bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of multilayer planar hybrid plasmonic waveguide and bends
Authors: Sharma P. , Kumar V.D.
Published: March 2016

Hybrid metal insulator metal plasmonic waveguide has been investigated at 1550 nm wavelength using frequency‐domain electromagnetic solver of computer simulation technology microwave studio. This waveguide overcomes the limitations of conventional plasmonic metal insulator metal waveguide and provides good balance between propagation length and confinement. Propagation length up to 2.5 mm and confinement factor more than 80% have been observed. Waveguide bends such as 90° and S‐shaped, based on the presented waveguide have been examined; these bends exhibit more than 90% transmission efficiency in a confinement area of 40 × 200 nm2. The application of these structures in the design of chip scale integrated circuitry is motivated.
Wearable antenna with tripolarisation diversity for WBAN communications
Authors: Yan S. , Vandenbosch G.A.E.
Published: March 2016

A wearable antenna with tripolarisation diversity is designed for wireless body area networks (WBANs). The antenna is fabricated with flexible materials. Three polarisations are realised by combining an inductive loaded circular monopolar patch antenna with a microstrip annular ring antenna. Simulated and measured results show that the antenna has sufficient bandwidth for a WBAN. The port isolation reaches 13.5 dB, and the correlation coefficients show a good diversity performance.
Dielectric and work function engineered TFET for ambipolar suppression and RF performance enhancement
Authors: Raad B. , Nigam K. , Sharma D. , Kondekar P.
Published: March 2016

A novel approach to suppress the ambipolar behaviour and enhance RF parameters is proposed for the first time. For this, the dielectric and gate material work function engineering is used to suppress the ambipolar behaviour individually. Further, the combination of gate dielectric and gate material work function engineering is used to suppress the ambipolar conduction in huge amount and to eliminate the hot carriers effects. Apart from these, the proposed work improves the ON‐state current and RF figures of merit for symmetric devices.
Performance analysis of IEEE 802.22 wireless regional area network in the presence of digital video broadcasting – second generation terrestrial broadcasting services
Authors: Popescu Vlad , Fadda Mauro , Murroni Maurizio
Published: March 2016

In Cognitive Radio (CR) networks unlicensed secondary users aim at transmitting in licensed bands while preserving primaries from harmful interference. CR communications have been especially studied in the white spaces of TV band (TVWS), defined as the TV free channels left unused in each territorial area by the reallocation of TV services as a direct consequence of the switchover plans. The first full CR standard, the IEEE 802.22 Wireless Regional Area Network (WRAN), has been developed to bring wireless broadband access to remote, rural areas where other wireless networks are not present due to low revenue impact or critical network deployment. IEEE 802.22 WRAN devices are designed to operate in the range of frequencies between 54MHz and 862MHz alongside digital terrestrial television (DTT) operation. In this work we perform a complete analysis to evaluate the performance of IEEE 802.22 WRAN devices coexisting with DVB‐T2 adjacent channel transmission in the TV bands in a rural environment. The link budget analysis for IEEE 802.22 WRAN in different coexistence scenarios, such as fixed DTT reception with indoor/outdoor IEEE 802.22 WRAN reception shows that its robustness is comparable to long term evolution (LTE) which represents the state‐of‐the art of cellular networks in rural scenario.
Low speed control and implementation of permanent magnet synchronous motor for mechanical elastic energy storage device with simultaneous variations of inertia and torque
Authors: Yu Yang , Mi Zengqiang , Guo Xudong , Xu Yikun , Zhao Tong
Published: March 2016

The spiral torsion spring‐based mechanical elastic energy storage (MEES) device presented previously with inherent characteristic of simultaneous variations of inertia and torque is disadvantage to be actuated by conventional control method. This study proposes an improved non‐linear backstepping control scheme based on combination of recursive least squares (RLS) and differential evolution (DE) optimisation to regulate permanent magnet synchronous motor (PMSM) at a very low speed and control MEES device effectively. For this presented control scheme, first, a single RLS method with forgetting factor is presented to simultaneously estimate the time‐varying inertia and torque of MEES device. Second, on the basis of estimation results, an improved non‐linear backstepping control algorithm considering parameter variations in derivation process is proposed to drive PMSM to operate at a very low speed. Finally, a self‐adaptive parameter DE method is designed to optimise the several control parameters. The performance of the proposed methodology is verified through simulations and experiments.
Overview of fast on‐board integrated battery chargers for electric vehicles based on multiphase machines and power electronics
Authors: Subotic Ivan , Bodo Nandor , Levi E. , Dumnic Boris , Milicevic Dragan , Katic Vladimir
Published: March 2016

The study provides an extensive overview of on‐board integrated chargers for electric vehicles that are based on multiphase (more than three phases) machines and power electronics. A common attribute of all discussed topologies is that they do not require a charger as a separate device since its role is transferred to the already existing drivetrain elements, predominantly a multiphase machine and an inverter. The study demonstrates how additional degrees of freedom that exist in multiphase systems can be conveniently utilised to achieve torque‐free charging operation. Therefore, although three‐phase (or multiphase) currents flow through machines’ stator windings, they do not generate any torque; thus the machines do not have to be mechanically locked. Cost and weight saving is achieved in this way, while the available space is increased. For each topology operating principles are explained, and its control elaborated in detail for both charging and vehicle‐to‐grid mode. Finally, the validity of theoretical considerations and control algorithms of some of the existing charging solutions is experimentally verified and experimental performance of all discussed topologies is compared.
Detecting asymmetry in the presence of symmetry with maximum likelihood three‐dimensional reconstructions of viruses from electron microscope images
Authors: Wang Kang , Fu Chi‐yu , Catalano Carlos E. , Prevelige Peter E. , Doerschuk Peter C. , Johnson John E.
Published: March 2016

