bluuebunny/crossref_metadata_2025 huggingface dataset:
A theoretical and experimental formalism of electronic structure of BFO:Cr thin films and modulation of their electrical properties upon visible light illumination
Authors: Ameer Shaan , Jindal Kajal , Tomar Monika , Kumar Ashok , Jha Pradip K. , Gupta Vinay
Published: October 2018

BiFeO3 (BFO) and BiFe1-xCrxO3 (BFCO) (x = 0, 0.01, 0.02, 0.03) thin films have been fabricated using chemical solution deposition technique. The bandgap of BFO and BFCO thin films is found to be lying in the visible region making these films suitable candidates for potential solar energy harvesting applications. Density functional theory based calculations have also been performed to study the effect of B-site (Cr) doping on the electronic properties of BFO and BFCO. The BiFe1-xCrxO3 (x = 0.02) thin films exhibited well saturated PE hysteresis loops with a maximum remanent and saturation polarization of about 43 μC/cm2 and 64 μC/cm2, respectively. In contrast to pure BFO, a high value of short circuit current density (Jsc) of magnitude 766.60 μA/cm2 along with the open circuit voltage (Voc) of 106 mV was obtained for BiFe0.98Cr0.02O3 thin film structure under illumination with a laser of wavelength 470 nm and intensity 20 mW/cm2. The Au/BiFe0.98Cr0.02O3/ITO/glass heterostructure displays a remarkably enhanced value of Ion/Ioff ratio (8.4 × 104). The observed results clearly highlight the potential of Cr doped BFO thin film structure for the development of cost effective light-driven devices.
Velocity-space sensitivity of the compact neutron emission spectrometers at EAST
Authors: Zhang Y. M. , Ge L. J. , Sun J. Q. , Hu Z. M. , Nocente M. , Gorini G. , Tardocchi M. , Zhong G. Q. , Hu L. Q. , Li X. Q. , Fan T. S.
Published: October 2018

Several compact neutron spectrometers are now installed at EAST (Experimental Advanced Superconducting Tokamak) to obtain information on fuel ions produced in the core of the plasma. In this paper, a stilbene crystal neutron spectrometer and an EJ301 liquid scintillator neutron spectrometer with n-γ discrimination capability will be discussed. Both spectrometers have a horizontal line of sight, while at different positions. In the last few experiment campaigns at EAST, they all proved to be reliable diagnostics for auxiliary heated D–D plasmas. Taking the response function simulated by dedicated Geant4 models into consideration, the velocity-space sensitivities given by the instrument-specific weight function of the beam-thermal part of neutron energy spectra in D–D plasmas are derived for both spectrometers with the Genesis code. This method makes it possible to directly relate the contribution of different deuteron velocity space regions to events in each channel of the neutron spectrum measured by the two instruments: http://rsi-htpd.peerx-press.org/.
Gallium nitride (GaN) devices as a platform technology for radiation hard inertial confinement fusion diagnostics
Authors: Sun K.-X. , Valles M. , Valencia H. , Nelson R.O.
Published: October 2018

Inertial Confinement Fusion (ICF) is undergoing more detailed research to increase neutron yield and will require high resolution imaging near the target. Neutron damage to diagnostics remains a serious issue in understanding and achieving ICF. We have demonstrated that Gallium Nitride (GaN) optoelectronic devices have exceptional neutron radiation hardness, by systematic testing of neutron radiation effects in GaN devices and materials with elevated neutron fluence levels and a broad neutron energy spectrum. During the 2013-2017 run cycles at Los Alamos Neutron Science Center (LANSCE), we irradiated various GaN materials and devices with fast and thermal plus resonance neutrons at several beamlines. This paper presents a radiation hardness study for Aluminum Gallium Nitride and Gallium Nitride (AlGaN/GaN) deep UV LEDs irradiated at the LANSCE 4FP60R beamline. The fluence level was up to 2.4 × 1013 neutrons/cm2 for neutrons with energies greater than 0.1 MeV. The device performance was monitored in real time. After three years of irradiation studies, we found that the GaN devices maintained operation in the forward active region. The current and voltage relation (I-V curves) varied insignificantly in the linear region. Our results demonstrate the radiation hardness needed for laser fusion diagnostics at least up to 1017 neutron yield per shot, if the diagnostics is placed 1 m away from the target, where the neutron fluence per shot is approximately 8 × 1011 n/cm2. The GaN devices can operate for multiple shots.
Tutorial: Photonic neural networks in delay systems
Authors: Brunner D. , Penkovsky B. , Marquez B. A. , Jacquot M. , Fischer I. , Larger L.
Published: October 2018

Photonic delay systems have revolutionized the hardware implementation of Recurrent Neural Networks and Reservoir Computing in particular. The fundamental principles of Reservoir Computing strongly facilitate a realization in such complex analog systems. Especially delay systems, which potentially provide large numbers of degrees of freedom even in simple architectures, can efficiently be exploited for information processing. The numerous demonstrations of their performance led to a revival of photonic Artificial Neural Network. Today, an astonishing variety of physical substrates, implementation techniques as well as network architectures based on this approach have been successfully employed. Important fundamental aspects of analog hardware Artificial Neural Networks have been investigated, and multiple high-performance applications have been demonstrated. Here, we introduce and explain the most relevant aspects of Artificial Neural Networks and delay systems, the seminal experimental demonstrations of Reservoir Computing in photonic delay systems, plus the most recent and advanced realizations.
Recent advances in Dirac spin-gapless semiconductors
Authors: Wang Xiaotian , Li Tingzhou , Cheng Zhenxiang , Wang Xiao-Lin , Chen Hong
Published: October 2018

