bluuebunny/crossref_metadata_2025 huggingface dataset:
Approaching the high intrinsic electrical resistivity of NbO2 in epitaxially grown films
Authors: Stoever Julian , Boschker Jos E. , Bin Anooz Saud , Schmidbauer Martin , Petrik Peter , Schwarzkopf Jutta , Albrecht Martin , Irmscher Klaus
Published: May 2020

NbO2 is a promising candidate for resistive switching devices due to an insulator-metal transition above room temperature, which is related to a phase transition from a distorted rutile structure to an undistorted one. However, the electrical resistivity of the NbO2 thin films produced so far has been too low to achieve high on-off switching ratios. Here, we report on the structural, electrical, and optical characterization of single-crystalline NbO2 (001) thin films grown by pulsed laser deposition on MgF2 (001) substrates. An annealing step reduced the full width at half maximum of the NbO2 (004) x-ray Bragg reflection by one order of magnitude, while the electrical resistivity of the films increased by two orders of magnitude to about 1 kΩcm at room temperature. Temperature-dependent resistivity measurements of an annealed sample revealed that below 650 K, two deep-level defects with activation energies of 0.25 eV and 0.37 eV dominate the conduction, while above 650 K, intrinsic conduction prevails. Optical characterization by spectroscopic ellipsometry and by absorption measurements with the electric field vector of the incident light perpendicular to the c-axis of the distorted rutile structure indicates the onset of fundamental absorption at about 0.76 eV at room temperature, while at 4 K, the onset shifts to 0.85 eV. These optical transitions are interpreted to take place across the theoretically predicted indirect bandgap of distorted rutile NbO2.
Analysis of a trilayer thermal cloak
Authors: Yeung Woon-Shing , Yang Fu-Yao , Yang Ruey-Jen
Published: May 2020

An analytical solution exists for a circular bilayer cloak against a background of linearly varying temperature distribution and under steady state. In particular, the ratio of the outer-layer and background conductivity is fixed, given the inner and outer radius of the outer layer. This conductivity ratio could be large, thus limiting the selection of bulk materials for the outer layer. This study reports a different design by adding a third layer of known conductivity between the inner and the outer layer of the bilayer cloak. The analysis extends the analytical solution of the bilayer cloak. For the same outer layer geometry between the bilayer and trilayer cloak, the proposed trilayer design gives a less limiting conductivity ratio between the outer layer and the background material than the bilayer design. Consequently, the trilayer design can enhance the selection of natural materials for the outer layer of the thermal cloak.
Light field imaging through a single multimode fiber for OAM-multiplexed data transmission
Authors: Zhao Qian , Yu Pan-Pan , Liu Yi-Fan , Wang Zi-Qiang , Li Yin-Mei , Gong Lei
Published: May 2020

Multimode fibers (MMFs) can support a large number of spatial modes, increasing the amount of transmitted information, a feature that benefits fields such as endoscopic imaging or optical communications. However, the transport of information encoded in the phase through a standard MMF has not been achieved due to strong mode coupling, hindering direct data transfer using light beams endowed with orbital angular momentum (OAM). Here, we present a computational light field imaging technique to achieve OAM-multiplexed transmission through a commercial MMF. Such a technique enables the retrieval of the incident field from the speckle intensity at the distant end of the fiber. Based on the recovered field, the extraction of the transferred data by addressing all the OAM channels can be achieved. Experimentally, light field imaging through a MMF is demonstrated by recovering a structured light field and a phase picture. For optical transmission, the crosstalk between OAM channels is tested first, and then we demonstrate high-fidelity image data transfer via 24 multiplexed OAM channels through a commercial MMF.
Low energy electron impact resonances of anthracene probed by 2D photoelectron imaging of its radical anion
Authors: Mensa-Bonsu Golda , Lietard Aude , Tozer David J. , Verlet Jan R. R.
Published: May 2020

Electron-molecule resonances of anthracene were probed by 2D photoelectron imaging of the corresponding radical anion up to 3.7 eV in the continuum. A number of resonances were observed in both the photoelectron spectra and angular distributions, and most resonances showed clear autodetachment dynamics. The resonances were assigned using density functional theory calculations and are consistent with the available literature. Competition between direct and autodetachment, as well as signatures of internal conversion between resonances, was observed for some resonances. For the 12B2g resonance, a small fraction of population recovers the ground electronic state as evidenced by thermionic emission. Recovery of the ground electronic state offers a route of producing anions in an electron–molecule reaction; however, the energy at which this occurs suggests that anthracene anions cannot be formed in the interstellar medium by electron capture through this resonance.
Layer-by-layer-stacked graphene/graphene-island supercapacitor
Authors: Lee Dongwook , Seo Jiwon
Published: May 2020