Various modes of transmission electron microscopy can provide unique structural information on nanometre‐scale biological machines such as viruses and ribosomes. A maximum‐likelihood statistical reconstruction algorithm using information from two such modalities, single‐particle cryo‐electron microscopy and computed electron tomography, is described for the problem where the machine is nearly symmetrical, but the localised regions of asymmetry are important for the functioning of the machine. The algorithm is demonstrated on experimental bacteriophage Lambda procapsid data. Key features of the algorithm are the use of probability density functions (pdfs) derived from normalised correlation rather than Gaussian pdfs and the solution of a constrained classification problem in which 11 out of 12 sites of asymmetry belong to one class while the 12th site belongs to a second class.
T‐type direct AC/AC converter structure
Authors: Khodabandeh Masih , Zolghadri Mohammad Reza , Shahbazi Mahmood , Noroozi Negar
Published: March 2016

In this study, a novel T‐type topology for single‐phase direct AC/AC conversion is proposed. In this topology, frequency changing takes place directly (without common DC voltage bus) through three converters that are connected in a T structure. Unity input power factor and precise output voltage and frequency regulation is achieved through appropriate control of these three converters. H‐bridge converters can be used in each branch of T to make the proposed converter. The converter is controlled such that the average active power of each H‐bridge remains zero. Therefore, capacitors are implemented in DC links of H‐bridges. Moreover, using half‐bridge converters, instead of H‐bridge ones, for T branch converters, leads to an AC/AC converter with only six semiconductor switches. Also, multilevel inverters, specially cascaded H‐bridge can be used in branches of T. This will lead to a multilevel AC/AC converter that is suitable for high‐power applications such as intertie connections and high‐power motor drives. Principle of operation and control schemes of the converter are then explained. Simulation and experimental results verify the performance of the converter while operating as a power supply at different frequencies.
Analysis of five‐phase voltage source inverter with dual frequency modulator
Authors: Chen Keng‐Yuan , Jiang Pei‐Syuan
Published: March 2016

This study presents an analysis of five‐phase voltage source inverter with dual frequency modulator to reduce baseband harmonics distortion. Analyses of five‐phase inverter load equation, error signal, system stability and states bounds are carried out. Further, the frequency domain analysis shows the noise shaping effect of the proposed dual frequency modulator. Three design examples with first, second and forth order dual frequency modulators are shown. Both simulations and experiments are illustrated, telling that the proposed modulator can reduce baseband harmonics distortion as discussed in the frequency domain analysis. Further, the states bounds obtained from simulations agree with the theoretical value, showing the correctness of the analysis. Both simulations and experiments correspond to each other, confirming the effectiveness of the proposed five‐phase inverter driven by dual frequency modulator.
Dynamics of photoexcited Ba+ cations in 4He nanodroplets
Authors: Leal Antonio , Zhang Xiaohang , Barranco Manuel , Cargnoni Fausto , Hernando Alberto , Mateo David , Mella Massimo , Drabbels Marcel , Pi Martí
Published: March 2016

We present a joint experimental and theoretical study on the desolvation of Ba+ cations in 4He nanodroplets excited via the 6p ← 6s transition. The experiments reveal an efficient desolvation process yielding mainly bare Ba+ cations and Ba+Hen exciplexes with n = 1 and 2. The speed distributions of the ions are well described by Maxwell-Boltzmann distributions with temperatures ranging from 60 to 178 K depending on the excitation frequency and Ba+ Hen exciplex size. These results have been analyzed by calculations based on a time-dependent density functional description for the helium droplet combined with classical dynamics for the Ba+. In agreement with experiment, the calculations reveal the dynamical formation of exciplexes following excitation of the Ba+ cation. In contrast to experimental observation, the calculations do not reveal desolvation of excited Ba+ cations or exciplexes, even when relaxation pathways to lower lying states are included.
Influence of interparticle electronic coupling on the temperature and size dependent optical properties of lead sulfide quantum dot thin films
Authors: Roland Paul J. , Bhandari Khagendra P. , Ellingson Randy J.
Published: March 2016

We report on the quantum dot (QD) size, temperature, and inter-dot coupling dependence on the optical absorption and emission for PbS QD thin films. Inter-dot coupling is induced by ligand exchange from oleic acid to 1,2-ethanedithiol, and the expected band gap red-shift observed for coupled QD thin films is accompanied by a modification to the temperature-dependence of the band gap energy. The amplitude and temperature dependence of the photoluminescence (PL) Stokes shift support recombination via a mid-gap state and also indicate that the application of band gap-specific models to fit the temperature dependence PL peak energy is inadequate. Electronically coupled QD thin films show PL quenching with decreasing temperature, following a Boltzmann model which is consistent with thermally activated carrier transport. Enhancing the inter-dot coupling results in the dynamic PL decay signal changing from single- to bi-exponential behavior, reveals a size-dependent transport activation energy, and yields a negative temperature dependent band gap energy for the smallest QD diameters.
Monopole antenna in quantitative near-field microwave microscopy of planar structures
Authors: Reznik Alexander N. , Korolyov Sergey A.
Published: March 2016

