bluuebunny/crossref_metadata_2025 huggingface dataset:
Methods for preparing quantum gases of lithium
Authors: Hulet Randall G. , Nguyen Jason H. V. , Senaratne Ruwan
Published: January 2020

Lithium is an important element in atomic quantum gas experiments because its interactions are highly tunable due to broad Feshbach resonances and zero-crossings and because it has two stable isotopes: 6Li, a fermion, and 7Li, a boson. Although lithium has special value for these reasons, it also presents experimental challenges. In this article, we review some of the methods that have been developed or adapted to confront these challenges, including beam and vapor sources, Zeeman slowers, sub-Doppler laser cooling, laser sources at 671 nm, and all-optical methods for trapping and cooling. Additionally, we provide spectral diagrams of both 6Li and 7Li and present plots of Feshbach resonances for both isotopes.
A new microwave coupling scheme for high intensity highly charged ion beam production by high power 24–28 GHz SECRAL ion source
Authors: Guo J. W. , Sun L. , Lu W. , Zhang W. H. , Feng Y. C. , Shen Z. , Li L. X. , Li J. B. , Zhang X. Z. , Hitz D. , Zhao H. W.
Published: January 2020

The efficiency of the microwave-plasma coupling is a key issue to enhance the performance of electron cyclotron resonance ion sources (ECRISs) in terms of higher ion beam intensity yield. The coupling properties are affected by the microwave coupling scheme, especially for the high frequency (f > 20 GHz) and high power (P > 5 kW) ECR ion sources. Based on the study of 24 GHz SECRAL ion source performances working at different launching systems, a new microwave coupling scheme, called the Vlasov launcher, is proposed, which can not only realize efficient power matching and feeding but also enhance the microwave power distribution on the ECR surface. The first promising results are presented in this article. Then, a prototype dedicated to the next generation ECRIS is described.
A novel clear-sky index for color sky imagery used in short-term irradiance forecasting
Authors: Manning Jeff , Baldick Ross
Published: January 2020

A method for mapping color sky images of convective fair-weather cumuli to a scalar irradiance metric is presented. While basic interpretations of irradiance from color sky imagery are sufficient for many irradiance forecasting applications, sky images containing convective fair-weather cumuli can often contain gray-colored regions. Gray regions of a cloud commonly relate cloud thickness, indicating a region that has a high potential to attenuate surface irradiance from the sun. However, existing irradiance metrics are not found to translate such gray regions in accordance with their importance to a clear-sky index for short-term forecasting. This method exploits the special structure of sky images in three-dimensional red-green-blue (RGB) Cartesian space. By applying principal component analysis and basic clustering operations, a planar discriminant for cloudy-to-clear-sky classification is found. Once the {cloudy, clear-sky} identity of all image pixels is determined, the cloudy and clear-sky pixel distributions are separately remapped in RGB space so that gray pixels score a higher optical depth value than white pixels, and clear-sky pixels are mapped to low optical depth values. The resulting clear-sky index is simply the grayscale interpretation of the remapped image. The method is described and demonstrated with two actual sky images, and errors for sequences of several hundred images are tabulated and discussed. Remapped images are shown to represent gray cloud regions with a relatively high cloud optical depth in comparison with white cloud regions. The proposed metric is shown, by comparison with experimentally measured irradiance time series, to produce a more accurate clear-sky index in comparison with other methods.
Geminate recombination in organic photovoltaic blend PCDTBT/PC71BM studied by out-of-phase electron spin echo spectroscopy
Authors: Beletskaya E. A. , Lukina E. A. , Uvarov M. N. , Popov A. A. , Kulik L. V.
Published: January 2020

The key process in organic solar cell operation is charge separation under light illumination. Due to the low dielectric constant of organic materials, the Coulomb attraction energy within the interfacial charge-transfer state (CTS) is larger than the thermal energy. Understanding the mechanism of charge separation at the organic donor/acceptor interface still remains a challenge and requires knowledge of the CTS temporal evolution. To address this problem, the CTS in the benchmark photovoltaic blend PCDTBT/PC71BM was studied by the out-of-phase Electron Spin Echo (ESE). The protocol for determining the CTS geminate recombination rate for certain electron-hole distances was developed. Simulating the out-of-phase ESE trace for the CTS in the PCDTBT/PC71BM blend allows precise determination of the electron-hole distance distribution function and its evolution with the increase in the delay after the laser flash. Distances of charge separation up to 6 nm were detected upon thermalization at a temperature of 20 K. Assuming the exponential decay of the recombination rate, the attenuation factor β = 0.08 Å−1 is estimated for the PCDTBT/PC71BM blend. Such a low attenuation factor is probably caused by a high degree of hole delocalization along the PCDTBT chain.
Low energy excited state vibrations revealed in conjugated copolymer PCDTBT
Authors: Irgen-Gioro Shawn , Roy Palas , Padgaonkar Suyog , Harel Elad
Published: January 2020

