bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparative study of CO adsorption on tetrahexahedral Pt nanocrystals and interrelated Pt single crystal electrodes by using cyclic voltammetry and in situ FTIR spectroscopy
Authors: Liu Hai-Xia , Tian Na , Ye Jin-Yu , Lu Bang-An , Ren Jie , Huangfu Zhi-Chao , Zhou Zhi-You , Sun Shi-Gang
Published: August 2014

This study focuses on CO adsorption at tetrahexahedral Pt nanocrystals (THH Pt NCs) by using cyclic voltammetry andin situFTIR spectroscopy. Since the electrochemically prepared THH Pt NCs in this study are enclosed by {730} facets which could be considered by a subfacet configuration of 2{210} + {310}, we have also studied CO adsorption on the interrelated Pt(310) and Pt(210) single crystal electrodes as a comparison. Cyclic voltammetry results demonstrated that CO adsorbs dominantly on the (100) sites of THH Pt NCs at low CO coverage (θCO≤ 0.135), while on both (100) and (110) sites at higher CO coverage. On ordered Pt(310) and Pt(210),i.e.they were flame annealed and then cooled in H2+ Ar, CO adsorption also illustrates relative priority on (100) sites at low CO coverage; while at high CO coverage or on oxygen-disordered Pt(310) and Pt(210) when they were cooled in air after flame annealing, the adsorption of CO presents a weak preference on (100) sites of Pt(310) and even no preference at all on (100) sites of Pt(210).In situFTIR spectroscopic studies illustrated that CO adsorption on THH Pt NCs yields anomalous infrared effects (AIREs), which are depicted by the Fano-like IR feature on a dense distribution (60 μm−2) and the enhancement of abnormal IR absorption on a sparse distribution (22 μm−2) of THH Pt NCs on glassy carbon substrate. Systematic investigation of CO coverage dependence of IR features revealed that, on THH Pt NCs, the IR band center (νCOL) of linearly bonded CO (COL) is rapidly shifted to higher wavenumbers along with the increase of CO coverage to 0.184, yielding a fast linear increase rate with a high slope (dνCOL/dθIRCO = 219 cm−1); whenθIRCO > 0.184, the increase ofνCOLwithθCOslows down and deviates drastically from linearity. In contrast, theνCOLon the ordered Pt(310) electrode maintains a linear increase withθIRCO for the whole range ofθIRCO variation, and gives a much smaller increase rate of slope 74.3 cm−1. The significant differences in CO adsorption behavior on THH Pt NCs and on interrelated Pt single crystal planes demonstrated clearly the unique properties of nanoparticles enclosed by high-index facets.
Nonlinear current–voltage characteristics and enhanced negative differential conductance in graphene field effect transistors
Authors: Wang Lin , Chen Xiaoshuang , Hu Yibin , Yu Anqi , Lu Wei
Published: August 2014

Observations of the negative differential conductance (NDC) phenomenon in graphene field-effect transistors (FET) open up new opportunities for their application in graphene-based fast switches, frequency multipliers and, most importantly, in high frequency oscillators up to the terahertz regime.
Comparative study of optical, structural and electrical properties of zinc phthalocyanine Langmuir–Blodgett thin film on annealing
Authors: Roy Dhrubojyoti , Das Nayan Mani , Shakti Nanda , Gupta P. S.
Published: August 2014

Model representing growth mechanism in the LB thin film during phase transformation from α- to β-phase on annealing.
Fluorophore-doped calcium phosphate nanoparticles for non-toxic biomedical applications
Authors: Anuradha Anuradha , Chandra Joshi Jagdish , Gulati Kavita , Ray Arunabha , Roy Indrajit
Published: August 2014

Cell viability assay showing absence of toxicity in cells treated with calcium phosphate nanoparticles, without (CP) and with (CP-CH) chitosan coating.
Synthesis of core–shell structured Fe3O4@α-MnO2microspheres for efficient catalytic degradation of ciprofloxacin
Authors: Zhao Huan , Cui Hao-Jie , Fu Ming-Lai
Published: August 2014

Three-dimensional core–shell structured Fe3O4@α-MnO2microspheres were successfully fabricated to activate persulfate for catalytic degradation of ciprofloxacin in wastewater.
Electronic transport properties of a dithienylethene-based polymer with different metallic contacts
Authors: Zhao Jingfen , Zhao Wenkai , Cui Bin , Fang Changfeng , Xu Yuqing , Kong Xiangru , Li Dongmei , Liu Desheng
Published: August 2014

We have studied the electronic transport behaviors of a dithienylethene-based polymer between two metal surfaces using nonequilibrium Green's functions combined with density functional theory.
Molecular interaction of fibrinogen with thermally modified titanium dioxide nanoparticles
Authors: Zhao A. S. , Zhou S. , Wang Y. , Chen J. , Ye C. R. , Huang N.
Published: August 2014