Spin-gapless semiconductors (SGSs), the new generation of spintronic materials, have received increasing attention recently owing to their various attractive properties such as fully spin-polarization and high carrier mobility. Based on their unique band structures, SGSs can be divided into two types: parabolic and Dirac-like linear. The linear-type SGSs, also called Dirac SGSs (DSGSs), have real massless fermions and dissipation-less transport properties, and thus are regarded as promising material candidates for applications in ultra-fast and ultra-low-power spintronic devices. DSGSs can be further classified into p-state type or d-state type depending on the degree of contribution of either the p-orbitals or d-orbitals to the Dirac states. Considering the importance of the research field and to cover its fast development, we reviewed the advances in DSGSs and proposed our own viewpoints. First, we introduced the computational algorithms of SGSs. Second, we found that the boundaries between DSGSs and Dirac half-metals were frequently blurred. Therefore, a simple classification is proposed in this work. Third, we collected almost all the studies on DSGSs published in the past six years. Finally, we proposed new guidance to search for DSGSs among 3D bulk materials on the basis of our latest results.
Adaptive coupling of a deep neural network potential to a classical force field
Authors: Zhang Linfeng , Wang Han , E Weinan
Published: October 2018

An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is decomposed into three types of regions. The first type captures the important phenomena in the system and requires high accuracy, for which we use the Deep Potential Molecular Dynamics (DeePMD) model in this work. The DeePMD model is trained to accurately reproduce the statistical properties of the ab initio molecular dynamics. The second type does not require high accuracy, and a classical force field is used to describe it in an efficient way. The third type is used for a smooth transition between the first and the second types of regions. By using a force interpolation scheme and imposing a thermodynamics force in the transition region, we make the DeePMD region embedded in the AMM simulated system as if it were embedded in a system that is fully described by the accurate potential. A representative example of the liquid water system is used to show the feasibility and promise of this method.
Analog reversible nonvolatile memcapacitance in metal-oxide-semiconductor memcapacitor with ITO/HfOx/Si structure
Authors: Park Daehoon , Yang Paul , Kim Hyung Jun , Beom Keonwon , Lee Hyun Ho , Kang Chi Jung , Yoon Tae-Sik
Published: October 2018

We demonstrate strong, analog, reversible, and nonvolatile memcapacitance in a Si-based MOS (metal-oxide-semiconductor) memcapacitor with an ITO (In-Sn-O)/HfOx/Si structure. Both accumulation and depletion capacitances change sequentially and reversibly upon repeating voltage application with respect to voltage polarity. This memcapacitance is thought to be induced by oxygen ions' migration between ITO and HfOx layers, which changes the HfOx permittivity and the depletion states in Si and ITO. The Si-based memcapacitor has potential to be applied to the gate stack of the MOS field-effect-transistor for nonvolatile memory and synaptic transistors through modulating drain current determined by the capacitance change of the MOS gate stack.
Probing the impact of energetic argon ions on the structural properties of ZnO:Al/TiO2 heterostructures
Authors: Saini C. P. , Barman A. , Kumar N. , Cours R. , Joulie S. , Serin V. , Claverie A. , Sinha A. K. , Kanjilal D. , Kanjilal A.
Published: October 2018

The efficacy of 50 keV Ar+-ion irradiation toward the interfacial and stoichiometric engineering of strained Al-doped ZnO (AZO)/TiO2 heterostructure is systematically investigated using a variety of experimental techniques, notably by cross-sectional transmission electron microscopy. Glancing-angle X-ray diffraction evidences the release of in-plane compressive stress from the as-grown AZO/TiO2 bilayer structure at a critical fluence of 1 × 1016 ions/cm2, and we discuss in the light of microcracks and voids formation combined with the dewetting phenomenon. Ion irradiation also leads to an improvement of stoichiometry in both top AZO and underneath amorphous TiO2 layers, as manifested by depth-dependent energy dispersive X-ray spectroscopy owing to the large diffusion of oxygen toward the AZO/TiO2 interfacial region through the AZO defect sites. Such ion beam induced self-healing in stoichiometry of AZO/TiO2 heterostructure has been attributed to a conjunction of sputtering and diffusion phenomena involving the constituent elements (Zn, Ti, and O). Further increase in ion fluence up to 5 × 1016 ions/cm2 causes a complete deterioration of the heterostructure with the formation of a graded layer via intermixing of these elements, followed by the evolution of voids.
A non-destructive method to calibrate the torsional spring constant of atomic force microscope cantilevers in viscous environments
Authors: Cafolla Clodomiro , Payam Amir F. , Voïtchovsky Kislon
Published: October 2018

