bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanostructure manipulation and its influence on functionalities in self-assembled oxide thin films
Authors: Li Weiwei , Wang Liuyong , Zhao Run , Tang Rujun , Liang Yan , Yang Hao
Published: November 2014

Self-assembled oxide thin films have tremendous potential applications in next generation of multifunctional systems. However, the manipulation of nanostructures and understanding on the relationship between nanostructures and functionalities remain as substantial challenges. Recently, an interesting architecture transformation between two basic nanocomposite structures has been demonstrated, i.e., from a horizontal layered structure to a vertical columnar structure, simply by tuning the film compositions in the (YBa2Cu3O7-δ)1-x:(BaZrO3)x system. In this work, the architecture dependence of functionalities has been investigated. The nanostructure manipulation has been revealed to largely affect the lattice structures and superconductive properties, especially at the critical composition of nanostructure transformation. The present work represents a novel approach to tune the self-assembled nanostructures and to further understand that how the nanostructures contribute to the functionalities in oxide thin films.
Entropy and enthalpy of interaction between amino acid side chains in nanopores
Authors: Vaitheeswaran S. , Thirumalai D.
Published: November 2014

Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.
Measurement of probability distributions for internal stresses in dislocated crystals
Authors: Wilkinson Angus J. , Tarleton Edmund , Vilalta-Clemente Arantxa , Jiang Jun , Britton T. Benjamin , Collins David M.
Published: November 2014

Here, we analyse residual stress distributions obtained from various crystal systems using high resolution electron backscatter diffraction (EBSD) measurements. Histograms showing stress probability distributions exhibit tails extending to very high stress levels. We demonstrate that these extreme stress values are consistent with the functional form that should be expected for dislocated crystals. Analysis initially developed by Groma and co-workers for X-ray line profile analysis and based on the so-called “restricted second moment of the probability distribution” can be used to estimate the total dislocation density. The generality of the results are illustrated by application to three quite different systems, namely, face centred cubic Cu deformed in uniaxial tension, a body centred cubic steel deformed to larger strain by cold rolling, and hexagonal InAlN layers grown on misfitting sapphire and silicon carbide substrates.
Simulation of nanoparticle based enhancement of cellular electroporation for biomedical applications
Authors: Qiu Hao , Joshi Ravindra P. , Pradhan Aswini
Published: November 2014

Introduction of nanoparticles can modify electrical properties such as the permittivity and conductivity of a medium. This model based study focuses on such modulated changes of an extracellular medium from the standpoint of enhancing electroporation to achieve more efficient delivery into biological cells. A finite element, time-dependent axisymmetric bio-model, coupled with the Smoluchowski equation, has been used to evaluate the transmembrane potentials and evolution of pore densities. Our simulation results show that a relatively small fraction of gold nanoparticles in the extracellular medium effectively enhances the transmembrane potentials, leads to much higher pore densities, and shifts the pore distribution towards larger radii. This collectively bodes well for enhancing drug delivery or gene transfection in cells.
Statistical modelling of discharge behavior of atmospheric pressure dielectric barrier discharge
Authors: Tay W. H. , Kausik S. S. , Wong C. S. , Yap S. L. , Muniandy S. V.
Published: November 2014

In this work, stochastic behavior of atmospheric pressure dielectric barrier discharge (DBD) has been investigated. The experiment is performed in a DBD reactor consisting of a pair of stainless steel parallel plate electrodes powered by a 50 Hz ac high voltage source. Current pulse amplitude distributions for different space gaps and the time separation between consecutive current pulses are studied. A probability distribution function is proposed to predict the experimental distribution function for the current pulse amplitudes and the occurrence of the transition regime of the pulse distribution. Breakdown voltage at different positions on the dielectric surface is suggested to be stochastic in nature. The simulated results based on the proposed distribution function agreed well with the experimental results and able to predict the regime of transition voltage. This model would be useful for the understanding of stochastic behaviors of DBD and the design of DBD device for effective operation and applications.
Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows
Authors: Dobson Matthew
Published: November 2014

This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box deforms with the flow, and it is possible for image particles to become arbitrarily close, causing a breakdown in the simulation. The KR boundary conditions avoid this problem for planar elongational flow and general planar mixed flow [T. A. Hunt, S. Bernardi, and B. D. Todd, J. Chem. Phys. 133, 154116 (2010)] through careful choice of the initial simulation box and by periodically remapping the simulation box in a way that conserves image locations. In this work, the ideas are extended to a large class of three-dimensional flows by using multiple remappings for the simulation box. The simulation box geometry is no longer time-periodic (which was shown to be impossible for uniaxial and biaxial stretching flows in the original work by Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)]. The presented algorithm applies to all flows with nondefective flow matrices, and in particular, to uniaxial and biaxial flows.
Doped silicon nanocrystals from organic dopant precursor by a SiCl4-based high frequency nonthermal plasma
Authors: Zhou Shu , Ding Yi , Pi Xiaodong , Nozaki Tomohiro
Published: November 2014

