bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct numerical simulation of a three-dimensional spatially evolving compressible mixing layer laden with particles. I. Turbulent structures and asymmetric properties
Authors: Dai Qi , Jin Tai , Luo Kun , Fan Jianren
Published: August 2019

With the Eulerian–Lagrangian point-source method, the effects of dispersed particles on turbulent structures and asymmetric properties are systematically investigated in a three-dimensional spatially evolving compressible mixing layer with the convective Mach number up to 1.2. Particles interact with the mixing layer through two-way coupling, and three simulations with different particle diameters are conducted and compared with the particle-free flow. The underlying mechanisms responsible for the mixing layer asymmetry are also revealed through analyzing the self-similar equations of the particle-laden spatially evolving compressible mixing layer. The compressible mixing layer is significantly asymmetric on the high- and low-speed sides. The low-speed layer possesses more vortices and less shocklets compared with the high-speed layer in the fully developed region, and the shear layer center tends to skew toward the low-speed stream, which is due to the streamwise momentum gradient. Small particles augment the mixing layer asymmetry with more vortices and shocklets in the low-speed stream, which is attributed to the small inertia and the larger streamwise velocity of particles than fluid across the mixing layer. However, large particles attenuate the asymmetry of the mixing layer where the vortical structures on the low-speed side are further reduced and the shocklets are barely existent in both the layers, which is ascribed to the large inertia and the stronger effect of particle back-reaction on the low-speed fluid than that on the high-speed fluid.
Reduction of defect generation and development of sinks at nanocluster boundary in oxide dispersion-strengthened steel
Authors: Higgins M. P. , Peng Q. , Shao L. , Gao F.
Published: August 2019

The radiation resistance mechanisms of nanoclusters (NCs) in oxide dispersion-strengthened (ODS) steels have been investigated. Molecular dynamics simulation has been used to investigate defect generation during the primary damage state of a displacement cascade in ODS steels for NCs of various radii and a range of primary knock-on atom (PKA) energies. Y2O3 NCs considerably enhance the radiation resistance of ODS steels by reducing the peak defect generation during the cascade within the Fe matrix. The NC also affects the morphology of the collision cascades, depending on PKA energy. At lower energies, the NC’s outer circumference act as a cessation point forming a dampened shockwave compared to a pure Fe system. At higher energies, the PKA energy is able to transfer through the NC, thus causing two smaller shockwaves in the Fe matrix. Along with the alteration of the cascade morphology, the NC boundary acts as a strong defect sink to absorb defects and defect clusters, leading to significant recombination of interstitials and vacancies away from the NC. The interfacial energy of the NCs with the Fe matrix increases with increasing diameter of the oxide NCs. The evolution of the NC is tracked through the primary damage state of a cascade, and the effects of ballistic dissolution play a key role in this evolution, most evident in the 2 nm NC.
Ion-neutral decoupling in the nonlinear Kelvin–Helmholtz instability: Case of field-aligned flow
Authors: Hillier A.
Published: August 2019

Nonlinear magnetic Kelvin-Helmholtz instability (KHI), and the turbulence it creates appear in many astrophysical systems. This includes those systems where the local plasma conditions are such that the plasma is not fully ionized, for example in the lower solar atmosphere and molecular clouds. In a partially ionized system, the fluids couple via collisions which occur at characteristic frequencies, therefore neutral and plasma species become decoupled for sufficiently high-frequency dynamics. Here, we present high-resolution 2D two-fluid simulations of the nonlinear KHI for a system that traverses the dynamic scales between decoupled fluids and coupled dynamics. We discover some interesting phenomena, including the presence of a density coupling that is independent of the velocity coupling. Using these simulations, we analyze the heating rate, and two regimes appear. The first is a regime where the neutral flow is decoupled from the magnetic field that is characterized by a constant heating rate, then at larger scales, the strong coupling approximation holds the heating rate with the KHI layer width to the power of –2. There is an energy cascade in the simulation, but the nature of the frictional heating means the heating rate is determined by the largest scale of turbulent motions, a fact that has consequences for understanding turbulent dissipation in multifluid systems.
Multiple fano resonances in a coupled plasmonic resonator system
Authors: Chen Yonghao , Chen Li , Wen Kunhua , Hu Yihua , Lin Weitao
Published: August 2019

A refractive index sensor based on metal-insulator-metal waveguides coupled with two rectangular cavities is proposed and investigated by using a finite-difference time-domain method and coupled mode theory. The calculation results show that dual Fano resonances can be manipulated independently through adjusting the parameters of the system due to the local discrete states caused by different cavities. Moreover, the line shape of the transmission spectrum can be tuned by changing the height of the output port. In addition, triple Fano resonances with considerable performances are also achieved after adding an extra slot cavity, and the sensitivity of up to 985 nm/RIU and the figure of merit of up to 54 are obtained. It is believed that the proposed structure can find wide applications in sensors, nonlinear devices, and slow-light devices.
III-V photonic integrated circuit with waveguide-coupled light-emitting diodes and WSi superconducting single-photon detectors
Authors: McDonald Corey , Moody Galan , Nam Sae Woo , Mirin Richard P. , Shainline Jeffrey M. , McCaughan Adam , Buckley Sonia , Silverman Kevin L.
Published: August 2019