A large surface area and high electrical conductivity are required for an ideal supercapacitor electrode. Novel electrode materials have been investigated to obtain high volumetric and gravimetric capacitances with long cycling lifetimes. Graphene, a highly promising material for energy storage systems, has attracted considerable interest owing to its desirable characteristics such as large surface area and excellent electrical conductivity. However, the stacking of layers blocks the permeation of electrolytes and deteriorates the function of the electrode. Supercapacitor electrodes consisting of three-dimensional (3D) graphitic structures with large surface areas, high electrical conductivities, and low charge-transfer resistances, facile permeations, and diffusion paths for the electrolyte are required for portable electronic devices. In this study, we fabricate a 3D graphene structured electrode with graphene islands as spacers, which exhibits a non-Faradaic behavior and an ultrahigh power density of up to 187 kW/g.
Hysteresis and criticality in hybrid percolation transitions
Authors: Park Jinha , Yi Sudo , Kahng B.
Published: May 2020

Phase transitions (PTs) are generally classified into second-order and first-order transitions, each exhibiting different intrinsic properties. For instance, a first-order transition exhibits latent heat and hysteresis when a control parameter is increased and then decreased across a transition point, whereas a second-order transition does not. Recently, hybrid percolation transitions (HPTs) are issued in diverse complex systems, in which the features of first-order and second-order PTs occur at the same transition point. Thus, the question whether hysteresis appears in an HPT arises. Herein, we investigate this fundamental question with a so-called restricted Erdős–Rényi random network model, in which a cluster fragmentation process is additionally proposed. A hysteresis curve of the order parameter was obtained. Depending on when the reverse process is initiated, the shapes of hysteresis curves change, and the critical behavior of the HPT is conserved throughout the forward and reverse processes.
Dense ferroelectric-ferroelastic domain structures in rhombohedral PMN-28PT single crystals
Authors: Ushakov A. D. , Turygin A. P. , Akhmatkhanov A. R. , Alikin D. O. , Hu Q. , Liu X. , Zhao Y. , Xu Z. , Wei X. , Ya Shur V.
Published: May 2020

We have studied a dense domain structure (DDS) appearing during polarization reversal in rhombohedral (111)-cut lead magnesium niobate-lead titanate single crystals. The complicated shape of the switching current was explained by means of non-uniform motion of the boundary between the DDS and c-domains using comparative analysis of the optical current and kinetic map. 2D-vector piezoresponse force microscopy revealed that DDS represented needle-like a-domains inside the a-domains with different vertical orientations of spontaneous polarization.
A tunable electromagnetic acoustic switch
Authors: Zhang Yumin , Wang Chunqi , Huang Lixi
Published: May 2020

An acoustic switch permits or forbids sound transmission through a partition, and its performance is governed by the stiffness and mass laws at low and high frequencies, respectively. The mechanism of artificial mass and stiffness, either positive or negative, is required to break these laws; all are demonstrated experimentally in this study. The switch consists of a suspended diaphragm with electric moving coil and a magnetic field, shunted by an essentially passive analog circuit. We show that electrically mediated damping is extremely large, and its mechanism as a powerful wave stopper can be very broadband, which contrasts with most resonance-based devices in the literature. We also show that a serial shunt capacitor introduces a mechanical mass that softens the diaphragm spring at low frequencies, while a shunt inductance is an electromagnetic spring that pacifies mechanical inertia at high frequencies. By manipulating the dynamic mass, stiffness, and damping electronically to enhance or defy the mass law and stiffness law, a switch effective in over one octave and working at a deep subwavelength scale is realized, and the maximum switch ratio is as high as 28 dB. As circuits can be miniaturized and easily tuned, these illustrated physics point to a versatile tool for digital control of sound waves.
The in-plane anisotropy of the effective g factors in Al0.25Ga0.75N/GaN based quantum point contacts with narrow channels
Authors: Lu Fangchao , Tang Ning , Ge Weikun , Xu Fujun , Wang Wenjie , Li Wei , Shen Bo
Published: May 2020

The effective g factors (g*) of the lowest three subbands of Al0.25Ga0.75N/GaN-based quantum point contacts (QPCs) are obtained in various magnetic field orientations. The g factors show an anisotropic enhancement compared to those in the two-dimensional electron gas, among which an in-plane anisotropy becomes manifested, when the QPC is depleted from the third to the first subband and the channel width shrinks from the order of 10−7 m–10−8 m. In the one-dimensional (1D) regime with only one subband in the QPC, the in-plane g* perpendicular to the current is evidently larger than the parallel one. The in-plane anisotropy can be attributed to the Rashba spin–orbit coupling (SOC) in the narrow confinement. The reason that the anisotropy can be observed in this work, but not in conventional III–V semiconductors studied previously, is due to the fact that the Al0.25Ga0.75N/GaN-based QPCs have larger polarization-field-induced Rashba SOC and much stronger 1D constriction.
Large-amplitude oscillatory shear flow loops for long-chain branching from general rigid bead-rod theory
Authors: Kanso M. A. , Giacomin A. J. , Saengow C.
Published: May 2020