Novelty lies in the attempt to connect protein changes and subsequent platelet activation to surface/chemical changes upon thermal treatment of TiO2NP's.
A novel strategy to prepare a Pt–SnO2 nanocomposite as a highly efficient counter electrode for dye-sensitized solar cells
Authors: Chen Xiao , Hou Yu , Yang Shuang , Yang Xiao Hua , Yang Hua Gui
Published: August 2014

A novel strategy was introduced to prepare Pt–SnO2 nanocomposite in one step. Pt–SnO2 nanocomposite counter electrode based dye-sensitized solar cells achieve an energy conversion efficiency of 8.83%, better than that for SnO2 CE and comparable with Pt CE based DSCs.
A novel graphene sheet-wrapped Co2(OH)3Cl composite as a long-life anode material for lithium ion batteries
Authors: Ma Jingjing , Yuan Tao , He Yu-Shi , Wang Jiulin , Zhang Weimin , Yang Dezhi , Liao Xiao-Zhen , Ma Zi-Feng
Published: August 2014

A novel graphene sheet-wrapped cobalt hydroxide chloride composite is synthesized as a long-life anode material for lithium ion battery via a facile one-pot in situ hydrothermal route.
Polymeric mold soft-patterned metal oxide field-effect transistors: critical factors determining device performance
Authors: Kim Seong Jip , Kim Aryeon , Jo Yejin , Yoon Jun-Young , Lee Sun Sook , Choi Youngmin , Won JongChan , Nahm Sahn , Jang Kwang-Suk , Kim Yun Ho , Jeong Sunho
Published: August 2014

The plausible origin of distinctively different device performances is clarified for spin-cast and soft-patterned soluble oxide transistors.
Chromatin and oxygen sensing in the context of JmjC histone demethylases
Authors: Shmakova Alena , Batie Michael , Druker Jimena , Rocha Sonia
Published: August 2014

Responding appropriately to changes in oxygen availability is essential for multicellular organism survival. Molecularly, cells have evolved intricate gene expression programmes to handle this stressful condition. Although it is appreciated that gene expression is co-ordinated by changes in transcription and translation in hypoxia, much less is known about how chromatin changes allow for transcription to take place. The missing link between co-ordinating chromatin structure and the hypoxia-induced transcriptional programme could be in the form of a class of dioxygenases called JmjC (Jumonji C) enzymes, the majority of which are histone demethylases. In the present review, we will focus on the function of JmjC histone demethylases, and how these could act as oxygen sensors for chromatin in hypoxia. The current knowledge concerning the role of JmjC histone demethylases in the process of organism development and human disease will also be reviewed.
Contact angle hysteresis on superhydrophobic stripes
Authors: Dubov Alexander L. , Mourran Ahmed , Möller Martin , Vinogradova Olga I.
Published: August 2014

We study experimentally and discuss quantitatively the contact angle hysteresis on striped superhydrophobic surfaces as a function of a solid fraction, ϕS. It is shown that the receding regime is determined by a longitudinal sliding motion of the deformed contact line. Despite an anisotropy of the texture the receding contact angle remains isotropic, i.e., is practically the same in the longitudinal and transverse directions. The cosine of the receding angle grows nonlinearly with ϕS. To interpret this we develop a theoretical model, which shows that the value of the receding angle depends both on weak defects at smooth solid areas and on the strong defects due to the elastic energy of the deformed contact line, which scales as \documentclass[12pt]{minimal}\begin{document}$\phi _S^2 \ln \phi _S$\end{document}ϕS2lnϕS. The advancing contact angle was found to be anisotropic, except in a dilute regime, and its value is shown to be determined by the rolling motion of the drop. The cosine of the longitudinal advancing angle depends linearly on ϕS, but a satisfactory fit to the data can only be provided if we generalize the Cassie equation to account for weak defects. The cosine of the transverse advancing angle is much smaller and is maximized at ϕS ≃ 0.5. An explanation of its value can be obtained if we invoke an additional energy due to strong defects in this direction, which is shown to be caused by the adhesion of the drop on solid sectors and is proportional to \documentclass[12pt]{minimal}\begin{document}$\phi _S^2$\end{document}ϕS2. Finally, the contact angle hysteresis is found to be quite large and generally anisotropic, but it becomes isotropic when ϕS ≤ 0.2.
Nonuniform radiation damage in permanent magnet quadrupoles
Authors: Danly C. R. , Merrill F. E. , Barlow D. , Mariam F. G.
Published: August 2014

We present data that indicate nonuniform magnetization loss due to radiation damage in neodymium-iron-boron Halbach-style permanent magnet quadrupoles. The proton radiography (pRad) facility at Los Alamos uses permanent-magnet quadrupoles for magnifying lenses, and a system recently commissioned at GSI-Darmsdadt uses permanent magnets for its primary lenses. Large fluences of spallation neutrons can be produced in close proximity to these magnets when the proton beam is, intentionally or unintentionally, directed into the tungsten beam collimators; imaging experiments at LANL’s pRad have shown image degradation with these magnetic lenses at proton beam doses lower than those expected to cause damage through radiation-induced reduction of the quadrupole strength alone. We have observed preferential degradation in portions of the permanent magnet quadrupole where the field intensity is highest, resulting in increased high-order multipole components.
Electronic and physico-chemical properties of nanometric boron delta-doped diamond structures
Authors: Chicot G. , Fiori A. , Volpe P. N. , Tran Thi T. N. , Gerbedoen J. C. , Bousquet J. , Alegre M. P. , Piñero J. C. , Araújo D. , Jomard F. , Soltani A. , De Jaeger J. C. , Morse J. , Härtwig J. , Tranchant N. , Mer-Calfati C. , Arnault J. C. , Delahaye J. , Grenet T. , Eon D. , Omnès F. , Pernot J. , Bustarret E.
Published: August 2014