Doped silicon nanocrystals (Si NCs) are of great interest in demanding low-cost nanodevices because of the abundance and nontoxicity of Si. Here, we demonstrate a cost-effective gas phase approach to synthesize phosphorous (P)-doped Si NCs in which the precursors used, i.e., SiCl4, trimethyl phosphite (TMP), are both safe and economical. It is found that the TMP-enabled P-doping does not change the crystalline structure of Si NCs. The surface of P-doped Si NCs is terminated by both Cl and H. The Si–H bond density at the surface of P-doped Si NCs is found to be much higher than that of undoped Si NCs. The X-ray photoelectron spectroscopy and electron spin resonance results indicate that P atoms are doped into the substitutional sites of the Si-NC core and electrically active in Si NCs. Unintentional impurities, such as carbon contained in TMP, are not introduced into Si NCs.
Spectral gain profile of a multi-stack terahertz quantum cascade laser
Authors: Bachmann D. , Rösch M. , Deutsch C. , Krall M. , Scalari G. , Beck M. , Faist J. , Unterrainer K. , Darmo J.
Published: November 2014

The spectral gain of a multi-stack terahertz quantum cascade laser, composed of three active regions with emission frequencies centered at 2.3, 2.7, and 3.0 THz, is studied as a function of driving current and temperature using terahertz time-domain spectroscopy. The optical gain associated with the particular quantum cascade stacks clamps at different driving currents and saturates to different values. We attribute these observations to varying pumping efficiencies of the respective upper laser states and to frequency dependent optical losses. The multi-stack active region exhibits a spectral gain full width at half-maximum of 1.1 THz. Bandwidth and spectral position of the measured gain match with the broadband laser emission. As the laser action ceases with increasing operating temperature, the gain at the dominant lasing frequency of 2.65 THz degrades sharply.
Improving triplet-triplet-annihilation based upconversion systems by tuning their topological structure
Authors: Zimmermann Jochen , Mulet Roberto , Scholes Gregory D. , Wellens Thomas , Buchleitner Andreas
Published: November 2014

Materials capable to perform upconversion of light transform the photon spectrum and can be used to increase the efficiency of solar cells by upconverting sub-bandgap photons, increasing the density of photons able to generate an electron-hole pair in the cell. Incoherent solar radiation suffices to activate upconverters based on sensitized triplet-triplet annihilation, which makes them particularly suited for this task. This process requires two molecular species, sensitizers absorbing low energy photons, and emitters generating higher frequency photons. Successful implementations exist in solutions and solids. However, solid upconverters exhibit lower efficiency than those in solution, which poses a serious problem for real applications. In the present work, we suggest a new strategy to increase the efficiency of sensitized upconverters that exploits the solid nature of the material. We show that an upconversion model system with molecules distributed as clusters outperforms a system with a random distribution of molecules, as used in current upconverters. Our simulations reveal a high potential for improvement of upconverter systems by exploring different structural configurations of the molecules. The implementation of advanced structures can push the performance of solid upconverters further towards the theoretical limit and a step closer to technological application of low power upconversion.
Ionization sensitization of doping in co-deposited organic semiconductor films
Authors: Shinmura Yusuke , Yamashina Yohei , Kaji Toshihiko , Hiramoto Masahiro
Published: November 2014

Sensitization of the dopant ionization in co-deposited films of organic semiconductors was found. The ionization rate of cesium carbonate (Cs2CO3), which acts as a donor dopant in single films of metal-free phthalocyanine (H2Pc) and fullerene (C60), was increased from 10% to 97% in a H2Pc:C60 co-deposited film. A charge separation superlattice model that includes electron transfer from the conduction band of H2Pc to that of C60, which increases the rate of dopant ionization, is proposed.
Analysis of electric-powered taxis: A cross national study
Authors: Park Eunil , Kim Heetae , Han Eunji , Kwon Sang Jib , Yoo Kyeongsik , Ohm Jay Y.
Published: November 2014

