proteins, HookA, as a factor required for dynein-mediated early endosome movement in the filamentous fungus Aspergillus nidulans. HookA contains a putative N-terminal microtubule-binding domain followed by coiled-coil domains and a C-terminal cargo-binding domain, an organization reminiscent of cytoplasmic linker proteins. HookA–early endosome interaction occurs independently of dynein–early endosome interaction and requires the C-terminal domain. Importantly, HookA interacts with dynein and dynactin independently of HookA–early endosome interaction but dependent on the N-terminal part of HookA. Both dynein and the p25 subunit of dynactin are required for the interaction between HookA and dynein–dynactin, and loss of HookA significantly weakens dynein–early endosome interaction, causing a virtually complete absence of early endosome movement. Thus, HookA is a novel linker important for dynein–early endosome interaction in vivo.
A general method for accurate estimation of false discovery rates in identification of differentially expressed genes
Authors: Tan Yuan-De , Xu Hongyan
Published: March 2014

Summary: The ‘omic’ data such as genomic data, transcriptomic data, proteomic data and single nucleotide polymorphism data have been rapidly growing. The omic data are large-scale and high-throughput data. Such data challenge traditional statistical methodologies and require multiple tests. Several multiple-testing procedures such as Bonferroni procedure, Benjamini–Hochberg (BH) procedure and Westfall–Young procedure have been developed, among which some control family-wise error rate and the others control false discovery rate (FDR). These procedures are valid in some cases and cannot be applied to all types of large-scale data. To address this statistically challenging problem in the analysis of the omic data, we propose a general method for generating a set of multiple-testing procedures. This method is based on the BH theorems. By choosing a C-value, one can realize a specific multiple-testing procedure. For example, by setting C = 1.22, our method produces the BH procedure. With C < 1.22, our method generates procedures of weakly controlling FDR, and with C > 1.22, the procedures strongly control FDR. Those with C = G (number of genes or tests) and C = 0 are, respectively, the Bonferroni procedure and the single-testing procedure. These are the two extreme procedures in this family. To let one choose an appropriate multiple-testing procedure in practice, we develop an algorithm by which FDR can be correctly and reliably estimated. Simulated results show that our method works well for an accurate estimation of FDR in various scenarios, and we illustrate the applications of our method with three real datasets.

Availability and implementation: Our program is implemented in Matlab and is available upon request.

Contact : hxu@gru.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants
Authors: Chorostecki Uciel , Palatnik Javier F.
Published: March 2014

Motivation: MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target messenger RNAs (mRNAs) by sequence complementarity and guide them to cleavage or translational arrest. So far, the prediction of plant miRNA–target pairs generally relies on the use of empirical parameters deduced from known miRNA–target interactions.

Results: We developed comTAR, a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in different species. We used data generated from a pipeline applied to transcript datasets of 33 angiosperms that was used to build a database of potential miRNA targets of different plant species. The database contains information describing each miRNA–target pair, their function and evolutionary conservation, while the results are displayed in a user-friendly interface. The tool also allows the search using new miRNAs.

Availability and implementation: The Web site is free to all users, with no login requirements, at http://rnabiology.ibr-conicet.gov.ar/comtar .

Contact:  palatnik@ibr-conicet.gov.ar or chorostecki@ibr-conicet.gov.ar
FSuite: exploiting inbreeding in dense SNP chip and exome data
Authors: Gazal Steven , Sahbatou Mourad , Babron Marie-Claude , Génin Emmanuelle , Leutenegger Anne-Louise
Published: March 2014

Summary: FSuite is a user-friendly pipeline developed for exploiting inbreeding information derived from human genomic data. It can make use of single nucleotide polymorphism chip or exome data. Compared with other software, the advantage of FSuite is that it provides a complete suite of scripts to describe and use the inbreeding information. It includes a module to detect inbred individuals and estimate their inbreeding coefficient, a module to describe the proportion of different mating types in the population and the individual probability to be offspring of different mating types that can be useful for population genetic studies. It also allows the identification of shared regions of homozygosity between affected individuals (homozygosity mapping) that can be used to identify rare recessive mutations involved in monogenic or multifactorial diseases.

Availability and implementation: FSuite is developed in Perl and uses R functions to generate graphical outputs. This pipeline is freely available under GNU GPL license at: http://genestat.cephb.fr/software/index.php/FSuite .

