bluuebunny/crossref_metadata_2025 huggingface dataset:
Equivalent circuit and numerical analyses of an inductively coupled plasma torch with a tapped induction coil
Authors: Lee Mi-Yeon , Nam Jun-Seok , Yang In-Mok , Seo Jun-Ho
Published: November 2018

Equivalent circuit and numerical analyses of an Ar-N2 inductively coupled plasma (ICP) were conducted in order to clarify the effect of the induction coil with a grounded tap on the electrical characteristics of an ICP torch system. First, from the computational results, it was revealed that the load resistance of tank circuit for a free running radio-frequency (RF) oscillator can be reduced to about 25% with a center-tap of the induction coil grounded. Despite the asymmetric distributions of the electric fields in the inside of the ICP torch, this effect was found due to the equivalent resistance and inductance of ICP that were divided in approximately half into each part of the center-tapped induction coil. The reduction of the load resistance by a grounded tap was also observed in generation experiments of Ar-N2 ICPs using a vacuum tube oscillator for various N2 contents ranging from 6.3 % to 25.0 %. By providing a way to reduce the load resistance of the tank circuit, the induction coil with a grounded tap can be used to improve the impedance matching condition of ICP systems with the load resistances higher than the internal resistance of a free running RF oscillator.
Magnetic structure of a non-centrosymmetric CePtSi3
Authors: Ueta D. , Yoshida M. , Ikeda Y. , Liu Y. , Hong T. , Masuda T. , Yoshizawa H.
Published: November 2018

Neutron diffraction experiments have been performed on single crystalline samples of CePtSi3. We found that the incommensurate magnetic propagation vector τ1 = (±0.283, 0, 0) in the phase I (2.2 ∼ 4.8 K) switches to the commensurate vectors τ2 = (±0.25, 0, 0) and τ3 = (±0.25, 0, ±1) in the phase III (∼ 2.8 K) at zero field. Although the magnetic structure of CePtSi3 in the phase I is a spin density wave similar to those in CeRhSi3, CeIrSi3, and CePdSi3, the magnetic structure in the phase III is commensurate unlike other CeTSi3 (T = Rh, Ir, Pd) compounds.
A piezoelectric cantilever with novel large mass for harvesting energy from low frequency vibrations
Authors: Wang Lu , Lu Dejiang , Jiang Zhuangde , Jia Chen , Wu Yumeng , Zhou Xiangyang , Zhao Libo , Zhao Yulong
Published: November 2018

The piezoelectric cantilever with a large proof mass is a classic vibration energy harvesting structure. In this study, in order to harvest much more energy from low frequency vibration in the finite volume, a novel L type mass block is proposed and compared with a traditional rectangular mass block for the piezoelectric cantilever. A theoretical modeling of lumped parameter system is carried out considering the effect of mass block length on mass, stiffness and damping. A series of PZT bimorph cantilevers with brass proof mass prototypes are fabricated for the experimental verification. Their eigenfrequency and maximum piezoelectric power output are analyzed by the experiment and simulation. The piezoelectric cantilever with L type mass block avoids the weakness of decreasing the effective length of piezoelectric cantilever, and has lower eigenfrequency and larger piezoelectric power output than that with rectangular mass block. Its piezoelectric power output of 192 mW/(g2) can be obtained at the low resonant frequency of 18.1 Hz and the optimal load impedance of 5kΩ, and the unit volume power density is as high as 24.6 mW/(cm3×g2).
Exchange coupling in FeCoB/Ru, Mo/FeCoB trilayer structures
Authors: McKinnon Tommy , Girt Erol
Published: November 2018

In this work, bilinear (J1) and biquadratic (J2) coupling between two FeCoB layers across Ru and Mo spacer layers is studied. The investigated structures are FM1/Ru and Mo(d)/FM2, where FM1 is Fe/FeCoB, FM2 is FeCoB/NiFe, and d is the thickness of the Ru and Mo spacer layers where d is varied from 0.3 to 1.5 nm. Using a ferromagnetic resonance(FMR) model, we are able to determine J1–2J2 of all as-deposited samples and those annealed at 200 and 300 °C. FMR measurements are also used to extract Gilbert damping of the magnetic films. We also use a micromagnetic model to fit magnetization as a function of field to determine J1 and J2 independently for antiferromagnetically coupled samples. This study shows that the spacer layer thickness range, for which antiferromagnetic coupling between FeCoB layer can be achieved, is reduced with increasing annealing temperature. Antiferromagnetic coupling is not realized in samples annealed at 300 °C. The damping of magnetic layers first rapidly increases and then gradually decreases with an increase in the spacer layer thickness. The exchange coupling and spin pumping in the studied structures are responsible for this trend.
A co-axial velocity map imaging spectrometer for electrons
Authors: Li S. , Champenois E. G. , Coffee R. , Guo Z. , Hegazy K. , Kamalov A. , Natan A. , O’Neal J. , Osipov T. , Owens M. , Ray D. , Rich D. , Walter P. , Marinelli A. , Cryan J. P.
Published: November 2018