With rapidly increasing interest in several significant environmental and transportation issues, namely, greenhouse gas emissions, there have been several attempts to transition the current transportation systems and vehicles to more environment-friendly vehicles. Following this trend, this study aimed to investigate drivers' motivations for adopting electric-powered taxis in two representative nations, South Korea and the U.S. This study conducted a main survey and collected data from professional taxi-drivers in the U.S. and South Korea to explore the differences between the two nations. In addition, an integrated adoption model for electric-powered taxis was proposed and a structural equation modelling method was employed to test the model. The results indicated that usefulness, services and system quality, and trust were positive factors that could predict driver acceptance of electric-powered taxis, while perceived risks and cost showed negative effects on acceptance. In addition, the driver acceptance patterns of two nations are significantly different. The results also illustrated that there are different sets of circumstances with various implications for practice and academia. Based on the findings of the current study, we examine its implications and limitations, as well as the potential for future studies.
Moisture assisted perovskite film growth for high performance solar cells
Authors: You Jingbi , Yang Yang (Michael) , Hong Ziruo , Song Tze-Bin , Meng Lei , Liu Yongsheng , Jiang Chengyang , Zhou Huanping , Chang Wei-Hsuan , Li Gang , Yang Yang
Published: November 2014

Moisture is assumed to be detrimental to organometal trihalide perovskite, as excess water can damage the crystallinity of the perovskite structure. Here, we report a growth mode for via thermal annealing of the perovskite precursor film in a humid environment (e.g., ambient air) to greatly improve the film quality, grain size, carrier mobility, and lifetime. Our method produces devices with maximum power conversion efficiency of 17.1% and a fill factor of 80%, revealing a promising route to achieve high quality perovskite polycrystalline films with superior optoelectronic properties that can pave the way towards efficient photovoltaic conversion.
Temperature-sensitive junction transformations for mid-wavelength HgCdTe photovoltaic infrared detector arrays by laser beam induced current microscope
Authors: Qiu Weicheng , Hu Weida , Lin Tie , Cheng Xiang'ai , Wang Rui , Yin Fei , Zhang Bo , Chen Xiaoshuang , Lu Wei
Published: November 2014

In this paper, we report on the disappearance of the photosensitive area extension effect and the unusual temperature dependence of junction transformation for mid-wavelength, n-on-p HgCdTe photovoltaic infrared detector arrays. The n-type region is formed by B+ ion implantation on Hg-vacancy-doped p-type HgCdTe. Junction transformations under different temperatures are visually captured by a laser beam induced current microscope. A physical model of temperature dependence on junction transformation is proposed and demonstrated by using numerical simulations. It is shown that Hg-interstitial diffusion and temperature activated defects jointly lead to the p-n junction transformation dependence on temperature, and the weaker mixed conduction compared with long-wavelength HgCdTe photodiode contributes to the disappearance of the photosensitive area extension effect in mid-wavelength HgCdTe infrared detector arrays.
Electro-optical and dielectric properties of CdSe quantum dots and 6CHBT liquid crystals composites
Authors: Singh U. B. , Dhar R , Pandey A. S. , Kumar S. , Dabrowski R. , Pandey M. B.
Published: November 2014

We have prepared the composites of a room temperature nematic liquid crystal namely 4-(trans-4-n-hexylcyclohexyl) isothiocyanatobenzoate (6CHBT) and Cadmium Selenide Quantum Dots (CdSe-QDs) and investigated their electro-optical and dielectric properties. Effect of dispersion of CdSe-QDs on various electro-optical and display parameters of host liquid crystalline material have been studied. Physical parameters, such as switching threshold voltage and splay elastic constant have been altered drastically for composites. Dispersion of QDs in a liquid crystals medium destabilizes nematic ordering of the host and decreases the nematic-to-isotropic transition temperature.
Graphene as transparent and current spreading electrode in silicon solar cell
Authors: Behura Sanjay K. , Mahala Pramila , Nayak Sasmita , Jani Omkar
Published: November 2014

Fabricated bi-layer graphene (BLG) has been studied as transparent and current spreading electrode (TCSE) for silicon solar cell, using TCAD-Silvaco 2D simulation. We have carried out comparative study using both Ag grids and BLG as current spreading electrode (CSE) and TCSE, respectively. Our study reveals that BLG based solar cell shows better efficiency of 24.85% than Ag-based cell (21.44%), in all of the critical aspects, including generation rate, recombination rate, electric field, potential and quantum efficiency. Further BLG based cell exhibits pronounce rectifying behavior, low saturation current, and good turn-on voltage while studying in dark.
Rovibrational State-Selectivity in Photoassociation through Multi-photon Transitions
Authors: Wang Rong , Qiu Ming-hui , Xiu Jun-ling
Published: November 2014

The rovibrational state-selectivity in photoassociation (PA) is investigated for the ground electronic state of OH radical. The calculated results show that population can be transferred from continuum state to the target states through three-, four-, and nine-photon transitions by choosing suitable pulse parameters and initial collision energy. To control population transfer to a lower rovibrational state, a shorter pulse frequency has to be chosen and the photon number transferred to target state should be increased. In PA process, some associated OH radicals can be dissociated via intermediate and background states, which decreases the final population of the target state.
Effect of Impurity on Critical Conditions of Colloidal Cluster Nucleation in Colloidal System
Authors: Deng Yuan-xiang , Xiao Chang-ming
Published: November 2014