We have developed an analytical model of a near-field microwave microscope based on a coaxial resonator with a sharpened tip probe. The probe interacts with a layered sample that features an arbitrary depth distribution of permittivity. The microscopic tip end with the accumulated charge is regarded as a monopole antenna radiating an electric field in near zone. The impedance of such an antenna is determined within a quasi-static approximation. The proposed model is used for calculating the sample-sensitive parameters of the microscope, specifically, resonance frequency f0 and quality factor Q0, as a function of probe-sample distance h. The theory has been verified experimentally in studies of semiconductor structures, both bulk and thin films. For measurements, we built a ∼2.1 GHz microscope with an effective tip radius of about 100 μm. The theoretical and experimental dependences f0(h) and Q0(h) were found to be in a good agreement. The developed theory underlies the method for determining sheet resistance Rsh of a semiconductor film on a dielectric substrate proposed in this article. Studies were performed on doped n-GaN films on an Al2O3 substrate. The effective radius and height of the probe determined from calibration measurements of etalon samples were used as the model fitting parameters. For etalon samples, we employed homogeneous sapphire and doped silicon plates. We also performed four-probe dc measurements of Rsh. The corresponding values for samples with Rsh > 1 kΩ were found to be 50% to 100% higher than the microwave results, which are attributed to the presence of microdefects in semiconductor films.
Anisotropic transport in the quasi-one-dimensional semiconductor Li0.33MoO3
Authors: Moshfeghyeganeh S. , Cote A. N. , Neumeier J. J. , Cohn J. L.
Published: March 2016

Transport measurements (electrical resistivity, Seebeck coefficient, and thermal conductivity) in the temperature range 80–500 K are presented for single crystals of the quasi-one-dimensional (Q1D) semiconductor Li0.33MoO3. Opposite signs are observed for the Seebeck coefficient along the trinclinic a and c axes, with Sc − Sa ≃ 250 μV/K near room temperature and ≃100 μV/K at 380 K. The thermal conductivity at room temperature in the a-c planes was ∼2 W/m K and ∼10 times smaller along b*. A weak structural anomaly at Ts ≈ 355 K, identified in the temperature-dependent lattice constants, coincides with anomalies in the electrical properties. Analysis of the electronic transport at T > Ts favors an intrinsic semiconductor picture for transport along the most conducting Q1D axis and small-polaronic transport along the other directions, providing insight into the origin of the Seebeck anisotropy.
CdZnTe position-sensitive drift detectors with thicknesses up to 5 cm
Authors: Bolotnikov A. E. , Camarda G. S. , Chen E. , Cheng S. , Cui Y. , Gul R. , Gallagher R. , Dedic V. , De Geronimo G. , Ocampo Giraldo L. , Fried J. , Hossain A. , MacKenzie J. M. , Sellin P. , Taherion S. , Vernon E. , Yang G. , El-hanany U. , James R. B.
Published: March 2016

We investigated the feasibility of long-drift-time CdZnTe (CZT) gamma-ray detectors, fabricated from CZT material produced by Redlen Technologies. CZT crystals with cross-section areas of 5 × 5 mm2 and 6 × 6 mm2 and thicknesses of 20-, 30-, 40-, and 50-mm were configured as 3D position-sensitive drift detectors and were read out using a front-end ASIC. By correcting the electron charge losses caused by defects in the crystals, we demonstrated high performance for relatively thick detectors fabricated from unselected CZT material.
Quasielastic neutron scattering with in situ humidity control: Water dynamics in uranyl fluoride
Authors: Miskowiec A. , Kirkegaard M. C. , Herwig K. W. , Trowbridge L. , Mamontov E. , Anderson B.
Published: March 2016

The structural phase diagram of uranyl fluoride (UO2F2), while incomplete, contains at least one anhydrous crystal structure and a second, zeolite-like structure with the formula [(UO2F2)(H2O)]7 ⋅ (H2O)4 that can be produced by adding water to the anhydrous structure. While traditional diffraction measurements can easily differentiate these crystals, additional aqueous structures (in general of the form UO2F2 + xH2O) have been proposed as well. We present results using a novel sample environment setup to intercalate water during a quasielastic neutron scattering measurement over the course of 86 h. Our sample environment allows low-pressure (<2 atm) humid air flow across the sample coupled with a system to control the relative humidity of this air flow between 10% and 70%. The water dynamics in UO2F2 and [(UO2F2)(H2O)]7 ⋅ (H2O)4 are sufficiently different to distinguish them, with water in the latter executing a restricted diffusion (D = 2.7 × 10−6 cm2/s) within the structure's accessible pores (r = 3.17 Å) such that the dynamics can be used as a fingerprinting tool. We confirm that water vapor pressure is the driving thermodynamic force for the conversion of the anhydrous structure to [(UO2F2)(H2O)]7 ⋅ (H2O)4, and we demonstrate the feasibility of extending this approach to aqueous forms of UO2F2 + xH2O. This method has general applicability to systems in which water content itself is a driving variable for structural or dynamical phase transitions.
Distinctive electrical properties in sandwich-structured Al2O3/low density polyethylene nanocomposites
Authors: Wang Si-Jiao , Zha Jun-Wei , Li Wei-Kang , Dang Zhi-Min
Published: March 2016