We demonstrate cryogenic, all on-chip, single-photon-level photonic integrated circuits on a III-V platform with waveguide-coupled quantum-well sources and tungsten silicide superconducting nanowire single-photon detectors. We have measured the dark count rates below 10−3 counts/s and have reduced the cross talk to an adjacent waveguide by 30 dB.
Broadband magnetotransport in La0.6Sr0.4Mn1−xGaxO3 (0.0 ≤ x ≤ 0.3) at room temperature
Authors: Chanda A. , Chaudhuri U. , Das R. , Mahendiran R.
Published: August 2019

We report the magnetic field (−2.5 kOe ≤ Hdc ≤ 2.5 kOe) dependence of ac magnetoresistance (ac MR) and magnetoreactance (MX) in bulk samples of La0.6Sr0.4Mn1−xGaxO3 (0 ≤ x ≤ 0.3) carrying radio frequency current (f = 10 MHz–3 GHz) at 300 K. Samples with x ≤ 0.10 are ferromagnetic (FM) and those with x ≥ 0.2 are paramagnetic (PM) at 300 K. While the ac MR in FM samples is negative and shows a single sharp peak at Hdc = 0 at low frequencies, positive double peaks emerge at Hdc = ±Hp for f > 500 MHz, and they shift toward higher Hdc with increasing f. The positive ac MR is larger (∼75% at Hdc = Hp = 800 Oe at 3000 MHz) than 20% negative ac MR for Hdc = 2.5 kOe at 10 MHz. The PM samples also show negative ac MR and single peak for 100 MHz < f ≤ 500 MHz, but the magnitude of ac MR is much reduced compared to the FM samples. Surprisingly, the ac MR increases abruptly at a critical value of the magnetic field for higher f, and this anomaly also shifts upward in Hdc as f increases. The MX shows distinct field dependence in FM and PM samples. The ac MR is dictated by the frequency and field dependence of magnetic permeability. We attribute observed features in the ac MR to ferromagnetic resonance for x = 0.0–0.1 and electron paramagnetic resonance for x ≥ 0.2.
Origin of the magnetic ground state developed upon Si, Ge, and Sb-substitution at Sn site in Fe2TiSn
Authors: Chaudhuri S. , Srihari Velaga , Nigam A. K. , Bhobe P. A.
Published: August 2019

A nonmagnetic full Heusler alloy, Fe2TiSn, was substituted with Si, Ge, and Sb at the Sn site with a primary aim of investigating the physical properties of these compositions that are much anticipated to result in a high thermoelectric power factor and generate a half-metallic ground state. The X-ray diffraction (XRD) study carried out using the synchrotron source confirms the solubility limit of substituent atoms to be a mere 5% for Si and Ge and 60% for Sb that results in a pure L21 Heusler phase. Rietveld refinement of the XRD profiles yields the lattice parameters. Despite the fact that chemical substitution should lead to atomic disorder and an increase in the scattering of charge carriers, resistivity measurements show a significant decrease in the magnitude with as little as 5% substitution of Sn by Si or Ge. The weak localization present in Fe2TiSn seems to drastically reduce in the substituted compositions, and the long range magnetic order seems to affect the transport of the charge carriers. The origin of magnetic interactions is investigated using extended X-ray absorption fine structure spectroscopy. The changes in the local crystal structure in terms of the Fe–Fe bond distance are determined. The inference drawn from the experimental study is further complemented with exchange coupling parameter, Jij, and orbital projected density of states calculations, thus presenting an overall understanding of the origin of magnetic interactions in these technologically relevant compositions.
On the origin of the stress spike decay in the elastic precursor in shocked metals
Authors: Kositski Roman , Mordehai Dan
Published: August 2019

High-strain rate experiments are commonly employed to study the dynamic strength of metals, by generating a plane shock wave and measuring the amplitude of the elastic precursor. In some cases, the shock wave is rapidly relaxed after the elastic precursor, leading to a spike in the stress wave. We propose that the observed spike and the following relaxation arise from the interplay between the rate by which dislocations are nucleated and the mobility of the existing ones. In addition, we suggest that the elastic precursor decays since glide takes a larger role in the plastic deformation as the plastic strain rate decreases. The interplay is demonstrated in a physically, dislocation-based dynamic strength model, using dislocation mobility rules from molecular dynamics simulations, as well as a dislocation nucleation model which is fitted using a metamodel optimization technique. Our results show that the stress spike and its decay in annealed body-centered cubic specimens arise from the need to nucleate dislocations to generate a plastic deformation when the mobility of existing dislocations is insufficient to accommodate plastic strain. Cold-rolled targets have sufficient amount of initial dislocations, so glide, rather than nucleation, can accommodate the plastic relaxation, and as such do not exhibit a spike. These insights shed light on the experimentally observed differences between dynamic and static strength of materials, and, in particular, on the anomalous dependence of the dynamic strength on temperature and pretreatment of materials at high-strain rates.
Squeezing a drop of nematic liquid crystal with strong elasticity effects
Authors: Cousins J. R. L. , Wilson S. K. , Mottram N. J. , Wilkes D. , Weegels L.
Published: August 2019