Due to depletion interactions, a few of colloidal spheres will be packed into cluster or clusters, even a phase transition may take place if the volume fraction of system is large enough. In a binary colloidal system, if the mole fraction of one component is very small, then it can be taken as the impurity of the other component. In this work, the effect of impurity on critical conditions of colloidal cluster nucleation was studied by Carnahan-Starling state equation and the principle of entropy maximum. The results show that, even the mole fraction of small-spheres is very small, the critical volume fraction is obvious smaller than that of one component system, so the influence on critical volume fraction from impurity is very huge and cannot be ignored. In addition, it is also found that, the larger the volume fraction of the system is, the larger cluster density can be packed, however, the critical size of nucleating cluster is almost independent of the density of the cluster.
Conversion of Bio-syngas to Liquid Hydrocarbon over CuCoMn-Zeolite Bifunctional Catalysts
Authors: Zhang Zhao-xia , Bi Pei-yan , Jiang Pei-wen , Li Quan-xin
Published: November 2014

A series of bifunctional catalysts composed of a component for higher alcohol synthesis (CuCoMn oxides, CCM) and an acidic zeolite (SAPO-34, ZSM-5, Y, MCM-41) were prepared for production of liquid hydrocarbon directly from a bio-syngas through a one-stage process. The effects of zeolite type, zeolite content, Si/Al ratio and preparation method on catalyst texture and its reaction performance were investigated. Higher selectivities and yields of liquid products were obtained by using bifunctional catalysts. The yields of liquid hydrocarbons decreased in the order CCM-ZSM-5>CCM-SAPO-34>CCM-Y>CCM-MCM-41. CCM-ZSM-5 (20wt%, Si/Al=100) prepared by coprecipitation method displayed the optimal catalytic performance with the highest CO conversion (76%) and yield of liquid products (30%). The catalysts were characterized by N2 adsorption/desorption, NH3-TPD, XRD, and H2-TPR analysis. The results showed that higher specific surface areas and pore volumes of bifunctional catalysts were achieved by adding zeolites into CuCoMn precursors. Medium pore dimension and moderate acidity in CCM-ZSM-5 were observed, which probably resulted in its excellent reaction performance. Additionally, a higher number of weaker acid sites (weak and/or medium acid sites) were formed by increasing ZSM-5 content in CCM-ZSM-5 or decreasing Si/Al ratio in ZSM-5. It was also seen that metal dispersion was higher and reducibility of metal ions was easier on the CCM-ZSM-5 catalyst prepared by coprecipitation. The higher alcohols-to-hydrocarbon process provides a promising route to hydrocarbon fuels via higher alcohols from syngas or biobased feedstocks.
Electrocatalytic Oxidation of Saccharides at MoOx/AuNPs Modified Electrode Towards Analytical Application
Authors: Wu Shou-guo , Zhang Zhi-xin , Zhao Qi-ping , Zhou Lei , Yao Yao
Published: November 2014

The MoOx/AuNPs composite film modified glassy carbon electrode was fabricated by electro-depositing simultaneously gold nanoparticles and molybdenum oxides using cyclic voltammetry. The morphology and topography of the MoOx/AuNPs composite were characterized by scan electron microscopy and X-ray photoelectron spectroscopy respectively, and the electrocatalytic oxidation of glucose at the MoOx/AuNPs composite film was investigated and analyzed in detail. It was shown that the MoOx/AuNPs composite was of strong electrocatalytic activity towards oxidation of glucose as well as other saccharides, so that an attempt was made for direct voltammetric determination of glucose. Then the positive scan polarization reverse catalytic voltammetry was proposed for the first time. Based on this method, the pure oxidation current was extracted by subtraction of the blank current in the reverse scan. The current sensitivity was enhanced tremendously and the signal to noise ratio was improved adequately. The electrocatalytic oxidation of glucose at the MoOx/AuNPs modified electrode was performed in alkaline medium, a wide linear range from 0.01 mmol/L to 4.0 mmol/L of glucose, a higher current sensitivity of 2.35 mA/(mmol/L·cm2), and a lower limit of detection of 9.01 µmol/L (at signal/noise=3) were achieved. In addition, the electrocatalytic oxidation of other saccharides such as lactose, fructose and sucrose was also evaluated.
Quantitative analysis of bariatric procedure trends 2001–13 in South Australia: implications for equity in access and public healthcare expenditure
Authors: Meyer Samantha B. , Booth Sue , Gray John , Hakendorf Paul , McNaughton Darlene , Mwanri Lillian , Thompson Campbell , Ward Paul R.
Published: November 2014

Objectives
The aims of the present study were to: (1) identify trends in bariatric surgery in South Australia (SA) from 2001 to 2013; and (2) compare public and private hospitals, and so discuss the implications of these trends as they relate to equity in access to bariatric procedures and public system healthcare expenditure.