The sandwich-structured Al2O3/low density polyethylene (Al2O3/LDPE) nanocomposite dielectrics consisting of layer-by-layer with different concentration Al2O3 loading were prepared by melt-blending and following hot pressing method. The space charge distribution from pulsed electro-acoustic method and breakdown strength of the nanocomposites were investigated. Compared with the single-layer Al2O3/LDPE nanocomposites, the sandwich-structured nanocomposites remarkably suppressed the space charge accumulation and presented higher breakdown strength. The charges in the sandwich-structured nanocomposites decayed much faster than that in the single-layer nanocomposites, which was attributed to an effective electric field caused by the formation of the interfacial space charges. The energy depth of shallow and deep traps was estimated as 0.73 eV and 1.17 eV in the sandwich-structured nanocomposites, respectively, according to the thermal excitation theoretical model we proposed. This work provides an attractive strategy of design and fabrication of polymer nanocomposites with excellent space charge suppression.
A thermalization energy analysis of the threshold voltage shift in amorphous indium gallium zinc oxide thin film transistors under positive gate bias stress
Authors: Niang K. M. , Barquinha P. M. C. , Martins R. F. P. , Cobb B. , Powell M. J. , Flewitt A. J.
Published: March 2016

Thin film transistors (TFTs) employing an amorphous indium gallium zinc oxide (a-IGZO) channel layer exhibit a positive shift in the threshold voltage under the application of positive gate bias stress (PBS). The time and temperature dependence of the threshold voltage shift was measured and analysed using the thermalization energy concept. The peak energy barrier to defect conversion is extracted to be 0.75 eV and the attempt-to-escape frequency is extracted to be 107 s−1. These values are in remarkable agreement with measurements in a-IGZO TFTs under negative gate bias illumination stress (NBIS) reported recently (Flewitt and Powell, J. Appl. Phys. 115, 134501 (2014)). This suggests that the same physical process is responsible for both PBS and NBIS, and supports the oxygen vacancy defect migration model that the authors have previously proposed.
Structural disorder and magnetism in the spin-gapless semiconductor CoFeCrAl
Authors: Choudhary Renu , Kharel Parashu , Valloppilly Shah R. , Jin Yunlong , O’Connell Andrew , Huh Yung , Gilbert Simeon , Kashyap Arti , Sellmyer D. J. , Skomski Ralph
Published: March 2016

Disordered CoFeCrAl and CoFeCrSi0.5Al0.5 alloys have been investigated experimentally and by first-principle calculations. The melt-spun and annealed samples all exhibit Heusler-type superlattice peaks, but the peak intensities indicate a substantial degree of B2-type chemical disorder. Si substitution reduces the degree of this disorder. Our theoretical analysis also considers several types of antisite disorder (Fe-Co, Fe-Cr, Co-Cr) in Y-ordered CoFeCrAl and partial substitution of Si for Al. The substitution transforms the spin-gapless semiconductor CoFeCrAl into a half-metallic ferrimagnet and increases the half-metallic band gap by 0.12 eV. Compared CoFeCrAl, the moment of CoFeCrSi0.5Al0.5 is predicted to increase from 2.01 μB to 2.50 μB per formula unit, in good agreement with experiment.
Using krabok (Irvingia malayana) seed oil and Flemingia macrophylla leaf meal as a rumen enhancer in an in vitro gas production system
Authors: Kang Sungchhang , Wanapat Metha , Phesatcha Kampanat , Norrapoke Thitima , Foiklang Suban , Ampapon Thiwakorn , Phesatcha Burarat
Published: March 2016

An in vitro gas production system was conducted to investigate the effect of krabok (Irvingia malayana) seed oil (KSO) and Flemingia (Flemingia macrophylla) leaf powder (FLM) supplementation on gas production kinetics, volatile fatty acid (VFA) and methane production with different ratios of rice straw to cassava chip (RS : CC). The treatments were arranged according to a 4 × 2 × 2 factorial arrangement in a completely randomised design using four different ratios of RS : CC (100 : 0; 60 : 40; 20 : 80; and 0 : 100), two levels of KSO supplement (0% and 2.5% of total dietary substrate) and two levels of FLM supplement (0% and 2.5% of total dietary substrate). The gas production kinetics were affected by RS : CC, KSO and FLM supplementation (P < 0.05). However, there was no interaction between RS : CC*FLM, FLM*KSO, or RS : CC*FLM*KSO; with the exception of RS : CC*KSO (P < 0.05). Cumulative gas at 96 h post incubation was increased with increasing RS : CC especially at 0 : 100. However, KSO supplementation suppressed gas production whereas FLM could enhance gas production from feed fraction (P < 0.05). Increasing RS : CC ratio resulted in increasing total VFA, propionic acid and butyric acid whereas acetic acid concentration was reduced; therefore, ratio of acetic acid : propionic acid was reduced. However, KSO supplementation depressed VFA production whereas the FLM supplement had no effect. The methane production was reduced with increasing level of RS : CC especially with supplementation of KSO. Based on this study, it is concluded that KSO addition could reduce methane production whereas FLM could enhance the gas production and fermentation end products; hence, the combined use is potentially beneficial. However, further research under in vivo conditions should be conducted.
The tale of two deer: management of Père David’s deer and sika deer in anthropogenic landscape of eastern Asia
Authors: Jiang Zhigang , Kaji Koichi , Ping Xiaoge
Published: March 2016