The One Drop Filling (ODF) method is widely used for the industrial manufacture of liquid crystal devices. Motivated by the need for a better fundamental understanding of the reorientation of the molecules due to the flow of the liquid crystal during this manufacturing method, we formulate and analyze a squeeze-film model for the ODF method. Specifically, we consider a nematic squeeze film in the asymptotic regime in which the drop is thin, inertial effects are weak, and elasticity effects are strong for four specific anchoring cases at the top plate and the substrate (namely, planar, homeotropic, hybrid aligned nematic, and π-cell infinite anchoring conditions) and for two different scenarios for the motion of the top plate (namely, prescribed speed and prescribed force). Analytical expressions for the leading- and first-order director angles, radial velocity, vertical velocity, and pressure are obtained. Shear and couple stresses at the top plate and the substrate are calculated and are interpreted in terms of the effect that flow may have on the alignment of the molecules at the plates, potentially leading to the formation of spurious optical defects (“mura”).
Direct numerical simulation of a three-dimensional spatially evolving compressible mixing layer laden with particles. II. Turbulence anisotropy and growth rate
Authors: Dai Qi , Jin Tai , Luo Kun , Xiao Wei , Fan Jianren
Published: August 2019

With the Eulerian–Lagrangian point-source method, turbulence modulation by dispersed particles is systematically investigated in a three-dimensional spatially evolving compressible mixing layer with the convective Mach number up to 1.2. Particles interact with the mixing layer through two-way coupling, and three simulations with different particle diameters are conducted and compared with the particle-free simulation. The underlying mechanisms responsible for turbulence modulation are revealed by analyzing the transport equations of the Reynolds stresses and turbulent kinetic energy, especially the two-way coupling terms. The compressible mixing layer turbulence is significantly anisotropic with strong three-dimensionality. The addition of particles augments turbulence anisotropy of the shear layer, and the augmentation becomes greater as the particle inertia increases, which is attributed to the different particle responsive features to the fluid fluctuations in the streamwise, normal, and spanwise directions. Particles respond fast to the fluid streamwise fluctuation but slowly to the normal and spanwise fluctuations because the streamwise turbulent intensity is larger compared with the normal and spanwise turbulent intensities. Consequently, the streamwise fluctuating velocity and the Reynolds shear stress are augmented and the normal and spanwise velocity fluctuations are attenuated. Besides, small particles slightly enhance the growth rate of the mixing layer, while large particles reduce the shear layer growth rate in the fully developed turbulence, which is due to the quick response of small particles and the slow response of large particles to the total fluid fluctuation.
Extra half-plane shortening of dislocations as an origin of tensile strain in Si-doped (Al)GaN
Authors: Weinrich J. , Mogilatenko A. , Brunner F. , Koch C. T. , Weyers M.
Published: August 2019

Si doping of (Al,Ga)N layers grown by metalorganic chemical vapor deposition induces an inclination of threading dislocations (TDs). This inclination leads to a change of the extra half-plane size of edge and mixed type dislocations. Depending on the dislocation density and the doping concentration, these effects are accompanied by the generation of tensile strain, which can also lead to crack formation. Several models have been published in the past in order to explain this process. Different models result in opposite TD inclination directions with respect to the extra half-plane position. Therefore, this work examines the correlation between the extra half-plane position and the inclination direction to clarify the origin of the tensile strain increase using scanning transmission electron microscopy. With this approach, it can be unambiguously experimentally verified that Si doping leads to a shortening of the dislocations half-plane. An analysis of in situ wafer curvature measurement proves that the increase of tensile strain in GaN caused by Si doping can be explained by this process. Aside from the inclination caused by Si doping, a TD inclination in undoped GaN layers has been analyzed. Possible explanations for the inclination process are discussed.
Pulsed spin wave propagation in a magnonic crystal
Authors: Ordóñez-Romero César L. , Lazcano-Ortiz Zorayda , Pirruccio Giuseppe , Drozdovskii Andrey , Kalinikos Boris , Urbanek Michal , Vigueras-Zúñiga Marco Osvaldo , Matatagui Cruz Daniel , Qureshi Naser , Kolokoltsev Oleg , Monsivais Guillermo
Published: August 2019

Amplitude, frequency, and time domain characteristics have been mapped for short spin wave pulses inside a magnonic crystal. A space- and time-resolved magnetoinductive probing system has been used to detail the spin wave spectral, propagation, and evolution characteristics in a geometrically structured yttrium iron garnet film. Experiments have been performed using magnetostatic surface spin waves excited in a chemically-etched magnonic crystal, ultrafast pulsed excitation of the spin waves, and direct spin wave detection using a scannable magnetoinductive probe connected to a synchronized fast oscilloscope. The results show how the frequency discriminating effect of a magnonic bandgap decreases as the excitation pulse width decreases. They also show how the use of rectangular pulses compromise the magnonic crystal performance because of the high frequency components of such pulses. Space and time maps show how these components are transmitted without additional damping.
Correlating fragility and heterogeneous dynamics in polystyrene through single molecule studies
Authors: Manz Alyssa S. , Aly Mariam , Kaufman Laura J.
Published: August 2019

Many macroscopic properties of polymers depend on their molecular weight, with one notable example being glass transition temperature: polymers with higher molecular weights typically have higher glass transition temperatures than their lower molecular weight polymeric and oligomeric counterparts. Polymeric systems close to their glass transition temperatures also exhibit interesting properties, showing both high (and molecular weight dependent) fragility and strong evidence of dynamic heterogeneity. While studies have detailed the correlations between molecular weight and fragility, studies clearly detailing correlations between molecular weight and degree of heterogeneous dynamics are lacking. In this study, we use single molecule rotational measurements to investigate the impact of molecular weight on polystyrene’s degree of heterogeneity near its glass transition temperature. To this end, two types of fluorescent probes are embedded in films composed of polystyrene ranging from 0.6 to 1364.0 kg mol−1. We find correlation between polystyrene molecular weight, fragility, and degree of dynamic heterogeneity as reported by single molecule stretching exponents but do not find clear correlation between these quantities and time scales associated with dynamic exchange.
Cell size effects in the molecular dynamics of the intrinsically disordered Aβ peptide
Authors: Mehra Rukmankesh , Kepp Kasper P.
Published: August 2019