Methods
An analysis of retrospective data of all bariatric procedures in public and private hospitals in SA was conducted using all SA public and private hospital administrative records between 2001 and 2013.

Results
Of all procedures conducted in SA, 22.6% were revisions or reversals. The number of revisions or reversals conducted in SA has increased at a rate higher than weight loss procedures (6.4- vs 3.8-fold increase). An increasing proportion of public surgeries are revisions or reversals of weight loss procedures that occurred outside of the SA public system (interstate or in the private system).

Conclusion
Further investigation is necessary to identify the pathways patients navigate to access bariatric surgery, the utilisation of public services following private procedures and why rates of revisions or reversals of bariatric procedures are increasing in SA.

What is known about the topic?
Rates of bariatric surgery are increasing internationally as a treatment for obesity.

What does this paper add?
Trends in bariatric procedures in SA have not been published. We have identified that: (1) rates of bariatric revisions or reversals in SA far surpass the rate at which bariatric weight loss procedures are increasing; (2) rates of revisions or reversals are increasing in public hospitals; and (3) an increasing number of the revision or reversal procedures in public hospitals are for weight loss procedures that have occurred outside the public system.

What are the implications for practitioners?
The data have implications for practitioners caring for patients interested in undergoing bariatric surgery for the treatment of obesity. The data suggest that rates of revisions or reversals are increasing in public hospitals, which suggests that further information is needed regarding the effectiveness of weight loss procedures and the implications of revision or reversal increases on waiting times for patients seeking weight loss treatment in a system with limited resources.
Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae)
Authors: Lopardo Lara , Uhl Gabriele
Published: November 2014

The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed Yule-coalescent Model) for species delimitation. We propose that the cox1 marker can potentially overestimate analyses of biodiversity and thus might not be the preferred marker for DNA species identification and delimitation methods in Oedothorax. Instead, our results suggest that the 16S marker appears to be a promising candidate for such endeavour. Evaluating the contribution and suitability of markers to the re-identification of species, measured by their recovery of well established morphological species, is critical for future studies and for reliable results in species identification in spiders.
N-Acetylcysteine improves oocyte and embryo quality in polycystic ovary syndrome patients undergoing intracytoplasmic sperm injection: an alternative to metformin
Authors: Cheraghi Ebrahim , Mehranjani Malek Soleimani , Shariatzadeh Mohammad Ali , Esfahani Mohammad Hossein Nasr , Ebrahimi Zahra
Published: November 2014

Polycystic ovary syndrome (PCOS) is associated with low-quality oocytes. The aim of the present study was to investigate the effects of metformin (MET), N-acetylcysteine (NAC) and their combination on follicular fluid parameters, oocytes and embryo quality in PCOS patients. A prospective randomised placebo-controlled pilot study on 60 Iranian women with PCOS (aged 25–35 years) undergoing intracytoplasmic sperm injection (ICSI) was designed. Women were divided into four groups (n = 15 in each): (1) an MET, administered 1500 mg day–1 MET; (2) an NAC group, administered 1800 mg day–1 NAC; (3) an NAC + MET group; and (4) a placebo group. Drugs were administered from the 3rd day of previous cycle until the day of oocyte aspiration (6 weeks treatment in total). Data were analysed by one-way ANOVA, with significance set at P < 0.05. The number of immature and abnormal oocytes decreased significantly in the NAC compared with placebo group, with a concomitant increase in the number of good-quality embryos in the NAC group (P < 0.05). Malondialdehyde levels decreased significantly in the NAC and NAC + MET groups compared with the placebo-treated group (P < 0.02). In addition, there were significant decreases in leptin levels in the NAC, MET and NAC + MET groups compared with the placebo group (P < 0.001). Insulin and LH levels were significantly lower in the MET and NAC groups compared with the placebo-treated group (P < 0.02). We concluded that NAC improves oocyte and embryo quality and could be administered as an alternative to MET.
The influence of a variable fire regime on woodland structure and composition
Authors: Burgess Emma E. , Moss Patrick , Haseler Murray , Maron Martine
Published: November 2014