Contact:  fsuite.software@gmail.com or steven.gazal@inserm.fr

Supplementary information:   Supplementary data is available at Bioinformatics online.
Comprehensive analysis of gene expression in human retina and supporting tissues
Authors: Li Mingyao , Jia Cheng , Kazmierkiewicz Krista L. , Bowman Anita S. , Tian Lifeng , Liu Yichuan , Gupta Neel A. , Gudiseva Harini V. , Yee Stephanie S. , Kim Mijin , Dentchev Tzvete , Kimble James A. , Parker John S. , Messinger Jeffrey D. , Hakonarson Hakon , Curcio Christine A. , Stambolian Dwight
Published: March 2014

Understanding the influence of gene expression on the molecular mechanisms underpinning human phenotypic diversity is fundamental to being able to predict health outcomes and treat disease. We have carried out whole transcriptome expression analysis on a series of eight normal human postmortem eyes by RNA sequencing. Here we present data showing that ∼80% of the transcriptome is expressed in the posterior layers of the eye and that there is significant differential expression not only between the layers of the posterior part of the eye but also between locations of a tissue layer. These differences in expression also extend to alternative splicing and splicing factors. Differentially expressed genes are enriched for genes associated with psychiatric, immune and cardiovascular disorders. Enrichment categories for gene ontology included ion transport, synaptic transmission and visual and sensory perception. Lastly, allele-specific expression was found to be significant forCFH,C3 andCFB, which are known risk genes for age-related macular degeneration. These expression differences should be useful in determining the underlying biology of associations with common diseases of the human retina, retinal pigment epithelium and choroid and in guiding the analysis of the genomic regions involved in the control of normal gene expression.
Reflections on the success of traditional fisheries management
Authors: Hilborn Ray , Ovando Daniel
Published: March 2014

The argument persists that the continued overexploitation by many fisheries around the world is evidence that current approaches to fisheries management are failing, and that more precautionary management approaches are needed. We review the available estimates of the status of fish stocks from three sources: the FAO's “State of Marine Resources”, a database on scientific stock assessments, and recent estimates from statistical models designed to determine the status of unassessed fish stocks. The two key results are (i) that stocks that are scientifically assessed are in better shape and indeed are not typically declining but rebuilding, and (ii) that large stocks appear to be in better shape than small stocks. These results support the view that stocks that are managed are improving, while stocks that are not managed are not. Large stocks receive far more management attention than small stocks in jurisdictions that have active fisheries management systems, and most unassessed stocks are simply not managed. We assert that fisheries management as currently practised can (and often does) lead to sustainable fisheries, and what is needed is to actively manage the unassessed fisheries of the world. More precautionary management is not necessarily needed to ensure the sustainability of managed fisheries.
Using correlations between cosmic microwave background lensing and large-scale structure to measure primordial non-Gaussianity
Authors: Giannantonio Tommaso , Percival Will J.
Published: March 2014

We apply a new method to measure primordial non-Gaussianity, using the cross-correlation between galaxy surveys and the cosmic microwave background (CMB) lensing signal to measure galaxy bias on very large scales, where local-type primordial non-Gaussianity predicts a k2 divergence. We use the CMB lensing map recently published by the Planck Collaboration, and measure its external correlations with a suite of six galaxy catalogues spanning a broad redshift range. We then consistently combine correlation functions to extend the recent analysis by Giannantonio et al., where the density–density and the density–CMB temperature correlations were used. Due to the intrinsic noise of the Planck lensing map, which affects the largest scales most severely, we find that the constraints on the galaxy bias are similar to the constraints from density–CMB temperature correlations. Including lensing constraints only improves the previous statistical measurement errors marginally, and we obtain fNL = 12 ± 21 (1σ) from the combined data set. However, the lensing measurements serve as an excellent test of systematic errors: we now have three methods to measure the large-scale, scale-dependent bias from a galaxy survey: auto-correlation, and cross-correlation with both CMB temperature and lensing. As the publicly available Planck lensing maps have had their largest scale modes at multipoles l < 10 removed, which are the most sensitive to the scale-dependent bias, we consider mock CMB lensing data covering all multipoles. We find that, while the effect of fNL indeed increases significantly on the largest scales, so do the contributions of both cosmic variance and the intrinsic lensing noise, so that the improvement is small.
Large-scale gas sloshing out to half the virial radius in the strongest cool core REXCESS galaxy cluster, RXJ2014.8-2430
Authors: Walker S. A. , Fabian A. C. , Sanders J. S.
Published: March 2014