Periodic molecular dynamics simulations of proteins may suffer from image interactions. Similarly, the hydrophobic effect required to keep a protein folded may not be enforced by small simulation cells. Accordingly, errors may arise both from the water concentration per se and the image interactions. Intrinsically disordered proteins are particularly sensitive, providing a worst-case estimate of the errors. Following this reasoning, we studied Aβ40 (Aβ), a disordered peptide central to Alzheimer’s disease, by 100 different simulations with variable cell size from very large (20 Å) to very small (3 Å). Even for this very disordered peptide, most properties are not cell-size dependent, justifying the common use of modest-sized (10 Å) cells for simulating proteins. The radius of gyration, secondary structure, intrapeptide, and peptide-water hydrogen bonds are similar relative to standard deviations at any cell size. However, hydrophobic surface area increases significantly in small cells (confidence 95%, two-tailed t-test), as does the standard deviation in exposure and backbone conformations (>40% and >27%). Similar results were obtained for the force fields OPLS3e, Ambersb99-ILDN, and Charmm22*. The similar prevalence of structures and α-β transitions in long and short simulations indicate small diffusion barriers, which we suggest is a defining hallmark of intrinsically disordered proteins. Whereas hydrophilic exposure dominates in large cells, hydrophobic exposure dominates in small cells, suggesting a weakening of the hydrophobic effect by image interactions and the few water layers available to keep the protein compact, with a critical limit of 2–3 water layers required to enforce the hydrophobic effect.
Turbulence in counter-flowing partially-ionized plasma may help explain astrophysical systems
Authors: Bandari Anashe
Published: August 2019

The study of turbulence where a neutral fluid and an ionized plasma are mixed together has potential astrophysical applications.
Crystal Structure of Burgess Inner Salts and their Hydrolyzed Ammonium Sulfaminates
Authors: Arduengo III Anthony J. , Uchiyama Yosuke , Dixon David A. , Vasiliu Monica
Published: August 2019

The solid-state structures of the Burgess reagent, and its analogous ethyl ester reveal structures indicative of triethylamine solvated sulfonyl imides rather than the more commonly depicted triethylammonium sulfonyl amidate. The existence of a reversibly formed hydrate of Burgess reagent is not supported by present studies, but rather a hydrosylate that does not revert to the Burgess reagent with gentle warming under vacuum was isolated and characterised. Structures of the hydrosylates from both the methyl- and ethyl-amidate esters were determined from X-ray crystallographic analysis and are reported. The crystal structures of the Burgess inner salts exhibit geometries at the sulfur atoms that are intermediate between a planar O2S=NCO2R unit and tetrahedral 4-coordinate sulfur centres that would be expected from a strong single (dative) bond between the triethylamine nitrogen and sulfur. The hydrolysed ammonium sulfaminates are water soluble intermolecular salts composed of triethylammonium ions, Et3NH+, and N-(alkoxycarbonyl)sulfaminate, O(−)SO2NHCO2R {R=CH3 or C2H5}.
Histone deacetylase 1 suppresses Krüppel homolog 1 gene expression and influences juvenile hormone action in
Tribolium castaneum
Authors: George Smitha , Gaddelapati Sharath Chandra , Palli Subba Reddy
Published: August 2019

Posttranslational modifications, including acetylation and deacetylation of histones and other proteins, modulate hormone action. In
Tribolium castaneum
TcA cells, Trichostatin A, a histone deacetylase (HDAC) inhibitor, mimics juvenile hormone (JH) in inducing JH response genes (e.g.,
Kr-h1
), suggesting that HDACs may be involved in JH action. To test this hypothesis, we identified genes coding for HDACs in
T. castaneum
and studied their function. Knockdown of 12
HDAC
genes showed variable phenotypes; the most severe phenotype was detected in insects injected with double-stranded RNA targeting
HDAC1
(dsHDAC1). The dsHDAC1-injected insects showed arrested growth and development and eventually died. Application of JH analogs hydroprene to
T. castaneum
larvae and JH III to TcA cells suppressed
HDAC1
expression. Sequencing of RNA isolated from control and dsHDAC1-injected larvae identified 1,720 differentially expressed genes, of which 1,664 were up-regulated in dsHDAC1-treated insects. The acetylation levels of core histones were increased in TcA cells exposed to dsHDAC1 or JH III. ChIP assays performed using histone H2BK5ac antibodies showed an increase in acetylation in the
Kr-h1
promoter region of cells exposed to JH III or dsHDAC1. Overexpression or knockdown of
HDAC1
,
SIN3
, or both resulted in a decrease or increase in
Kr-h1
mRNA levels and its promoter activity, respectively. Overexpression of the JH receptor Methoprene tolerant (
Met
) was unable to induce
Kr-h1
in the presence of HDAC1 or SIN3. These data suggest that epigenetic modifications influence JH action by modulating acetylation levels of histones and by affecting the recruitment of proteins involved in the regulation of JH response genes.
Ross Levine: Focus on the critical questions
Authors: Houston Stephanie
Published: August 2019