Père David’s deer (Elaphurus davidianus) and sika deer (Cervus nippon) occupy two contrasting types of niches in eastern Asia: Père David’s deer is a swamp deer adapted to wetlands, while the sika deer mainly live in forested areas. Both Père David’s deer and sika deer have been hunted since the early days of the hunting and gathering civilisation; however, these two deer have undergone different population histories. As human society entered the era of agriculture civilisation, Père David’s deer gradually lost its habitats to farmlands, and the population was greatly reduced until, finally, it became extinct in the wild in 1900. Fortunately, after 30 years of restoration and introduction, more than 4000 Père David’s deer thrive in nature reserves, zoos and safari parks in China, and more than 500 Père David’s deer could be found in the wild in 2014. Populations of wild sika deer were reduced as well due to hunting and deforestation, and were restricted in the forest patches in the mountains in eastern Asia. Nevertheless, the sika deer in China and Japan have different fortunes. Sika deer in China did not escape the prevalent tragedy of domestication, in that wild sika deer was endangered or extirpated in its original habitats, while the farmed sika deer thrived since late 1950s. Sika deer populations in Japan also remained at low density in the mid-1950s due to over-hunting, including poaching. After one-quarter of a century of in situ protection, sika populations are still small in China and some populations were found to leave the nature reserve to areas with high human densities, while the wild sika deer in Japan have markedly increased in numbers and extended their geographic distribution during the past few decades. Accordingly, the management strategies in China and Japan were completely different. The Chinese government is seeking all the efforts on the conservation of sika deer, while the Japanese government is revising laws to harvest and to reduce sika deer population.
Zinc Oxide Nanoparticles-Immobilized Mesoporous Hollow Silica Spheres for Photodegradation of Sodium Dodecylbenzenesulfonate
Authors: Pourdayhimi Parisa , Koh Pei Wen , Salleh Mohamed Mohd , Nur Hadi , Lee Siew Ling
Published: March 2016

ZnO-Immobilized mesoporous hollow silica spheres (ZnO/xMHSS; x = 15, 30, 50 molar ratio of Zn/Si) were synthesized and examined as photocatalysts toward the degradation of sodium dodecylbenzenesulfonate (SDBS). The hollow structures of MHSS and ZnO-immobilized MHSS composite were evidenced by transmission electron microscopy analysis. X-ray diffraction results confirmed the presence of ZnO and a mesoporous structure in the synthesized materials. N2 adsorption–desorption analysis also depicted the formation of a mesoporous structure and the increased surface area for the ZnO/xMHSS materials. Fourier transform infrared spectroscopy analysis revealed the formation of Si–O–Zn bonds due to interaction between ZnO and MHSS. The photocatalytic testing results indicated that all the ZnO/xMHSS materials showed improved efficiencies of 10–21 % toward the photodegradation of SDBS when compared with bare ZnO. Among the prepared materials, ZnO/15MHSS was the best photocatalyst, which photodegraded 68 % SDBS after 1 h reaction. The kinetic study demonstrated that the photocatalytic reaction followed the second-order model.
Integrating animal welfare into wild herbivore management: lessons from the Australian Feral Camel Management Project
Authors: Hampton Jordan O. , Jones Bidda , Perry Andrew L. , Miller Corissa J. , Hart Quentin
Published: March 2016

The Australian Feral Camel Management Project (AFCMP) was initiated in 2009 to manage the growing impacts of feral camels (Camelus dromedarius) in Australia. One of the most important considerations for the project was achieving high standards of animal welfare and demonstrating this to stakeholders and the public. The novelty of feral camels as an invasive species meant that relatively little was known about the animal welfare aspects of the available management techniques. To address this knowledge gap, quantitative animal-based assessment tools were developed to allow independent observers to perform repeatable in situ field auditing of the two main control methods used: aerial (helicopter) shooting and live capture (mustering and transport for slaughter). Although observation protocols allowed most stages of aerial shooting (in situ killing) to be assessed, not all stages of live capture operations could be assessed (namely transport and slaughter at ex situ abattoirs) due to the limitations of the jurisdiction of the Australian Feral Camel Management Project. For assessments that were performed, audit results were made available to project partners to allow procedures to be reviewed and published through peer-reviewed literature to improve transparency. Empirical evidence produced through the audit system was also used to refine humaneness ranking assessments comparing management methods. We present the lessons learnt through the animal welfare approach of the AFCMP to assist future wild herbivore management programs.
Inhibitory effect ofPterocarpus indicusWilld water extract on IgE/Ag-induced mast cell and atopic dermatitis-like mouse models
Authors: Cha Hae-Sim , Kim Wan-Joong , Lee Myung-Hun , Kim Sun-Young , Kim Seo Ho , Lee Kwang-Ho , Kim Tack-Joong
Published: March 2016