Low energy vibrations in the excited state have been hypothesized to play an important role in quickly and efficiently generating free charges in bulk heterojunctions of some conjugated polymer systems. While time-resolved vibrational spectroscopies seemingly are well poised to address the relationship between kinetics and vibrational motions after initial photoexcitation, uncertainty in the measurement arises due to overlapping signals and difficulties in assigning observed oscillatory signals to the molecular response. Here, we demonstrate a high sensitivity strategy to distinguish between signal oscillations originating from lab noise and those molecular in origin in order to isolate the low energy excited-state vibrations in the model conjugated copolymer PCDTBT. Furthermore, to distinguish modes that may be implicated in different kinetic pathways, coherent signal oscillations extracted from 2-dimensional electronic spectroscopy (2DES) are compared for the polymer in two solvents with different polarities resulting in different kinetics. We observe that the change in solvent affects dynamics on the >2 ps scale but not on the time scale required for free charge generation in heterojunctions (∼200 fs time scale). By the same token, the excited state vibrational modes that appear and disappear based on solvent polarity may also be associated with the slower kinetic process. The observation of low energy vibrational motions coupled to the excited state manifold that persists through the solvent change and thus can be associated with the fast kinetic process supports the hypothesis that direct polaron formation, rather than exciton formation and diffusion followed by interfacial charge separation, is a more likely route toward free charges in organic heterostructures.
Multi-scale dynamics of atmospheric-pressure discharges ignited over liquid electrodes
Authors: Levko Dmitry , Arslanbekov Robert R. , Kolobov Vladimir I.
Published: January 2020

A multiphase computational model of atmospheric-pressure gas discharges ignited over liquid electrodes is developed. The model takes into account both the liquid electrode motion under applied electric fields and plasma generation in the gas phase. The influence of the applied voltage and liquid properties (density, viscosity, and surface tension) on the liquid surface deformation is analyzed. It is shown that the shape of dynamic cones formed on the liquid surface differs from the static Taylor's cones. The influence of the liquid surface protrusions on gas breakdown dynamics is demonstrated. It is shown that the breakdown develops in two stages: first, a fast ionization wave propagates from the cathode to the anode, and then the cathode sheath collapses due to secondary electron emission from the liquid surface. It is shown that dynamics of the multiphase system containing gas, plasma, and liquid states is characterized by three disparate time scales: the fast electron time scale, the intermediate ion time scale, and the slow liquid dynamics time scale.
Tunneling electroresistance effects in epitaxial complex oxides on silicon
Authors: Abuwasib Mohammad , Serrao Claudy R. , Stan Liliana , Salahuddin Sayeef , Bakaul Saidur Rahman
Published: January 2020

Complex oxide-based ferroelectric tunnel junctions (FTJs) show excellent nonvolatile memory characteristics promising for emerging technology. However, integration of these epitaxially grown FTJs electrically with a silicon substrate remains challenging due to their incompatible lattice structures and poor electronic interfaces resulting from the direct synthesis techniques. Here, we present an epitaxial SrRuO3/PbZr0.2Ti0.8O3/SrRuO3 FTJ integrated electrically with a doped silicon substrate after a layer transfer process. The tunnel currents of the FTJ on silicon show a large tunneling electroresistance (∼1 × 105%) effect, which is explained by a numerical FTJ model incorporating pinned dipoles at the interfaces. This proof of concept of the integration of functional oxide heterostructures with silicon opens a pathway to beyond-CMOS computing devices using unconventional materials.
Resistive wall modes and related sideways forces in tokamak
Authors: Martynov A. A. , Medvedev S. Yu.
Published: January 2020

This paper presents the results of analytical and numerical calculations of the sideways force acting on the resistive wall due to eddy currents induced by n=1 kink instability. The inertia-less ideal MHD model for resistive wall mode is explicitly shown to be compatible with the condition of vanishing sideways force in the ideal wall limit. In the frame of standard high aspect ratio approximation, assuming that tokamak plasma is separated from the coaxial resistive wall by a vacuum layer, we calculate analytically the sideways force as a function of the growth rate γ taking into account the known relation between γ and the value of the safety factor q. It is noted that this dependence is determined by the single mode m/n=1/1 instability in the range of q-values q<1 giving the maximal force at γτw≥2, where τw is the resistive wall time. The numerically estimated magnitude of the sideways force for ITER relevant cases with q>1 is smaller because the sideways force is generated by toroidally coupled satellite harmonic m/n=1/1. The forces due to resistive wall mode with conformal and one-sided wall proximity to the plasma boundary are compared.
Inertial effects of self-propelled particles: From active Brownian to active Langevin motion
Authors: Löwen Hartmut
Published: January 2020

Active particles that are self-propelled by converting energy into mechanical motion represent an expanding research realm in physics and chemistry. For micrometer-sized particles moving in a liquid (“microswimmers”), most of the basic features have been described by using the model of overdamped active Brownian motion. However, for macroscopic particles or microparticles moving in a gas, inertial effects become relevant such that the dynamics is underdamped. Therefore, recently, active particles with inertia have been described by extending the active Brownian motion model to active Langevin dynamics that include inertia. In this perspective article, recent developments of active particles with inertia (“microflyers,” “hoppers,” or “runners”) are summarized both for single particle properties and for collective effects of many particles. These include inertial delay effects between particle velocity and self-propulsion direction, tuning of the long-time self-diffusion by the moment of inertia, effects of fictitious forces in noninertial frames, and the influence of inertia on motility-induced phase separation. Possible future developments and perspectives are also proposed and discussed.
Influence of polymer topology on crystallization in thin films
Authors: Giuntoli Andrea , Chremos Alexandros , Douglas Jack F.
Published: January 2020