Ross Levine is a physician-scientist at Memorial Sloan Kettering Cancer Center in New York, where his laboratory studies the genetic basis of myeloid malignancies. Work from Ross’ laboratory has shown how mutations in the JAK–STAT pathway and epigenetic regulators play a role in myeloproliferative neoplasms, and JAK inhibitors are now successfully used to treat myeloproliferative neoplasms. We spoke to Ross about his journey in science so far.
Determining the anisotropy and exchange parameters of polycrystalline spin-1 magnets
Authors: Blackmore W J A , Brambleby J , Lancaster T , Clark S J , Johnson R D , Singleton J , Ozarowski A , Schlueter J A , Chen Y-S , Arif A M , Lapidus S , Xiao F , Williams R C , Blundell S J , Pearce M J , Lees M R , Manuel P , Villa D Y , Villa J A , Manson J L , Goddard P A
Published: August 2019

Although low-dimensional S = 1 antiferromagnets remain of great interest, difficulty in obtaining high-quality single crystals of the newest materials hinders experimental research in this area. Polycrystalline samples are more readily produced, but there are inherent problems in extracting the magnetic properties of anisotropic systems from powder data. Following a discussion of the effect of powder-averaging on various measurement techniques, we present a methodology to overcome this issue using thermodynamic measurements. In particular we focus on whether it is possible to characterise the magnetic properties of polycrystalline, anisotropic samples using readily available laboratory equipment. We test the efficacy of our method using the magnets [Ni(H2O)2(3,5-lutidine)4](BF4)2 and Ni(H2O)2(acetate)2(4-picoline)2, which have negligible exchange interactions, as well as the antiferromagnet [Ni(H2O)2(pyrazine)2](BF4)2, and show that we are able to extract the anisotropy parameters in each case. The results obtained from the thermodynamic measurements are checked against electron-spin resonance and neutron diffraction. We also present a density functional method, which incorporates spin–orbit coupling to estimate the size of the anisotropy in [Ni(H2O)2(pyrazine)2](BF4)2.
Anisotropic Landau level splitting and Lifshitz transition induced magnetoresistance enhancement in ZrTe5 crystals
Authors: Zhou L , Ramiere A , Chen P B , Tang J Y , Wu Y H , Lei X , Guo G P , He J Q , He H T
Published: August 2019

Magneto-transport study has been performed in ZrTe5 single crystals. The observed Shubnikov–de Hass quantum oscillation at low temperature clearly demonstrates the existence of a nontrivial band with small effective mass in ZrTe5. Furthermore, we also revealed the highly anisotropic nature of high-field Landau level splitting in ZrTe5, suggesting the dominant role of orbital contribution to the splitting. Besides these, an abnormal large enhancement of magnetoresistance appears at high temperatures, which is believed to arise from the Lifshitz transition induced two-carrier transport in ZrTe5. Our study provides more understanding of the physical properties of ZrTe5 and sheds light on potential application of ZrTe5 in spintronics.
Stoichiometric edges during the intrinsic growth of hexagonal boron nitride on Ir(111)
Authors: Poelsema Bene , Zandvliet Harold J W , van Houselt Arie
Published: August 2019

The growth of hexagonal boron nitride, hBN, on Ir(111) at 1150–1200 K by thermal decomposition of borazine has been monitored in situ by means of low energy electron microscopy, LEEM. A major and unexpected hBN growth induced transformation of the step morphology on Ir(111) is observed. The dominant orientation of the steps evolves persistently from 〈1–10〉 during the initial experiment(s), towards 〈11–2〉 after numerous experiments. The latter orientation was established directly from an involved analysis of the profile of the specular beam in a selected area diffraction pattern. Images of the hBN islands grown on surface regions with dominant 〈1–10〉 steps reveal that the hBN edges are oriented along 〈1–10〉 and 〈11–2〉 directions in about equal abundance. Using the direct ascertainment of the step orientations we are able to identify unequivocally the nature of the edges of individual hBN islands on areas with predominant 〈11–2〉 steps as solely of the armchair type. This assessment consolidates both the major evolution of the step morphology from 〈1–10〉 into dominant 〈11–2〉 steps during hBN growth on Ir(111) and the earlier reported alignment of the moiré pattern with the substrate.
Near-surface elevated pollution: what we don’t know doesn’t hurt? A numerical study over Mt. Carmel
Authors: Haikin Nitsa , Alpert Pinhas
Published: August 2019