We search the cool core galaxy clusters in the REXCESS sample for evidence of large-scale gas sloshing, and find clear evidence for sloshing in RXJ2014.8-2430, the strongest cool core cluster in the REXCESS cluster sample. The residuals of the surface brightness distribution from the azimuthal average for RXJ2014 show a prominent swirling excess feature extending out to an abrupt surface brightness discontinuity at 800 kpc from the cluster core (half the virial radius) to the south, which the XMM–Newton observations confirm to be cold, low-entropy gas. The gas temperature is significantly higher outside this southern surface brightness discontinuity, indicating that this is a cold front 800 kpc from the cluster core. Chandra observations of the central 200 kpc show two clear younger cold fronts on opposite sides of the cluster. The scenario appears qualitatively consistent with simulations of gas sloshing due to minor mergers which raise cold, low-entropy gas from the core to higher radius, resulting in a swirling distribution of opposing cold fronts at increasing radii. However, the scale of the observed sloshing is much larger than that which has been simulated at present, and is similar to the large-scale sloshing recently observed in the Perseus cluster and Abell 2142.
Domains of the cucumber mosaic virus 2b silencing suppressor protein affecting inhibition of salicylic acid-induced resistance and priming of salicylic acid accumulation during infection
Authors: Zhou Tao , Murphy Alex M. , Lewsey Mathew G. , Westwood Jack H. , Zhang Heng-Mu , González Inmaculada , Canto Tomás , Carr John P.
Published: March 2014

The cucumber mosaic virus (CMV) 2b silencing suppressor protein allows the virus to overcome resistance to replication and local movement in inoculated leaves of plants treated with salicylic acid (SA), a resistance-inducing plant hormone. InArabidopsis thalianaplants systemically infected with CMV, the 2b protein also primes the induction of SA biosynthesis during this compatible interaction. We found that CMV infection of susceptible tobacco (Nicotiana tabacum) also induced SA accumulation. Utilization of mutant 2b proteins expressed during infection of tobacco showed that the N- and C-terminal domains, which had previously been implicated in regulation of symptom induction, were both required for subversion of SA-induced resistance, while all mutants tested except those affecting the putative phosphorylation domain had lost the ability to prime SA accumulation and expression of the SA-induced marker genePR-1.
GABA-mediated presynaptic inhibition is required for precision of long-term memory
Authors: Cullen Patrick K. , Dulka Brooke N. , Ortiz Samantha , Riccio David C. , Jasnow Aaron M.
Published: March 2014

Though much attention has been given to the neural structures that underlie the long-term consolidation of contextual memories, little is known about the mechanisms responsible for the maintenance of memory precision. Here, we demonstrate a rapid time-dependent decline in memory precision in GABAB(1a) receptor knockout mice. First, we show that GABAB(1a) receptors are required for the maintenance, but not encoding, of a precise fear memory. We then demonstrate that GABAB(1a) receptors are required for the maintenance, but not encoding, of spatial memories. Our findings suggest that GABA-mediated presynaptic inhibition regulates the maintenance of memory precision as a function of memory age.
Sleep benefits in parallel implicit and explicit measures of episodic memory
Authors: Weber Frederik D. , Wang Jing-Yi , Born Jan , Inostroza Marion
Published: March 2014

Research in rats using preferences during exploration as a measure of memory has indicated that sleep is important for the consolidation of episodic-like memory, i.e., memory for an event bound into specific spatio-temporal context. How these findings relate to human episodic memory is unclear. We used spontaneous preferences during visual exploration and verbal recall as, respectively, implicit and explicit measures of memory, to study effects of sleep on episodic memory consolidation in humans. During encoding before 10-h retention intervals that covered nighttime sleep or daytime wakefulness, two groups of young adults were presented with two episodes that were 1-h apart. Each episode entailed a spatial configuration of four different faces in a 3 × 3 grid of locations. After the retention interval, implicit spatio-temporal recall performance was assessed by eye-tracking visual exploration of another configuration of four faces of which two were from the first and second episode, respectively; of the two faces one was presented at the same location as during encoding and the other at another location. Afterward explicit verbal recall was assessed. Measures of implicit and explicit episodic memory retention were positively correlated (r = 0.57, P < 0.01), and were both better after nighttime sleep than daytime wakefulness (P < 0.05). In the sleep group, implicit episodic memory recall was associated with increased fast spindles during nonrapid eye movement (NonREM) sleep (r = 0.62, P < 0.05). Together with concordant observations in rats our results indicate that consolidation of genuinely episodic memory benefits from sleep.
The orexin component of fasting triggers memory processes underlying conditioned food selection in the rat
Authors: Ferry Barbara , Duchamp-Viret Patricia
Published: March 2014