We investigate how varying molecular topology of polymers influences crystallization in thin polymer films. In particular, we simulate linear and star polymers of fixed mass having a progressively increasing number of arms (f ≤ 16) in a system where the linear polymer exhibits crystallization in a thin film geometry, but no apparent crystallization in the corresponding bulk material. The degree of crystallization of the polymer film at long times decreases progressively with increasing f, and no crystallization is observed beyond f = 8. Crystallization for smaller values of f develops as a sigmoidally shaped wavefront initiating from the supporting crystalline interface. We suggest that large shape fluctuations and the competition of length scales of star polymers with high f lead to inhibited crystallization.
A numerical investigation of puddle jumping
Authors: Avhad Amit , Tan Hua , Al-Jubaree Taif , Torres Logan , Weislogel Mark
Published: January 2020

The nearly step reduction in gravity arising in routine drop tower tests leads to numerous interesting large-length-scale capillary flow phenomena. For example, a liquid puddle at equilibrium on a hydrophobic substrate is observed to spontaneously jump from the substrate during such tests. Implementing a modified version of the open-source Gerris code, we numerically investigate such a puddle jump phenomenon for a variety of water puddles on flat substrates. We quantify a range of puddle jump characteristics including jump time, jump velocity, and free puddle oscillation modes for an unearthly range of drop volumes between 0.001 ml and 15 ml and substrate contact angles between 60° and 175°. A numerical regime map is constructed identifying no jump, standard jump, bubble ingestion, geyser formation, drop fission, and satellite puddle jump regimes. Favorable agreement is found between the simulations, experiments, simple theoretical models, and scaling laws.
Enhancement of temperature change induced by anomalous Ettingshausen effect in thin Ni films on suspended membrane substrates
Authors: Modak Rajkumar , Uchida Ken-ichi
Published: January 2020

We demonstrate the effect of substrates on the temperature change induced by the anomalous Ettingshausen effect in ferromagnetic thin films. The experimental results show that, in comparison with conventional experiments using bulk substrates, the temperature modulation due to the anomalous Ettingshausen effect in Ni films can be enhanced by more than an order of magnitude using suspended membrane substrates, which reduce thermal dissipation from the films to the substrates. The temperature modulation can be further enhanced with the help of a simple suspended thermopile configuration consisting of two Ni strips separated by a small distance. These demonstrations will provide a guideline for the thermal design of thin-film-based spin-caloritronic devices.
Mapping atmospheric waves and unveiling phase coherent structures in a global surface air temperature reanalysis dataset
Authors: Zappala Dario A. , Barreiro Marcelo , Masoller Cristina
Published: January 2020

In the analysis of empirical signals, detecting correlations that capture genuine interactions between the elements of a complex system is a challenging task with applications across disciplines. Here, we analyze a global dataset of surface air temperature (SAT) with daily resolution. Hilbert analysis is used to obtain phase, instantaneous frequency, and amplitude information of SAT seasonal cycles in different geographical zones. The analysis of the phase dynamics reveals large regions with coherent seasonality. The analysis of the instantaneous frequencies uncovers clean wave patterns formed by alternating regions of negative and positive correlations. In contrast, the analysis of the amplitude dynamics uncovers wave patterns with additional large-scale structures. These structures are interpreted as due to the fact that the amplitude dynamics is affected by processes that act in long and short time scales, while the dynamics of the instantaneous frequency is mainly governed by fast processes. Therefore, Hilbert analysis allows us to disentangle climatic processes and to track planetary atmospheric waves. Our results are relevant for the analysis of complex oscillatory signals because they offer a general strategy for uncovering interactions that act at different time scales.
Pinning of energy transitions of defects, complexes, and surface states in AlGaN alloys
Authors: Reddy Pramod , Bryan Zachary , Bryan Isaac , Kim Ji Hyun , Washiyama Shun , Kirste Ronny , Mita Seiji , Tweedie James , Irving Douglas L. , Sitar Zlatko , Collazo Ramón
Published: January 2020

In this work, we determine the dependence of the defect transition energies, electronic bands, and surface charge neutrality levels in AlGaN. With Vacuum level as reference, we show that energy transitions of localized defects and the surface Fermi level are independent of the alloy composition as electronic bands diverge with the increase in the bandgap as a function of alloy composition. The invariance of localized states on the alloy composition creates a convenient internal reference energy with respect to which other energy states may be measured. We demonstrate a higher generality to the universality rule with the independence of deep transition states of otherwise shallow donor type defects [(+1/+3) transition for VN] and defect complexes (CN+SiIII) in addition to the earlier predicted independent nature of mid-gap states when they are either the antibonding state between cationic impurities and host anion or acceptors at anion sites.
Observation of polymer-like flow mechanism in a short-chain phosphate glass-forming liquid
Authors: Xia Yiqing , Zhu Weidi , Sen Jishnu , Sen Sabyasachi
Published: January 2020