Many air pollution events are occasionally difficult to explain. While most monitoring-based air pollution assessment studies deal with surface analysis, the near-surface elevated pollutants are challenging. The lack of data and understanding of those elevated layers, leaves us ‘blind’ and with no clue where, when and how intensively these pollutants may hit the surface. Here, this challenge at the specific domain of Mt. Carmel is addressed. The atmospheric numerical models RAMS and HYPACT were employed on Haifa Bay in the Eastern Mediterranean with nested horizontal grids down to 0.5 km, in order to resolve the fine-scale flow, along an air pollution episode which serves as a case study. Sixteen locations were determined, representing monitored and non-monitored sites in the complex terrain sub-domains. Results show multi-inversion profiles, which are consistent with an earlier observational study over the region. Concentration differences up to an order of magnitude between adjacent sites (∼2 km) were found, often associated with near-zero surface values, while some simulated peaks were at elevations of 100–400 m above ground level (AGL). The current event offers a view on the near-surface elevated layers, and points at limitations of ground-level monitoring as an indicator of air pollution. This study highlights the importance of near-surface pollution, which is often an unknown source for surface pollution. Overall, steep vertical gradient of pollution as shown here is associated with a combination of deep inversion (or multi-inversion profile), vertical circulation due to topography or synoptic flow, and small scale circulation induced by the complex topography. Since monitoring of the elevated layers is limited by the technology, it is suggested that high resolution advanced models should be used for further exploration of the near-surface pollution.
Recycling of a wastewater to iron oxide micro structures
Authors: Horvath G , Szalay Zs , Simo F , Salgo K , Krcma F , Matejova S
Published: August 2019

The proposed work describes new perspectives for recycling of a salty industrial wastewater to micro-structured iron oxides with capturing potential for minor carbon- and metallic contaminations. By-products generated by electrochemical treatment of a rubber wastewater with sacrificial steel anode were separated, dried, desalinated, and thermally processed at 800 and 1100 °C in a nitrogen atmosphere to investigate the effects of chemically bound oxygen on iron oxide formation. The obtained powder products were different phases of iron oxides, such as hematite, maghemite, magnetite; depending on the annealing temperature. All of the phases are interesting from a recycling point of view, the microstructure, elementary composition and crystallinity of the solid products before and after thermal treatment were investigated via SEM-EDX and PXRD techniques.
Catalan functions and 𝑘-Schur positivity
Authors: Blasiak Jonah , Morse Jennifer , Pun Anna , Summers Daniel
Published: August 2019

We prove that gradedkk-Schur functions areGG-equivariant Euler characteristics of vector bundles on the flag variety, settling a conjecture of Chen-Haiman. We expose a new miraculous shift invariance property of the gradedkk-Schur functions and resolve the Schur positivity andkk-branching conjectures in the strongest possible terms by providing direct combinatorial formulas using strong marked tableaux.
Secularism: A Very Short Introduction
Authors: Copson Andrew
Published: August 2019

Until the modern period, the integration of church and state had been taken for granted. But from the 18th century onwards, some European states began to set up their political order on a different basis. The rule of law through non-religious values embedded in constitutions became the foundation of some states—a movement we now call secularism. Secularism: A Very Short Introduction tells the story of secularism and considers the role of secularism when engaging with some of the most contentious political and legal issues of our time: ‘blasphemy’, ‘apostasy’, religious persecution, religious discrimination, religious schools, and freedom of belief and freedom of thought in a divided world.
Geoffrey Chaucer: A Very Short Introduction
Authors: Wallace David
Published: August 2019

Originally writing over 600 years ago, Geoffrey Chaucer is today enjoying a global renaissance. Why do poets, translators, and audiences from so many cultures and different parts of the world find Chaucer so inspiring? In part, it is down to the character and sheer inventiveness of Chaucer’s work. His writing covered a range of social registers, from noble tragedy to barnyard farce, and his tale-telling geography is vast, his fascination with varieties of religious belief endless, and his desire to voice female experience especially remarkable. Geoffrey Chaucer: A Very Short Introduction introduces the life, performance, and poetry of Chaucer, and analyses his astonishing and enduring appeal, including what made his writing unique.
2. Schoolrooms, science, female intuition
Authors: Wallace David
Published: August 2019

‘Schoolrooms, science, female intuition’ describes the teaching in the medieval schoolroom and explains that few women at the time of Chaucer learned to read and write. Schoolboys entered the educational scheme at the trivium, which was dedicated to grammar, rhetoric, and logic. Beyond this lay the higher arts of the quadrivium (arithmetic, geometry, astronomy, and music). Chaucer’s engagement with these levels is shown in his works the Boece and Treatise on the Astrolabe. In The Wife of Bath’s Tale and Man of Law’s Tale, Chaucer shows how he is sympathetic to women, depends upon their patronage and protection, imitates their voices, and tries to please them.
4. Poetry at last
Authors: Wallace David
Published: August 2019

‘Poetry at last: Troilus and Criseyde’ describes the structure and content of Chaucer’s Troilus and Criseyde. Since London styled itself ‘Troynovant’ or ‘New Troy’, imagining itself founded by the Trojan-Latin Brutus, Chaucer immediately saw great potential in Boccaccio’s ottava rima tale, Il Filostrato. The Boccaccio-inspired Troilus and Criseyde tells of a doomed love affair in a doomed city. For three-fifths of its length its trajectory is seemingly comic, or upward-moving, but it is defined as a tragedy. The dense allusiveness of Troilus and Criseyde suggests that Chaucer is writing a poem to be pondered over, many times, rather than listened to once.
5. Organizing, disorganizing
Authors: Wallace David
Published: August 2019

‘Organizing, disorganizing: The Canterbury Tales’ describes the structure and content of Chaucer’s The Canterbury Tales. The chief precedent for this work as a framed collection is the Decameron, heroically written in response to the 1348 plague, but then retouched by Boccaccio until his death in 1375. Chaucer heard much about Boccaccio during his visit to Florence in 1373, the year of the world’s first lecturae Dantis (Dante lectures, organized and given by Boccaccio). Chaucer’s Tales exist over fifty-five manuscripts; tale orders vary and ‘fragments’ float. For Chaucer, the framed collection provided a convenient workshop and repository for all kinds of writing, some of it drafted much earlier.
7. Performance and new Chaucers
Authors: Wallace David
Published: August 2019