We present the design of an electron velocity map imaging (VMI) spectrometer where the ionizing laser source propagates along the symmetry axis of the spectrometer. The co-axial geometry is useful in a variety of experiments, because it provides a unique 2-dimensional projection of the 3-dimensional electron momentum distribution. Initial simulations show that this co-axial VMI can work with both high energy (more than 100 eV) and low energy (tens of eV) electrons. We demonstrate the performance of this co-axial VMI spectrometer at the Linac Coherent Light Source X-ray Free Electron Laser facility.
Electrochemistry in ultra-high vacuum: The fully transferrable ultra-high vacuum compatible electrochemical cell
Authors: Kerger P. , Vogel D. , Rohwerder M.
Published: November 2018

A new experimental setup for in situ/operando investigations of redox reactions is introduced. This setup, in combination with ultra-high vacuum (UHV) methods from the field of surface science, provides completely new possibilities to investigate electrochemical redox reactions. Two types of cells are distinguished conceptionally: in the permeation configuration, the working electrode is electrochemically polarised on one side of a membrane (entry side), leading to atomic hydrogen uptake, and allowing proton and electron exchange between the entry and the other side (exit side) of the membrane. Here it is found that the applied potential on the entry side shows a 1:1 correlation with the measured potential on the exit side. The concept of the “window” cell requires ultra-thin, electron transparent “windows,” such as single layer graphene, for X-ray photoelectron spectroscopy or X-ray transparent silicon nitride “windows” for X-ray absorption spectroscopy. In this case, the solid/liquid interface can be directly probed under applied potentials. In both configurations, the applied potential is measured with a palladium hydride reference electrode, with so far unseen precision and long-term stability. The cell design is constructed with regard to transferability within a UHV system, allowing sample preparation, and a modular construction, allowing a straightforward changeover between these two configurations. As a first application, an approach based on atomic hydrogen is presented. Further application concepts are discussed. The setup functionality is demonstrated by the example of in situ/operando investigation of the palladium oxide reduction.
Non-thermal and low-destructive X-ray induced graphene oxide reduction
Authors: Mikoushkin V. M. , Kriukov A. S. , Nikonov S. Yu. , Dideikin A. T. , Vul A. Ya. , Vilkov O. Yu.
Published: November 2018

Large-scale graphene fabrication by thermal and chemical reductions of graphene oxide has faced the problem of defect formation. To solve the problem, we have considered a physically alternative reduction process including electronic excitation followed by the oxygen group detachment from the carbon sheet without capturing a sheet of carbon atoms. Single-layer graphene oxide films were studied by photoemission spectroscopy in the course of monochromatic synchrotron X-ray radiation with in situ control of the layer thickness, chemical composition, atomic ordering, and defect concentration exactly in the modified area. The radiation flux was too low to heat the film. A non-thermal and low-destructive effect of X-ray induced graphene oxide reduction has been revealed. Transformation of the sp3 σ bonds into sp2 π ordered bonds, bandgap closing, and significant diminishing of the oxygen content (below 5 at. %) have been observed without any signs of defects in the photoemission spectra. The effective cross section of the oxygen group detachment induced by a soft X-ray photon (hν = 130 eV) was estimated to be σ* ∼ 3 × 10−18 cm2. A reduced single-layer graphene oxide with a narrow bandgap (0.4 – 0.8 eV) attractive for many applications was obtained, as well as almost pure graphene.
Time resolved imaging of the non-linear bullet mode within an injection-locked nano-contact spin Hall nano-oscillator
Authors: Spicer T. M. , Keatley P. S. , Dvornik M. , Loughran T. H. J. , Awad A. A. , Dürrenfeld P. , Houshang A. , Ranjbar M. , Åkerman J. , Kruglyak V. V. , Hicken R. J.
Published: November 2018

Time-resolved scanning Kerr microscopy (TRSKM) has been used to image precessional magnetization dynamics excited by a DC current within a nano-contact (NC) spin Hall nano-oscillator (SHNO). Injection of a radio frequency (RF) current was used to phase lock the SHNO to TRSKM. The out of plane magnetization was detected by means of the polar magneto optical Kerr effect (MOKE). However, longitudinal MOKE images were dominated by an artifact arising from the edges of the Au NCs. Time resolved imaging revealed the simultaneous excitation of a non-linear “bullet” mode at the centre of the device, once the DC current exceeded a threshold value, and ferromagnetic resonance (FMR) induced by the RF current. However, the FMR response observed for sub-critical DC current values exhibits an amplitude minimum at the centre, which is attributed to spreading of the RF spin current due to the reactance of the device structure. This FMR response can be subtracted to yield images of the bullet mode. As the DC current is increased above threshold, the bullet mode appears to increase in size, suggesting increased translational motion. The reduced spatial overlap of the bullet and FMR modes, and this putative translational motion, may impede the injection locking and contribute to the reduced locking range observed within NC-SHNO devices. This illustrates a more general need to control the geometry of an injection-locked oscillator so that the autonomous dynamics of the oscillator exhibit strong spatial overlap with those resulting from the injected signal.
Increased luminescent efficiency of perovskite light emitting diodes based on modified two-step deposition method providing gradient concentration
Authors: Kim Joo Sung , Cho Himchan , Wolf Christoph , Yun Hyung Joong , Heo Jung-Min , Lee Tae-Woo
Published: November 2018