Heavily boron doped diamond epilayers with thicknesses ranging from 40 to less than 2 nm and buried between nominally undoped thicker layers have been grown in two different reactors. Two types of [100]-oriented single crystal diamond substrates were used after being characterized by X-ray white beam topography. The chemical composition and thickness of these so-called delta-doped structures have been studied by secondary ion mass spectrometry, transmission electron microscopy, and spectroscopic ellipsometry. Temperature-dependent Hall effect and four probe resistivity measurements have been performed on mesa-patterned Hall bars. The temperature dependence of the hole sheet carrier density and mobility has been investigated over a broad temperature range (6 K < T < 450 K). Depending on the sample, metallic or non-metallic behavior was observed. A hopping conduction mechanism with an anomalous hopping exponent was detected in the non-metallic samples. All metallic delta-doped layers exhibited the same mobility value, around 3.6 ± 0.8 cm2/Vs, independently of the layer thickness and the substrate type. Comparison with previously published data and theoretical calculations showed that scattering by ionized impurities explained only partially this low common value. None of the delta-layers showed any sign of confinement-induced mobility enhancement, even for thicknesses lower than 2 nm.
Neoclassical theory of elementary charges with spin of 1/2
Authors: Babin Anatoli , Figotin Alexander
Published: August 2014

We advance here our neoclassical theory of elementary charges by integrating into it the concept of spin of 1/2. The developed spinorial version of our theory has many important features identical to those of the Dirac theory such as the gyromagnetic ratio, expressions for currents including the spin current, and antimatter states. In our theory, the concepts of charge and anticharge relate naturally to their “spin” in its rest frame in two opposite directions. An important difference with the Dirac theory is that both the charge and anticharge energies are positive whereas their frequencies have opposite signs.
Extendability of Kirchhoff elastic rods in complete Riemannian manifolds
Authors: Kawakubo Satoshi
Published: August 2014

The Kirchhoff elastic rod is a classical mathematical model of equilibrium configurations of thin elastic rods, and is defined to be a solution of the Euler-Lagrange equations associated to the energy with the effect of bending and twisting. We consider the initial-value problem for the Euler-Lagrange equations in a Riemannian manifold. In a previous paper, the author proved the existence and uniqueness of global solutions of the initial-value problem in the case where the ambient space is a space form. In the present paper, we extend this result to the case where the ambient space is a general complete Riemannian manifold. This implies that an arbitrary Kirchhoff elastic rod of finite length in a complete Riemannian manifold extends to that of infinite length.
Tuning of deep level emission in highly oriented electrodeposited ZnO nanorods by post growth annealing treatments
Authors: Simimol A. , Manikandanath N. T. , Anappara Aji A. , Chowdhury Prasanta , Barshilia Harish C.
Published: August 2014

Highly dense and c-axis oriented zinc oxide (ZnO) nanorods with hexagonal wurtzite facets were deposited on fluorine doped tin oxide coated glass substrates by a simple and cost-effective electrodeposition method at low bath temperature (80 °C). The as-grown samples were then annealed at various temperatures (TA = 100–500 °C) in different environments (e.g., zinc, oxygen, air, and vacuum) to understand their photoluminescence (PL) behavior in the ultra-violet (UV) and the visible regions. The PL results revealed that the as-deposited ZnO nanorods consisted of oxygen vacancy (VO), zinc interstitial (Zni), and oxygen interstitial (Oi) defects and these can be reduced significantly by annealing in different environments at optimal annealing temperatures. However, the intensity of deep level emission increased for TA greater than the optimized values for the respective environments due to the introduction of various defect centers. For example, for TA ≥ 450 °C in the oxygen and air environments, the density of Oi defects increased, whereas, the green emission associated with VO is dominant in the vacuum annealed (TA = 500 °C) ZnO nanorods. The UV peak red shifted after the post-growth annealing treatments in all the environments and the vacuum annealed sample exhibited highest UV peak intensity. The observations from the PL data are supported by the micro-Raman spectroscopy. The present study gives new insight into the origin of different defects that exist in the electrodeposited ZnO nanorods and how these defects can be precisely controlled in order to get the desired emissions for the opto-electronic applications.
Cryogenic temperature relaxor-like dielectric responses and magnetodielectric coupling in Aurivillius Bi5Ti3FeO15 multiferroic thin films
Authors: Bai Wei , Yin Wenhao , Yang Jing , Tang Kai , Zhang Yuanyuan , Lin Tie , Meng Xiangjian , Duan Chun-Gang , Tang Xiaodong , Chu Junhao
Published: August 2014