Pterocarpus indicus Willd has been widely used as a traditional medicine to treat edema, cancer, and hyperlipidemia, but its antiallergic properties and underlying mechanisms have not yet been studied. The purpose of this study was to evaluate the antiallergic activity of Pterocarpus indicus Willd water extract (PIW) using activated mast cells and an atopic dermatitis (AD)-like mouse model. PIW decreased IgE/Ag-induced mast cell degranulation and the phosphorylation of Syk and downstream signaling molecules such as PLC-γ, Akt, Erk 1/2, JNK compared to stimulated mast cells. In DNCB-induced AD-like mice, PIW reduced IgE level in serum, as well as AD-associated scratching behavior and skin severity score. These results indicate that PIW inhibits the allergic response by reducing mast cell activation and may have clinical potential as an antiallergic agent for disorders such as AD.
Control of protein trafficking by reversible masking of transport signals
Authors: Abraham Omer , Gotliv Karnit , Parnis Anna , Boncompain Gaelle , Perez Franck , Cassel Dan
Published: March 2016

Systems that allow the control of protein traffic between subcellular compartments have been valuable in elucidating trafficking mechanisms. Most current approaches rely on ligand or light-controlled dimerization, which results in either retardation or enhancement of the transport of a reporter. We developed an alternative approach for trafficking regulation that we term “controlled unmasking of targeting elements” (CUTE). Regulated trafficking is achieved by reversible masking of the signal that directs the reporter to its target organelle, relying on the streptavidin–biotin system. The targeting signal is generated within or immediately after a 38–amino acid streptavidin-binding peptide (SBP) that is appended to the reporter. The binding of coexpressed streptavidin to SBP causes signal masking, whereas addition of biotin causes complex dissociation and triggers protein transport to the target organelle. We demonstrate the application of this approach to the control of nuclear and peroxisomal protein import and the generation of biotin-dependent trafficking through the endocytic and COPI systems. By simultaneous masking of COPI and endocytic signals, we were able to generate a synthetic pathway for efficient transport of a reporter from the plasma membrane to the endoplasmic reticulum.
MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis
Authors: Kim SungHwan , Lin Chien-Wei , Tseng George. C.
Published: March 2016

Motivation: Supervised machine learning is widely applied to transcriptomic data to predict disease diagnosis, prognosis or survival. Robust and interpretable classifiers with high accuracy are usually favored for their clinical and translational potential. The top scoring pair (TSP) algorithm is an example that applies a simple rank-based algorithm to identify rank-altered gene pairs for classifier construction. Although many classification methods perform well in cross-validation of single expression profile, the performance usually greatly reduces in cross-study validation (i.e. the prediction model is established in the training study and applied to an independent test study) for all machine learning methods, including TSP. The failure of cross-study validation has largely diminished the potential translational and clinical values of the models. The purpose of this article is to develop a meta-analytic top scoring pair (MetaKTSP) framework that combines multiple transcriptomic studies and generates a robust prediction model applicable to independent test studies.

Results: We proposed two frameworks, by averaging TSP scores or by combining P-values from individual studies, to select the top gene pairs for model construction. We applied the proposed methods in simulated data sets and three large-scale real applications in breast cancer, idiopathic pulmonary fibrosis and pan-cancer methylation. The result showed superior performance of cross-study validation accuracy and biomarker selection for the new meta-analytic framework. In conclusion, combining multiple omics data sets in the public domain increases robustness and accuracy of the classification model that will ultimately improve disease understanding and clinical treatment decisions to benefit patients.

Availability and Implementation: An R package MetaKTSP is available online. (http://tsenglab.biostat.pitt.edu/software.htm).

Contact: ctseng@pitt.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Assortative mating can impede or facilitate fixation of underdominant alleles
Authors: Newberry Mitchell G , McCandlish David M , Plotkin Joshua B
Published: March 2016

Although underdominant mutations have undoubtedly fixed between divergent species, classical models of population genetics suggest underdominant alleles should be purged quickly, except in small or subdivided populations. Here we study the fixation of underdominant alleles at loci that also influence mate choice, such as loci encoding coloration patterns visible to mates and predators alike. We analyze a mechanistic model of positive assortative mating in which individuals havenchances to sample compatible mates. This one-parameter model naturally spans the two classical extremes of random mating (n= 1) and complete assortment (n→ ∞), and yet it produces a complex form of sexual selection that depends non-monotonically on the number of mating opportunities,n. The resulting interaction between viability selection and sexual selection can either inhibit or facilitate fixation of underdominant alleles, compared to random mating. As the number of mating opportunities increases, underdominant alleles can fix at rates that even approach the neutral substitution rate. This result is counterintuitive because sexual selection and underdominance each suppress rare alleles in this model, and yet in combination they can promote the fixation of rare alleles. This phenomenon constitutes a new mechanism for the fixation of underdominant alleles in large populations, and it illustrates how incorporating life history characteristics can alter the predictions of population-genetic models for evolutionary change.
Establishing elements of a synthetic biology platform for Vaccinia virus production: BioBrick™ design, serum-free virus production and microcarrier-based cultivation of CV-1 cells
Authors: Liu Shuchang , Ruban Ludmila , Wang Yaohe , Zhou Yuhong , Nesbeth Darren N.
Published: March 2016