We increased the luminescent efficiency of perovskite light-emitting diodes (PeLEDs) by using a modified two-step deposition method combined with an interdiffusion process without additional solvent engineering or additive molecules. Methylammonium lead bromide (MAPbBr3) polycrystalline films with nanosized grains and low electronic disorder were fabricated by a modified two-step deposition process. The as-fabricated MAPbBr3 films showed gradient concentration characteristics as a result of a gradient distribution of the MABr. Also, the MABr-gradient concentration structure was intensified by the interdiffusion process, showing improved performance of MAPbBr3 PeLEDs with maximum current efficiency CEmax = 0.861 cd A−1 and maximum luminance = 604 cd m−2 with very narrow electroluminescence spectral width. This is the highest CEmax among MAPbBr3-based PeLEDs deposited by the two-step deposition method.
Power-law decay in the nonadiabatic photodissociation dynamics of alkali halides due to quantum wavepacket interference
Authors: Mizuno Yuta , Hukushima Koji
Published: November 2018

The nonadiabatic photodissociation dynamics of alkali halide molecules excited by a femtosecond laser pulse in the gas phase are investigated theoretically, and it is shown that the population of the photoexcited molecules exhibits power-law decay with exponent −1/2, in contrast to exponential decay, which is often assumed in femtosecond spectroscopy and unimolecular reaction theory. To elucidate the mechanism of the power-law decay, a diagrammatic method that visualizes the structure of the nonadiabatic reaction dynamics as a pattern of occurrence of dynamical events, such as wavepacket bifurcation, turning, and dissociation, is developed. Using this diagrammatic method, an analytical formula for the power-law decay is derived, and the theoretical decay curve is compared with the corresponding numerical decay curve computed by a wavepacket dynamics simulation in the case of lithium fluoride. This study reveals that the cause of the power-law decay is the quantum interference arising from the wavepacket bifurcation and merging due to nonadiabatic transitions.
Characterizing the electrical breakdown properties of single n-i-n-n+:GaN nanowires
Authors: Qu Juntian , Wang Renjie , Sun Yu , Shih Ishiang , Mi Zetian , Liu Xinyu
Published: November 2018

The electrical transport properties and breakdown behaviors of single n-i-n-n+ GaN nanowires (NWs) are investigated through in-situ nanoprobing inside a scanning electron microscope (SEM). The nanoprobing contact resistance is dramatically reduced by increasing the Si-doping concentration of the top n+-GaN segment of the NW. The dependence of the NW breakdown parameters (i.e., breakdown voltage, power, and current density) on the n+-GaN Si-doping concentration and the NW diameter is experimentally quantified and explained by the localized thermal decomposition mechanism of the NW. Enabled by the low NW-nanoprobe contact resistance, a breakdown current density of 4.65 MA/cm2 and a breakdown power of 96.84 mW are achieved, both the highest among the previously reported results measured on GaN NWs.
Theoretical analysis of non-linear Joule heating effects on an electroosmotic flow with patterned surface charges
Authors: Sánchez S. , Ascanio G. , Méndez F. , Bautista O.
Published: November 2018

In this work, non-linear Joule heating effects induced on an electroosmotic flow with patterned surface charges driven inside of a slit microchannel are analyzed. Here, the movement of the fluid is controlled by placing electro-thermal forces, which are induced through an imposed longitudinal electric field, E0, and the wall electric potential generated by electrodes inserted along the surface of the microchannel wall. For this analysis, the physical properties of the fluid are included as known functions, which depend on the temperature. Therefore, in order to determine the flow, temperature, and electric potential fields together with their simultaneous interactions, the governing equations have to be solved in a coupled manner. For a strong Joule heating, the non-isothermal flow regime reveals that with the presence of thermal gradients, the local electro-thermal and viscous forces, F¯χ and F¯v,χ, are affected in a sensible manner, which results in changes in the flow pattern causing the interruption or intensification of recirculations along the microchannel. In parallel, increments of flow rate or pressure are observed due to electro-thermal interactions associated with the mentioned thermal dependence of the physical properties; here the corresponding effects induced in those regions where thermal gradients are located prevail. The present analytical formulation allows determining the local electro-thermal rotational moment, Mχ, which clearly reveals the fundamental importance of when thermal gradients interact with the electric and flow fields. Thus, the local electro-thermal rotational moment can be used to interpret alterations in the flow pattern linked to the temperature rise.
Electromigration in gold nanowires under AC driving
Authors: Sawtelle Sonya D. , Kobos Zachary A. , Reed Mark A.
Published: November 2018