Calibration of the torsional spring constant of atomic force microscopy cantilevers is fundamental to a range of applications, from nanoscale friction and lubrication measurements to the characterization of micro-electromechanical systems and the response of biomolecules to external stimuli. Existing calibration methods are either time consuming and destructive (ex situ static approaches), or rely on models using the frequency and quality factor (Q-factor) of the cantilever torsional resonance as input parameters (in situ dynamical approaches). While in situ approaches are usually preferred for their easy implementation and preservation of the cantilever, their dependence on the torsional resonance Q-factor renders calibration in highly viscous environments challenging. This is problematic, for example, in many nanoscale tribological applications. Here, we propose a calibration method that does not depend on the cantilever torsional Q-factor and show how the cantilever deflection can be converted into a lateral force. The method is tested with six cantilevers of different shapes and material composition and in six fluid media. The derived spring constants are compared with predictions from existing methods, demonstrating a higher precision, in particular, for highly viscous liquids.
Material influence on GHz split-ring resonator plasma ignition performance
Authors: Cohick Z. , Perini S. , Wolfe D. , Lanagan M.
Published: October 2018

Split-ring resonators have been popularized by their application in metamaterials, but their ability to concentrate electric fields has also made them useful as microwave plasma generators. Despite the existence of much work on plasma generation using ring resonators, a comparative study of the effect of different materials on plasma generation performance has been absent. This work focuses on the study of material effects on ring resonators' microwave properties and plasma generation performance at pressures ranging from 4 to 100 Torr. To achieve this end, screen-printed silver and gold ring resonators are studied due to their high conductivity, relatively low reactivity, and differences in conductivity and work function. The surface morphology and chemistry of the ring resonators are studied using optical profilometry, scanning electron microscopy, and X-ray photoelectron spectroscopy. It is found that the main factor influencing performance between these two materials is Q-factor, which is determined using both conventional bandwidth measurements and measurements of conductivity. Q-factor is further isolated by modifying a silver ring resonator such that its Q-factor matches gold ring resonators. In addition, a film formed on the silver resonators after plasma exposure provides an opportunity to study a material, which, unlike gold, is quite different from silver. With the film present, plasma generation performance is decreased with increasing severity as pressure is decreased—20% more power is required for breakdown at 4 Torr. This change is qualitatively consistent with a model of microwave plasma breakdown where boundary effects are expected to increase as pressure is decreased.
Collisional dissipation of the laser-induced alignment of ethane gas: A requantized classical model
Authors: Hartmann J.-M. , Boulet C. , Zhang H. , Billard F. , Faucher O. , Lavorel B.
Published: October 2018

We present the first theoretical study of collisional dissipation of the alignment of a symmetric-top molecule (ethane gas) impulsively induced by a linearly polarized non-resonant laser field. For this, Classical Molecular Dynamics Simulations (CMDSs) are carried out for an ensemble of C2H6 molecules based on knowledge of the laser-pulse characteristics and on an input intermolecular potential. These provide, for a given gas pressure and initial temperature, the orientations of all molecules at all times from which the alignment factor is directly obtained. Comparisons with measurements show that these CMDSs well predict the permanent alignment induced by the laser pulse and its decay with time but, as expected, fail in generating alignment revivals. However, it is shown that introducing a simple requantization procedure in the CMDS “creates” these revivals and that their predicted dissipation decay agrees very well with measured values. The calculations also confirm that, as for linear molecules, the permanent alignment of ethane decays more slowly than the transient revivals. The influence of the intermolecular potential is studied as well as that of the degree of freedom associated with the molecular rotation around the symmetry axis. This reveals that ethane practically behaves as a linear molecule because the intermolecular potential is only weakly sensitive to rotation around the C–C axis.
Experimental tests of an infrared video bolometer on Alcator C-Mod
Authors: Reinke M. L. , Terry J. L. , van Eden G. G. , Peterson B. J. , Mukai K. , Gray T. K. , Stratton B. C.
Published: October 2018

A prototype of an infrared imaging bolometer (IRVB) was successfully tested on the Alcator C-Mod tokamak at the end of its 2016 campaign. The IRVB method interprets the power radiated from the plasma by measuring the temperature rise of a thin, ∼2 μm, Pt absorber that is placed in the torus vacuum and exposed, using a pinhole camera, to the full-spectrum of plasma’s photon emission. The IRVB installed on C-Mod viewed the poloidal cross section of the core plasma and observed Ohmic and ion cyclotron range of frequency (ICRF)-heated plasmas. Analysis of total radiated power and on-axis emissivity from IRVB is summarized, and quantitative comparisons made to data from both resistive bolometers and AXUV diodes. IRVB results are clearly within a factor of two, but additional effort is needed for it to be used to fully support power exhaust research. The IRVB is shown to be immune to electromagnetic interference from ICRF which strongly impacts C-Mod’s resistive bolometers. Results of the bench-top calibration are summarized, including a novel temperature calibration method useful for IRVBs.
Bubble regime of plasma wakefield in 2D and 3D geometries
Authors: Golovanov A. A. , Kostyukov I. Yu.
Published: October 2018