Vaccinia virus (VACV) is an established tool for vaccination and is beginning to prove effective as an oncolytic agent. Industrial production of VACV stands to benefit in future from advances made by synthetic biology in genome engineering and standardisation. As a step toward realising these benefits we analysed the Lister Vaccinia virus genome with respect to refactoring options and propose a VACV genome engineering BioBrick™. We then used the CV-1 cell line to produce a conventional recombinant Lister strain VACV, VACVL-15 RFP in a serum-free process. CV-1 cells grown in 5% foetal bovine serum (FBS) Dulbecco’s Modified Eagle Medium (DMEM) were adapted to growth in OptiPRO and VP-SFM brands of serum-free media. Specific growth rates of 0.047 h−1and 0.044 h−1were observed for cells adapted to OptiPRO and VP-SFM respectively, compared to 0.035 h−1in 5% FBS DMEM. Cells adapted to OptiPRO and to 5% FBS DMEM achieved recovery ratios of over 96%, an indication of their robustness to cryopreservation. Cells adapted to VP-SFM showed a recovery ratio of 82%. VACV production in static culture, measured as plaque forming units (PFU) per propagator cell, was 75 PFU/cell for cells in 5% FBS DMEM. VP-SFM and OptiPRO adaptation increased VACV production to 150 PFU/cell and 350 PFU/cell respectively. Boosted PFU/cell from OptiPRO-adapted cells persisted when 5% FBS DMEM or OptiPRO medium was present during the infection step and when titre was measured using cells adapted to 5% FBS DMEM or OptiPRO medium. Finally, OptiPRO-adapted CV-1 cells were successfully cultivated using Cytodex-1 microcarriers to inform future scale up studies.
RNA-guided endonuclease-driven mutagenesis in tobacco followed by efficient fixation of mutated sequences in doubled haploid plants
Authors: Schedel Sindy , Pencs Stefanie , Hensel Göetz , Müller Andrea , Kumlehn Jochen
Published: March 2016

Background

Customizable endonucleases are providing an effective tool for genome engineering. The resulting primary transgenic individuals are typically heterozygous and/or chimeric with respect to any mutations induced. To generate genetically fixed mutants, they are conventionally allowed to self-pollinate, a procedure which segregates individuals into mutant heterozygotes/homozygotes and wild types. The chances of recovering homozygous mutants among the progeny depends not only on meiotic segregation but also on the frequency of mutated germline cells in the chimeric mother plant.

Results

RNA-guided endonuclease-mediated mutagenesis was targeted to the green fluorescent protein gene (gfp) harboured by a transgenic tobacco line. Upon retransformation using agfp-specific endonuclease construct, the T0plants were allowed to either self-pollinate, or were propagated via regeneration fromin vitrocultured embryogenic pollen which give rise to haploid/doubled haploid plants or from leaf explants that form plants vegetatively. Single or multiple mutations were detected in 80% of the T0plants. The majority of these mutations proved heritable by each of the three propagation systems used. Regeneration fromin vitrocultured embryogenic pollen allowed for homozygous mutants to be produced more efficiently than via sexual reproduction. The recovery of mutations that were not found among sexually produced progeny was shown to be achievable through vegetative plant propagationin vitro. In addition, a number of mutations not detected in the primary gRNA/Cas9-expressing plants were uncovered in the progeny, irrespective of the mode of propagation.

Conclusion

Regeneration from embryogenic pollen culture provides a convenient method to rapidly generate a variety of genetically fixed mutants following site-directed mutagenesis. Induced mutations that are not sexually transmitted can be recovered through vegetative plant regeneration from somatic tissue.
The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes
Authors: Janoušek Václav , Laukaitis Christina M. , Yanchukov Alexey , Karn Robert C.
Published: March 2016

We explored genome-wide patterns of RT content surrounding lineage-specific gene family expansions in the human and mouse genomes. Our results suggest that the size of a gene family is an important predictor of the RT distribution in close proximity to the family members. The distribution differs considerably between the three most common RT classes (LINEs, LTRs and SINEs). LINEs and LTRs tend to be more abundant around genes of multi-copy gene families, whereas SINEs tend to be depleted around such genes. Detailed analysis of the distribution and diversity of LINEs and LTRs with respect to gene family size suggests that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role, promoting gene duplication. This suggests that gene family expansions, especially in the mouse genome, might undergo two phases, the first is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Our observations also suggest that specific differences exist in this gene family expansion process between human and mouse genomes.
Transposable Element Evolution in the AllotetraploidCapsella bursa-pastoris
Authors: Ågren J. Arvid , Huang Hui-Run , Wright Stephen I.
Published: March 2016

Premise of the study

Shifts in ploidy affect the evolutionary dynamics of genomes in a myriad of ways. Population genetic theory predicts that transposable element (TE) proliferation may follow because the genome wide efficacy of selection should be reduced and the increase in gene copies may mask the deleterious effects of TE insertions. Moreover, in allopolyploids TEs may further accumulate because of hybrid breakdown of TE silencing. However, to date the evidence of TE proliferation following an increase in ploidy is mixed, and the relative importance of relaxed selection vs. silencing breakdown remains unclear.