Dielectric responses and magnetodielectric (MD) behavior of Aurivillius Bi5Ti3FeO15 multiferroics were systemically studied at cryogenic temperatures. Dielectric anomaly at ∼145 K was found by the temperature dependent dielectric spectroscopy, and relaxor-like relaxation dynamics was further confirmed unambiguously. Besides the two abnormal MD transitions at about 98 K and 220 K, remarkable MD couplings were observed near relaxation peak over the whole frequency range of 102–106 Hz. Finally, the possible mechanisms of the relaxation and MD properties were discussed in association with the occurrence of local Fe-O nano-clusters because of the antisite disorder defects in Aurivillius multiferroic phases.
Analysis of the phase transition and magneto-thermal properties in La2CoMnO6 single crystals
Authors: Balli M. , Fournier P. , Jandl S. , Truong K. D. , Gospodinov M. M.
Published: August 2014

Structural, magnetic, and magnetocaloric properties of the double perovskite La2CoMnO6 single crystals are investigated. The nature of the magnetic phase transition is analysed in terms of magnetic measurements and the Landau theory. The proportion of cationic order and the Co/Mn oxidation states were identified from the effective magnetic moment and Raman spectroscopy studies. La2CoMnO6 single crystals exhibit a significant refrigerant capacity. For a magnetic field change of 5 T, a refrigerant capacity of 222 J/kg is obtained. The magnetocaloric performance of La2CoMnO6 single crystals in the vicinity of the ferromagnetic-paramagnetic transition region (TC = 170 K) is discussed and compared with that of a polycrystalline sample.
Energy band modulation of graphane by hydrogen-vacancy chains: A first-principles study
Authors: Wu Bi-Ru , Yang Chih-Kai
Published: August 2014

We investigated a variety of configurations of hydrogen-vacancy chains in graphane by first-principles density functional calculation. We found that graphane with two zigzag H-vacancy chains segregated by one or more H chain is generally a nonmagnetic conductor or has a negligible band gap. However, the same structure is turned into a semiconductor and generates a magnetic moment if either one or both of the vacancy chains are blocked by isolated H atoms. If H-vacancy chains are continuously distributed, the structure is similar to a zigzag graphene nanoribbon embedded in graphane. It was also found that the embedded zigzag graphene nanoribbon is antiferromagnetic, and isolated H atoms left in the 2-chain nanoribbon can tune the band gap and generate net magnetic moments. Similar effects are also obtained if bare carbon atoms are present outside the nanoribbon. These results are useful for designing graphene-based nanoelectronic circuits.
Single mode interband cascade lasers based on lateral metal gratings
Authors: Weih Robert , Nähle Lars , Höfling Sven , Koeth Johannes , Kamp Martin
Published: August 2014

Single mode distributed feedback (DFB) interband cascade lasers were realized by placing metal gratings laterally to dry etched ridges. A discrete tuning range of 104 nm could be realized on the same gain material by a variation of the grating period. At room temperature, a 2.4 mm long and 9.8 μm wide ridge with as-cleaved facets emitted more than 6 mW of single mode output power in continuous-wave (cw) mode at a wavelength around 3.8 μm. With typical temperature- and current-tuning rates of 0.31 nm/ °C and 0.065 nm/mA, respectively, a total tuning bandwidth of more than 10 nm could be covered with a single device.
Spectrally resolved intraband transitions on two-step photon absorption in InGaAs/GaAs quantum dot solar cell
Authors: Tamaki Ryo , Shoji Yasushi , Okada Yoshitaka , Miyano Kenjiro
Published: August 2014

Two-step photon absorption processes in a self-organized In0.4Ga0.6As/GaAs quantum dot (QD) solar cell have been investigated by monitoring the mid-infrared (IR) photoinduced modulation of the external quantum efficiency (ΔEQE) at low temperature. The first step interband and the second step intraband transitions were both spectrally resolved by scanning photon energies of visible to near-IR CW light and mid-IR pulse lasers, respectively. A peak centered at 0.20 eV corresponding to the transition to virtual bound states and a band above 0.42 eV probably due to photoexcitation to GaAs continuum states were observed in ΔEQE spectra, when the interband transition was above 1.4 eV, directly exciting wetting layers or GaAs spacer layers. On the other hand, resonant excitation of the ground state of QDs at 1.35 eV resulted in a reduction of EQE. The sign of ΔEQE below 1.40 eV changed from negative to positive by increasing the excitation intensity of the interband transition. We ascribe this to the filling of higher energy trap states.
Influence of graphene-substrate interactions on configurations of organic molecules on graphene: Pentacene/epitaxial graphene/SiC
Authors: Jung W. , Oh D.-H. , Song I. , Shin H.-C. , Ahn S. J. , Moon Y. , Park C.-Y. , Ahn J. R.
Published: August 2014