Considering the popularity of two-dimensional particle-in-cell simulations, a planar 2D model of plasma wakefield in the strongly nonlinear (bubble) regime in transversely non-uniform plasma is developed. A differential equation for the boundary of the bubble in the 2D geometry is obtained, and its analytic solution is derived. 2D particle-in-cell simulations are used to confirm the validity of our model. The results are compared to the conventional axisymmetric bubble in the realistic 3D geometry. For uniform plasma, it is shown that the 2D bubble is elongated and has stronger focusing forces, while the structure of the accelerating field remains completely unchanged. A method of generating a quasi-2D bubble in the 3D space is proposed.
Determining whether diabolical singularities limit the accuracy of molecular property based diabatic representations: The 1,21A states of methylamine
Authors: Wang Yuchen , Yarkony David R.
Published: October 2018

An efficient, easily implemented method for locating singularities attributable to the failure of the defining equations in a molecular property based diabatization, termed diabolical singular points, is reported. For two state diabatizations, the singular points form a seam of dimension Nint − 2, where Nint is the number of internal degrees of freedom. The dynamical outcomes of nuclear trajectories that reach the region of this seam are flawed. The algorithm easily identifies these otherwise hard to anticipate regions of fallaciously large derivative coupling. The fact that the algorithm is easily incorporated into a two state diabatization code based on molecular properties makes it a practical tool for determining whether the existence of diabolical singularities is relevant to the problem being considered. The algorithm is illustrated using a multireference single and double excitation configuration interaction description of the 1,21A states of CH3NH2.
Effect of carbon on boron diffusion and clustering in silicon: Temperature dependence study
Authors: Tu Y. , Shimizu Y. , Kunimune Y. , Shimada Y. , Katayama T. , Ide T. , Inoue M. , Yano F. , Inoue K. , Nagai Y.
Published: October 2018

Atom probe tomography and secondary ion mass spectrometry were used to investigate the effects of carbon (C) co-implantation and subsequent annealing at 600 to 1200 °C on the behavior of implanted boron (B) atoms in silicon. When B alone was implanted, annealing at 600 to 800 °C caused it to form clusters in the peak region (1020 cm−3) of the concentration profile, and diffusion only occurred in the low-concentration tail region (<1018 cm−3), which is thought to be the well-known transient enhanced diffusion. However, when co-implantation with C was performed, this diffusion was almost completely suppressed in the same annealing temperature range. In the absence of C implantation, annealing at 1000 °C caused B clusters to begin to dissolve and B to diffuse out of the peak concentration region. However, this diffusion was also suppressed by C implantation because C atoms trapped B atoms in the kink region found at the B concentration level of 2 × 1019 cm−3. At 1200 °C, B clusters were totally dissolved and a strong B diffusion occurred. In contrast to lower annealing temperatures, this diffusion was actually enhanced by C implantation. It is believed that Si interstitials play an important role in the interaction between B and C. This kind of comprehensive investigation yields important information for optimizing ion implantation and annealing processes.
Materials for optical fiber lasers: A review
Authors: Dragic P. D. , Cavillon M. , Ballato J.
Published: October 2018

Over the past two decades, fiber laser technologies have matured to such an extent that they have captured a large portion of the commercial laser marketplace. Yet, there still is a seemingly unquenchable thirst for ever greater optical power to levels where certain deleterious light-matter interactions that limit continued power scaling become significant. In the past decade or so, the industry has focused mainly on waveguide engineering to overcome many of these hurdles. However, there is an emerging body of work emphasizing the enabling role of the material. In an effort to underpin these developments, this paper reviews the relevance of the material in high power fiber laser technologies. As the durable material-of-choice for the application, the discussion will mainly be limited to silicate host glasses. The discussion presented herein follows an outward path, starting with the trivalent rare earth ions and their spectroscopic properties. The ion then is placed into a host, whose impact on the spectroscopy is reviewed. Finally, adverse interactions between the laser lightwave and the host are discussed, and novel composition glass fiber design and fabrication methodologies are presented. With deference to the symbiosis required between material and waveguide engineering in active fiber development, this review will emphasize the former. Specifically, where appropriate, materials-based paths to the enhancement of laser performance will be underscored.
Changes in output parameters of 1 MeV electron irradiated upright metamorphic GaInP/GaInAs/Ge triple junction solar cell
Authors: Heini M. , Aierken A. , Li Z. H. , Zhao X. F. , Sailai M. , Shen X. B. , Xu Y. , Liu H. T. , Li Y. D. , Guo Q. , Liu C. M.
Published: October 2018

The changes in output parameters of 1 MeV electron irradiated MOCVD grown upright metamorphic (UMM) GaInP/GaInAs/Ge triple junction solar cells have been studied. Non-ionizing energy loss (NIEL) approach and MULASSIS simulation were applied for analyzing the effects of irradiation induced displacement damage on cell performance. The influence of base thickness on radiation resistance has been studied by changing the base thickness of top GaInP and middle GaInAs subcell, respectively. The experimental results show that the electrical parameters, Voc, Isc, and Pmax of UMM cell degrade with the increase of electron fluence. The change of spectra response indicates middle GaInAs subcell degrades more severe than top GaInP subcells, and the base thickness of two subcells has different effects on spectra response of UMM cell.
Impact of molecular orientation on energy level alignment at C60/pentacene interfaces
Authors: Nishi Toshio , Kanno Masato , Kuribayashi Miki , Nishida Yasuyo , Hattori Shinnosuke , Kobayashi Hajime , von Wrochem Florian , Rodin Vadim , Nelles Gabriele , Tomiya Shigetaka
Published: October 2018