The dynamics of the phosphate chains and the attendant shear relaxation in a short-chain silver phosphate glass-forming liquid with the composition 51.5%Ag2O-48.5% P2O5 are studied using a combination of high-temperature 31P NMR spectroscopy and parallel plate rheometry. The temperature-dependent evolution of the 31P NMR spectral line shapes indicates that the constituent PO4 tetrahedral chains in this liquid undergo rapid rotational reorientation. The time scale of this dynamics is in complete agreement with that of shear relaxation and, thus, must be responsible for the viscous flow of this liquid. These results demonstrate for the first time that, although the shear relaxation of the network oxide glass-forming liquids is typically controlled by the scission and renewal of bonds between the network-forming cations and oxygen atoms, such a scenario may not always be tenable for liquids with low-dimensional structures consisting of chains.
Combining three time-resolved photoemission techniques in a single instrument
Authors: Kim Meeri
Published: January 2020

A new article describes a versatile instrument that enables time-resolved momentum microscopy, time-resolved X-ray photoelectron spectroscopy and time-resolved X-ray photoelectron diffraction in a single experimental setup.
Trachycladindoles H–M: Molecular Networking Guided Exploration of a Library of Southern Australian Marine Sponges
Authors: Khushi Shamsunnahar , Nahar Laizuman , Salim Angela A. , Capon Robert J.
Published: January 2020

A global natural product social (GNPS) molecular network guided search of a library of 960 southern Australian marine sponge extracts successfully detected a deep-water Great Australian Bight sponge, Geodia sp. (CMB-01063), as a new source of a rare class of indolo-imidazole alkaloids previously believed to be unique to a single specimen of Trachycladus laevispirulifer (CMB-03397). Chemical analysis of CMB-01063 detected the known trachycladindoles A–G (1–7), and led to the isolation, characterisation, and structure elucidation of the new trachycladindoles H–M (8–13). Structures for 8–13 were assigned on the basis of detailed spectroscopic analysis, with comparison to authentic standards of 1–7.
A reference library for assigning protein subcellular localizations by image-based machine learning
Authors: Schormann Wiebke , Hariharan Santosh , Andrews David W.
Published: January 2020

Confocal micrographs of EGFP fusion proteins localized at key cell organelles in murine and human cells were acquired for use as subcellular localization landmarks. For each of the respective 789,011 and 523,319 optically validated cell images, morphology and statistical features were measured. Machine learning algorithms using these features permit automated assignment of the localization of other proteins and dyes in both cell types with very high accuracy. Automated assignment of subcellular localizations for model tail-anchored (TA) proteins with randomly mutated C-terminal targeting sequences allowed the discovery of motifs responsible for targeting to mitochondria, endoplasmic reticulum, and the late secretory pathway. Analysis of directed mutants enabled refinement of these motifs and characterization of protein distributions in within cellular subcompartments.
A life in pictures—Marilyn Gist Farquhar
Authors: Stow Jennifer L. , Saraste Jaakko , Brown William J.
Published: January 2020

Marilyn Gist Farquhar is remembered for her contributions over seven decades as a pioneering microscopist, an inspiring researcher, mentor, and eminent leader of cell biology.
Plaque-associated myeloid cells derive from resident microglia in an Alzheimer’s disease model
Authors: Reed-Geaghan Erin G. , Croxford Andrew L. , Becher Burkhard , Landreth Gary E.
Published: January 2020

Alzheimer’s disease (AD) is accompanied by a robust inflammatory response mediated by plaque-associated myeloid cells of the brain. These cells exhibit altered gene expression profiles and serve as a barrier, preventing neuritic dystrophy. The origin of these cells has been controversial and is of therapeutic importance. Here, we genetically labeled different myeloid populations and unequivocally demonstrated that plaque-associated myeloid cells in the AD brain are derived exclusively from resident microglia, with no contribution from circulating peripheral monocytes.
Decision by injection without infection
Authors: Sasai Miwa , Yamamoto Masahiro
Published: January 2020

The protozoan pathogen Toxoplasma gondii co-opts host immunity by secreting various effector proteins into host cells. In this issue of JEM, Chen et al. (https://doi.org/10.1084/jem.20181757) report that T. gondii injects an effector called ROP16 without invasion to polarize macrophages toward M2 cells.
Biophysical mechanisms for QRS- and QTc-interval prolongation in mice with cardiac expression of expanded CUG-repeat RNA
Authors: Tylock Kevin M. , Auerbach David S. , Tang Zhen Zhi , Thornton Charles A. , Dirksen Robert T.
Published: January 2020

Myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults, results from the expression of toxic gain-of-function transcripts containing expanded CUG-repeats. DM1 patients experience cardiac electrophysiological defects, including prolonged PR-, QRS-, and QT-intervals, that increase susceptibility to sudden cardiac death (SCD). However, the specific biophysical and molecular mechanisms that underlie the electrocardiograph (ECG) abnormalities and SCD in DM1 are unclear. Here, we addressed this issue using a novel transgenic mouse model that exhibits robust cardiac expression of expanded CUG-repeat RNA (LC15 mice). ECG measurements in conscious LC15 mice revealed significantly prolonged QRS- and corrected QT-intervals, but a normal PR-interval. Although spontaneous arrhythmias were not observed in conscious LC15 mice under nonchallenged conditions, acute administration of the sodium channel blocker flecainide prolonged the QRS-interval and unveiled an increased susceptibility to lethal ventricular arrhythmias. Current clamp measurements in ventricular myocytes from LC15 mice revealed significantly reduced action potential upstroke velocity at physiological pacing (9 Hz) and prolonged action potential duration at all stimulation rates (1–9 Hz). Voltage clamp experiments revealed significant rightward shifts in the voltage dependence of sodium channel activation and steady-state inactivation, as well as a marked reduction in outward potassium current density. Together, these findings indicate that expression of expanded CUG-repeat RNA in the murine heart results in reduced sodium and potassium channel activity that results in QRS- and QT-interval prolongation, respectively.
Hyperboloidal framework for the Kerr spacetime
Authors: Macedo Rodrigo Panosso
Published: January 2020

Motivated by the need of a robust geometrical framework for the calculation of long, and highly accurate waveforms for extreme-mass-ratio inspirals, this work presents an extensive study of the hyperboloidal formalism for the Kerr spacetime and the Teukolsky equation. In a first step, we introduce a generic coordinate system foliating the Kerr spacetime into hypersurfaces of constant time extending between the black-hole horizon and future null infinity, while keeping track of the underlying degrees of freedom. Then, we express the Teukolsky equation in terms of these generic coordinates with focus on applications in both the time and frequency domains. Specifically, we derive a wave-like equation in 2  +  1 dimensions, whose unique solution follows directly from the prescription of initial data (no external boundary conditions). Moreover, we extend the hyperboloidal formulation into the frequency domain. A comparison with the standard form of the Teukolsky equations allows us to express the regularisation factors in terms of the hyperboloidal degrees of freedom. In the second part, we discuss several hyperboloidal gauges for the Kerr solution. Of particular importance, this paper introduces the minimal gauge. The resulting expressions for the Kerr metric and underlying equations are simple enough for eventual (semi)-analytical studies. Despite the simplicity, the gauge has a very rich structure as it naturally leads to two possible limits to extremality, namely the standard extremal Kerr spacetime and its near-horizon geometry. When applied to the Teukolsky equation in the frequency domain, we show that the minimal gauge actually provides the spacetime counterpart of the well-known Leaver’s formalism. Finally, we recast the hyperboloidal gauges for the Kerr spacetime available in the literature within the framework introduced here.
Sharp-selectivity in-line topology low temperature superconducting bandpass filter for superconducting quantum applications
Authors: He Yuxing , Michibayashi Shiori , Takeuchi Naoki , Yoshikawa Nobuyuki
Published: January 2020

This paper presents a new class of sharp-selectivity low-temperature superconducting filter that incorporates lumped element resonant couplings. Dependent on a novel synthesis approach, the proposed filter exhibits great advantages such as: (1) a very simple in-line topology (without any cross coupling), (2) extremely compact size based on lumped inductor-capacitor (LC) elements, and (3) multiple transmission zeros (TZs) independently generated and controlled (via each resonant coupling). To facilitate the physical implementation, a group of lumped element circuit models are detailed, where series LC units are adopted for both the resonators and the resonant couplings. Considering an in-line topology here, the entire filter layout is then designed by cascading the lumped models one after another. For verification, a 5th-order bandpass filter centered at 5 GHz, with 500 MHz bandwidth and 3 TZs, is designed, simulated, and tested at cryogenic temperature (4.2 K). Moreover, preliminary simulations of the presented filter in series with an on-chip rapid single-flux-quantum microwave pulse generator are discussed for superconducting quantum applications.
The growth and superconducting properties of RE–Ba–Cu–O single grains with combined RE elements (RE = Gd and Y)
Authors: Shi Yunhua , Bergamo-Andreis Giovanni , Dennis Anthony R , Durrell John H , Cardwell David A
Published: January 2020

The superconducting properties, melting temperatures and crystal growth rates of single grain, RE–Ba–Cu–O [(RE)BCO] bulk superconductors (where RE = a rare earth element or yttrium) decrease with the RE-element sequence of Nd, Sm, Eu, Gd, Dy and Y. The mechanical properties of these technologically important materials, on the other hand, however, improve in the same sequence. Consequently, one promising approach for optimising the balance between mechanical and superconducting properties of bulk (RE)BCO superconductors, or for adjusting growth rate, is the use of combinations of different rare earth elements. In this study, we explore combinations of Gd and Y in the formation of (Gd–Y)–Ba–Cu–O single grains. We describe the optimisation of the growth process for this multi-RE element system and use optical and scanning electron microscopy to study the microstructure of both non-superconducting (Gd–Y)2BaCuO5 [(Y–Gd)-211] phase inclusions and the (Y–Gd)Ba2Cu3O7-δ
[(Y–Gd)-123] phase matrix itself. We demonstrate that (Gd–Y)–Ba–Cu–O single grains can be fabricated reliably and that they exhibit reasonably good superconducting properties. We observe that there is an increase in RE-211 particle size in this mixed rare earth system, which, ultimately, limits sample performance, and conclude that this may be a general disadvantage of this approach to the synthesis of single grains for high field engineering applications.
Realization of Weyl semimetal phases in topoelectrical circuits
Authors: Rafi-Ul-Islam S M , Siu Zhuo Bin , Sun Chi , Jalil Mansoor B A
Published: January 2020