We investigate the relationship between temperature and electron wind force in electromigration (EM) of ultrathin gold nanowires by monitoring power and current density at breakdown under a generalized AC bias (AC with a DC offset). Based on model calculations, our driving frequency of 10 MHz is low enough to maintain steady state self-heating behavior of our wires but high enough that the direction of the wind force switches quickly relative to the time-scale of atomic motion through the junction. The maximum and time-average of the squared current density (which dictate the temperature) both exhibit a minimum in DC offset (which dictates the wind force). This is explained by wind force driven annealing of the wire under long-range atomic displacements. Our hypothesis is supported by observations of changing device resistance on the voltage ramp prior to EM onset and by subsequent SEM inspection of electromigrated devices. The frequency dependence of pure AC EM breaking is also presented and interpreted in terms of the effectiveness of damage healing upon current reversal and the degree of wind force driven annealing.
Observation of particle assisted nano-ring, bump, pit structures on semiconductor substrates by dry laser exposure
Authors: Sugathan Bijoy , Nilaya J. Padma , Pillai V. P. Mahadevan , Biswas Dhruba J.
Published: November 2018

We report on the generation of nano-structures on semiconductor substrates through particle assisted dry laser exposure technique. Of particular interest is the formation of nano rings in case of Silicon substrate following exposure with sub nano-second laser pulse at 532 nm wavelength. Usage of such a laser pulse enabled us to realise a condition wherein the dominating thermo-capillary force allowed the formation of nano rings. With gradual increase in the laser fluence the nano rings gave way to formation of nano bumps and nano pits. In case of GaAs, on the other hand, nano rings could be observed for irradiation at 1064 nm at substantially higher value of fluence, in line with its poor absorption in the substrate. For exposure to 532 nm wavelength, onset of ablation even for low incident fluence precluded the formation of rings or bumps.
Optimization methodology for control strategy of parallel hybrid electric vehicle based on chaos prediction
Authors: Hu Donghai , Hu Leli , Yan Yanzhi
Published: November 2018

Irregular internal excitation (engine excitation and motor excitation) and external excitation (road excitation) can cause torsional vibration which even leads to the break of shaft of parallel hybrid electric vehicle (HEV) powertrain. Moreover, the current energy management control strategy ignores the significance of torsional stability of HEV powertrain when formulates the operating domain. The objective of this paper is to optimize the control strategy of parallel hybrid electric vehicle with multiple excitation sources to improve the torsional stability. To achieve the goal, the simplified two-mass nonlinear dynamic model of HEV powertrain is established. Then we apply the nonlinear dynamics to predict the torsional instability range of HEV powertrain. The theoretical analytical results are used to instruct to optimize the control strategy. Finally we set up the experimental platform and perform the experiment to verify the optimization of control strategy. The experimental results show that the HEV powertrain experience torsional instability under current control strategy. The critical speed when the operation mode of HEV switches from electric driving mode to hybrid driving mode was optimized to vc = 16km/h. The operating domain of engine was optimized to 1670 < n1 < 1850rpm under hybrid driving mode and driving and charging mode. The results reveals that optimization of control strategy can improve torsional stability of HEV powertrain effectively.
Quantum dynamics study of rotational transitions of NCCN induced by He collision
Authors: Kumar Sanchit , Kushwaha Apoorv , Dhilip Kumar T. J.
Published: November 2018

Quantum dynamics of the molecule cyanogen (NCCN) and its collision with helium taking place in the interstellar medium has been studied. An ab initio potential energy surface of NCCN—He, a van der Waals complex, is generated using the high-level single reference coupled-cluster with single and double and perturbative triple excitation method and aug-cc-pVQZ basis sets. Using the multipole expansion, Legendre coefficients have been calculated and utilized in determining collisional cross sections. Close-coupling calculations have been performed to study rotational excitations for He collision with NCCN. Due to nuclear spin statistics, collision induced transitions have even Δj, while odd Δj transitions are forbidden. The presence of resonances arising from rapid oscillation of cross sections in the low energy region is the result of quasi-bound states in the NCCN—He van der Waals complex. Among all the transitions, Δj = 2 are found to be predominant for excitation. Thereafter, for each transition, the rate coefficients have been calculated which decrease with increasing values of j and Δj. The result of this work will be helpful to accurately model the abundance of cyanogen in stellar atmospheres and interstellar gas.
A Tasmanian devil breeding program to support wild recovery
Authors: Grueber C. E. , Peel E. , Wright B. , Hogg C. J. , Belov K.
Published: November 2018

Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an ‘insurance population’ to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.
Implementation of a community pharmacy-based pre-exposure prophylaxis service: a novel model for pre-exposure prophylaxis care
Authors: Tung Elyse L. , Thomas Annalisa , Eichner Allyson , Shalit Peter
Published: November 2018