The molecular orientation and the electronic structure at molecular donor/acceptor interfaces play an important role in the performance of organic optoelectronic devices. Here, we show that graphene substrates can be used as templates for tuning the molecular orientation of pentacene (PEN), selectively driving the formation of either face-on or edge-on arrangements by controlling the temperature of the substrate during deposition. The electronic structure and morphology of the two resulting C60/PEN heterointerfaces were elucidated using ultraviolet photoelectron spectroscopy and atomic force microscopy, respectively. While the C60/PEN (edge-on) interface exhibited a vacuum level alignment, the C60/PEN (face-on) interface exhibited a vacuum level shift of 0.2 eV, which was attributed to the formation of an interface dipole that resulted from polarization at the C60/PEN boundary.
Free field structure of the model with a spin-32 Rarita-Schwinger field directly coupled to a spin-12 field
Authors: Adler Stephen L.
Published: October 2018

In earlier work we introduced an abelianized gauge field model in which a Rarita-Schwinger field is directly coupled to a spin-12 field, and showed that this model admits a perturbative expansion in the gauge field coupling. As a preliminary to further study of the coupled model, in this paper we present a detailed analysis of the free field structure that obtains when the dimensionless gauge coupling is set to zero, but the dimension one coupling of the spin-32 and spin-12 fields remains nonzero.
Cancer cell death by cold atmospheric plasma gets a boost with nitrogen supplements
Authors: Johnson-Groh Mara
Published: October 2018

By introducing nitrate and nitrite, cancer cell death by cold atmospheric plasma is improved without changing the discharge parameters.
Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations
Authors: Quinn Caitlin M. , Wang Mingzhang , Fritz Matthew P. , Runge Brent , Ahn Jinwoo , Xu Chaoyi , Perilla Juan R. , Gronenborn Angela M. , Polenova Tatyana
Published: October 2018

Significance

The mechanisms of how TRIM5α interferes with the integrity of the HIV-1 capsid to restrict HIV-1 infectivity remain poorly understood. We examined, at atomic resolution, the interactions with TRIM5α in the assembled capsid and the dynamics of capsid’s hexameric and pentameric building blocks. Remarkably, assemblies in the presence of the pentameric subunits are more rigid on microsecond to millisecond timescales at the sites of pentamer incorporation than tubes containing only hexamers. Furthermore, TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces, essential for higher-order capsid assembly. TRIM5α thus uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our results suggest that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.
Mutant UBQLN2 promotes toxicity by modulating intrinsic self-assembly
Authors: Sharkey Lisa M. , Safren Nathaniel , Pithadia Amit S. , Gerson Julia E. , Dulchavsky Mark , Fischer Svetlana , Patel Ronak , Lantis Gabrielle , Ashraf Naila , Kim John H. , Meliki Alia , Minakawa Eiko N. , Barmada Sami J. , Ivanova Magdalena I. , Paulson Henry L.
Published: October 2018

Significance

UBQLN2, a ubiquitin-linked quality-control protein, accumulates in common neurodegenerative diseases and, when mutated, directly causes neurodegeneration. Employing a range of model systems, we show that UBQLN2 is intrinsically prone to self-assemble, leading to the formation of liquid-like droplets and amyloid aggregates. A disease-causing mutation in UBQLN2 impairs droplet dynamics and favors amyloid-like aggregation associated with neurotoxicity. Self-assembly is regulated by ubiquitin-linked domains in UBQLN2, implying a functional relationship between oligomerization and ubiquitin-dependent protein quality control. Our results emphasize a critical link between UBQLN2’s role in ubiquitin-dependent pathways and its propensity to self-assemble and aggregate in neurodegenerative diseases.
Identification of triterpene biosynthetic genes from Momordica charantia using RNA-seq analysis
Authors: Takase Shohei , Kera Kota , Hirao Yuya , Hosouchi Tsutomu , Kotake Yuki , Nagashima Yoshiki , Mannen Kazuto , Suzuki Hideyuki , Kushiro Tetsuo
Published: October 2018

Cucurbitaceae plants contain characteristic triterpenoids. Momordica charantia, known as a bitter melon, contains cucurbitacins and multiflorane type triterpenes, which confer bitter tasting and exhibit pharmacological activities. Their carbon skeletons are biosynthesized from 2,3-oxidosqualene by responsible oxidosqualene cyclase (OSC). In order to identify OSCs in M. charantia, RNA-seq analysis was carried out from ten different tissues. The functional analysis of the resulting four OSC genes revealed that they were cucurbitadienol synthase (McCBS), isomultiflorenol synthase (McIMS), β-amyrin synthase (McBAS) and cycloartenol synthase (McCAS), respectively. Their distinct expression patterns based on RPKM values and quantitative RT-PCR suggested how the characteristic triterpenoids were biosynthesized in each tissue. Although cucurbitacins were finally accumulated in fruits, McCBS showed highest expression in leaves indicating that the early step of cucurbitacins biosynthesis takes place in leaves, but not in fruits.