Creative responses to Chaucer, across the world, have never been more varied and vibrant. This repairs some shortcomings of earlier centuries, where imitators have generally reworked entrenched ideas of a fatherly, and occasionally misbehaving, Chaucer, although an exception must be made for Shakespeare, who was a brilliant early reader of Chaucer. ‘Performance and new Chaucers’ considers the globalization of Chaucer and looks at how his work has influenced the poetry of Sylvia Plath, Ted Hughes, Lavinia Greenlaw. Marilyn Nelson, and Caroline Bergvall. The extraordinary growth of translations worldwide since 2000 suggests new esteem for Chaucer as the poet of an unfinished Englishness ripe for translation, adaptation, and local variation.
Socrates: A Very Short Introduction
Authors: Taylor C. C. W.
Published: August 2019

Socrates has a unique position in the history of philosophy; had it not been for his influence on Plato, the whole development of Western philosophy might have been unimaginably different. Socrates wrote nothing himself so our knowledge of him is derived primarily from the engaging and infuriating figure who appears in Plato’s dialogues. Socrates: A Very Short Introduction explores Socrates’ life and his philosophical activity, before considering the responses his philosophical doctrines have evoked in the centuries since his death. It examines the relationship between the historical Socrates and the Platonic character, and explores the enduring image of Socrates as the ideal exemplar of the philosophic life.
Plato’s Socrates
Authors: Taylor C. C. W.
Published: August 2019

‘Plato’s Socrates’ considers the portrayal of Socrates’ doctrines and methods of argument in twelve dialogues plus Apology. It shows that Socrates is predominantly characterized, not as a teacher, but as an enquirer. He disclaims wisdom and seeks, normally in vain, elucidation of problematic questions from his interlocutors, by the method of elenchus. All the dialogues are concerned with ethics in the broad sense of how one should live. Many focus on the attempt to define a virtue or other ethically significant concept. The discussion invariably ends in failure. Others take the form of a confrontation between Socrates and various sophists and/or their pupils and associates over the aims of education.
The iconic Socrates
Authors: Taylor C. C. W.
Published: August 2019

‘The iconic Socrates’ considers Socrates’ role as a gay icon and an icon for civil disobedience. In the Platonism revival of the Florentine Renaissance, the high-minded picture of Platonic/Socratic love focused on the spiritual and intellectual perfection of the beloved, but in an alternative ancient tradition Socrates was presented as a sexual enthusiast, with a penchant for attractive boys. The context of Socrates’ emergence as a major political icon of the 20th century was provided by the US civil rights movement and the anti-Vietnam War movement, but there is no evidence that Socrates ever actually espoused civil disobedience as a political ideology or performed any act of civil disobedience. Socrates remains a pioneer of systematic ethical thought and a paragon of moral and intellectual integrity.
EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology
Authors: Bartolome Jordi , Alves Rui , Solsona Francesc , Teixido Ivan
Published: August 2019

EasyModel is a new user-friendly web application that contains ready-for-simulation versions of the BioModels Database, and allows for the intuitive creation of new models. Its main target audience is the experimental biologist and students of bioinformatics or systems biology without programming skills. Expert users can also benefit from it by implementing basic models quickly and downloading the code for further tailoring.

Availability and implementation

Freely available on the web at https://easymodel.udl.cat. Implementation is described in its own section.
Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes
Authors: Chen Ziyi , Ji Chengyang , Shen Qin , Liu Wei , Qin F Xiao-Feng , Wu Aiping
Published: August 2019

Motivation

Many methods have been developed to estimate immune cell composition from tissue transcriptomes. One common characteristic of these methods is that they are trained using a set of general immune cell transcriptomes that ignores tissue specificities. However, as immune cells are localized in different tissues, they may have distinct expression profiles. Hence, calculations that use general signature matrices may hinder the deconvolution accuracy.

Results

This study used single cell RNA-sequencing (scRNA-Seq) data from different mouse tissues instead of general signature expression values to generate tissue-specific signature gene matrices that are used as the input of the deconvolution model. First, the transcriptome of immune cells in each tissue was extracted from scRNA-Seq data and used to construct the entire expression matrix of tissue immune cells. Then, after comparing different gene selection strategies, the expressions of 162 seq-ImmuCC derived signature genes in tissue immune cell scRNA-Seq data were regarded as the tissue specific signature matrices. Finally, a modest improvement in performance was observed in multiple tissues that refer to a traditional general signature matrix in the deconvolution model. With the fast accumulation of scRNA-Seq data, the introduction of these data into an estimation of immune cell compositions for different tissues will open a new window for avoiding tissue bias for immune cell expression.

Availability and implementation

The signature matrices were available at https://github.com/wuaipinglab/ImmuCC/tree/master/tissue_immucc/SignatureMatrix).