The post-fire response of vegetation reflects not only a single fire event but is the result of cumulative effects of previous fires in the landscape. For effective ecological fire management there is a need to better understand the relationship between different fire regimes and vegetation structure. The study investigated how different fire regimes affect stand structure and composition in subtropical eucalypt woodlands of central Queensland. We found that fire history category (i.e. specific combinations of time since fire, fire frequency and season of last burn) strongly influenced richness and abundance of species categorised as mid-storey trees and those individuals currently in the mid-level strata. Time since fire and fire frequency appeared to have the strongest influence. A longer time since fire (>4 years since last burn), combined with infrequent fires (<2 fires in 12 year period) appeared to promote a dense mid-storey with the opposite conditions (<4 years since last burn; >2 fires in 12 year period) promoting more-open woodlands. Consideration of these combined fire regime attributes will allow fire managers to plan for a particular range of fire-mediated patches to maintain the desired diversity of vegetation structures.
Transcriptional program of Kpna2/Importin-α2 regulates cellular differentiation-coupled circadian clock development in mammalian cells
Authors: Umemura Yasuhiro , Koike Nobuya , Matsumoto Tsuguhiro , Yoo Seung-Hee , Chen Zheng , Yasuhara Noriko , Takahashi Joseph S. , Yagita Kazuhiro
Published: November 2014

Significance

The emergence of the cell-autonomous circadian oscillator is coupled with cellular differentiation. Cellular differentiation, as well as reprogramming, results in global alterations of the transcriptional program via epigenetic modification such as DNA methylation. We here demonstrate that
c-Myc
constitutive expression and
Dnmt1
ablation disrupt the differentiation-coupled emergence of the clock from mouse ES cells (ESCs). Using these model ESCs, 484 genes were identified by global gene expression analysis as factors correlated with circadian clock development. Among them, we find that misregulation of
Kpna2
(
Importin-α2
) during the differentiation culture of ESCs significantly impairs clock development, and KPNA2 facilitates cytoplasmic localization of PER1/2. These results suggest that the programmed gene expression network regulates the differentiation-coupled circadian clock development in mammalian cells.
Requesting help with null or limited knowledge
Authors: Fele Giolo
Published: November 2014

The chapter deals with the issue of knowledge displays in conversation and the rights and obligations in social interaction connected to the fact of knowing something. My contribution has three main goals: first, it is a contribution to the study of the social distribution of knowledge in social interaction, in particular of “not knowing” where a display of knowledge is requested; second, it contributes to the study of the relations between request design and the display of commensurate knowledge that make the speaker fully entitled to make a request; finally, it is a contribution to the study of emergency calls, in particular with a focus on the relations between the terms of knowledge, the grounding of the request, and the provision of the service requested.
The journey to advice
Authors: Fatigante Marilena , Bafaro Saverio
Published: November 2014

The paper deals with the formulation of advice delivered by the doctor in routine gynecological consultations with pregnant patients. We analyze episodes in which the patients solicit advice for a number of concerns related to their health and overall life habits during their pregnancy. We show how the doctor’s formulation of the advice is sequentially elaborated through rounds and how it changes from its initial delivery to the final formulation. In these rounds, we show that the doctor’s advice may progressively lose certainty and coherence, encountering changes from its initial delivery to the final formulation. This is sequentially dealt as a strategic resource to adjust to the patient’s expression of resistance and to solicit her to choose the preferred course of action.
Embodying epistemicity
Authors: Klein Gabriella B. , Dossou Koffi M. , Pasquandrea Sergio
Published: November 2014

The present paper analyses a corpus of bureaucratic-institutional interactions between migrants and civil servants, in order to investigate the role of objects in negotiating the certainty of information. During the encounters, documents are employed as means to provide and assess information; furthermore, the encounters produce a final artifact (e.g., a filled form), which constitutes the basis for providing a public service. Such objects are both related to, and constitutive of, the activities performed: they are “called into existence” by the interactants, within the temporal development and spatial arrangement of the interaction. Building on data collected within two European Grundtvig projects, the paper takes into account the semiotic resources deployed by the interactants for dealing with the objects, the patterns of actions in which objects are involved their relevance for negotiating the certainty of information.
On the third homology of 𝑆𝐿₂ and weak homotopy invariance
Authors: Hutchinson Kevin , Wendt Matthias
Published: November 2014

The goal of the paper is to achieve - in the special case of the linear group

S

L
2

SL_2

- some understanding of the relation between group homology and its

A

1

\mathbb {A}^1

-invariant replacement. We discuss some of the general properties of the

A

1

\mathbb {A}^1

-invariant group homology, such as stabilization sequences and Grothendieck-Witt module structures. Together with very precise knowledge about refined Bloch groups, these methods allow us to deduce that in general there is a rather large difference between group homology and its

A

1

\mathbb {A}^1

-invariant version. In other words, weak homotopy invariance fails for

S

L
2

SL_2

over many families of non-algebraically closed fields.
GlycoRDF: an ontology to standardize glycomics data in RDF
Authors: Ranzinger Rene , Aoki-Kinoshita Kiyoko F. , Campbell Matthew P. , Kawano Shin , Lütteke Thomas , Okuda Shujiro , Shinmachi Daisuke , Shikanai Toshihide , Sawaki Hiromichi , Toukach Philip , Matsubara Masaaki , Yamada Issaku , Narimatsu Hisashi
Published: November 2014

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information.

Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases.

Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/).

Contact:  rene@ccrc.uga.edu or kkiyoko@soka.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Development of a robust classifier for quality control of reverse-phase protein arrays
Authors: Ju Zhenlin , Liu Wenbin , Roebuck Paul L. , Siwak Doris R. , Zhang Nianxiang , Lu Yiling , Davies Michael A. , Akbani Rehan , Weinstein John N. , Mills Gordon B. , Coombes Kevin R.
Published: November 2014

Motivation: High-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in approximately 1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing and amplified detection) may create substantial variability in data quality. We are not aware of any other quality control algorithm that is tuned to the special characteristics of RPPAs.

Results: We have developed a novel classifier for quality control of RPPA experiments using a generalized linear model and logistic function. The outcome of the classifier, ranging from 0 to 1, is defined as the probability that a slide is of good quality. After training, we tested the classifier using two independent validation datasets. We conclude that the classifier can distinguish RPPA slides of good quality from those of poor quality sufficiently well such that normalization schemes, protein expression patterns and advanced biological analyses will not be drastically impacted by erroneous measurements or systematic variations.

Availability and implementation: The classifier, implemented in the “SuperCurve” R package, can be freely downloaded at http://bioinformatics.mdanderson.org/main/OOMPA:Overview or http://r-forge.r-project.org/projects/supercurve/. The data used to develop and validate the classifier are available at http://bioinformatics.mdanderson.org/MOAR.

Contact:  Kevin.Coombes@osumc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analysis of Genotype, Environment, and Their Interaction Effects on the Phytochemicals and Antioxidant Capacities of Red Rice (Oryza sativa L.)
Authors: Shao Yafang , Xu Feifei , Chen Yaling , Huang Yan , Beta Trust , Bao Jinsong
Published: November 2014

Fourteen red rice varieties were planted in two locations during summer (Hangzhou) and winter (Hainan) to study the effect of genotype and environment on the phytochemicals and antioxidant capacities of rice grain. B‐type proanthocyanidins in red rice were detected by LC‐MS/MS and quantified by using the vanillin assay. Analysis of variance showed that total phenolic content (TPC), total flavonoid content (TFC) and 2,2′‐azino‐bis‐(3‐ethylbenzothiazoline‐6‐sulfonic acid) (ABTS) radical scavenging capacity were mainly affected by environmental factors, which accounted for more than 60% of the total variance. However, total proanthocyanidin content (TPAC) and 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical scavenging capacity were equally affected by both genotype and environment. The genotype × environment effects were significant for all traits. The pairwise correlations among TPC, TFC, TPAC, ABTS, and DPPH were also significant (r > 0.900, P < 0.001). Principal component analysis identified the genotypes that had higher contents of antioxidants and more stability across environments. This study showed that indirect selection of a simple trait (i.e., TPC) is an effective way to select rice high in antioxidant capacity in breeding programs. This study also suggests that rice should be produced specifically in a certain environment for the end user to minimize the variation in the functional properties and maximize their contents.
Why are so many trees hollow?
Authors: Ruxton Graeme D.
Published: November 2014

In many living trees, much of the interior of the trunk can be rotten or even hollowed out. Previously, this has been suggested to be adaptive, with microbial or animal consumption of interior wood producing a rain of nutrients to the soil beneath the tree that allows recycling of those nutrients into new growth via the trees roots. Here I propose an alternative (non-exclusive) explanation: such loss of wood comes at very little cost to the tree and so investment in costly chemical defence of this wood is not economic. I discuss how this theory can be tested empirically.
Non-uniform breaking of molecular bonds, peripheral morphology and releasable adhesion by elastic anisotropy in bio-adhesive contacts
Authors: Liu Yan , Gao Yanfei
Published: November 2014

Biological adhesive contacts are usually of hierarchical structures, such as the clustering of hundreds of sub-micrometre spatulae on keratinous hairs of gecko feet, or the clustering of molecular bonds into focal contacts in cell adhesion. When separating these interfaces, releasable adhesion can be accomplished by asymmetric alignment of the lowest scale discrete bonds (such as the inclined spatula that leads to different peeling force when loading in different directions) or by elastic anisotropy. However, only two-dimensional contact has been analysed for the latter method (Chen & Gao 2007J. Mech. Phys. Solids55, 1001–1015 (doi:10.1016/j.jmps.2006.10.008)). Important questions such as the three-dimensional contact morphology, the maximum to minimum pull-off force ratio and the tunability of releasable adhesion cannot be answered. In this work, we developed a three-dimensional cohesive interface model with fictitious viscosity that is capable of simulating the de-adhesion instability and the peripheral morphology before and after the onset of instability. The two-dimensional prediction is found to significantly overestimate the maximum to minimum pull-off force ratio. Based on an interface fracture mechanics analysis, we conclude that (i) the maximum and minimum pull-off forces correspond to the largest and smallest contact stiffness, i.e. ‘stiff-adhere and compliant-release’, (ii) the fracture toughness is sensitive to the crack morphology and the initial contact shape can be designed to attain a significantly higher maximum-to-minimum pull-off force ratio than a circular contact, and (iii) since the adhesion is accomplished by clustering of discrete bonds or called bridged crack in terms of fracture mechanics terminology, the above conclusions can only be achieved when the bridging zone is significantly smaller than the contact size. This adhesion-fracture analogy study leads to mechanistic predictions that can be readily used to design biomimetics and releasable adhesives.
On the origin of sex chromosomes from meiotic drive
Authors: Úbeda Francisco , Patten Manus M. , Wild Geoff
Published: November 2014