Background National guidelines for the provision of HIV pre-exposure prophylaxis (PrEP) to reduce a person’s risk of acquiring HIV were made available in 2014. We created a pharmacist-managed HIV PrEP clinic in a community pharmacy setting at Kelley-Ross Pharmacy in Seattle, WA, USA. Methods: The clinic operates under a collaborative drug therapy agreement based on these guidelines. This allows pharmacists to initiate and manage tenofovir disoproxil fumarate/emtricitabine under the supervision of a physician medical director. Results: Between March 2015 and February 2018, 714 patients were evaluated and 695 (97.3%) initiated PrEP. Five hundred and thirteen (74%) patients began medication the same day as their initial appointment. Of the prescriptions filled in our pharmacy, 90% of patients had a mean proportion of days covered (PDC) greater than 80%, and 98% had a zero-dollar patient responsibility per month, including uninsured individuals. 19% of patients were lost to follow up, with an effective drop-out rate of 25%. Two hundred and seven diagnoses of sexually transmissible infections were made. There were no HIV seroconversions in the service. Conclusion: The pharmacist-managed PrEP clinic proved to be a successful alternative model of PrEP care, with high initiation rates and low drop-out and lost-to-follow-up rates. This may benefit individuals who do not access PrEP in traditional health care settings or where PrEP access is scarce. Financial sustainability of the model was dependent on the ability of pharmacists in the clinic to bill insurance plans for their services in accordance with Washington State legislative changes requiring commercial insurances to recognise pharmacists as providers.
A comparison of unmanned aerial vehicles (drones) and manned helicopters for monitoring macropod populations
Authors: Gentle Matthew , Finch Neal , Speed James , Pople Anthony
Published: November 2018

Context
Developments in the use of remote aircraft, or unmanned aerial systems (UAS), for ecological study have been rapid. Helicopter surveys have proven to be a reliable, repeatable method for broad-scale monitoring of harvested kangaroo populations in Australia’s rangelands, but the recent availability of long-range UAS may offer improvements in detectability and cost efficiency.

Aims
We aimed to test the ability of a long-range UAS (Spylite, Bluebird Aero Systems Ltd, Kadima, Israel) to survey macropod populations at a landscape scale, and validate the results against those from the current best-practice helicopter surveys.

Methods
Four 80-km transects in south-western Queensland were surveyed using a helicopter and UAS. Two observers, occupying the rear seats of the helicopter, recorded animals observed in distance classes perpendicular to either side of the aircraft. Continuous electro-optical (EO) or infrared (IR) video from the UAS were recorded for later processing. Animal densities were calculated using line-transect methods for both techniques. The efficiency and cost effectiveness of each survey technique were also assessed using the flight and data processing times.

Key results
The encounter rate for macropods during the UAS was significantly lower compared with the helicopter survey, resulting in low estimates of macropod density (3.2 versus 53.8 animals km–2 respectively). The UAS technique recorded between 2.9 and 12.7% of the macropod density observed on each transect during the helicopter survey. The helicopter surveys were less expensive and more efficient and cost effective, requiring less flight and data processing time than the UAS surveys.

Conclusions
Utilising long-range UAS to detect and count groups of wild animals for landscape-scale wildlife monitoring has potential, but improvements in detection and identification technology are needed to match or exceed the accuracy of the conventional aerial survey technique for kangaroos.

Implications
Recent advances in camera technology and methodological refinements are encouraging for aerial survey of wildlife using UAS. However, significant improvements are required to survey for kangaroos and new technology should again be tested against current benchmarks.
Key comparison BIPM.RI(I)-K1 of the air-kerma standards of VSL, The Netherlands, and the BIPM in 60Co gamma radiation
Authors: Kessler C , Burns D , Jansen B J , Pooter J A de , Prez L A de
Published: November 2018

A key comparison of the standards for air kerma of VSL, Dutch Metrology Institute, The Netherlands (VSL) and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in December 2017. The comparison result, based on the calibration coefficients for two transfer chambers and expressed as a ratio of the VSL and the BIPM standards for air kerma, is 0.9963 with a combined standard uncertainty of 2.1 x 10-3. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

KEY WORDS FOR SEARCH

Comparison, radiation dosimetry, air kerma, 60Co

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Simulation Analysis of Influence of Boundary Parameters on the Performance of Gasoline Compression Ignition Engine
Authors: Lei peng , Zhang Guangde , Xie Kunpeng , Peng Chunmeng , Wang Huan
Published: November 2018