General rigid bead-rod theory [O. Hassager, “Kinetic theory and rheology of bead-rod models for macromolecular solutions. II. Linear unsteady flow properties,” J. Chem. Phys. 60, 4001–4008 (1974)] explains polymer viscoelasticity from macromolecular orientation. By means of this theory, we relate the complex viscosity of polymeric liquids to the architecture of axisymmetric branched macromolecules. In this work, we explore how adding long-chain branching to polymers affects the shapes of large-amplitude oscillatory shear (LAOS) flow loops. By loops, we mean plots of the alternant part of the shear stress response vs the cosinusoidal shear rate. We choose LAOS for its ability to amplify subtle differences in small-amplitude oscillatory shear flow at a high Weissenberg number. When non-dimensionalized with the product of the zero-shear viscosity and the shear rate amplitude, the loop shapes depend on the sole dimensionless architectural parameter, the macromolecular lopsidedness of the long-chain branched macromolecule. In this work, in this way, we compare and contrast the loop shapes of macromolecular chains that are straight with those branched. Specifically, we explore symmetric branch multiplicity, branch functionality, branch length, branch position, branch distribution, and multiple branch asymmetry. We find that adding branching collapses and distorts the loops. We then find that so long as branch length, branch position, and branch distribution are held constant and so long as the branching is symmetric about the center of mass, the peak shear stress increases with branch multiplicity. We also find that branch functionality hardly affects the loops. The structural details explored in this paper have yet to be explored in the laboratory.
Are donkey sentences and bare conditionals family or friends?
Authors: Lin Wei-ling Eileen , Chen Chun-yin Doris , Fernandez-Salgueiro Gerardo
Published: May 2020

The present study investigates children’s first language acquisition of donkey sentences and bare conditionals in Mandarin Chinese, both of which are concerned with quantification. Kindergarteners, Grade 2 and Grade 4 were recruited for experimental groups, each group consisting of 18 subjects, and 18 adults comprised a control group against which to compare their interpretations. Each subject finished two Truth-Value Judgment tasks, which were sentences in isolation and sentences in context. The results of this research identified a developmental pattern regarding the acquisition of donkey sentences and bare conditionals in Mandarin Chinese. It was found that overall children under seven years of age had difficulty interpreting quantificational sentences. First, concerning the relatedness of the two constructions, all four groups showed a tendency to find donkey sentences easier to interpret than bare conditionals. With respect to contextual effects, by Grade 2, children could obtain adult-like interpretations of donkey sentences in a biasing context, but it was not until they were in Grade 4 that they could interpret both donkey sentences and bare conditionals in their supporting context with adult-like readings. As a result, the subjects’ interpretations were greatly affected by context, but the two constructions were affected in different ways.
CD73+ extracellular vesicles inhibit angiogenesis through adenosine A2B receptor signalling
Authors: Angioni Roberta , Liboni Cristina , Herkenne Stephanie , Sánchez‐Rodríguez Ricardo , Borile Giulia , Marcuzzi Elisabetta , Calì Bianca , Muraca Maurizio , Viola Antonella
Published: May 2020

Pathological angiogenesis is a hallmark of several conditions including eye diseases, inflammatory diseases, and cancer. Stromal cells play a crucial role in regulating angiogenesis through the release of soluble factors or direct contact with endothelial cells. Here, we analysed the properties of the extracellular vesicles (EVs) released by bone marrow mesenchymal stromal cells (MSCs) and explored the possibility of using them to therapeutically target angiogenesis. We demonstrated that in response to pro‐inflammatory cytokines, MSCs produce EVs that are enriched in TIMP‐1, CD39 and CD73 and inhibit angiogenesis targeting both extracellular matrix remodelling and endothelial cell migration. We identified a novel anti‐angiogenic mechanism based on adenosine production, triggering of A2B adenosine receptors, and induction of NOX2‐dependent oxidative stress within endothelial cells. Finally, in pilot experiments, we exploited the anti‐angiogenic EVs to inhibit tumour progression in vivo. Our results identify novel pathways involved in the crosstalk between endothelial and stromal cell and suggest new therapeutic strategies to target pathological angiogenesis.
Breather Interaction Properties Induced by Self-Steepening and Space-Time Correction*
Authors: Wu Yu-Han , Liu Chong , Yang Zhan-Ying , Yang Wen-Li
Published: May 2020

We study the properties of breather interactions in nonlinear Kerr media with self-steepening and spacetime correction and with either self-focusing or self-defocusing nonlinearity, and present a new family of exact breather solutions via the Darboux transformation with a special-designed quadratic spectral parameter. In contrast to the previous results of the nonlinear Schrödinger equation (NLSE) hierarchy, we show that the relative phase of colliding breathers has a significant effect on the collision manifestation. In particular, only the out-of-phase interactions can generate small amplitude waves at the collision center, which are analogous to the NLSE super-regular breathers. Our results will deepen our understanding of the properties of breather interactions and they will offer the possibility of experimental observations of super-regular breather dynamics in systems with self-steepening and spacetime correction.
A New Path to Improve High β
p Plasma Performance on EAST for Steady-State Tokamak Fusion Reactor*
Authors: Wan Baonian
Published: May 2020