To test the selectivity of the orexin A (OXA) system in olfactory sensitivity, the present study compared the effects of fasting and of central infusion of OXA on the memory processes underlying odor–malaise association during the conditioned odor aversion (COA) paradigm. Animals implanted with a cannula in the left ventricle received ICV infusion of OXA or artificial cerebrospinal fluid (ACSF) 1 h before COA acquisition. An additional group of intact rats were food-deprived for 24 h before acquisition. Results showed that the increased olfactory sensitivity induced by fasting and by OXA infusion was accompanied by enhanced COA performance. The present results suggest that fasting-induced central OXA release influenced COA learning by increasing not only olfactory sensitivity, but also the memory processes underlying the odor–malaise association.
Systems Analysis of Auxin Transport in the Arabidopsis Root Apex
Authors: Band Leah R. , Wells Darren M. , Fozard John A. , Ghetiu Teodor , French Andrew P. , Pound Michael P. , Wilson Michael H. , Yu Lei , Li Wenda , Hijazi Hussein I. , Oh Jaesung , Pearce Simon P. , Perez-Amador Miguel A. , Yun Jeonga , Kramer Eric , Alonso Jose M. , Godin Christophe , Vernoux Teva , Hodgman T. Charlie , Pridmore Tony P. , Swarup Ranjan , King John R. , Bennett Malcolm J.
Published: March 2014

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin's shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues.
The life and times of a senior scholar: an interview with Jane Dutton
Authors: Moore Karl
Published: March 2014

Purpose

– The aim of this paper was to interview a senior scholar in the field of management.

Design/methodology/approach

– A structured interview method was used.

Findings

– Jane discussed her life and times, a fascinating recounting of history.

Originality/value

– The paper provides a unique perspective on the career of a management scholar.
Persistent pruritic papules and plaques associated with adult‐onset Still's disease: Report of six cases
Authors: Kikuchi Nobuyuki , Satoh Masataka , Ohtsuka Mikio , Yamamoto Toshiyuki
Published: March 2014

Typical skin rash, which appears and disappears along with respective rise and fall of fever, is well‐known, and included as one of the major criteria of adult‐onset Still's disease (AOSD) (Yamaguchi's criteria). In addition, various skin lesions are occasionally observed in association with AOSD. Persistent pruritic eruptions present with some clinical features, such as urticarial erythema, flagellate erythema, erythematous, slightly scaly or crusted papules, and/or plaques on the trunk and extremities. These lesions show unique histological features such as dyskeratosis with a peculiar, distinctive distribution in the upper epidermis and cornified layers with focal hyperkeratosis. We describe herein six cases of AOSD, which presented with skin lesions of persistent pruritic papules and plaques. All six cases were female, and three of them were elderly women. The patients presented with linear erythematous streaks, scaly erythema, keratotic papules, infiltrative plaques and irregular coalesced erythemas. By contrast, histological features were characteristic, and dyskeratotic cells were found in the horny layers as well as in the upper layers of the epidermis. Persistent pruritic eruption is an important cutaneous sign for the diagnosis of AOSD.
Case of giant basal cell carcinoma around the base of the penis in an elderly patient
Authors: Suyama Takayuki , Teramoto Yukiko , Yamamoto Akifumi , Kuroda Isao , Yoshikawa Shusuke , Kiyohara Yoshio
Published: March 2014

We report a case of an 85‐year‐old man with a doughnut‐shaped basal cell carcinoma around the base of the penis invading the cavernosum urethra. In cases in which curative resection is planned, the penis is resected, cystostomy is performed, and postoperative self‐management is required. In line with the patient's wishes and the fact that he was an elderly person living alone without family support, we decided to perform penis‐conserving surgery. Relapse occurred once, for which additional resection was conducted. Two years after the resection, there was no evidence of tumor recurrence. The therapeutic plan for elderly patients should be modified after considering the patient's social background, wishes, activity and life expectancy.
Cases with a spontaneous regression of an infiltrating non‐crateriform keratoacanthoma and squamous cell carcinoma with a keratoacanthoma‐like component
Authors: Misago Noriyuki , Takai Toshihiro , Murata Yozo , Nagase Kotaro , Narisawa Yutaka
Published: March 2014

We herein report the natural course of an early/proliferative stage keratoacanthoma (KA) with infiltrating islands of cytological malignancy (case 1) and a squamous cell carcinoma (SCC) with a KA‐like component (case 2), which were observed until their complete regression. The presented case 1 suggests that one of the histopathological forms of KA includes this unusual, infiltrating, non‐crateriform architecture, and also indicates the possibility of complete remission in the KA associated with infiltrating islands of cytological malignancy. In the presented case 2, the peripherally‐associated KA‐like focus was histopathologically considered to be either a remnant of KA focus or verrucous keratosis (hyperplasia). Therefore, the complete spontaneous regression of case 2 suggests that SCC arising in KA still has the potential of spontaneous regression, or that an extremely rare event, namely, the spontaneous regression of (traditional) SCC occurred in the present case.