In order to solve the problems of combustion instability and excessive discharge of gasoline compression ignition (GCI) engine at low load, three-dimensional numerical simulation software CONVERGE is used to establish engine simulation model, and the main factors controlling combustion such as the oxygen content and the intake pressure are simulated and analyzed. The results show that when the volume fraction of the oxygen content of intake is 23%, higher thermal efficiency and lower emissions can be achieved. When the intake pressure is 0.12MPa, the peak of heat release rate is the highest and the combustion efficiency is high. The research results provide basic data and theoretical basis for achieving stable combustion at low load conditions.
RETRACTED: Construction of the Course System of Mechanical and Electronic Specialty for Applied Undergraduate Course -- Teaching Direction of Industrial Robot
Authors: Lu Yaping , Liu Hejian
Published: November 2018

Under the background of “Internet + Made in China 2025” production and education integration innovation promotion plan. According to the professional uniqueness and social needs of applied undergraduate education. Take the teaching direction of industrial robots in the field of mechanical electronics as an example. The paper proposed the teaching of professional basic courses as the basis, the professional direction of curriculum teaching as the focus, professional quality and innovative entrepreneurship education curriculum as a fundamental, three training courses for the innovation of the curriculum system. All kinds of courses include in-class courses (the first class) and extra-curricular courses (the second class), the two classes with other courses, enrich the entire teaching system. And through the series of industrial robotic laboratory construction and management model innovations, it can achieve the true experience of students’ corporate life and the wide range of students’ second classroom activities; it can cultivate excellent applied talents.
Different SUMO paralogues determine the fate of wild-type and mutant CFTRs: biogenesis versus degradation
Authors: Gong Xiaoyan , Liao Yong , Ahner Annette , Larsen Mads Breum , Wang Xiaohui , Bertrand Carol A. , Frizzell Raymond A.
Published: November 2018

A pathway for cystic fibrosis transmembrane conductance regulator (CFTR) degradation is initiated by Hsp27, which cooperates with Ubc9 and binds to the common F508del mutant to modify it with SUMO-2/3. These SUMO paralogues form polychains, which are recognized by the ubiquitin ligase, RNF4, for proteosomal degradation. Here, protein array analysis identified the SUMO E3, protein inhibitor of activated STAT 4 (PIAS4), which increased wild-type (WT) and F508del CFTR biogenesis in CFBE airway cells. PIAS4 increased immature CFTR threefold and doubled expression of mature CFTR, detected by biochemical and functional assays. In cycloheximide chase assays, PIAS4 slowed immature F508del degradation threefold and stabilized mature WT CFTR at the plasma membrance. PIAS4 knockdown reduced WT and F508del CFTR expression by 40–50%, suggesting a physiological role in CFTR biogenesis. PIAS4 modified F508del CFTR with SUMO-1 in vivo and reduced its conjugation to SUMO-2/3. These SUMO paralogue-specific effects of PIAS4 were reproduced in vitro using purified F508del nucleotide-binding domain 1 and SUMOylation reaction components. PIAS4 reduced endogenous ubiquitin conjugation to F508del CFTR by ∼50% and blocked the impact of RNF4 on mutant CFTR disposal. These findings indicate that different SUMO paralogues determine the fates of WT and mutant CFTRs, and they suggest that a paralogue switch during biogenesis can direct these proteins to different outcomes: biogenesis versus degradation.
Construction and next-generation sequencing analysis of a large phage-displayed VNAR single-domain antibody library from six naïve nurse sharks
Authors: Feng Mingqian , Bian Hejiao , Wu Xiaolin , Fu Tianyun , Fu Ying , Hong Jessica , Fleming Bryan D , Flajnik Martin F , Ho Mitchell
Published: November 2018

Background

Shark new antigen receptor variable domain (VNAR) antibodies can bind restricted epitopes that may be inaccessible to conventional antibodies.

Methods

Here, we developed a library construction method based on polymerase chain reaction (PCR)-Extension Assembly and Self-Ligation (named “EASeL”) to construct a large VNAR antibody library with a size of 1.2 × 1010 from six naïve adult nurse sharks (Ginglymostoma cirratum).

Results

The next-generation sequencing analysis of 1.19 million full-length VNARs revealed that this library is highly diversified because it covers all four classical VNAR types (Types I–IV) including 11% of classical Type I and 57% of classical Type II. About 30% of the total VNARs could not be categorized as any of the classical types. The high variability of complementarity determining region (CDR) 3 length and cysteine numbers are important for the diversity of VNARs. To validate the use of the shark VNAR library for antibody discovery, we isolated a panel of VNAR phage binders to cancer therapy-related antigens, including glypican-3, human epidermal growth factor receptor 2 (HER2), and programmed cell death-1 (PD1). Additionally, we identified binders to viral antigens that included the Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) spike proteins. The isolated shark single-domain antibodies including Type I and Type II VNARs were produced in Escherichia coli and validated for their antigen binding. A Type II VNAR (PE38-B6) has a high affinity (Kd = 10.1 nM) for its antigen.