High β
p
scenario is foreseen to be a promising candidate operational mode for steady-state tokamak fusion reactors. Dedicated experiments on EAST and data analysis find that density gradient ∇n is a control knob to improve energy confinement in high β
p
plasmas at low toroidal rotation as projected for a fusion reactor. Different from previously known turbulent stabilization mechanisms such as E × B shear and Shafranov shift, high density gradient can enhance the Shafranov shift stabilizing effect significantly in high β
p
regime, giving that a higher density gradient is readily accessible in future fusion reactors with lower collisionality. This new finding is of great importance for the next-step fusion development because it may open a new path towards even higher energy confinement in the high β
p
scenario. It has been demonstrated in the recent EAST experiments, i.e., a fully non-inductive high β
p
(∼2) H-mode plasma (H
98y2 ≥ 1.3) has been obtained for a duration over 100 current diffusion times, which sets another new world record of long-pulse high-performance tokamak plasma operation with the normalized performance approaching the ITER and CFETR regimes.
Effects of Total-Ionizing-Dose Irradiation on Single-Event Burnout for Commercial Enhancement-Mode AlGaN/GaN High-Electron Mobility Transistors*
Authors: Chen Si-Yuan , Yu Xin , Lu Wu , Yao Shuai , Li Xiao-Long , Wang Xin , Liu Mo-Han , Xi Shan-Xue , Wang Li-Bin , Sun Jing , He Cheng-Fa , Guo Qi
Published: May 2020

We investigate the synergism effect of total ionizing dose (TID) on single-event burnout (SEB) for commercial enhancement-mode AlGaN/GaN high-electron mobility transistors. Our experimental results show that the slight degradation of devices caused by gamma rays can affect the stability of the devices during the impact of high energy particles. During heavy ion irradiation, the safe working values of drain voltage are significantly reduced for devices which have already been irradiated by
60
Co gamma rays before. This could be attributed to more charges trapped caused by
60
Co gamma rays, which make GaN devices more vulnerable to SEB. Moreover, the electrical parameters of GaN devices after
60
Co gamma and heavy-ion irradiations are presented, such as the output characteristic curve, effective threshold voltages, and leakage current of drain. These results demonstrate that the synergistic effect of TID on SEB for GaN power devices does in fact exist.
Pressure-Stabilized New Phase of CaN4*
Authors: Shi Xu-Han , Liu Bo , Yao Zhen , Liu Bing-Bing
Published: May 2020

We propose a new CaN4 high pressure structure with the P21/m space group. The P21/m-CaN4 structure is constituted by the infinite armchair N-chain. The dynamical stability and mechanical stability are verified by the calculations of phonon dispersion curves and elastic constants. The enthalpy difference calculation shows that the P21/m phase is more stable than the reported P41212 phase. The advantaged properties of P21/m-CaN4, such as high nitrogen content (58.3%) and low polymerization pressure (18.3 GPa), allow it to be a potential high energy material. Band structure calculation shows that the P21/m-CaN4 structure is a metallic phase. The nonpolar covalent single N–N bond is a sigma bond. The charge transfer between the Ca and N atoms results in an ionic bond interaction.
High-Pressure Ultrafast Dynamics in Sr2IrO4: Pressure-Induced Phonon Bottleneck Effect*
Authors: Wu Yanling , Yin Xia , Hasaien Jiazila , Ding Yang , Zhao Jimin
Published: May 2020

By integrating pump-probe ultrafast spectroscopy with diamond anvil cell (DAC) technique, we demonstrate a time-resolved ultrafast dynamics study on non-equilibrium quasiparticle (QP) states in Sr
2
IrO
4
under high pressure. On-site in situ condition is realized, where both the sample and DAC have fixed position during the experiment. The QP dynamics exhibits a salient pressure-induced phonon bottleneck feature at 20 GPa, which corresponds to a gap shrinkage in the electronic structure. A structural transition is also observed at 32 GPa. In addition, the slowest relaxation component reveals possible heat diffusion or pressure-controlled local spin fluctuation associated with the gap shrinkage. Our work enables precise pressure dependence investigations of ultrafast dynamics, paving the way for reliable studies of high-pressure excited state physics.
Chemical Vapor Deposition of Two-Dimensional PbS Nanoplates for Photodetection*
Authors: Gu Yi-Yi , Wang Yi-Fan , Xia Jing , Meng Xiang-Min
Published: May 2020

Non-layered two-dimensional (2D) lead sulfide (PbS) has attracted growing interest recently due to its direct narrow bandgap (0.4 eV) and broad spectral detection from visible to mid-IR region, which lead to remarkable electronic and optoelectronic properties promising for real applications. We report the chemical vapor deposition growth of highly crystalline 2D PbS crystals on mica substrates. The high quality and uniformity of 2D PbS nanoplates are confirmed by atomic force microscopy, x-ray powder diffraction, transmission electron microscopy and x-ray photoelectron spectroscopy. The morphology and lateral size are controllable by different growth temperatures. Photodetectors made from 2D PbS nanoplates reveal good stability, high photoresponsivity, and fast response time, which indicates their promising applications for ultrathin optoelectronics.
Advanced data analysis procedure for hard x-ray resonant magnetic reflectivity discussed for Pt thin film samples of various complexity
Authors: Krieft Jan , Graulich Dominik , Moskaltsova Anastasiia , Bouchenoire Laurence , Francoual Sonia , Kuschel Timo
Published: May 2020

X-ray resonant magnetic reflectivity (XRMR) is a powerful method to determine the optical, structural and magnetic depth profiles of a variety of thin film systems. Here, we investigate samples of different complexity all measured at the Pt