Abbreviations: OSC: oxidosqualene cyclase; RPKM: reads perkilobase of exon per million mapped reads
Core executive functions are selectively related to different facets of motor competence in preadolescent children
Authors: Ludyga Sebastian , Pühse Uwe , Gerber Markus , Herrmann Christian
Published: October 2018

Background: Although accumulating evidence suggests that motor and cognitive development is interrelated, only a few studies have investigated links between executive function and motor control. Therefore, the present cross‐sectional study examined the relationship between motor competences and core components of executive functioning, including inhibitory control, working memory and cognitive flexibility. Methods: In 89 preadolescent children, motor competences were assessed using the MOBAK‐5 test battery. Additionally, all participants completed computer‐based versions of the Flanker task, which included standard and switch blocks, and the 2‐Back task. Results: Partial correlations (correcting for age, gender and body mass index) revealed that locomotor skills were associated with the adjusted hit‐rate on the 2‐Back task (r = 0.34) whereas object control was linked with conflict score on the Flanker task (r = −0.39). In contrast, there was no correlation between switch costs and motor competences. Conclusion: In preadolescent children, high competences in locomotor skills and object control skills are associated with high performance on specific executive function tasks. This finding supports the current view that motor competences and cognitive control share some common underlying processes.
A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine
Authors: Kasimova Marina A. , Yazici Aysenur Torun , Yudin Yevgen , Granata Daniele , Klein Michael L. , Rohacs Tibor , Carnevale Vincenzo
Published: October 2018

The transient receptor potential channel vanilloid type 1 (TRPV1) is activated by a variety of endogenous and exogenous stimuli and is involved in nociception and body temperature regulation. Although the structure of TRPV1 has been experimentally determined in both the closed and open states, very little is known about its activation mechanism. In particular, the conformational changes that occur in the pore domain and result in ionic conduction have not yet been identified. Here we suggest a hypothetical molecular mechanism for TRPV1 activation, which involves rotation of a conserved asparagine in S6 from a position facing the S4–S5 linker toward the pore. This rotation is associated with hydration of the pore and dehydration of the four peripheral cavities located between each S6 and S4–S5 linker. In light of our hypothesis, we perform bioinformatics analyses of TRP and other evolutionary related ion channels, evaluate newly available structures, and reexamine previously reported water accessibility and mutagenesis experiments. These analyses provide several independent lines of evidence to support our hypothesis. Finally, we show that our proposed molecular mechanism is compatible with the prevailing theory that the selectivity filter acts as a secondary gate in TRPV1.
Emerin induces nuclear breakage inXenopusextract and early embryos
Authors: Dilsaver Matthew R. , Chen Pan , Thompson Trey A. , Reusser Traci , Mukherjee Richik N. , Oakey John , Levy Daniel L.
Published: October 2018

Emerin is an inner nuclear membrane protein often mutated in Emery–Dreifuss muscular dystrophy. Because emerin has diverse roles in nuclear mechanics, cytoskeletal organization, and gene expression, it has been difficult to elucidate its contribution to nuclear structure and disease pathology. In this study, we investigated emerin’s impact on nuclei assembled in Xenopus laevis egg extract, a simplified biochemical system that lacks potentially confounding cellular factors and activities. Notably, these extracts are transcriptionally inert and lack endogenous emerin and filamentous actin. Strikingly, emerin caused rupture of egg extract nuclei, dependent on the application of shear force. In egg extract, emerin localized to nonnuclear cytoplasmic membranes, and nuclear rupture was rescued by targeting emerin to the nucleus, disrupting its membrane association, or assembling nuclei with lamin A. Furthermore, emerin induced breakage of nuclei in early-stage X. laevis embryo extracts, and embryos microinjected with emerin were inviable, with ruptured nuclei. We propose that cytoplasmic membrane localization of emerin leads to rupture of nuclei that are more sensitive to mechanical perturbation, findings that may be relevant to early development and certain laminopathies.
Cardioprotective Effects of Paricalcitol Alone and in Combination With FGF23 Receptor Inhibition in Chronic Renal Failure: Experimental and Clinical Studies
Authors: Czaya Brian , Seeherunvong Wacharee , Singh Saurav , Yanucil Christopher , Ruiz Phillip , Quiroz Yasmir , Grabner Alexander , Katsoufis Chryso , Swaminathan Sethuraman , Abitbol Carolyn , Rodriguez-Iturbe Bernardo , Faul Christian , Freundlich Michael
Published: October 2018

BACKGROUND

In uremic animals, vitamin D receptor (VDR) agonists like paricalcitol (Pc) attenuate cardiac hypertrophy, but this effect has not been replicated consistently in humans with chronic kidney disease. Elevated fibroblast growth factor 23 (FGF23) levels cause cardiac hypertrophy with activation of the myocardial calcineurin/nuclear factor of activated T cell (NFAT) axis and may antagonize the cardioprotective effects of VDR agonist therapy. We hypothesized that the effectiveness of Pc may depend on the prevailing circulating levels of FGF23 and could be potentiated by the combined administration of a pan-FGF23 receptor (FGFR) blocker agent (PD173074).