Most animals and many plants make use of specialized chromosomes (sex chromosomes) to determine an individual's sex. Best known are the XY and ZW sex-determination systems. Despite having evolved numerous times, sex chromosomes present something of an evolutionary puzzle. At their origin, alleles that dictate development as one sex or the other (primitive sex chromosomes) face a selective penalty, as they will be found more often in the more abundant sex. How is it possible that primitive sex chromosomes overcome this disadvantage? Any theory for the origin of sex chromosomes must identify the benefit that outweighs this cost and enables a sex-determining mutation to establish in the population. Here we show that a new sex-determining allele succeeds when linked to a sex-specific meiotic driver. The new sex-determining allele benefits from confining the driving allele to the sex in which it gains the benefit of drive. Our model requires few special assumptions and is sufficiently general to apply to the evolution of sex chromosomes in outbreeding cosexual or dioecious species. We highlight predictions of the model that can discriminate between this and previous theories of sex-chromosome origins.
Secondary contact seeds phenotypic novelty in cichlid fishes
Authors: Nichols Paul , Genner Martin J. , van Oosterhout Cock , Smith Alan , Parsons Paul , Sungani Harold , Swanstrom Jennifer , Joyce Domino A.
Published: November 2014

Theory proposes that genomic admixture between formerly reproductively isolated populations can generate phenotypic novelty for selection to act upon. Secondary contact may therefore be a significant promoter of phenotypic novelty that allows species to overcome environmental challenges and adapt to novel environments, including during adaptive radiation. To date, this has largely been considered from the perspective of interspecific hybridization at contact zones. However, it is also possible that this process occurs more commonly between natural populations of a single species, and thus its importance in adaptive evolution may have been underestimated. In this study, we tested the consequences of genomic introgression during apparent secondary contact between phenotypically similar lineages of the riverine cichlid fishAstatotilapia calliptera. We provide population genetic evidence of a secondary contact zone in the wild, and then demonstrate using mate-choice experiments that both lineages can reproduce together successfully in laboratory conditions. Finally, we show that genomically admixed individuals display extreme phenotypes not observed in the parental lineages. Collectively, the evidence shows that secondary contact can drive the evolution of phenotypic novelty, suggesting that pulses of secondary contact may repeatedly seed genetic novelty, which when coupled with ecological opportunity could promote rapid adaptive evolution in natural circumstances.
Lutibacter oricola sp. nov., a marine bacterium isolated from seawater
Authors: Sung Hye-Ri , Shin Kee-Sun , Ghim Sa-Youl
Published: November 2014

A bacterial strain, UDC377T, was isolated from seawater samples collected at Seo-do on the coast of Dokdo island in the East Sea, and was subjected to taxonomic study using a polyphasic approach. Strain UDC377T was pale-yellow, Gram-staining-negative, non-motile, rod-shaped and aerobic. The strain grew optimally at 25–28 °C, in the presence of 2 % (w/v) NaCl and at pH 7.0–7.5. Strain UDC377T produced carotenoid pigments; however, it did not produce flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UDC377T clustered with members of the genus

Lutibacter

and appeared most closely related to

Lutibacter agarilyticus

KYW566T (96.0 % 16S rRNA gene sequence similarity) followed by

L. aestuarii

MA-My1T (95.0 %),

L. litoralis

CL-TF09T (94.9 %),

L. maritimus

S7-2T (94.1 %) and

L. flavus

IMCC1507T (94.0 %). The DNA G+C content of strain UDC377T was 30.8 mol%. Strain UDC377T contained MK-6 as the predominant menaquinone, iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 0 3-OH as the major fatty acids, and phosphatidylethanolamine, two unknown aminolipids and six unknown lipids as the major polar lipids. Based on phenotypic properties and phylogenetic data presented, strain UDC377T is considered to represent a novel species of the genus

Lutibacter

, for which the name Lutibacter oricola sp. nov. is proposed. The type strain is UDC377T ( = DSM 24956T = KCTC 23668T).