L

3

absorption edge to determine the optimal procedure for the analysis of the experimental XRMR curves, especially for nontrivial bi- and multilayer samples that include differently bonded Pt from layer to layer. The software tool ReMagX is used to fit these data and model the magnetooptic depth profiles based on a highly adaptable layer stack which is modified to be a more precise and physically consistent representation of the real multilayer system. Various fitting algorithms, iterative optimization approaches and a detailed analysis of the asymmetry ratio features as well as χ
2 (goodness of fit) landscapes are utilized to improve the agreement between measurements and simulations. We present a step-by-step analysis procedure tailored to the Pt thin film systems to take advantage of the excellent magnetic sensitivity and depth resolution of XRMR.
One-pot synthesis of manganese oxide/graphene composites via a plasma-enhanced electrochemical exfoliation process for supercapacitors
Authors: Dang Minh Nhat , Nguyen Thanh Hai , Nguyen To Van , Thu Tran Viet , Le Hoang , Akabori Masashi , Ito Nobuaki , Nguyen Hai Yen , Le Trong Lu , Nguyen Tuan Hong , Nguyen Van Thao , Phan Ngoc Hong
Published: May 2020

In this work, a feasible one-pot approach to synthesize manganese oxide/graphene composites, the so-called plasma-enhanced electrochemical exfoliation process (PE3P), has been developed. Herein, a composite of graphene decorated with manganese oxide nanoparticles was prepared via PE3P from a KMnO4 solution and graphite electrode under a voltage of 70 V in an ambient environment. By controlling the initial KMnO4 concentration, we obtained distinct MnO2/graphene samples. The prepared samples were characterized by scanning electron microscopy, transmission electron microscopy, x-ray diffraction, x-ray photoelectron spectroscopy, and Raman spectroscopy. The electrochemical measurements of the MnO2/graphene composites revealed that the specific capacitance of the samples is approximately 320 F g–1 at a scan rate of 10 mV s–1, which is comparably very high for manganese oxide/carbon-based supercapacitor electrode materials. Considering the simple, low-cost, one-step and environmentally friendly preparation, our approach has the potential to be used for the fabrication of MnO2/graphene composites as the electrode materials of supercapacitors.
Deformable image registration of the treatment planning CT with proton radiographies in perspective of adaptive proton therapy
Authors: Palaniappan Prasannakumar , Meyer Sebastian , Kamp Florian , Belka Claus , Riboldi Marco , Parodi Katia , Gianoli Chiara
Published: May 2020

The purpose of this work is to investigate the potentiality of using a limited number of in-room proton radiographies to compensate anatomical changes in adaptive proton therapy. The treatment planning CT is adapted to the treatment delivery scenario relying on 2D-3D deformable image registration (DIR). The proton radiographies, expressed in water equivalent thickness (WET) are simulated for both list-mode and integration-mode detector configurations in pencil beam scanning. Geometrical and analytical simulations of an anthropomorphic phantom in the presence of anatomical changes due to breathing are adopted. A Monte Carlo simulation of proton radiographies based on a clinical CT image in the presence of artificial anatomical changes is also considered. The accuracy of the 2D-3D DIR, calculated as root mean square error, strongly depends on the considered anatomical changes and is considered adequate for promising adaptive proton therapy when comparable to the accuracy of conventional 3D-3D DIR. In geometrical simulation, this is achieved with a minimum of eight/nine radiographies (more than 90% accuracy). Negligible improvement (sim1%) is obtained with the use of 180 radiographies. Comparing different detector configurations, superior accuracy is obtained with list-mode than integration-mode max (WET with maximum occurrence) and mean (average WET weighted by occurrences). Moreover, integration-mode max performs better than integration-mode mean. Results are minimally affected by proton statistics. In analytical simulation, the anatomical changes are approximately compensated (about 60%–70% accuracy) with two proton radiographies and minor improvement is observed with nine proton radiographies. In clinical data, two proton radiographies from list-mode have demonstrated better performance than nine from integration-mode (more than 100% and about 50%–70% accuracy, respectively), even avoiding the finer grid spacing of the last numerical optimization stage. In conclusion, the choice of detector configuration as well as the amount and complexity of the considered anatomical changes determine the minimum number of radiographies to be used.
Asymmetric-waveguide, short cavity designs with a bulk active layer for high pulsed power eye-safe spectral range laser diodes
Authors: Ryvkin Boris S , Avrutin Eugene A , Kostamovaara Juha T
Published: May 2020

It is shown, by calculations calibrated against the authors’ recent experimental data, that an eye-safe wavelength range InGaAsP/InP high pulsed power laser design using a bulk active layer, which has a large refractive index step with respect to the optical confinement layer and is located close to the p-cladding, can provide substantial performance improvement compared to the best results achieved so far for this operating regime and wavelength. The dependence of the laser performance on the design parameters such as the thicknesses of the active layer and the waveguide, as well as the cavity length, are analysed. It is shown that the relatively thick bulk active layer in such InGaAsP/InP lasers allows the use of short cavity lengths (∼1 mm or even shorter), for achieving high pulsed power while maintaining a low p-cladding series resistance (making for high efficiency) and a narrow far field (making for high brightness). A single-asymmetry structure with the asymmetric active layer location but symmetric optical confinement layer/cladding refractive index steps gives performance only marginally inferior to that of a double-asymmetric one including asymmetric refractive index steps.
HiFLEx—A Highly Flexible Package to Reduce Cross-dispersed Echelle Spectra
Authors: Errmann Ronny , Cook Neil , Anglada-Escudé Guillem , Sithajan Sirinrat , Mkrtichian David , Semenko Eugene , Martin William , Tanvir Tabassum S. , Feng Fabo , Collett James L. , Jones Hugh R. A.
Published: May 2020