Supplementary information

Supplementary data are available at Bioinformatics online.
Longitudinal Trajectory of Fatigue With Initiation of Biologic Therapy in Inflammatory Bowel Diseases: A Prospective Cohort Study
Authors: Borren Nienke Z , Tan William , Colizzo Francis P , Luther Jay , Garber John J , Khalili Hamed , van Der Woude C Janneke , Ananthakrishnan Ashwin N
Published: August 2019

Backgrounds and Aims

Fatigue is prevalent in patients with inflammatory bowel diseases [IBD]. Biologic therapy is effective in achieving symptomatic and endoscopic remission, but its impact on fatigue is less well established. Our aim is to define the longitudinal trajectory of fatigue over 1 year in patients initiating biologic therapy.

Methods

This prospective cohort enrolled patients diagnosed with Crohn’s disease [CD] or ulcerative colitis [UC] initiating biologic therapy with infliximab, adalimumab, ustekinumab, or vedolizumab. Fatigue was quantified using the seven-point fatigue question in the Short Inflammatory Bowel Disease Questionnaire [SIBDQ]. A score of ≤4 for this question was used to define fatigue. Multivariable regression models adjusting for relevant confounders examined the independent association between attaining clinical remission and resolution of fatigue.

Results

Our study included 326 patients [206 CD, 120 UC] initiating biologic therapy [144 anti-tumour necrosis factor, 129 vedolizumab, 63 ustekinumab]. A total of 61% of the included patients reported significant fatigue at baseline. This was associated with female gender, depressive symptoms, active disease, and disturbed sleep [p < 0.001]. Among the 198 patients who were fatigued at therapy initiation, 86 [70%], 55 [63%], and 44 [61%] remained fatigued at Week 14, 30, and 54, respectively. At each of these time points, achieving clinical remission was associated with lower likelihood of persistent fatigue. However, despite achieving remission, 35%, 30%, and 28% of patients experienced persistent fatigue at Week 14, 30, and 54, respectively.

Conclusions

Fatigue is common in IBD. Though biologic therapy improves fatigue parallel symptomatic improvement, a significant proportion continue to experience persistent fatigue up to 1 year.
Aorto-right pulmonary venous fistula after mitral valve replacement for prosthetic mitral valve infective endocarditis: a case report
Authors: Hirata Kazuhito , Fukuyama Asako , Tengan Toshiho , Takara Hiroaki
Published: August 2019

Background

Aorto-cavitary fistula is a rare condition, and the most common underlying aetiology is infective endocarditis (IE) of the native or the prosthetic aortic valve. We report a case of aorto-right inferior pulmonary venous fistula following redo mitral valve replacement (MVR) for prosthetic mitral valve IE.

Case summary

A 74-year-old woman underwent urgent redo MVR for prosthetic mitral valve IE. The post-operative course was complicated with heart failure and mediastinal haematoma compressing the left atrium. The haematoma was surgically removed and laceration of the left atrial wall was suture ligated; this was attributed to the surgical trauma dissection of the adhesive tissues. One-week post-operatively, a continuous murmur emerged, which prompted an evaluation of the left to right shunt. Transthoracic echocardiography revealed an echolucent area posterior to the aorta, with continuous flow on colour Doppler. Three-dimensional computed tomography showed a fistula between the aorta and the right inferior pulmonary vein. There was a high risk involved in surgical management; therefore, she was managed medically. Fortunately, the continuous murmur and echolucent space disappeared after 6 months. The fistula was considered to be obstructed by spontaneous thrombus formation in the narrowed segment of the fistula tract.

Discussion

The cause of fistula was attributed to possible surgical trauma in the presence of infection. The present case was unique, as it showed spontaneous healing of an aorto-cavitary fistula, which is very rare. The patient was alive with good health status, 6 years after the MVR.
Future Time Perspective in Mid-to-Later Life: The Role of Personality
Authors: Nelson Niccole A , Bergeman Cindy S , Jacobucci Ross
Published: August 2019

Objectives

Future time perspective (FTP), or the way individuals orient to and consider their futures, is fundamental to motivation and well-being across the life span. There is a relative paucity of studies, however, that explore its contributing factors in mid-to-later life, specifically. Therefore, uncovering which variables contribute to individual differences in FTP, as well as the ways these variables interact, is paramount to developing a strong understanding of this construct during this life-span stage.

Method

This study used three data mining techniques (ie, elastic net, decision tree, and tree ensemble analyses) to simultaneously test several potential contributors identified in the literature, including the five-factor personality domains, several health indices, and age.

Results

Personality, especially neuroticism, extraversion, conscientiousness, and agreeableness, had the most influence on FTP. Age and health were not among the most salient FTP contributors in mid-to-later life. Furthermore, decision tree analyses uncovered interactive effects of personality; several profiles of neuroticism, extraversion, and/or conscientiousness were linked with differing FTP levels.

Discussion

Although the extant literature has indicated that FTP, age, and health are inextricably tied, these results indicate that there is more variability to be explained in FTP, perhaps especially when looking within specific age groups.
Pulmonary mucormycosis with diaphragm and liver involvement in a patient with haematopoietic stem cell transplant
Authors: Leung Jason Hongting , Chew Khong-Yik , Chung Alexander Yaw-Fui , Koh Tina Puay Theng
Published: August 2019

Pulmonary mucormycosis is a rare but life-threatening fungal infection. We report a post-haematopoietic stem cell transplant patient with pulmonary mucormycosis that extended to the diaphragm and subphrenic space. He underwent lung and diaphragm resection, debridement of liver capsule and diaphragm reconstruction using a pedicled latissimus dorsi flap. Following surgery, the patient remained well and has resumed his regular daily activities.