In this work, we demonstrate a simple and effective method to design and realize various Weyl semimetal (WSM) states in a three-dimensional periodic circuit lattice composed of passive electric circuit elements such as inductors and capacitors (LC). The experimental accessibility of such LC circuits offers a ready platform for the realization of not only various WSM phases but also for exploring transport properties in topological systems. The characteristics of such LC circuits are described by the circuit admittance matrices, which are mathematically related to the Hamiltonian of the quantum tight-binding model. The system can be switched between the Type-I and Type-II WSM phases simply by an appropriate choice of inductive or capacitive coupling between certain nodes. A peculiar phase with a flat admittance band emerges at the transition between the Type-I and Type-II Weyl phases. Impedance resonances occur in the LC circuits at certain frequencies associated with vanishing eigenvalues of the admittance matrix. The impedance readout can be used to classify the Type-I and Type-II WSM states. A Type-I WSM shows impedance peaks only at the Weyl points (WPs) whereas a Type-II WSM exhibits multiple secondary peaks near the WPs. This impedance behaviour reflects the vanishing and non-vanishing density of states at the Weyl nodes in the Type-I and Type-II WSM phases, respectively.
Electronic and photonic counting statistics as probes of non-equilibrium quantum dynamics
Authors: Kubala Björn , Ankerhold Joachim , Armour Andrew D
Published: January 2020

We analyse the full counting statistics (FCS) of photons flowing in and out of a microwave cavity coupled to a voltage-biased Josephson junction. Tunnelling of Cooper pairs generates a coherent flow of photons into the cavity whilst at the same time photons can also leak out incoherently. We use a very general unitary transformation method to demonstrate that there is a simple connection between the FCS of the charges and the photons in the long time limit, revealing that all the cumulants of the coherent and the incoherent processes match in that limit. We also explore some of the interesting features in the counting statistics of the charges and photons which arise from the strongly nonlinear dynamics of the system. These include very narrow distributions associated with the emergence of coherent transport and regimes where counting of either an odd or an even number of photons leaving the cavity can result in strongly non-classical cat states within the cavity.
Role of matrix elements in the time-resolved photoemission signal
Authors: Boschini F , Bugini D , Zonno M , Michiardi M , Day R P , Razzoli E , Zwartsenberg B , Schneider M , da Silva Neto E H , dal Conte S , Kushwaha S K , Cava R J , Zhdanovich S , Mills A K , Levy G , Carpene E , Dallera C , Giannetti C , Jones D J , Cerullo G , Damascelli A
Published: January 2020

Time- and angle-resolved photoemission spectroscopy (TR-ARPES) provides access to the ultrafast evolution of electrons and many-body interactions in solid-state systems. However, the momentum- and energy-resolved transient photoemission intensity may not be unambiguously described by the intrinsic relaxation dynamics of photoexcited electrons alone. The interpretation of the time-dependent photoemission signal can be affected by the transient evolution of the electronic distribution, and both the one-electron removal spectral function as well as the photoemission matrix elements. Here we investigate the topological insulator Bi1.1Sb0.9Te2S to demonstrate, by means of a detailed probe-polarization dependent study, the transient contribution of matrix elements to TR-ARPES.
Numerical methods for the deterministic second moment equation of parabolic stochastic PDEs
Authors: Kirchner Kristin
Published: January 2020

Numerical methods for stochastic partial differential equations typically estimate moments of the solution from sampled paths. Instead, we shall directly target the deterministic equations satisfied by the mean and the spatio-temporal covariance structure of the solution process.

In the first part, we focus on stochastic ordinary differential equations. For the canonical examples with additive noise (Ornstein–Uhlenbeck process) or multiplicative noise (geometric Brownian motion) we derive these deterministic equations in variational form and discuss their well-posedness in detail. Notably, the second moment equation in the multiplicative case is naturally posed on projective–injective tensor product spaces as trial–test spaces. We then propose numerical approximations based on Petrov–Galerkin discretizations with tensor product piecewise polynomials and analyze their stability and convergence in the natural tensor norms.

In the second part, we proceed with parabolic stochastic partial differential equations with affine multiplicative noise. We prove well-posedness of the deterministic variational problem for the second moment, improving an earlier result. We then propose conforming space-time Petrov–Galerkin discretizations, which we show to be stable and quasi-optimal.

In both parts, the outcomes are validated by numerical examples.
Many cusped hyperbolic 3-manifolds do not bound geometrically
Authors: Kolpakov Alexander , Reid Alan , Riolo Stefano
Published: January 2020

In this note we show that there exist cusped hyperbolic

3
3

-manifolds that embed geodesically but cannot bound geometrically. Thus, being a geometric boundary is a non-trivial property for such manifolds. Our result complements the work by Long and Reid on geometric boundaries of compact hyperbolic

4
4

-manifolds and by Kolpakov, Reid, and Slavich on embedding arithmetic hyperbolic manifolds.
Bidirectional relations between cognitive function and oral health in ageing persons: a longitudinal cohort study
Authors: Kang Jing , Wu Bei , Bunce David , Ide Mark , Aggarwal Vishal R , Pavitt Sue , Wu Jianhua
Published: January 2020

Background

evidence suggests a reciprocal relationship between cognitive function (CF) and oral health (OH), but no study has demonstrated this inter-relationship in a longitudinal population.