We describe a flexible data reduction package for high resolution cross-dispersed echelle data. This open-source package is developed in Python and includes optional GUIs for most of the steps. It does not require any pre-knowledge about the form or position of the echelle-orders. It has been tested on cross-dispersed echelle spectrographs between 13k and 115k resolution (bifurcated fiber-fed spectrogaph ESO-HARPS and single fiber-fed spectrograph TNT-MRES). HiFLEx can be used to determine radial velocities and is designed to use the TERRA package but can also control the radial velocity packages such as CERES and SERVAL to perform the radial velocity analysis. Tests on HARPS data indicates radial velocities results within ±3 m s−1 of the literature pipelines without any fine tuning of extraction parameters.
Mapping the evidence of climate change adaptation policy instruments in Europe
Authors: Biesbroek Robbert , Delaney Aogan
Published: May 2020

With climate change impacts being felt across Europe, governments have started to invest in designing and implementing adaptation actions. The means through which governments adapt is generally referred to as policy instruments. Although there is a large body of adaptation policy literature emerging, our comprehensive understanding of policy instruments is limited nor do we know much about how scholarship on adaptation is addressing critical questions about policy instrument choice and effectiveness to support policy practice. In this article we map academic scholarship on climate change adaptation policy instruments in Europe. Using systematic approaches, we identify 184 relevant articles published 2014–2019. Our findings show that research is heavily concentrated on a limited number of western-European countries, with hardly any insights from eastern Europe and smaller countries. Most studies do not connect climate change impacts and risks with policy instruments, making assessment of policy effectiveness difficult, if not impossible. We argue that expanding the geographical scope of future research and enhancing the diversity of study types across Europe is critical for advancing theories on climate change adaptation policy, as well as providing useful recommendations for policy makers to strengthen the solution space and accelerate climate change adaptation.
Electrospun poly(lactic acid) nanofiber mats for controlled transdermal delivery of essential oil from Zingiber cassumunar Roxb
Authors: Wongkanya Ratchada , Teeranachaideekul Veerawat , Makarasen Arthit , Chuysinuan Piyachat , Yingyuad Peerada , Nooeaid Patcharakamon , Techasakul Supanna , Chuenchom Laemthong , Dechtrirat Decha
Published: May 2020

A controlled release system of Plai (Zingiber cassumunar Roxb.) oil based on electrospun poly(lactic) acid (PLA) nanofiber mat was successfully developed. The physicochemical properties of the nanofibers loaded with select amounts of oil (15%, 20%, and 30% wt) were characterized using various techniques, including a morphological study using scanning electron microscopy (SEM), structural determination using Fourier transform infrared spectrometry (FTIR) and x-ray diffraction (XRD), as well as thermal properties study using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The loading content and the entrapment efficiency of Plai oil within the fiber mats were evaluated and were found to be remarkably high, ensuring that PLA was an appropriate material for Plai oil loading. The ability of the nanofiber mats to release (E)-1-(3,4-dimethoxyphenyl) butadiene (DMPBD) was also examined and the fiber mats showed controlled release characteristics. As the nanofiber mats have particularly high specific surface area with fully accessible and interconnected pore structures, a liquid medium with active ingredients will not be trapped in blind pores but can be fully released out of the fiber matrix. Furthermore, in vitro skin permeation of the active compound as well as a skin irritation were assessed using reconstructed human epidermis (EpiSkinTM). It was found that DMPBD could efficiently penetrate through the skin model. Moreover, the nanofiber mats containing Plai oil also showed no skin irritation, indicating them as promising prototypes for medical applications.
Efficient unitary method for simulation of driven quantum dot systems
Authors: Talkington Spenser , Jiang HongWen
Published: May 2020

Density matrices evolved according the von Neumann equation are commonly used to simulate the dynamics of driven quantum systems. However, computational methods using density matrices are often too slow to explore the large parameter spaces of solid state quantum systems. Here we develop a unitary computation method to quickly perform simulations for closed quantum systems, where dissipation to the environment can be ignored. We use three techniques to optimize simulations, apply them to six time-dependent pulses for a semiconductor quantum dot qubit system, and predict the dynamic evolutions. We compare computational times between our unitary method and the density matrix method for a variety of image sizes. As an example, we implement our unitary method for a realistic four-state system (Z. Shi et al, Nat. Commun. 5, 3020 (2014)), and find that it is over two orders of magnitude faster than the corresponding density matrix method implemented in the popular quantum simulation software QuTiP.
Numerical methodology for treating static and dynamic dislocation problems near a free surface
Authors: Siddique Abu Bakar , Khraishi Tariq
Published: May 2020