Methods

We used high-coverage whole genome sequence data to evaluate the abundance, genomic distribution, and population frequencies of TEs in the self-fertilizing recent allotetraploidCapsella bursa-pastoris(Brassicaceae). We then compared theC. bursa-pastorisTE profile with that of its two parental diploid species, outcrossingC. grandifloraand self-fertilizingC. orientalis.

Key results

We found no evidence thatC. bursa-pastorishas experienced a large genome wide proliferation of TEs relative to its parental species. However, when centromeric regions are excluded, we find evidence of significantly higher abundance of retrotransposons inC. bursa-pastorisalong the gene-rich chromosome arms, compared to C.grandifloraandC. orientalis.

Conclusions

The lack of a genome-wide effect of allopolyploidy on TE abundance, combined with the increases TE abundance in gene-rich regions suggest that relaxed selection rather than hybrid breakdown of host silencing explains the TE accumulation inC. bursa-pastoris
Dynamics and Control of Phloem Loading of Indoleacetic Acid in Seedling Cotyledons ofRicinus CommunisDuring Germination
Authors: Tamas Imre A , Davies Peter J
Published: March 2016

During seed germination sugars and auxin are produced from stored precursors or conjugates respectively and transported to the seedling axis. To elucidate the mode of travel of IAA into the phloem a solution of [3H]indoleacetic acid (IAA), together with [14C]sucrose, was injected in the endosperm cavity harboring the cotyledons of germinating seedlings ofRicinus communis. Phloem exudate from the cut hypocotyl was collected and the radioactivity recorded. Sucrose loading in the phloem was inhibited at higher IAA levels, and the rate of filling of the transient pool(s) was reduced by IAA. IAA was detected within 10 minutes, with the concentration increasing over 30 min and reaching a steady-state by 60 min. The kinetics indicated that phloem loading of IAA involving both an active, carrier-based, and a passive, diffusion-based component, with IAA traveling along a pathway containing an intermediary pool, possibly the protoplasts of mesophyll cells. Phloem loading of IAA was altered by sucrose, K+and a range of non-specific and IAA-specific analogues and inhibitors in a manner that showed that IAA moves into the phloem from the extra cotyledonary solution by multiple pathways, with a carrier mediated pathway playing a principal role.

Summary Statement

Indoleacetic acid is transported from the peri-cotyledonary space into the phloem of germinatingRicinusseedlings by both trans-membrane carriers and diffusive pathways, with the cells of the cotyledons forming an intermediate reservoir.
Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing
Authors: Parker Jeremy D.K. , Shen Yaoqing , Pleasance Erin , Li Yvonne , Schein Jacqueline E. , Zhao Yongjun , Moore Richard , Wegrzyn-Woltosz Joanna , Savage Kerry J. , Weng Andrew P. , Gascoyne Randy D. , Jones Steven , Marra Marco , Laskin Janessa , Karsan Aly
Published: March 2016

In an attempt to assess potential treatment options, whole-genome and transcriptome sequencing were performed on a patient with an unclassifiable small lymphoproliferative disorder. Variants from genome sequencing were prioritized using a combination of comparative variant distributions in a spectrum of lymphomas, and meta-analyses of gene expression profiling. In this patient, the molecular variants that we believe to be most relevant to the disease presentation most strongly resemble a diffuse large B-cell lymphoma (DLBCL), whereas the gene expression data are most consistent with a low-grade chronic lymphocytic leukemia (CLL). The variant of greatest interest was a predicted NOTCH2-truncating mutation, which has been recently reported in various lymphomas.
Crystal structure of (E)-9-(4-nitrobenzylidene)-8,9-dihydropyrido[2,3-d]pyrrolo[1,2-a]pyrimidin-5(7H)-one
Authors: Khodjaniyazov Khamid U. , Ashurov Jamshid M.
Published: March 2016

The title compound, C17H12N4O3, a pyridopyrrolopyrimidine derivative, is almost planar. The nitrobenzene ring is inclined to the mean plane of the 8,9-dihydropyrido[2,3-d]pyrrolo[1,2-a]pyrimidin-5(7H)-one moiety (r.m.s. deviation = 0.023 Å) by 6.8 (1)°. In the crystal, molecules are linkedviaC—H...O and C—H...N hydrogen bonds, forming layers parallel to (101).
A day in the life of a peer support worker: endings
Authors: Watson Emma
Published: March 2016

Purpose

– The purpose of this paper is to describe the experiences of a day in the life of a peer support worker based within an NHS trust and to use these experiences as a basis for reflection on key issues in recovery focused practice and peer support.

Design/methodology/approach

– A reflective approach is used to consider the experience of ending peer support relationships and the emotion which this creates for both parties.

Findings

– Reflections are offered relating to boundaires, grieving and the experience of endings within peer support and other contexts.

Originality/value

– As a narrative account of the experience of a peer support worker, this paper adds to the small number of reflective pieces in this area.