We demonstrate that molecular ordering of pentacene (Pn) on graphene depends on the interaction between graphene and its underlying SiC substrate. The adsorption of Pn molecules on zero-layer (ZL) and single-layer (SL) graphene, which were grown on a Si-faced 6H-SiC(0001) wafer, was studied using scanning tunneling microscopy (STM). Pn molecules form a quasi-amorphous layer on ZL graphene, which interacts strongly with the underlying SiC substrate. In contrast, they form a uniformly ordered layer on the SL graphene having a weak graphene-SiC interaction. Furthermore, we could change the configuration of Pn molecules on the SL graphene by using STM tips. The results suggest that the molecular ordering of Pn on graphene and the Pn/graphene interface structure can be controlled by a graphene-substrate interaction.
Active acoustic metamaterials with tunable effective mass density by gradient magnetic fields
Authors: Chen Xing , Xu Xianchen , Ai Shigang , Chen HaoSen , Pei Yongmao , Zhou Xiaoming
Published: August 2014

Magnetically controlled acoustic metamaterials are designed and experimentally studied. Magneto-acoustic metamaterials are fabricated by covering an aluminum circular ring with magnetorheological elastomer. The resonant frequency of the structured elastomer is actively tunable by external gradient magnetic field, allowing for values of effective mass density of metamaterials to be adjusted in the low-frequency region. A prestressed plate theory is proposed to explain the shifting of the resonant frequency induced by the magnetic field and coincides very well with the experimental results. It is found that the tunability of magneto-acoustic metamaterials is attributed to the competition between the magnetic-field-induced prestress and the structural flexural rigidity. The proposed magneto-acoustic metamaterials realize the dynamic tuning of effective mass density with non-contact and fast-response gradient magnetic fields, providing a degree of freedom for full control of sound.
Controllable underwater anisotropic oil-wetting
Authors: Yong Jiale , Chen Feng , Yang Qing , Farooq Umar , Bian Hao , Du Guangqing , Hou Xun
Published: August 2014

This Letter demonstrates a simple method to achieve underwater anisotropic oil-wetting using silicon surfaces with a microgroove array produced by femtosecond laser ablation. The oil contact angles along the direction perpendicular to the grooves are consistently larger than those parallel to the microgroove arrays in water because the oil droplet is restricted by the energy barrier that exists between the non-irradiated domain and the trapped water in the laser-ablated microgrooves. This underwater anisotropic oil-wetting is able to be controlled, and the anisotropy can be tuned from 0° to ∼20° by adjusting the period of the microgroove arrays.
Tuning nucleation density of metal island with charge doping of graphene substrate
Authors: Ming Wenmei , Liu Feng
Published: August 2014

We have demonstrated that the island nucleation in the initial stage of epitaxial thin film growth can be tuned by substrate surface charge doping. This charge effect was investigated using spin density functional theory calculation in Fe-deposition on graphene substrate as an example. It was found that hole-doping can noticeably increase both Fe-adatom diffusion barrier and Fe inter-adatom repulsion energy occurring at intermediate separation, whereas electron-doping can decrease Fe-adatom diffusion barrier but only slightly modify inter-adatom repulsion energy. Further kinetic Monte Carlo simulation showed that the nucleation island number density can be increased up to six times larger under hole-doping and can be decreased down to ten times smaller under electron doping than that without doping. Our findings indicate a route to tailor the growth morphology of magnetic metal nanostructure for spintronics and plasmonic applications via surface charge doping.
Issues in developing unified systems for contextual Field and Mode
Authors: Bowcher Wendy L.
Published: August 2014

‘Context of situation’ is a central concept in Systemic Functional Linguistic (SFL) theory, and recently there has been a renewed interest in modelling context and developing a set of features for the contextual parameters Field, Tenor, and Mode. Much of this work has been inspired by Hasan’s and Butt’s development of ‘contextualisation system networks’ (Butt 2004; Hasan 1999, 2009). However, a single comprehensive descriptive framework has still not yet been agreed upon. The current Field and Mode networks include contextual features that are under some debate: ‘the role of language’, ‘ancillary’, ‘constitutive’, and ‘material action’. This paper reviews these features and presents a unified set of primary systems for Field and for Mode. Further, the paper proposes that the primary systems should reflect the core defining features of the contextual parameters, in this case, Field and Mode: the nature of the activity in terms of the kind of experience around which the situation revolves, and the nature of the activity in terms of the mode through which it is expressed respectively. Reference is made to key notions within SFL theory that need to be considered in modelling the contextual parameters as sets of choices in system networks: the relations of realisation and instantiation, inter- and intra-stratal interdependency, and the concept of ‘semiotic’. Where relevant, choices in the system networks are explained using illustrative examples.
SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome
Authors: Hooper Cornelia M. , Tanz Sandra K. , Castleden Ian R. , Vacher Michael A. , Small Ian D. , Millar A. Harvey
Published: August 2014

Motivation: Knowing the subcellular location of proteins is critical for understanding their function and developing accurate networks representing eukaryotic biological processes. Many computational tools have been developed to predict proteome-wide subcellular location, and abundant experimental data from green fluorescent protein (GFP) tagging or mass spectrometry (MS) are available in the model plant, Arabidopsis. None of these approaches is error-free, and thus, results are often contradictory.