Simulation of dislocation dynamics enables researchers and scientists to explore the plastic behavior of crystalline materials under loading. Analytic solutions for the stress field due to a linear dislocation segment near a free surface are case-specific, e.g. dealing with either a horizontal segment or a vertical segment, and therefore hard to implement in time-dependent dislocation dynamics simulations as different dislocation segments could be differently oriented. This article presents a generalized numerical framework to find the stress field beneath a free surface due to the presence of a dislocation segment. The framework can be expanded to non-flat surfaces. Also, three-dimensional discrete dislocation dynamics simulations are performed here, which clearly show the effect of free surfaces on the flow stress of a material.
Chosroes II, Parvēz, Sasanian king, 590–628 CE
Authors: Börm Henning
Published: May 2020

Chosroes II was one of the most important Sasanian rulers of Late Antiquity. After having prevailed with the help of Emperor Maurice in a civil war against the usurper Bahrām Čōbin, in 591 ce, the king attacked the Roman Empire after the fall of Maurice in 602. By 622, the Persians had conquered Syria and Egypt, but after the failure of the siege of Constantinople in 626, Chosroes, whose empire was attacked in the east by the Turks, was overthrown by dissatisfied aristocrats in 628. After his death, civil wars broke out that decisively weakened the Sasanian Empire in the wake of the Islamic conquests.
rape
Authors: James Sharon
Published: May 2020

Only the rape of citizens was taken seriously by law. Sexual assaults on non-citizens were lesser matters. Rape of enslaved persons, a daily reality, was a crime only if committed by someone other than their owner. Rape of citizen males damaged their reputations; rape of citizen females could render them ineligible for marriage. Ancient myth features almost countless stories of rape, usually of human females by divine males. These tales were common subjects in ancient art and literature. Overwhelmingly, the victims are unmarried girls, who may suffer brutal treatment afterward and frequently bear miraculous offspring, some of whom establish cities (e.g., Romulus and Remus). Rape by human men is rarer in myth; rape of a wife causes massive militarized response (e.g., Helen of Troy, Lucretia). War-rape and post-war rape were standard practice around the Mediterranean.
Survey and comparative assessments of computational multi-omics integrative methods with multiple regulatory networks identifying distinct tumor compositions across pan-cancer data sets
Authors: Wei Zhuohui , Zhang Yue , Weng Wanlin , Chen Jiazhou , Cai Hongmin
Published: May 2020

The significance of pan-cancer categories has recently been recognized as widespread in cancer research. Pan-cancer categorizes a cancer based on its molecular pathology rather than an organ. The molecular similarities among multi-omics data found in different cancer types can play several roles in both biological processes and therapeutic developments. Therefore, an integrated analysis for various genomic data is frequently used to reveal novel genetic and molecular mechanisms. However, a variety of algorithms for multi-omics clustering have been proposed in different fields. The comparison of different computational clustering methods in pan-cancer analysis performance remains unclear. To increase the utilization of current integrative methods in pan-cancer analysis, we first provide an overview of five popular computational integrative tools: similarity network fusion, integrative clustering of multiple genomic data types (iCluster), cancer integration via multi-kernel learning (CIMLR), perturbation clustering for data integration and disease subtyping (PINS) and low-rank clustering (LRACluster). Then, a priori interactions in multi-omics data were incorporated to detect prominent molecular patterns in pan-cancer data sets. Finally, we present comparative assessments of these methods, with discussion over key issues in applying these algorithms. We found that all five methods can identify distinct tumor compositions. The pan-cancer samples can be reclassified into several groups by different proportions. Interestingly, each method can classify the tumors into categories that are different from original cancer types or subtypes, especially for ovarian serous cystadenocarcinoma (OV) and breast invasive carcinoma (BRCA) tumors. In addition, all clusters of the five computational methods show notable prognostic values. Furthermore, both the 9 recurrent differential genes and the 15 common pathway characteristics were identified across all the methods. The results and discussion can help the community select appropriate integrative tools according to different research tasks or aims in pan-cancer analysis.
Weighted minimizer sampling improves long read mapping
Authors: Jain Chirag , Rhie Arang , Zhang Haowen , Chu Claudia , Walenz Brian P , Koren Sergey , Phillippy Adam M
Published: May 2020

Motivation

In this era of exponential data growth, minimizer sampling has become a standard algorithmic technique for rapid genome sequence comparison. This technique yields a sub-linear representation of sequences, enabling their comparison in reduced space and time. A key property of the minimizer technique is that if two sequences share a substring of a specified length, then they can be guaranteed to have a matching minimizer. However, because the k-mer distribution in eukaryotic genomes is highly uneven, minimizer-based tools (e.g. Minimap2, Mashmap) opt to discard the most frequently occurring minimizers from the genome to avoid excessive false positives. By doing so, the underlying guarantee is lost and accuracy is reduced in repetitive genomic regions.

Results

We introduce a novel weighted-minimizer sampling algorithm. A unique feature of the proposed algorithm is that it performs minimizer sampling while considering a weight for each k-mer; i.e. the higher the weight of a k-mer, the more likely it is to be selected. By down-weighting frequently occurring k-mers, we are able to meet both objectives: (i) avoid excessive false-positive matches and (ii) maintain the minimizer match guarantee. We tested our algorithm, Winnowmap, using both simulated and real long-read data and compared it to a state-of-the-art long read mapper, Minimap2. Our results demonstrate a reduction in the mapping error-rate from 0.14% to 0.06% in the recently finished human X chromosome (154.3 Mbp), and from 3.6% to 0% within the highly repetitive X centromere (3.1 Mbp). Winnowmap improves mapping accuracy within repeats and achieves these results with sparser sampling, leading to better index compression and competitive runtimes.