Conclusions

The naïve nurse shark VNAR library is a useful source for isolating single-domain antibodies to a wide range of antigens. The EASeL method may be applicable to the construction of other large diversity gene expression libraries.
Trap Crops: How Far We Are From Using Them in Cereal Crops?
Authors: Sharma Anamika , Shrestha Govinda , Reddy Gadi V P
Published: November 2018

Trap crops are plants grown along with the main crop in order to manipulate insect behavior to manage the insect pests and are used as a cultural management strategy in several crops. Trap crops also provide habitat to natural enemies and can reduce the need for insecticides and hence reduce the development of insecticide resistance. The attractiveness of the trap crop, the timing of planting, and the space it occupies are major factors to consider before selecting and using a trap crop. The addition of semiochemicals and incorporation of ‘stimulo-deterrent diversion’ can increase the efficiency of trap crops. The important insect pests of cereal crops reported to managed by using trap crops include the wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), on wheat and the stem borers Chilo partellus (Swinhoe) and Busseola fusca (Fuller) on maize and sorghum. Other insect pests such as soil-dwelling wireworms [Agriotes obscurus L., Limonius californicus (Mannerheim) (Coleoptera: Elateridae)] on potatoes and the aphids Schizaphis graminum (Rondani) (Hemiptera: Aphididae), and Rhopalosiphum padi L. on wheat and the brown planthopper Nilaparvata lugens (Stål) on rice are also possible to manage by using trap crops. Cereal crops such as maize and wheat are sometimes themselves used as trap crops, yet there have been only a handful of attempts made to use trap crops in cereal crops. The major limiting factors in using trap crops in cereal crops are environmental conditions, variation in landscape and cultivation practices. Nonetheless, trap crops remain an important tool of integrated pest management, and future studies should work to improve the efficacy, cost efficiency, and availability of alternative trap crops for use in cereal cultivation.
Evaluation of Exposure Assessment Tools under REACH: Part II—Higher Tier Tools
Authors: Lee Eun Gyung , Lamb Judith , Savic Nenad , Basinas Ioannis , Gasic Bojan , Jung Christian , Kashon Michael L , Kim Jongwoon , Tischer Martin , van Tongeren Martie , Vernez David , Harper Martin
Published: November 2018

Stoffenmanager®v4.5 and Advanced REACH Tool (ART) v1.5, two higher tier exposure assessment tools for use under REACH, were evaluated by determining accuracy and robustness. A total of 282 exposure measurements from 51 exposure situations (ESs) were collected and categorized by exposure category. In this study, only the results of liquids with vapor pressure (VP) > 10 Pa category having a sufficient number of exposure measurements (n = 251 with 42 ESs) were utilized. In addition, the results were presented by handling/activity description and input parameters for the same exposure category. It should be noted that the performance results of Stoffenmanager and ART in this study cannot be directly compared for some ESs because ART allows a combination of up to four subtasks (and nonexposed periods) to be included, whereas the database for Stoffenmanager, separately developed under the permission of the legal owner of Stoffenmanager, permits the use of only one task to predict exposure estimates. Thus, it would be most appropriate to compare full-shift measurements against ART predictions (full shift including nonexposed periods) and task-based measurements against task-based Stoffenmanager predictions. For liquids with VP > 10 Pa category, Stoffenmanager®v4.5 appeared to be reasonably accurate and robust when predicting exposures [percentage of measurements exceeding the tool’s 90th percentile estimate (%M > T) was 15%]. Areas that could potentially be improved include ESs involving the task of handling of liquids on large surfaces or large work pieces, allocation of high and medium VP inputs, and absence of local exhaust ventilation input. Although the ART’s median predictions appeared to be reasonably accurate for liquids with VP > 10 Pa, the %M > T for the 90th percentile estimates was 41%, indicating that variance in exposure levels is underestimated by ART. The %M > T using the estimates of the upper value of 90% confidence interval (CI) of the 90th percentile estimate (UCI90) was considerably reduced to 18% for liquids with VP > 10 Pa. On the basis of this observation, users might be to consider using the upper limit value of 90% CI of the 90th percentile estimate for predicting reasonable worst case situations. Nevertheless, for some activities and input parameters, ART still shows areas to be improved. Hence, it is suggested that ART developers review the assumptions in relation to exposure variability within the tool, toward improving the tool performance in estimating percentile exposure levels. In addition, for both tools, only some handling/activity descriptions and input parameters were considered. Thus, further validation studies are still necessary.
BacPaCS—Bacterial Pathogenicity Classification via Sparse-SVM
Authors: Barash Eran , Sal-Man Neta , Sabato Sivan , Ziv-Ukelson Michal
Published: November 2018

Motivation

Bacterial infections are a major cause of illness worldwide. However, most bacterial strains pose no threat to human health and may even be beneficial. Thus, developing powerful diagnostic bioinformatic tools that differentiate pathogenic from commensal bacteria are critical for effective treatment of bacterial infections.