METHODS

In rats with 5/6 nephrectomy treated with Pc or PD173074 or both agents concurrently, myocardial mRNA expression of renin–angiotensin system, VDR, FGFR4, and calcineurin/NFAT target genes was determined. In adolescents on hemodialysis, we analyzed sequential echocardiograms, blood pressures and serial FGF23 measurements, and their relations to the cumulative administered dose of parenteral Pc.

RESULTS

The ratio of Pc dose/plasma levels of FGF23 correlated inversely (P < 0.005) with the cardiac mass in uremic rats and in hemodialysis patients, independently of hypertension. Despite persistently elevated FGF23 levels and myocardial FGFR4 activation, Pc suppressed upregulated myocardial calcineurin/NFAT target genes, and the effects were amplified by coadministration of PD173074.

CONCLUSIONS

The beneficial effects of Pc on uremic cardiac hypertrophy are counterbalanced by the increased FGF23 levels. Blockade of FGF23-mediated signaling increased the Pc-induced suppression of the myocardial calcineurin/NFAT system. Higher doses of Pc should be considered in the treatment of patients with uremic cardiomyopathy.
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles
Authors: Sun Saisai , Wu Qi , Peng Zhenling , Yang Jianyi
Published: October 2018

Motivation

The de novo prediction of RNA tertiary structure remains a grand challenge. Predicted RNA solvent accessibility provides an opportunity to address this challenge. To the best of our knowledge, there is only one method (RNAsnap) available for RNA solvent accessibility prediction. However, its performance is unsatisfactory for protein-free RNAs.

Results

We developed RNAsol, a new algorithm to predict RNA solvent accessibility. RNAsol was built based on improved sequence profiles from the covariance models and trained with the long short-term memory (LSTM) neural networks. Independent tests on the same datasets from RNAsnap show that RNAsol achieves the mean Pearson’s correlation coefficient (PCC) of 0.43/0.26 for the protein-bound/protein-free RNA molecules, which is 26.5%/136.4% higher than that of RNAsnap. When the training set is enlarged to include both types of RNAs, the PCCs increase to 0.49 and 0.46 for protein-bound and protein-free RNAs, respectively. The success of RNAsol is attributed to two aspects, including the improved sequence profiles constructed by the sequence-profile alignment and the enhanced training by the LSTM neural networks.

Availability and implementation

http://yanglab.nankai.edu.cn/RNAsol/

Supplementary information

Supplementary data are available at Bioinformatics online.
Disease gene identification based on generic and disease-specific genome networks
Authors: Nam Yonghyun , Jhee Jong Ho , Cho Junhee , Lee Ji-Hyun , Shin Hyunjung
Published: October 2018

Immune diseases have a strong genetic component with Mendelian patterns of inheritance. While the tight association has been a major understanding in the underlying pathophysiology for the category of immune diseases, the common features of these diseases remain unclear. Based on the potential commonality among immune genes, we design Gene Ranker for key gene identification. Gene Ranker is a network-based gene scoring algorithm that initially constructs a backbone network based on protein interactions. Patient gene expression networks are added into the network. An add-on process screens the networks of weighted gene co-expression network analysis (WGCNA) on the samples of immune patients. Gene Ranker is disease-specific; however, any WGCNA network that passes the screening procedure can be added on. With the constructed network, it employs the semi-supervised learning for gene scoring.

Results

The proposed method was applied to immune diseases. Based on the resulting scores, Gene Ranker identified potential key genes in immune diseases. In scoring validation, an average area under the receiver operating characteristic curve of 0.82 was achieved, which is a significant increase from the reference average of 0.76. Highly ranked genes were verified through retrieval and review of 27 million PubMed literatures. As a typical case, 20 potential key genes in rheumatoid arthritis were identified: 10 were de facto genes and the remaining were novel.

Availability and Implementation

Gene Ranker is available at http://www.alphaminers.net/GeneRanker/

Supplementary information

Supplementary data are available at Bioinformatics online.
Propagation of Information Along the Cortical Hierarchy as a Function of Attention While Reading and Listening to Stories
Authors: Regev Mor , Simony Erez , Lee Katherine , Tan Kean Ming , Chen Janice , Hasson Uri
Published: October 2018

How does attention route information from sensory to high-order areas as a function of task, within the relatively fixed topology of the brain? In this study, participants were simultaneously presented with 2 unrelated stories—one spoken and one written—and asked to attend one while ignoring the other. We used fMRI and a novel intersubject correlation analysis to track the spread of information along the processing hierarchy as a function of task. Processing the unattended spoken (written) information was confined to auditory (visual) cortices. In contrast, attending to the spoken (written) story enhanced the stimulus-selective responses in sensory regions and allowed it to spread into higher-order areas. Surprisingly, we found that the story-specific spoken (written) responses for the attended story also reached secondary visual (auditory) regions of the unattended sensory modality. These results demonstrate how attention enhances the processing of attended input and allows it to propagate across brain areas.
Resilience and protective factors among refugee children post-migration to high-income countries: a systematic review
Authors: Marley Charles , Mauki Beatus
Published: October 2018

Background

Increasing numbers of children have been forced to flee and seek asylum in high-income countries. Current research indicates that focussing on resilience and protective factors is an important long-term goal for positive mental health and psychological functioning of refugee children.