Availability and implementation

Winnowmap is built on top of the Minimap2 codebase and is available at https://github.com/marbl/winnowmap.
Unsupervised topological alignment for single-cell multi-omics integration
Authors: Cao Kai , Bai Xiangqi , Hong Yiguang , Wan Lin
Published: May 2020

Motivation

Single-cell multi-omics data provide a comprehensive molecular view of cells. However, single-cell multi-omics datasets consist of unpaired cells measured with distinct unmatched features across modalities, making data integration challenging.

Results

In this study, we present a novel algorithm, termed UnionCom, for the unsupervised topological alignment of single-cell multi-omics integration. UnionCom does not require any correspondence information, either among cells or among features. It first embeds the intrinsic low-dimensional structure of each single-cell dataset into a distance matrix of cells within the same dataset and then aligns the cells across single-cell multi-omics datasets by matching the distance matrices via a matrix optimization method. Finally, it projects the distinct unmatched features across single-cell datasets into a common embedding space for feature comparability of the aligned cells. To match the complex non-linear geometrical distorted low-dimensional structures across datasets, UnionCom proposes and adjusts a global scaling parameter on distance matrices for aligning similar topological structures. It does not require one-to-one correspondence among cells across datasets, and it can accommodate samples with dataset-specific cell types. UnionCom outperforms state-of-the-art methods on both simulated and real single-cell multi-omics datasets. UnionCom is robust to parameter choices, as well as subsampling of features.

Availability and implementation

UnionCom software is available at https://github.com/caokai1073/UnionCom.

Supplementary information

Supplementary data are available at Bioinformatics online.
Chromatin network markers of leukemia
Authors: Malod-Dognin N , Pancaldi V , Valencia A , Pržulj N
Published: May 2020

Motivation

The structure of chromatin impacts gene expression. Its alteration has been shown to coincide with the occurrence of cancer. A key challenge is in understanding the role of chromatin structure (CS) in cellular processes and its implications in diseases.

Results

We propose a comparative pipeline to analyze CSs and apply it to study chronic lymphocytic leukemia (CLL). We model the chromatin of the affected and control cells as networks and analyze the network topology by state-of-the-art methods. Our results show that CSs are a rich source of new biological and functional information about DNA elements and cells that can complement protein–protein and co-expression data. Importantly, we show the existence of structural markers of cancer-related DNA elements in the chromatin. Surprisingly, CLL driver genes are characterized by specific local wiring patterns not only in the CS network of CLL cells, but also of healthy cells. This allows us to successfully predict new CLL-related DNA elements. Importantly, this shows that we can identify cancer-related DNA elements in other cancer types by investigating the CS network of the healthy cell of origin, a key new insight paving the road to new therapeutic strategies. This gives us an opportunity to exploit chromosome conformation data in healthy cells to predict new drivers.

Availability and implementation

Our predicted CLL genes and RNAs are provided as a free resource to the community at https://life.bsc.es/iconbi/chromatin/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Geometric potentials from deep learning improve prediction of CDR H3 loop structures
Authors: Ruffolo Jeffrey A , Guerra Carlos , Mahajan Sai Pooja , Sulam Jeremias , Gray Jeffrey J
Published: May 2020

Motivation

Antibody structure is largely conserved, except for a complementarity-determining region featuring six variable loops. Five of these loops adopt canonical folds which can typically be predicted with existing methods, while the remaining loop (CDR H3) remains a challenge due to its highly diverse set of observed conformations. In recent years, deep neural networks have proven to be effective at capturing the complex patterns of protein structure. This work proposes DeepH3, a deep residual neural network that learns to predict inter-residue distances and orientations from antibody heavy and light chain sequence. The output of DeepH3 is a set of probability distributions over distances and orientation angles between pairs of residues. These distributions are converted to geometric potentials and used to discriminate between decoy structures produced by RosettaAntibody and predict new CDR H3 loop structures de novo.

Results

When evaluated on the Rosetta antibody benchmark dataset of 49 targets, DeepH3-predicted potentials identified better, same and worse structures [measured by root-mean-squared distance (RMSD) from the experimental CDR H3 loop structure] than the standard Rosetta energy function for 33, 6 and 10 targets, respectively, and improved the average RMSD of predictions by 32.1% (1.4 Å). Analysis of individual geometric potentials revealed that inter-residue orientations were more effective than inter-residue distances for discriminating near-native CDR H3 loops. When applied to de novo prediction of CDR H3 loop structures, DeepH3 achieves an average RMSD of 2.2 ± 1.1 Å on the Rosetta antibody benchmark.

Availability and Implementation

DeepH3 source code and pre-trained model parameters are freely available at https://github.com/Graylab/deepH3-distances-orientations.

Supplementary information

Supplementary data are available at Bioinformatics online.