Results

We propose a machine-learning approach for classifying human-hosted bacteria as pathogenic or non-pathogenic based on their genome-derived proteomes. Our approach is based on sparse Support Vector Machines (SVM), which autonomously selects a small set of genes that are related to bacterial pathogenicity. We implement our approach as a tool—‘Bacterial Pathogenicity Classification via sparse-SVM’ (BacPaCS)—which is fully automated and handles datasets significantly larger than those previously used. BacPaCS shows high accuracy in distinguishing pathogenic from non-pathogenic bacteria, in a clinically relevant dataset, comprising only human-hosted bacteria. Among the genes that received the highest positive weight in the resulting classifier, we found genes that are known to be related to bacterial pathogenicity, in addition to novel candidates, whose involvement in bacterial virulence was never reported.

Availability and implementation

The code and the resulting model are available at: https://github.com/barashe/bacpacs.

Supplementary information

Supplementary data are available at Bioinformatics online.
DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence
Authors: Xue Li , Tang Bin , Chen Wei , Luo Jiesi
Published: November 2018

Motivation

Various bacterial pathogens can deliver their secreted substrates also called effectors through Type III secretion systems (T3SSs) into host cells and cause diseases. Since T3SS secreted effectors (T3SEs) play important roles in pathogen–host interactions, identifying them is crucial to our understanding of the pathogenic mechanisms of T3SSs. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to develop a novel and effective method to screen and select putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments.

Results

We develop a deep convolution neural network to directly classify any protein sequence into T3SEs or non-T3SEs, which is useful for both effector prediction and the study of sequence-function relationship. Different from traditional machine learning-based methods, our method automatically extracts T3SE-related features from a protein N-terminal sequence of 100 residues and maps it to the T3SEs space. We train and test our method on the datasets curated from 16 species, yielding an average classification accuracy of 83.7% in the 5-fold cross-validation and an accuracy of 92.6% for the test set. Moreover, when comparing with known state-of-the-art prediction methods, the accuracy of our method is 6.31–20.73% higher than previous methods on a common independent dataset. Besides, we visualize the convolutional kernels and successfully identify the key features of T3SEs, which contain important signal information for secretion. Finally, some effectors reported in the literature are used to further demonstrate the application of DeepT3.

Availability and implementation

DeepT3 is freely available at: https://github.com/lje00006/DeepT3.

Supplementary information

Supplementary data are available at Bioinformatics online.
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
Authors: Smaili Fatima Zohra , Gao Xin , Hoehndorf Robert
Published: November 2018

Motivation

Ontologies are widely used in biology for data annotation, integration and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information that characterize ontology classes. Annotation axioms commonly used in ontologies include class labels, descriptions or synonyms. Despite being a rich source of semantic information, the ontology meta-data are generally unexploited by ontology-based analysis methods such as semantic similarity measures.

Results

We propose a novel method, OPA2Vec, to generate vector representations of biological entities in ontologies by combining formal ontology axioms and annotation axioms from the ontology meta-data. We apply a Word2Vec model that has been pre-trained on either a corpus or abstracts or full-text articles to produce feature vectors from our collected data. We validate our method in two different ways: first, we use the obtained vector representations of proteins in a similarity measure to predict protein–protein interaction on two different datasets. Second, we evaluate our method on predicting gene–disease associations based on phenotype similarity by generating vector representations of genes and diseases using a phenotype ontology, and applying the obtained vectors to predict gene–disease associations using mouse model phenotypes. We demonstrate that OPA2Vec significantly outperforms existing methods for predicting gene–disease associations. Using evidence from mouse models, we apply OPA2Vec to identify candidate genes for several thousand rare and orphan diseases. OPA2Vec can be used to produce vector representations of any biomedical entity given any type of biomedical ontology.

Availability and implementation

https://github.com/bio-ontology-research-group/opa2vec

Supplementary information

Supplementary data are available at Bioinformatics online.
Age-Related Differences in Brain Morphology and the Modifiers in Middle-Aged and Older Adults
Authors: Zhao Lu , Matloff William , Ning Kaida , Kim Hosung , Dinov Ivo D , Toga Arthur W
Published: November 2018

Brain structural morphology differs with age. This study examined age-differences in surface-based morphometric measures of cortical thickness, volume, and surface area in a well-defined sample of 8137 generally healthy UK Biobank participants aged 45–79 years. We illustrate that the complexity of age-related brain morphological differences may be related to the laminar organization and regional evolutionary history of the cortex, and age of about 60 is a break point for increasing negative associations between age and brain morphology in Alzheimer’s disease (AD)-prone areas. We also report novel relationships of age-related cortical differences with individual factors of sex, cognitive functions of fluid intelligence, reaction time and prospective memory, cigarette smoking, alcohol consumption, sleep disruption, genetic markers of apolipoprotein E, brain-derived neurotrophic factor, catechol-O-methyltransferase, and several genome-wide association study loci for AD and further reveal joint effects of cognitive functions, lifestyle behaviors, and education on age-related cortical differences. These findings provide one of the most extensive characterizations of age associations with major brain morphological measures and improve our understanding of normal structural brain aging and its potential modifiers.