Objective

to investigate the bidirectional relationship between CF and OH in an ageing cohort.

Design

cohort study.

Setting

general community.

Subjects

participants from the English Longitudinal Study of Ageing.

Methods

OH, measured by teeth status, self-reported OH and OH-related quality of life (OHRQoL), and CFs were collected at three time points in 2006/07, 2010/11 and 2014/15. Cross-lagged structural equation models were used to investigate the association between CF and OH, adjusted for potential confounding factors.

Results

5477 individuals (56.4% women) were included (mean age = 63.1 years at 2006/07, 67.2 at 2010/11 and 70.4 at 2014/15, SD = 8.9) in analyses. The average CF score was 46.5(SD = 12.3) at baseline and 41.2 (SD = 13.4) at follow-up. 3350 (61.2%) participants had natural teeth only and 622 (11.2%) were edentulous. In the fully adjusted model, better cognition at baseline was associated with better OH at follow-up (beta coefficient = 0.02, 95% CI: 0.01–0.03); conversely better OH at baseline predicted better cognition (beta coefficient = 0.12, 95% CI: 0.06–0.18). Similar magnitude and direction of the reciprocal association was evident between cognition and OHRQoL.

Conclusions

This is the first longitudinal study to demonstrate the positive reciprocal association between CF and OH. The findings suggest the importance of maintaining both good CF and OH in old age.
β
2-Agonists and the Incidence of Parkinson Disease
Authors: Giorgianni Francesco , Ernst Pierre , Dell’Aniello Sophie , Suissa Samy , Renoux Christel
Published: January 2020

A recent study found a decreased risk of Parkinson disease (PD) associated with the β2 adrenergic agonist (β2-agonist) salbutamol. However, other mechanisms might explain this apparent association. Using the UK Clinical Practice Research Datalink, we formed a cohort of 2,430,884 patients aged 50 years or older between 1995 and 2016. During follow-up, 8,604 cases of PD were identified and matched to 86,040 controls on sex, age, date of cohort entry, and duration of follow-up, after applying a 1-year latency time window. Incidence rate ratios of PD associated with use of β2-agonists were estimated using conditional logistic regression. Ever-use of β2-agonists was associated with a 17% decreased rate of PD (rate ratio = 0.83, 95% confidence interval: 0.75, 0.91) compared with no use. However, this association was limited to early short-term use and was no longer observed after more than 2 years of cumulative duration of use (rate ratio = 0.97, 95% confidence interval: 0.80, 1.17). A similar pattern was observed when stratifying by time since first β2-agonist prescription and by duration of follow-up. The apparent association of β2-agonists with a decreased risk of PD is likely the result of reverse causality rather than a biological effect of these drugs on the risk of PD.
DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion
Authors: Zhang Wenjuan , Xu Hunan , Li Xiaozhong , Gao Qiang , Wang Lin
Published: January 2020

Motivation

One of the most important problems in drug discovery research is to precisely predict a new indication for an existing drug, i.e. drug repositioning. Recent recommendation system-based methods have tackled this problem using matrix completion models. The models identify latent factors contributing to known drug-disease associations, and then infer novel drug-disease associations by the correlations between latent factors. However, these models have not fully considered the various drug data sources and the sparsity of the drug-disease association matrix. In addition, using the global structure of the drug-disease association data may introduce noise, and consequently limit the prediction power.

Results

In this work, we propose a novel drug repositioning approach by using Bayesian inductive matrix completion (DRIMC). First, we embed four drug data sources into a drug similarity matrix and two disease data sources in a disease similarity matrix. Then, for each drug or disease, its feature is described by similarity values between it and its nearest neighbors, and these features for drugs and diseases are mapped onto a shared latent space. We model the association probability for each drug-disease pair by inductive matrix completion, where the properties of drugs and diseases are represented by projections of drugs and diseases, respectively. As the known drug-disease associations have been manually verified, they are more trustworthy and important than the unknown pairs. We assign higher confidence levels to known association pairs compared with unknown pairs. We perform comprehensive experiments on three benchmark datasets, and DRIMC improves prediction accuracy compared with six stat-of-the-art approaches.

Availability and implementation

Source code and datasets are available at https://github.com/linwang1982/DRIMC.