Results: To help unify these multiple data sources, we have developed the SUBcellular Arabidopsis consensus (SUBAcon) algorithm, a naive Bayes classifier that integrates 22 computational prediction algorithms, experimental GFP and MS localizations, protein–protein interaction and co-expression data to derive a consensus call and probability. SUBAcon classifies protein location in Arabidopsis more accurately than single predictors.

Availability: SUBAcon is a useful tool for recovering proteome-wide subcellular locations of Arabidopsis proteins and is displayed in the SUBA3 database (http://suba.plantenergy.uwa.edu.au). The source code and input data is available through the SUBA3 server (http://suba.plantenergy.uwa.edu.au//SUBAcon.html) and the Arabidopsis SUbproteome REference (ASURE) training set can be accessed using the ASURE web portal (http://suba.plantenergy.uwa.edu.au/ASURE).

Contact:  cornelia.hooper@uwa.edu.au or ian.castleden@uwa.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Can graphene keep its promise?
Authors: Ball Philip
Published: August 2014

Over the past decade, the carbon material known as graphene has been hailed as a ‘wonder material’, which might revolutionize everything from microelectronic circuitry to ultra-strong composite engineering. Graphene displays several striking properties: it conducts electricity, it is transparent, and exceedingly strong and lightweight. But will it live up to its promise?
Computational modelling of the inflammatory response in trauma, sepsis and wound healing: implications for modelling resilience
Authors: Vodovotz Yoram
Published: August 2014

Resilience refers to the ability to recover from illness or adversity. At the cell, tissue, organ and whole-organism levels, the response to perturbations such as infections and injury involves the acute inflammatory response, which in turn is connected to and controlled by changes in physiology across all organ systems. When coordinated properly, inflammation can lead to the clearance of infection and healing of damaged tissues. However, when either overly or insufficiently robust, inflammation can drive further cell stress, tissue damage, organ dysfunction and death through a feed-forward process of inflammation → damage → inflammation. To address this complexity, we have obtained extensive datasets regarding the dynamics of inflammation in cells, animals and patients, and created data-driven and mechanistic computational simulations of inflammation and its recursive effects on tissue, organ and whole-organism (patho)physiology. Through this approach, we have discerned key regulatory mechanisms, recapitulatedin silicokey features of clinical trials for acute inflammation and captured diverse, patient-specific outcomes. These insights may allow for the determination of individual-specific tolerances to illness and adversity, thereby defining the role of inflammation in resilience.
Sleep and inflammation in resilient aging
Authors: Irwin Michael R.
Published: August 2014

Sleep quality is important to health, and increasingly viewed as critical in promoting successful, resilient aging. In this review, the interplay between sleep and mental and physical health is considered with a focus on the role of inflammation as a biological pathway that translates the effects of sleep on risk of depression, pain and chronic disease risk in aging. Given that sleep regulates inflammatory biologic mechanisms with effects on mental and physical health outcomes, the potential of interventions that target sleep to reduce inflammation and promote health in aging is also discussed.
The hypothalamic–pituitary–adrenal–leptin axis and metabolic health: a systems approach to resilience, robustness and control
Authors: Aschbacher Kirstin , Rodriguez-Fernandez Maria , van Wietmarschen Herman , Tomiyama A. Janet , Jain Shamini , Epel Elissa , Doyle Francis J. , van der Greef Jan
Published: August 2014

Glucocorticoids contribute to obesity and metabolic syndrome; however, the mechanisms are unclear, and prognostic measures are unavailable. A systems level understanding of the hypothalamic–pituitary–adrenal (HPA)–leptin axis may reveal novel insights. Eighteen obese premenopausal women provided blood samples every 10 min over 24 h, which were assayed for cortisol, adrenocorticotropin releasing hormone (ACTH) and leptin. A published personalized HPA systems model was extended to incorporate leptin, yielding three parameters: (i) cortisol inhibitory feedback signalling, (ii) ACTH–adrenal signalling, and (iii) leptin–cortisol antagonism. We investigated associations between these parameters and metabolic risk profiles: fat and lean body mass (LBM; using dual-energy X-ray absorptiometry), and insulin resistance. Decreased cortisol inhibitory feedback signalling was significantly associated with greater fat (kg;
p
= 0.01) and insulin resistance (
p
= 0.03) but not LBM. Leptin significantly antagonized cortisol dynamics in eight women, who exhibited significantly lower 24 h mean leptin levels, LBM and higher ACTH–adrenal signalling nocturnally (all
p
< 0.05), compared with women without antagonism. Traditional neuroendocrine measures did not predict metabolic health, whereas a dynamic systems approach revealed that lower central inhibitory cortisol feedback signalling was significantly associated with greater metabolic risk. While exploratory, leptin–cortisol antagonism may reflect a ‘neuroendocrine starvation’ response.
The mathematician's control toolbox for management of type 1 diabetes
Authors: Csete Marie , Doyle John
Published: August 2014