Methods

We performed a systematic review of quantitative literature regarding psychological and contextual factors that contribute to resilience in refugee children residing in high-income countries. Our procedure followed guidelines from the Centre for Reviews and Dissemination.

Results

We identified a number of protective factors as related to positive outcomes. They are drawn from several ecological domains and include age, self-esteem, maintenance of cultural identity, social support, belonging and safety and innovative social care services. A key overarching point reported by the studies we reviewed was that for refugee settlement specific policies and approaches to be beneficial, they were required to be embedded within a positive socially inclusive society. We also identified several limitations across the reported studies.

Conclusion

The factors we identified would assist clinicians to adopt a resilience-focussed approach. However, a continued pre-occupation with psychopathology was evident across the studies, which we argue as holding back the development of resilience-focussed approaches.
Perceptions of an online ‘train-the-champion’ approach to increase workplace movement
Authors: Goode Ana D , Hadgraft Nyssa T , Neuhaus Maike , Healy Genevieve N
Published: October 2018

Prolonged sitting is now recognized as an emergent work health and safety issue. To address the need for a scalable sitting-reduction intervention for workplaces, the BeUpstanding™ Champion Toolkit was developed. This free, online toolkit uses a ‘train-the-champion’ approach, providing a step-by-step guide and resources to workplace champions to assist them in raising awareness and building a supportive culture to reduce sitting time in their team. This qualitative study explored champion and staff perceptions of the beta (test) version of the toolkit. Seven work teams, from a range of workplace sectors (blue-/white-collar), sizes (small/medium/large) and locations (urban/regional) participated; all team members were exposed to the program (n = 603). Approximately 4 months after program initiation, semi-structured interviews were conducted with all champions (n = 7); focus groups were conducted with a random sample of staff (n = 40). Champions were followed-up again at 12 months (n = 5). Transcripts were coded by two researchers, with codes organized into overarching themes. All champions found the ‘train-the-champion’ approach, and the toolkit acceptable. Common enablers for intervention delivery included: champion passion for staff health and wellbeing; perceived fit of the program within existing practice; and, management support. Champions and staff reported improvements in knowledge/awareness about sitting, cultural norms, perceived stress, productivity and resilience. Facilitators for sustained change over time included a stable organizational climate and ongoing management support; barriers included workload intensification. The beta version of the BeUpstanding™ Champion Toolkit was highly acceptable to workplace champions and staff, and was perceived to have benefits for team culture and staff knowledge and wellbeing.
Comment on “A new approach for estimating stock status from length frequency data” by Froese et al. (2018)
Authors: Hordyk Adrian R , Prince Jeremy D , Carruthers Thomas R , Walters Carl J
Published: October 2018

Potential users of the model proposed by Froese et al. (2018) should be aware of several issues. First, the method to calculate equilibrium numbers-at-length is incomplete and leads to negatively biased estimates of fishing mortality. Second, inadequate simulation testing fails to reveal that the method is highly sensitive to assumptions of equilibrium conditions and that the population average asymptotic length (L∞) can be approximated by the largest observed size (Lmax). Finally, the Froese et al. (2018) model relies on the assumption that the ratio of natural mortality (M) to the von Bertalanffy growth parameter (K; M/K) is typically around 1.5, which they argue is supported by the literature for most fish stocks. We believe that this conclusion is based on an insufficient reading of the literature and, in fact, there is strong evidence to support the claim that M/K is outside the narrow bounds of 1.2–1.8 for many exploited species. Potential users of the method are alerted to these issues and alternative approaches are recommended to avoid these biases.
Barbara Strozzi, Appresso ai molli argenti (1659)
Authors: Kolb Richard , Swanson Barbara
Published: October 2018

This chapter explores the ways in which Appresso ai molli argenti exemplifies Barbara Strozzi’s sophisticated approach to the mid-seventeenth-century cantata. On the surface, Appresso is a five-section work consisting of opening and closing recitatives that enclose three aria sections. Strozzi makes judicious choices in setting Giovanni Pietro Monesi’s text, drawing attention to two contrasting aspects of lament, each defined by two distinct trends in the operatic lament tradition—the recitative lament and the aria-based descending-tetrachord lament. By giving voice to despair and creating room for reprieve through well-defined musical idioms and tonal plans, Strozzi shapes the cantata into a tightly knit and musically compelling narrative.
Marianna Martines, Sonata in A Major, I (1765)
Authors: Poundie Burstein L.
Published: October 2018

Marianna Martines, a Viennese contemporary of Haydn and Mozart, combined the fruits of instruction in the strict style with the devices and schemata of the new galant style. She was an excellent harpsichordist and singer as well as composer, and her compositional craft is amply displayed in the opening movement of her Sonata in A Major for Keyboard, written around 1765. This movement skillfully handles various layouts, schemata, and compositional devices that were standard at the time. Furthermore, it cleverly manipulates these features with rhythmic and formal devices—some of which are quite daring—in an expressive and dramatic fashion.