Supplementary information

Supplementary data are available at Bioinformatics online.
Bovine sperm samples induce different NET phenotypes in a NADPH oxidase-, PAD4-, and Ca++-dependent process†
Authors: Fichtner Theresa , Kotarski Franziska , Gärtner Ulrich , Conejeros Iván , Hermosilla Carlos , Wrenzycki Christine , Taubert Anja
Published: January 2020

Deposition of sperm during artificial insemination in the bovine female reproductive tract results in early host innate immune reactions of polymorphonuclear neutrophils (PMNs). Furthermore, sperm-mediated neutrophil extracellular trap (NET) formation (NETosis) was recently reported to occur in different mammalian species, including humans. We, here, investigated the interactions of bovine PMN with different semen-derived samples and analyzed in more depth molecular aspects of this effector mechanism. Overall, confrontation of PMN with sperm/cell preparation (SCP) resulted in a rapid and dose-dependent NET formation leading to effective spermatozoa entrapment. Thereby, spermatozoa induced different phenotypes of NETs. Immunostaining analyses revealed the presence of histones (H3), neutrophil elastase (NE), and pentraxin (PTX) in sperm-triggered NET structures. Fresh SCP strongly induced NETosis than frozen-thawed ones. The level of NETosis was not related to spermatozoa viability. SCP as well as purified sperm cells (SCs) and supernatant (SN) induce NETosis, although the reaction in SC was lower. Enhanced levels of oxygen consumption and proton leak in PMN revealed sperm SNs but not purified SCs as PMN activators. Functional inhibition experiments revealed sperm-triggered NETosis as an NADPH oxidase- and peptidylarginine deiminase 4-dependent process and proved to be dependent on intra- and extracellular Ca++ influxes while myeloperoxidase activity and as ERK1/2- and PI3K-related signaling pathways did not seem to play a pivotal role in this effector mechanism. From these findings, we speculate that sperm-derived NETosis might also occur in vivo during artificial insemination and might therefore play a role related to reduced fertility.
Abrupt, Asynchronous Changes in Action Representations by Anterior Cingulate Cortex Neurons during Trial and Error Learning
Authors: Emberly Eldon , Seamans Jeremy K
Published: January 2020

The ability to act on knowledge about the value of stimuli or actions factors into simple foraging behaviors as well as complex forms of decision-making. In striatal regions, action representations are thought to acquire value through a gradual (reinforcement-learning based) process. It is unclear whether this is also true for anterior cingulate cortex (ACC) where neuronal representations tend to change abruptly. We recorded from ensembles of ACC neurons as rats deduced which of 3 levers was rewarded each day. The rat’s lever preferences changed gradually throughout the sessions as they eventually came to focus on the rewarded lever. Most individual neurons changed their responses to both rewarded and nonrewarded lever presses abruptly (<2 trials). These transitions occurred asynchronously across the population but peaked near the point where the rats began to focus on the rewarded lever. Because the individual transitions were asynchronous, the overall change at the population level appeared gradual. Abrupt transitions in action representations of ACC neurons may be part of a mechanism that alters choice strategies as new information is acquired.
Improved Methods of Analysis for Oxygen, Carbon Monoxide, and Iron on Fingertip Blood
Authors: Natelson Samuel , Menning Carol M
Published: January 2020

Improved gasometric methods of analyses for oxygen and carbon monoxide in fingertip blood are described. The accuracy of the method for oxygen is evaluated by comparison with the iron concentration of the blood. The accuracy of the method for carbon monoxide is evaluated by analyzing samples of blood saturated with carbon monoxide serially diluted with the same blood saturated with oxygen.

Technics are described for obtaining the blood for analysis from fingertip puncture.
Effect of Shaking on the Accuracy of Salt Fractionation Methods For Serum Albumin
Authors: Saifer Abraham , Zymaris Michael C
Published: January 2020

1. The important factors causing albumin denaturation in the presence of sodium sulfite when shaking with ether or ether-Span, are the method and time of shaking, and the free air space available for shaking.

2. Gentle inversion with ether-Span for 30 seconds or less, and a free air space of about 1.3 cm.3 gave results with the Wolfson-Cohn procedure (10) which were in close agreement with the electrophoretic method in 42 normal and pathologic sera.

3. There is little or no albumin denaturation from shaking with ether in the presence of 21.2% sodium sulfate as used in the procedure of Wolfson-Cohn (10)for albumin plus α-globulins.
Seromucoid in Hepatobiliary Disease
Authors: Mandel Emanuel E , Gorsuch Thomas L , Cooper Gerald E
Published: January 2020

Seromucoid was determined in 165 patients with jaundice or hepato. megaly, or both. Subnormal seromucoid concentrations were found in 39 per cent of 44 cases of viral hepatitis and in 15 per cent of 41 cases of alcoholic cirrhosis. This incidence increased to 50 and 43 per cent, respectively, when patients with complicating extrahepatic disease processes were excluded. No subnormal values were encountered in 55 cases of benign and malignant biliary obstruction which, however, yielded about 80 per cent of elevated values.

The empirical data point to the lower limit of the normal seromucoid range as providing a useful dividing line between obstructive and parenchymal jaundice: the finding of a subnormal level is strongly indicative of the latter. Normal or elevated levels may only occasionally be expected to make a decisive diagnostic contribution.

A more definitive evaluation of the clinical utility of this type of test must await improvements in analytic standardization, based on a more detailed knowledge of the chemical and physiologic identity of the compound than is available at present.
Calcium Determination in Biologic Material
Authors: Berger Eugene Y
Published: January 2020

A method has been described for the determination of calcium in plasma, urine, and tissue and feces. Calcium is precipitated as the oxalate salt and the oxalate is determined by cerate oxidimetry.