Blood glucose levels are controlled by well-known physiological feedback loops: high glucose levels promote insulin release from the pancreas, which in turn stimulates cellular glucose uptake. Low blood glucose levels promote pancreatic glucagon release, stimulating glycogen breakdown to glucose in the liver. In healthy people, this control system is remarkably good at maintaining blood glucose in a tight range despite many perturbations to the system imposed by diet and fasting, exercise, medications and other stressors. Type 1 diabetes mellitus (T1DM) results from loss of the insulin-producing cells of the pancreas, the beta cells. These cells serve as both sensor (of glucose levels) and actuator (insulin/glucagon release) in a control physiological feedback loop. Although the idea of rebuilding this feedback loop seems intuitively easy, considerable control mathematics involving multiple types of control schema were necessary to develop an artificial pancreas that still does not function as well as evolved control mechanisms. Here, we highlight some tools from control engineering used to mimic normal glucose control in an artificial pancreas, and the constraints, trade-offs and clinical consequences inherent in various types of control schemes. T1DM can be viewed as a loss of normal physiologic controls, as can many other disease states. For this reason, we introduce basic concepts of control engineering applicable to understanding pathophysiology of disease and development of physiologically based control strategies for treatment.
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power
Authors: Angaroni Fabrizio , Chen Kevin , Damiani Chiara , Caravagna Giulio , Graudenzi Alex , Ramazzotti Daniele
Published: August 2014

Motivation

Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive models of cancer evolution. Yet, available methods cannot infer logical formulas connecting events to represent alternative evolutionary routes or convergent evolution.

Results

We introduce PMCE, an expressive framework that leverages mutational profiles from crosssectional sequencing data to infer probabilistic graphical models of cancer evolution including arbitrary logical formulas, and which outperforms the state-of-the-art in terms of accuracy and robustness to noise, on simulations.

The application of PMCE to 7866 samples from the TCGA database allows us to identify a highly significant correlation between the predicted evolutionary paths and the overall survival in 7 tumor types, proving that our approach can effectively stratify cancer patients in reliable risk groups.

Availability

PMCE is freely available athttps://github.com/BIMIB-DISCo/PMCE, in addition to the code to replicate all the analyses presented in the manuscript.

Contacts

daniele.ramazzotti@unimib.it,alex.graudenzi@ibfm.cnr.it.
Modeling human population separation history using physically phased genomes
Authors: Song Shiya , Sliwerska Elzbieta , Emery Sarah , Kidd Jeffrey M.
Published: August 2014

Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Massai and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati and CEPH European populations and analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We find that statistically phased haplotypes yield an earlier split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation (ABC) approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard Isolation-with-Migration model. We inferred that the separation between hunter-gather populations and other populations happened around 120.0 to 140,000 years ago with gene flow continuing until 30,000 to 40,000 years ago; separation between west African and out of African populations happened around 70,000 to 80.0 years ago, while the separation between Massai and out of African populations happened around 50,000 years ago.
Factors influencing quality corporate governance in Sub Saharan Africa: an empirical study
Authors: Waweru Nelson
Published: August 2014

Purpose

– This study aims to examine the factors influencing the quality of corporate governance in South Africa (SA). Firm-level variables including performance, firm size, leverage, investment opportunities and audit quality were identified from the corporate governance literature.

Design/methodology/approach

– The study used ordinary least squares regression on firm-specific and corporate governance variables obtained from panel data of 247-firm years obtained from the annual reports of the 50 largest companies listed on the Johannesburg Stock Exchange (JSE) Securities Exchange of SA.

Findings

– This study found leverage, firm size and investment opportunities as the main factors influencing the quality of corporate governance in SA.

Research limitations/implications

– The research findings should be interpreted in the light of the following limitations. First, the study sample consists of the 50 largest firms listed in the JSE of SA. Because these are large companies, the results may not be generalized to other smaller firms operating in SA. Second, this study is constrained to SA. Firms in other developing countries may differ from their SA counterparts.

Originality/value

– The results of this study are important to the King Committee and other corporate governance regulators in Sub-Saharan Africa, in their effort to improve corporate governance practices and probably minimize corporate failure and protect the well-being of the minority shareholders. Furthermore, the study contributes to our understanding of the variables affecting the quality of corporate governance in developing economies of Africa.
An evaluation of the functionality and accessibility of e-readers for individuals with print disabilities
Authors: L. Maatta Stephanie , J. Bonnici Laurie
Published: August 2014

Purpose

– This study aims to examine the usability of three popular electronic reading devices (e-readers) to determine which device provides the best functionality for individuals with print disabilities. Adaptability and flexibility for use with assistive technology are also evaluated.

Design/methodology/approach

– This study reports the results of a usability test of e-readers and their potential for use by individuals with print disabilities. Students enrolled in a School of Library and Information Science evaluated and compared the devices through a series of tasks designed to measure functionality. Participants completed a series of questionnaires and engaged in small group discussion about the efficacy of the devices. Likert scales and open-ended evaluation were employed in the evaluation and analysis.

Findings

– Two of the three devices examined offered no accessibility features for individuals with low or no vision who require assistive technologies to use information and communication technologies. The third device, while offering greater universal access functionality for individuals with mild-to-moderate print disabilities, also had weaknesses for individuals with severe print disabilities.

Originality/value

– With the rapid deployment of e-readers, little research has been completed measuring the accessibility and functionality for individuals with print disabilities in library or educational environments. The paper provides data on the usability of e-readers for users with print disabilities and recommendations for adopting e-reader use in libraries and educational environments. It will inform and guide information professionals seeking to provide greater access to resources for patrons with specialized access needs.
Comparing electronic short books from the USA and the UK to South Africa
Authors: Moller Jana
Published: August 2014

Purpose

– This paper aims to investigate the electronic short books phenomenon from the USA and the UK which has spilled over to South Africa. By looking at the benefits these short books have for readers and authors, and the possible reasons for their success, the aim is to determine whether or not these books can be as successful a venture in South Africa as it has been elsewhere.

Design/methodology/approach

– Information about electronic short books, or e-singles, is gathered from various sources, including press releases and sales results. Information is gathered to determine the receptiveness to electronic short books of the South African trade book reading market, the way South African publishers are presenting e-singles to the market and what the future for e-singles may be.

Findings

– The findings of this paper make it clear that e-singles have found a gap in the market, providing various benefits to authors and readers, which may have contributed to their success. In South Africa, the success of e-singles faces unique obstacles, like a weaker reading culture and a poor awareness of e-books. Publishers need to make a bigger effort to become visible in the eyes of their readers and need to think about better distribution strategies.

Research limitations/implications

– With comparisons, accuracy is dependent on information provided by organizations (on their Web sites).

Originality/value

– This paper offers information about a new publishing trend – only a few months in South Africa. It offers a look into the state of the trade book industry in South Africa, how e-singles may function in it and what publishers of e-singles may do to ensure more success. It predicts the future of e-singles in South Africa based on its unique situation, pointing out what obstacles there may be to their uptake.
Exploring switch intention of users’ reading behaviour
Authors: Chiang Hsiu-Sen , Chen Chia-Chen
Published: August 2014

Purpose

– This study aims to explore switch intention of users’ reading behaviour. Amazon’s 2007 introduction of the Kindle e-book reader launched a new way of reading. The popularity of e-book readers has exploded over past several years. However, the Chinese e-book reader market is still relatively underdeveloped and underexploited when compared with North America or other regions. At the time, it remained unclear whether consumers could be persuaded to abandon conventional printed books for the new device in the Chinese market.

Design/methodology/approach

– This research has gathered 352 valid questionnaire samples on an Internet survey from the general population. Path analysis was used to investigate the causal relationships which were hypothesized by the structural equation modelling methodology to identify key factors in intention to switch to the e-book reader.

Findings

– The results indicate that convenience and social influence were found to have a significant effect on consumer switching intention, while switching cost was found to be a significant obstacle to switching. This research also found that convenience of carry and operation of new technological products will lower switching costs. Furthermore, it will lead consumers to have higher switching intention when surrounding friends and families have good experiences and impressions of using new products. Thus, the manufacturers and sellers of e-readers have to consider the easy-to-handle convenient-to-carry while designing products. And the concept of higher social influence and lower switching cost shall lead the marketing strategies.

Originality/value

– Recently, some studies address what factors drive users’ willingness to use this new device for reading based on innovation diffusion theory or the technology acceptance model. Few studies have investigated adoption of e-readers for consumers’ perceived innovative and their perception of the costs. Hence, this paper studies the switching intention of readers through dimensions including new product attributes (compatibility, complexity, convenience and e-book content), social influence, price and switching costs and verifies the relationships among these dimensions on Chinese market.
The futures of the Singapore association of social workers: an analysis using CLA and the “Futures Triangle”
Authors: Fan Gilbert , Nee Wey Khng Joan
Published: August 2014

Purpose

– This paper aims to study the future of the Singapore association of social workers using causal layered analysis (CLA) and the Futures Triangle. In today’s rapidly changing world, professional associations have to re-evaluate their roles to remain relevant. This paper presents an analysis of findings from a study on the level of alliance of social workers with their professional association. By critically examining underlying issues beneath common beliefs held by social workers that impede, promote or sustain change with their professional association, we can gain a deeper understanding into their level of alliance with their association. Insights toward current issues faced by the association as well as its alternative and preferred futures could be illuminated.

Design/methodology/approach

– Inayatullah’s “Futures Triangle” was used to deepen the findings of the study on the level of alliance of social workers with their professional association from the lens of CLA (Inayatullah, 2004). The study employed interviews with 27 social workers in Singapore, selected through purposive sampling.

Findings

– Alternative scenarios and preferred futures of the Singapore Association of Social Workers (SASW) that were postulated from the interviews reinforce a need for more targeted recruitment campaigns. It also calls for regionalization and globalization of SASW to maximize its potentials.

Originality/value

– The paper suggests how a social work association might be able to reposition its role in relation to its stakeholders to promote and sustain itself. SASW could do so through positioning itself as the “National Geographic” beacon for social workers in Singapore to reach out to the world.